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2023-01-01 00:00:00
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29150433
|
10.15252/embj.201796484
|
[BioStudies]_Tyrosine phosphorylation of Munc18-1 inhibits synaptic transmission by preventing SNARE assembly
|
2017
|
Figure 5
|
<sd-panel> <p><strong>Figure 5. Promoting helix 12 extension partly rescues the inhibitory effect of Y473D</strong></p> <p>(A) Left: closed helical <sd-pretag role='assayed' id='sdPretag1180427143sme' type='geneprod' >hairpin</sd-pretag> in domain 3a as identified in the <sd-pretag parent-gene-tag-id='63' parent-protein-tag-id='3' id='sdPretag508637466sd'>Munc18-1</sd-pretag>:closed-<sd-pretag role='assayed' id='sdPretag187252177sme' type='geneprod' >Syntaxin1</sd-pretag> <sd-pretag role='component' id='sdPretag365076735sme' type='tissue' >crystal</sd-pretag> structure (<sd-pretag role='component' id='sdPretag1537041183sme' type='organism' >Misura</sd-pretag> et al., 2000). Right: extended helical <sd-pretag role='assayed' id='sdPretag1042947496sme' type='geneprod' >hairpin</sd-pretag> as observed in the <sd-pretag role='component' id='sdPretag1787965939sme' type='tissue' >crystal</sd-pretag> of <sd-pretag parent-gene-tag-id='63' parent-protein-tag-id='3' id='sdPretag1568822234sd'>Munc18-1</sd-pretag> bound to the N-peptide of <sd-pretag role='component' id='sdPretag998223658sme' type='undefined' >Syntaxin-4</sd-pretag> (Hu et al., 2011).</p> <p>(B) <sd-pretag parent-tag-id='387' id='sdPretag1093383335sd'>GST</sd-pretag>-<sd-pretag parent-gene-tag-id='63' parent-protein-tag-id='3' id='sdPretag1994480591sd'>Munc18-1</sd-pretag> constructs were immobilized on <sd-pretag parent-tag-id='389' id='sdPretag395392721sd'>glutathione beads</sd-pretag> and incubated with the indicated molar excess of <sd-pretag parent-tag-id='68' id='sdPretag1784359567sd'>Synaptobrevin</sd-pretag>/<sd-pretag parent-tag-id='67' id='sdPretag1544925470sd'>VAMP2</sd-pretag> (over <sd-pretag parent-gene-tag-id='63' parent-protein-tag-id='3' id='sdPretag386862566sd'>Munc18-1</sd-pretag>) for 1.5 h at 4°C. Bound <sd-pretag parent-tag-id='68' id='sdPretag1026111614sd'>Synaptobrevin</sd-pretag>/<sd-pretag parent-tag-id='67' id='sdPretag1038009928sd'>VAMP2</sd-pretag> was analyzed by <sd-pretag parent-tag-id='394' id='sdPretag898720557sd'>Western blot</sd-pretag> and immune decorating with an anti-<sd-pretag parent-tag-id='68' id='sdPretag956832748sd'>Synaptobrevin</sd-pretag>/<sd-pretag parent-tag-id='67' id='sdPretag257901669sd'>VAMP2</sd-pretag> antibody and quantified by the LICORE <sd-pretag role='component' id='sdPretag1072342948sme' type='tissue' >system</sd-pretag> and <sd-pretag role='assayed' id='sdPretag878875358sme' type='geneprod' >ImageJ</sd-pretag> software. <sd-pretag parent-tag-id='68' id='sdPretag185560319sd'>Synaptobrevin</sd-pretag>/<sd-pretag parent-tag-id='67' id='sdPretag1515750866sd'>VAMP2</sd-pretag> bound to the <sd-pretag parent-tag-id='387' id='sdPretag1371395879sd'>GST</sd-pretag>-<sd-pretag parent-gene-tag-id='63' parent-protein-tag-id='3' id='sdPretag1315214453sd'>Munc18-1</sd-pretag> mutants is represented as percentage of <sd-pretag parent-tag-id='68' id='sdPretag504198735sd'>Synaptobrevin</sd-pretag>/<sd-pretag parent-tag-id='67' id='sdPretag314664378sd'>VAMP2</sd-pretag> bound to <sd-pretag parent-tag-id='387' id='sdPretag1696787886sd'>GST</sd-pretag>-<sd-pretag parent-gene-tag-id='63' parent-protein-tag-id='3' id='sdPretag185541810sd'>Munc18-1</sd-pretag> WT. Error bars indicate s.e.m., n=3.</p> <p>(C) GUVs (14 nmol <sd-pretag parent-tag-id='30' id='sdPretag1112548572sd'>lipid</sd-pretag>) containing <sd-pretag role='component' id='sdPretag815350407sme' type='geneprod' >Syx1</sd-pretag> (14 pmol) were pre-incubated with the indicated <sd-pretag parent-gene-tag-id='63' parent-protein-tag-id='3' id='sdPretag944030212sd'>Munc18-1</sd-pretag> constructs (90 pmol) at room temperature for 30 min. Subsequently, samples were incubated with soluble <sd-pretag role='component' id='sdPretag1291788329sme' type='molecule' >SNAP-25</sd-pretag> (128 pmol) and <sd-pretag parent-tag-id='419' id='sdPretag560906391sd'>SUVs</sd-pretag> (2.5 nmol <sd-pretag parent-tag-id='30' id='sdPretag248567042sd'>lipid</sd-pretag>) containing Synaptotagmin1 (3 pmol) and SSynaptobrevin/<sd-pretag parent-tag-id='67' id='sdPretag1857442sd'>VAMP2</sd-pretag> (8 pmol) for 15 min on ice. <sd-pretag parent-tag-id='54' id='sdPretag1774366439sd'>Lipid mixing</sd-pretag> was started by increasing the temperature to 37 °C.</p> <p>(D) <sd-pretag parent-tag-id='54' id='sdPretag289618111sd'>Lipid mixing</sd-pretag> was monitored by the increase of <sd-pretag parent-tag-id='414' id='sdPretag686013242sd'>Atto 655</sd-pretag> fluorescence for 30 minutes. Data were normalized to the maximum fluorescence after <sd-pretag parent-tag-id='29' id='sdPretag2078867111sd'>liposome</sd-pretag> lysis by detergent. The minimum fluorescence was set to 0%. Error bars = s.e.m., <em>N</em> = 3.</p> <p>(E) Trans-<sd-pretag parent-tag-id='420' id='sdPretag368749218sd'>SNARE</sd-pretag> Formation Assay: t- and v-<sd-pretag parent-tag-id='420' id='sdPretag661640523sd'>SNARE</sd-pretag> <sd-pretag parent-tag-id='419' id='sdPretag1173429513sd'>SUVs</sd-pretag> were incubated in the presence or absence of different <sd-pretag parent-gene-tag-id='63' parent-protein-tag-id='3' id='sdPretag1456507416sd'>Munc18-1</sd-pretag> constructs for 30min at 4°C. After solubilization and precipitation of the t-<sd-pretag parent-tag-id='420' id='sdPretag449555121sd'>SNAREs</sd-pretag> using nickel beads, presence of full-<sd-pretag parent-tag-id='669' id='sdPretag8530155sd'>length</sd-pretag> <sd-pretag parent-tag-id='67' id='sdPretag758247952sd'>VAMP2</sd-pretag> in the precipitates was probed by <sd-pretag parent-tag-id='421' id='sdPretag506915541sd'>immunoblotting</sd-pretag>, which was used as an indicator for trans-<sd-pretag parent-tag-id='420' id='sdPretag1635625656sd'>SNARE</sd-pretag> assembly between <sd-pretag parent-tag-id='419' id='sdPretag69278866sd'>SUVs</sd-pretag>.</p> </sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=16695
|
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"ext_tax_names": "Homo sapiens",
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"A0A0D9SG72",
"A0A1B0GTP9",
"A0A1B0GVQ5",
"A0A1B0GWF2"
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},
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}
] |
|
29150433
|
10.15252/embj.201796484
|
[BioStudies]_Tyrosine phosphorylation of Munc18-1 inhibits synaptic transmission by preventing SNARE assembly
|
2017
|
Figure 6
|
<sd-panel> <p><strong>Figure 6. Promoting helix 12 extension partly rescues <sd-pretag parent-tag-id='62' id='sdPretag562301709sd'>synaptic transmission</sd-pretag></strong></p> <p>Evoked and spontaneous release in autaptic <sd-pretag parent-gene-tag-id='63' parent-protein-tag-id='3' id='sdPretag108143713sd'>m<em>unc18-1</em></sd-pretag> null <sd-pretag parent-tag-id='57' id='sdPretag763677736sd'>hippocampal neurons</sd-pretag> expressing M18<sub>Y473D</sub>, M18<sub>Y473D/P335A</sub> or wild-type <sd-pretag parent-gene-tag-id='63' parent-protein-tag-id='3' id='sdPretag153413141sd'>Munc18-1</sd-pretag> as control.</p> <p>(A) Typical examples of single <sd-pretag role='component' id='sdPretag1005035773sme' type='cell' >EPSCs</sd-pretag>. <sd-pretag parent-tag-id='114' id='sdPretag665134415sd'>EPSC</sd-pretag> <sd-pretag parent-tag-id='705' id='sdPretag1387688476sd'>amplitude</sd-pretag> (M18<sub>WT</sub>: 2.98 ± 0.76 nA, n=11; M18<sub>Y473D</sub>: 0.042 ± 0.018 nA, n=11, M18<sub>Y473D/P335A</sub>: 2.02 ± 0.67 nA, n=7, Kruskal-Wallis test, p < 0.0004).</p> <p>(B) Typical traces of spontaneous release.</p> <p>(C) <sd-pretag parent-tag-id='651' id='sdPretag475945142sd'>mEPSC</sd-pretag> frequency (M18<sub>WT</sub>: 8.23 ± 2.29 Hz, n=11; M18<sub>Y473D</sub>: 0.096 ± 0.056 Hz, n=8, M18<sub>Y473D/P335A</sub>: 2.18 ± 1.02 Hz, n=11, Kruskal-Wallis test, p = 0.2390), <sd-pretag parent-tag-id='651' id='sdPretag1903083229sd'>mEPSC</sd-pretag> <sd-pretag parent-tag-id='705' id='sdPretag1215281450sd'>amplitude</sd-pretag> (M18<sub>WT</sub>: 16.7 ± 1.0 pA, n=11; M18<sub>Y473D</sub>: 21.6 ± 5.2 pA, n=10, M18<sub>Y473D/P335A</sub>: 14.8 ± 1.2 pA, n=6, ANOVA, p = 0.1465) and <sd-pretag parent-tag-id='648' id='sdPretag534886656sd'>decay time</sd-pretag> (M18<sub>WT</sub>: 2.53 ± 0.29 ms, n=11; M18<sub>Y473D</sub>: 3.79 ± 0.71 ms, n=10, M18<sub>Y473D/P335A</sub>: 2.85 ± 0.36 pA, n=6, Kruskal-Wallis test, p < 0.0003).</p> <p>(D) Depression of <sd-pretag parent-tag-id='114' id='sdPretag242227132sd'>EPSC</sd-pretag> <sd-pretag parent-tag-id='705' id='sdPretag802136901sd'>amplitude</sd-pretag> during a 10 Hz train. Inset shows first 4 pulses normalized to the first <sd-pretag parent-tag-id='114' id='sdPretag1985176399sd'>EPSC</sd-pretag>.</p> </sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=16696
|
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{
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] |
|
29150433
|
10.15252/embj.201796484
|
[BioStudies]_Tyrosine phosphorylation of Munc18-1 inhibits synaptic transmission by preventing SNARE assembly
|
2017
|
Figure 7
|
<sd-panel> <p><strong>Figure 7. Preventing <sd-pretag parent-tag-id='11' id='sdPretag1922911585sd'>tyrosine phosphorylation</sd-pretag> on <sd-pretag role='component' id='sdPretag80283068sme' type='organism' >Y473</sd-pretag> has no effect on <sd-pretag parent-tag-id='62' id='sdPretag915399370sd'>synaptic transmission</sd-pretag>.</strong></p> <p><sd-pretag parent-tag-id='62' id='sdPretag2127190895sd'>Synaptic transmission</sd-pretag> in <sd-pretag role='component' id='sdPretag1049434410sme' type='tissue' >autaptic</sd-pretag> excitatory <sd-pretag parent-gene-tag-id='63' parent-protein-tag-id='3' id='sdPretag1954738808sd'>m<em>unc18-1</em></sd-pretag> <sd-pretag parent-tag-id='60' id='sdPretag807665798sd'>neurons</sd-pretag> expressing M18<sub>WT</sub> or a non-phosphorylatable <sd-pretag parent-gene-tag-id='63' parent-protein-tag-id='3' id='sdPretag12022640sd'>Munc18-1</sd-pretag> variant, M18<sub>Y473F</sub>, was tested with whole-cell <sd-pretag parent-tag-id='91' id='sdPretag542318374sd'>patch clamp</sd-pretag> <sd-pretag parent-tag-id='92' id='sdPretag1853725259sd'>electrophysiology</sd-pretag>.</p> <p>(A) Evoked release upon action potential stimulation. Average <sd-pretag parent-tag-id='114' id='sdPretag551873957sd'>EPSC</sd-pretag> <sd-pretag parent-tag-id='705' id='sdPretag1039182310sd'>amplitude</sd-pretag> (M18<sub>WT</sub>: 3.78 ± 0.58 nA, n=22; M18<sub>Y473F</sub>: 4.10 ± 0.61 nA, n=20, Mann-Whitney U test, p = 0.7915). Typical responses are depicted on the top.</p> <p>(B) Average <sd-pretag parent-tag-id='651' id='sdPretag548459840sd'>mEPSC</sd-pretag> frequency (M18<sub>WT</sub>: 5.42 ± 1.86 Hz, n=17; M18<sub>Y473F</sub>: 4.42 ± 1.01 Hz, n=14, t-test with Welch correction, p = 0.6424), <sd-pretag parent-tag-id='651' id='sdPretag331337416sd'>mEPSC</sd-pretag> <sd-pretag parent-tag-id='705' id='sdPretag295272228sd'>amplitude</sd-pretag> (M18<sub>WT</sub>: 20.72 ± 0.7 pA, n=17; M18<sub>Y473F</sub>: 20,5 ± 0.9 pA, n=14, t-test, p = 0.8373) and <sd-pretag parent-tag-id='651' id='sdPretag1573553024sd'>mEPSC</sd-pretag> <sd-pretag parent-tag-id='648' id='sdPretag1563911046sd'>decay time</sd-pretag> (M18<sub>WT</sub>: 2.54 ± 0.20 ms, n=17; M18<sub>Y473F</sub>: 2.46 ± 0.18 ms, n=14, t-test, p = 0.7550). Example traces of spontaneous release are depicted on top.</p> <p>(C) <sd-pretag parent-tag-id='114' id='sdPretag1091630769sd'>EPSC</sd-pretag> depression during 10 Hz stimulation is normal.</p> <p>(D) Depression of <sd-pretag parent-tag-id='114' id='sdPretag1525566561sd'>EPSC</sd-pretag> charge during 40 Hz stimulation is normal. Inset shows the first 5 pulses.</p> <p>(E) <sd-pretag parent-tag-id='114' id='sdPretag1842696151sd'>EPSC</sd-pretag> <sd-pretag parent-tag-id='705' id='sdPretag2078437751sd'>amplitude</sd-pretag> recovery two seconds after an <sd-pretag parent-tag-id='106' id='sdPretag1783787377sd'>RRP</sd-pretag> depleting 40 Hz train. Average <sd-pretag parent-tag-id='114' id='sdPretag2102000388sd'>EPSC</sd-pretag> recovery (M18<sub>WT</sub>: 82.2 ± 6.7 %, n=17; M18<sub>Y473F</sub>: 65.5 ± 11.0 %, n=12, t-test, p = 0.1805).</p> <p>(F) The amount of <sd-pretag parent-tag-id='557' id='sdPretag987827262sd'>DSE</sd-pretag>-triggered <sd-pretag parent-tag-id='114' id='sdPretag1627037649sd'>EPSC</sd-pretag> depression was quantified by the ratio of the average <sd-pretag parent-tag-id='114' id='sdPretag487925486sd'>EPSC</sd-pretag> <sd-pretag parent-tag-id='705' id='sdPretag1549604723sd'>amplitude</sd-pretag> (taken over 4 pulses given at 0.2 Hz) before or immediately following 10 seconds depolarization to 0mV. Typical <sd-pretag role='component' id='sdPretag1088983674sme' type='cell' >EPSCs</sd-pretag> before and following <sd-pretag parent-tag-id='557' id='sdPretag669107691sd'>DSE</sd-pretag> induction are depicted on the left. Average <sd-pretag parent-tag-id='557' id='sdPretag375061048sd'>DSE</sd-pretag> (M18<sub>WT</sub>: 0.57 ± 0.04 fold, n=20; M18<sub>Y473F</sub>: 0.53 ± 0.04 fold, n=16, t-test, p = 0.5227).</p> <p>(G) <sd-pretag parent-tag-id='382' id='sdPretag1965085172sd'>PDBu</sd-pretag> was bath applied during 0.05 Hz stimulation. Maximum potentiation of <sd-pretag parent-tag-id='114' id='sdPretag2005720657sd'>EPSC</sd-pretag> <sd-pretag parent-tag-id='705' id='sdPretag980481007sd'>amplitude</sd-pretag> (M18<sub>WT</sub>: 2.56 ± 0.48 fold, n=7; M18<sub>Y473F</sub>: 2.82 ± 0.98 fold, n=8, t-test with Welch correction, p = 0.8168).</p> </sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=16697
|
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"ext_dbs": "NCBI gene",
"ext_ids": "20910",
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"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "20910",
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"type": "geneprod",
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},
{
"ext_dbs": "NCBI gene",
"ext_ids": "20910",
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"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "20910",
"original_type": "gene",
"role": "intervention",
"text": "M18",
"type": "geneprod",
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"O08599"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "20910",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "20910",
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"text": "Munc18-1",
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}
] |
|
29150433
|
10.15252/embj.201796484
|
[BioStudies]_Tyrosine phosphorylation of Munc18-1 inhibits synaptic transmission by preventing SNARE assembly
|
2017
|
Figure 8
|
<sd-panel> <p><strong>Figure 8. Structural modifications to Tyr473 strongly affect <sd-pretag parent-tag-id='62' id='sdPretag2053496059sd'>synaptic transmission</sd-pretag></strong></p> <p>(A) Using denatured IP, <sd-pretag parent-gene-tag-id='63' parent-protein-tag-id='3' id='sdPretag1979676455sd'>Munc18-1</sd-pretag> was pulled-down from cell lysate of <sd-pretag parent-tag-id='4' id='sdPretag1902617152sd'>HEK293T</sd-pretag> cells expressing M18<sub>WT</sub> or M18<sub>Y473A</sub> together with <sd-pretag role='component' id='sdPretag439890578sme' type='organism' >SFK</sd-pretag> kinases or an empty vector as control. <sd-pretag parent-gene-tag-id='63' parent-protein-tag-id='3' id='sdPretag4276310sd'>Munc18-1</sd-pretag> was then <sd-pretag parent-tag-id='421' id='sdPretag508983162sd'>immunoblotted</sd-pretag> for <sd-pretag parent-tag-id='11' id='sdPretag573829938sd'>tyrosine phosphorylation</sd-pretag> using the <sd-pretag role='assayed' id='sdPretag23982985sme' type='geneprod' >4G10</sd-pretag> antibody. The total amount of <sd-pretag parent-gene-tag-id='63' parent-protein-tag-id='3' id='sdPretag1100629476sd'>Munc18-1</sd-pretag> was detected after stripping and reblotting for <sd-pretag parent-gene-tag-id='63' parent-protein-tag-id='3' id='sdPretag2016772016sd'>Munc18-1</sd-pretag>.</p> <p>(B-G) <sd-pretag parent-gene-tag-id='63' parent-protein-tag-id='3' id='sdPretag1474897137sd'><em>Munc18-1</em></sd-pretag> null <sd-pretag parent-tag-id='57' id='sdPretag1129860483sd'>hippocampal neurons</sd-pretag> were rescued with wildtype <sd-pretag parent-tag-id='24' id='sdPretag1377474486sd'>Munc18</sd-pretag>-1a or a <sd-pretag parent-gene-tag-id='63' parent-protein-tag-id='3' id='sdPretag590282625sd'>Munc18-1</sd-pretag> mutant, Y473A, in which Y473 was replaced with alanine.</p> <p>(B) Typical <sd-pretag parent-tag-id='587' id='sdPretag1085814497sd'>confocal images</sd-pretag> of <sd-pretag parent-tag-id='60' id='sdPretag1893669197sd'>neurons</sd-pretag> stained for <sd-pretag parent-tag-id='66' id='sdPretag1590908298sd'>MAP2</sd-pretag>, <sd-pretag parent-tag-id='68' id='sdPretag1464310238sd'>Synaptobrevin</sd-pretag>/<sd-pretag parent-tag-id='67' id='sdPretag39835493sd'>VAMP2</sd-pretag> and <sd-pretag parent-gene-tag-id='63' parent-protein-tag-id='3' id='sdPretag575021855sd'>Munc18-1</sd-pretag>. Scale bar = 50πm.</p> <p>(C) Quantification of <sd-pretag parent-tag-id='587' id='sdPretag1875861432sd'>confocal images</sd-pretag>. Average <sd-pretag parent-tag-id='74' id='sdPretag2065333636sd'>synaptic</sd-pretag> <sd-pretag parent-gene-tag-id='63' parent-protein-tag-id='3' id='sdPretag1755070615sd'>Munc18-1</sd-pretag> intensity (M18<sub>WT</sub>: 389 ± 85 a.u., n=21; M18<sub>Y473A</sub>: 321 ± 48 a.u., n=20, t-test with Welch correction, p = 0.4868), <sd-pretag parent-tag-id='79' id='sdPretag1545472523sd'>somatic</sd-pretag> <sd-pretag parent-gene-tag-id='63' parent-protein-tag-id='3' id='sdPretag1977342674sd'>Munc18-1</sd-pretag> intensity (M18<sub>WT</sub>: 328 ± 49 a.u., n=21; M18<sub>Y473A</sub>: 245 ± 42 a.u., n=20, t-test, p = 0.2810), <sd-pretag parent-tag-id='77' id='sdPretag1212760309sd'>synapse number</sd-pretag> (M18<sub>WT</sub>: 129 ± 14, n=21; M18<sub>Y473A</sub>: 159 ± 16, n=20, t-test, p = 0.1548) and <sd-pretag parent-tag-id='78' id='sdPretag1522243343sd'>dendrite length</sd-pretag> (M18<sub>WT</sub>: 0.433 ± 0.028, n=21; M18<sub>Y473A</sub>: 0.461 ± 0.037, n=20, t-test, p = 0.5473).</p> <p>(D) Evoked release upon action potential stimulation. Average <sd-pretag parent-tag-id='114' id='sdPretag1209624382sd'>EPSC</sd-pretag> <sd-pretag parent-tag-id='705' id='sdPretag1081559606sd'>amplitude</sd-pretag> (M18<sub>WT</sub>: 7.96 ± 0.94 nA, n=30; M18<sub>Y473A</sub>: 1.44 ± 0.34 nA, n=33, t-test with Welch correction, p < 0.0001). Typical responses are depicted on the right.</p> <p>(E) Release by hyperosmotic <sd-pretag parent-tag-id='101' id='sdPretag1428433649sd'>sucrose</sd-pretag> application (500mM, 3.5sec.) was used to assess the <sd-pretag parent-tag-id='106' id='sdPretag885569781sd'>RRP</sd-pretag>. Left: <sd-pretag parent-tag-id='106' id='sdPretag1533373317sd'>RRP</sd-pretag> charge (M18<sub>WT</sub>: 1.68 ± 0.64 nC, n=13; M18<sub>Y473A</sub>: 0.27 ± 0.08 nC, n=13, t-test with Welch correction, p = 0.0487). Typical responses are depicted in the middle. Right: vesicular release probability per <sd-pretag parent-tag-id='60' id='sdPretag192944543sd'>neuron</sd-pretag> (<sd-pretag parent-tag-id='114' id='sdPretag2049219749sd'>EPSC</sd-pretag> charge / <sd-pretag parent-tag-id='106' id='sdPretag1470693293sd'>RRP</sd-pretag> charge). Mean <sd-pretag role='intervention' id='sdPretag1542185263sme' type='geneprod' >Pves</sd-pretag> (M18<sub>WT</sub>: 6.75 ± 0.77%, n=13; M18<sub>Y473A</sub>: 1.98 ± 0.72%, n=13, t-test, p = 0.0001).</p> <p>(F) Top: example traces of <sd-pretag parent-tag-id='658' id='sdPretag1328787213sd'>spontaneous release of single vesicles</sd-pretag> (<sd-pretag parent-tag-id='651' id='sdPretag1051130482sd'>mEPSCs</sd-pretag>). Average <sd-pretag parent-tag-id='651' id='sdPretag639694794sd'>mEPSC</sd-pretag> frequency (M18<sub>WT</sub>: 20.18 ± 5.18 Hz, n=15; M18<sub>Y473A</sub>: 0.48 ± 0.15 Hz, n=20, t-test with Welch correction, p = 0.0019), <sd-pretag parent-tag-id='705' id='sdPretag1246416449sd'>amplitude</sd-pretag> (M18<sub>WT</sub>: 26.0 ± 1.7 pA, n=15; M18<sub>Y473A</sub>: 24.5 ± 1.6 pA, n=20, t-test, p = 0.5334) and <sd-pretag parent-tag-id='648' id='sdPretag2118252641sd'>decay time</sd-pretag> (M18<sub>WT</sub>: 1.98 ± 0.10 ms, n=15; M18<sub>Y473A</sub>: 2.13 ± 0.17 ms, n=20, t-test with Welch correction, p = 0.4499).</p> <p>(G) <sd-pretag category='assay' id='sdPretag823394951sme'>Typical electron microscopy</sd-pretag> images from rescued autaptic <sd-pretag role='component' id='sdPretag68570553sme' type='tissue' >hippocampal</sd-pretag> <sd-pretag parent-gene-tag-id='63' parent-protein-tag-id='3' id='sdPretag639297529sd'><em>Munc18-1</em></sd-pretag> null <sd-pretag parent-tag-id='60' id='sdPretag884614512sd'>neurons</sd-pretag> (scale bar = 100 nm). <sd-pretag parent-tag-id='60' id='sdPretag44045985sd'>Neurons</sd-pretag> expressing M18<sub>Y473A</sub> have less <sd-pretag parent-tag-id='665' id='sdPretag1631288937sd'>synaptic vesicles</sd-pretag> (SV) <sd-pretag parent-tag-id='224' id='sdPretag1146857975sd'>docked</sd-pretag> at the <sd-pretag parent-tag-id='183' id='sdPretag1768987907sd'>active zone</sd-pretag>. Average <sd-pretag parent-tag-id='216' id='sdPretag1853833704sd'>number of docked SV</sd-pretag> (M18<sub>WT</sub>: 7.63 ± 0.15 <sd-pretag role='component' id='sdPretag1719741424sme' type='subcellular' >SVs</sd-pretag>; M18<sub>Y473A</sub>: 5.71 ± 0.28 <sd-pretag role='component' id='sdPretag1614147742sme' type='subcellular' >SVs</sd-pretag>, multilevel analysis, p < 0.001), total number of <sd-pretag role='component' id='sdPretag820854014sme' type='subcellular' >SVs</sd-pretag> (M18<sub>WT</sub>: 142 ± 11 <sd-pretag role='component' id='sdPretag1004939276sme' type='subcellular' >SVs</sd-pretag>; M18<sub>Y473A</sub>: 120 ± 12 <sd-pretag role='component' id='sdPretag194609083sme' type='subcellular' >SVs</sd-pretag>, multilevel analysis, p = 0.077), <sd-pretag parent-tag-id='183' id='sdPretag1015886443sd'>active zone</sd-pretag> (Munch et al.) <sd-pretag parent-tag-id='669' id='sdPretag1735932453sd'>length</sd-pretag> (M18<sub>WT</sub>: 561 ± 24 nm; M18<sub>Y473A</sub>: 501 ± 21 nm, multilevel analysis, p = 0.015) and <sd-pretag parent-tag-id='224' id='sdPretag121985505sd'>docked</sd-pretag> <sd-pretag role='component' id='sdPretag62844698sme' type='subcellular' >SVs</sd-pretag> per <sd-pretag parent-tag-id='215' id='sdPretag967434887sd'>AZ length</sd-pretag> (M18<sub>WT</sub>: 0.0140 ± 0.0006 <sd-pretag parent-tag-id='224' id='sdPretag330388909sd'>docked</sd-pretag> <sd-pretag role='component' id='sdPretag1779823754sme' type='subcellular' >SVs</sd-pretag>/nm AZ; M18<sub>Y473A</sub>: 0.0117 ± 0.0005 <sd-pretag parent-tag-id='224' id='sdPretag87990962sd'>docked</sd-pretag> <sd-pretag role='component' id='sdPretag1236388032sme' type='subcellular' >SVs</sd-pretag>/nm AZ, multilevel analysis, p = 0.003). M18<sub>WT</sub> : N=6 <sd-pretag parent-tag-id='173' id='sdPretag542310306sd'>autaptic neurons</sd-pretag>, n=137 <sd-pretag parent-tag-id='144' id='sdPretag23229179sd'>synapses</sd-pretag>; M18<sub>Y473A</sub>: N=8 <sd-pretag parent-tag-id='173' id='sdPretag767718292sd'>autaptic neurons</sd-pretag>, n=136 <sd-pretag parent-tag-id='144' id='sdPretag131200703sd'>synapses</sd-pretag>.</p> </sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=16698
|
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},
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}
] |
|
29150433
|
10.15252/embj.201796484
|
[BioStudies]_Tyrosine phosphorylation of Munc18-1 inhibits synaptic transmission by preventing SNARE assembly
|
2017
|
Figure 9
|
<sd-panel> <p><strong>Figure 9. Altered short-term plasticity in <sd-pretag parent-tag-id='60' id='sdPretag224003702sd'>neurons</sd-pretag> expressing M18<sub>Y473A</sub>.</strong></p> <p><sd-pretag role='component' id='sdPretag999559242sme' type='tissue' >Autaptic</sd-pretag> excitatory <sd-pretag parent-protein-tag-id='3' id='sdPretag2043882801sd' parent-gene-tag-id='63'><em>munc18-1</em></sd-pretag> <sd-pretag parent-tag-id='60' id='sdPretag809625707sd'>neurons</sd-pretag> expressing M18<sub>WT</sub> or M18<sub>Y473A</sub> were subjected to stimulation trains of 100 pulses at different frequencies.</p> <p>(A) Absolute <sd-pretag parent-tag-id='114' id='sdPretag2129061305sd'>EPSC</sd-pretag> <sd-pretag parent-tag-id='705' id='sdPretag461563421sd'>amplitudes</sd-pretag> during a 10 Hz train.</p> <p>(B) <sd-pretag parent-tag-id='114' id='sdPretag783915936sd'>EPSC</sd-pretag> <sd-pretag parent-tag-id='705' id='sdPretag1693055326sd'>amplitudes</sd-pretag> during a 10 Hz train normalized to the first <sd-pretag parent-tag-id='114' id='sdPretag1164847659sd'>EPSC</sd-pretag>.</p> <p>(C) Top: example traces of the currents evoked by 40 Hz stimulation. Bottom right: first 5 pulses of the 40 Hz train. Far right: transferred charge during 40 Hz train. Insert shows total charge transferred during entire 40 Hz train (M18<sub>WT</sub>: 2.63 ± 0.38 nC; M18<sub>Y473A</sub>: 2.93 ± 0.54 nC, t test, p = 0.6630).</p> <p>(D) <sd-pretag parent-tag-id='114' id='sdPretag1059348216sd'>EPSC</sd-pretag> augmentation is calculated by dividing the <sd-pretag parent-tag-id='114' id='sdPretag885896490sd'>EPSC</sd-pretag> <sd-pretag parent-tag-id='705' id='sdPretag425567471sd'>amplitude</sd-pretag> of a single pulse after a stimulation train by the <sd-pretag parent-tag-id='705' id='sdPretag343167893sd'>amplitude</sd-pretag> of the first <sd-pretag parent-tag-id='114' id='sdPretag1896521978sd'>EPSC</sd-pretag> within this train. Mean augmentation after 5 Hz train (M18<sub>WT</sub>: 0.54 ± 0.05, n=8; M18<sub>Y473A</sub>: 2.88 ± 0.47, n=10; Unpaired t-test with Welch correction, p = 0.0008), 10 Hz train (M18<sub>WT</sub>: 0.70 ± 0.10, n=8; M18<sub>Y473A</sub>: 5.39 ± 0.77, n=10; Unpaired t-test with Welch correction, p = 0.0002) and 40 Hz train (M18<sub>WT</sub>: 0.93 ± 0.11, n=8; M18<sub>Y473A</sub>: 8.77 ± 1.52, n=10; Unpaired t-test with Welch correction, p = 0.0006).</p> <p>(E) A single action potential or <sd-pretag parent-tag-id='101' id='sdPretag797940444sd'>sucrose</sd-pretag> application (500 mM, 3.5 sec.) was given before (naive) or two seconds after <sd-pretag parent-tag-id='334' id='sdPretag521830782sd'>HFS</sd-pretag> (100 pulses at 40 Hz). Average <sd-pretag parent-tag-id='114' id='sdPretag1109798742sd'>EPSC</sd-pretag> charge M18<sub>WT</sub> (Naive: 70.9 ± 19.5 pC, after <sd-pretag parent-tag-id='334' id='sdPretag215557698sd'>HFS</sd-pretag>: 75.4 ± 17.4 pC, n=12, Paired t-test, p = 0.4049). Average <sd-pretag parent-tag-id='114' id='sdPretag1739169240sd'>EPSC</sd-pretag> charge M18<sub>Y473A</sub> (naive: 10.3 ± 4.5 pC, after <sd-pretag parent-tag-id='334' id='sdPretag142951065sd'>HFS</sd-pretag>: 46.2 ± 14.5 pC, n=13, Wilcoxon matched-pairs signed-ranks test, p = 0.0005). Average <sd-pretag parent-tag-id='106' id='sdPretag1663399992sd'>RRP</sd-pretag> size M18<sub>WT</sub> (naive: 1.73 ± 0.69 nC, after <sd-pretag parent-tag-id='334' id='sdPretag84104186sd'>HFS</sd-pretag>: 1.34 ± 0.54 nC, n=12, paired t-test, p = 0.0557) Average <sd-pretag parent-tag-id='106' id='sdPretag249611877sd'>RRP</sd-pretag> size M18<sub>Y473A</sub> (naive: 0.268 ± 0.075 nC, after <sd-pretag parent-tag-id='334' id='sdPretag1127861370sd'>HFS</sd-pretag>: 0.439 ± 0.107 nC, n=13, paired t-test, p = 0.0100). Average Pves M18<sub>WT</sub> (<sd-pretag parent-tag-id='114' id='sdPretag1938307779sd'>EPSC</sd-pretag> charge / <sd-pretag parent-tag-id='106' id='sdPretag1362902227sd'>RRP</sd-pretag> charge * 100) (Naive: 7.07 ± 0.76 %, after <sd-pretag parent-tag-id='334' id='sdPretag1882502711sd'>HFS</sd-pretag>: 10.6 ± 1.6 %, n=12, paired t-test, p = 0.0201). Average Pves M18<sub>Y473A</sub> (naive: 1.98 ± 0.72 %, 12.2 ± 2.8 %, n=13, paired t-test, p = 0.0021).</p> <p>Expanded View Figure Legends</p> </sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=16699
|
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|
10.15252/embj.2021108016
|
AKT2 reduces IFNβ1 production to modulate anti-viral responses and systemic lupus erythematosus
|
2021
|
Figure 1
|
<p><strong>Figure 1. <em>Akt2</em> expression is negatively correlated with IFNβ1 production</strong></p><p>A The mRNA value of <em>AKT2</em> was analyzed in the GEO Profiles from the liver explant of Hepatitis B virus (HBV)-associated acute liver failure (ALF) patients (GDS4387/225471_s_at), and from bronchial epithelial cells with pandemic and seasonal H1N1 influenza virus infections <em>in vitro</em> (GDS4855/203808_at). normal, n=10; HBV, n=17; control, n=3; influenza A, n=9.</p><p>B The mRNA expression of <em>Akt2</em> in the brain homogenates of WT mice with JEV injection (5.0×10<sup>6</sup> PFU/g, i.v.) or in the lung of WT mice with H7N9 (10<sup>5.5</sup> EID50, i.n.) and PR8 infection (10 LD50, i.n.) were detected by quantitative reverse transcription-PCR (qRT-PCR). Mock, n=4; JEV, n=12; PBS, n=6; H7N9, n=4; PR8, n=8.</p><p>C The qRT-PCR analysis of <em>Akt2</em> mRNA in PEMs stimulated with lipo-poly(I:C) (1 μg/mL), lipo-poly(A:T) (1 μg/mL), lipo-ISD (3 μg/mL) or HSV-1 (MOI, 1) for 6 hours. n=3, respectively.</p><p>D The mRNA of <em>Akt2</em> (red line) and <em>Ifnb1</em> (black line) were analyzed by qRT-PC in the mock and VSV (MOI, 1) or LM (MOI, 1)-stimulated PEMs or BMDMs at the indicated time. Mock and VSV, n=4; mock and LM, n≥3.</p><p>E The mRNA levels of <em>Akt2</em> in WT (n=3) and <em>Ifnar1</em> KO (n=3) PEMs stimulated with VSV and lipo-ISD for 6 hours were detected by qRT-PCR.</p><p>F PEMs were pretreated with the indicate inhibitors for 2 hours and stimulated with recombined of IFNβ1 (1 μg/mL) for another 3 hours, followed by qRT-PCR for detection of the <em>Akt2</em> mRNA levels. DMSO, n=2; inhibitors, n=3.</p><p>G-H PEMs were pretreated with DMSO or AKT2 inhibitor CCT128930 (10 μM) (G) for 2 hours, or knocked down of <em>Akt2</em> with si<em>Akt2</em>-1 (20 nM) for 48 hours (H), then the mRNA level of <em>Ifnb1</em> was measured by qRT-PCR after lipo-poly(I:C), lipo-poly(A:T), lipo-ISD, VSV, or HSV-1 stimulation for another 6 hours. n=3, respectively.</p><p>Data information: *<em>P</em> < 0.05, **<em>P</em> < 0.01, ***<em>P</em> < 0.001, ****<em>P</em> < 0.0001 and ns, not significant (<em>P</em> > 0.05); using unpaired <em>t</em>-test (A, B left panel), or one-way ANOVA test (B right panel, C and F), or two-way ANOVA test (E, G and H). Data are from two (F) or at least three independent biological replicates (C-E, G, H). Error bars (A and B, mean ± SD; C-H, mean ± SEM). Source data are available online for this figure.</p>
|
https://api.sourcedata.io/file.php?figure_id=45878
|
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||
10.15252/embj.2021108016
|
AKT2 reduces IFNβ1 production to modulate anti-viral responses and systemic lupus erythematosus
|
2021
|
Figure 2
|
<p><strong>Figure 2. AKT2 kinase activity is indispensable to attenuate I-IFN production in macrophages and in zebrafish larvae</strong></p><p>A-B qRT-PCR detection for the mRNA expression of <em>Ifnb1</em> (A), <em>Ifna4</em>, <em>Cxcl10</em> and <em>Ccl5</em> (B) in WT (n=3) and <em>Akt2</em> KO (n=3) PEMs stimulated with lipo-poly(I:C), VSV, lipo-poly(A:T), lipo-ISD or HSV-1 for 6 hours.</p><p>C The expression of <em>Ifnb1</em> mRNA level by qRT-PCR in WT (n=3) and <em>Akt2</em> KO (n=3) PEMs treated with poly(I:C) (10 μg/mL) for 6 hours (left panel) or LPS (1 μg/mL) for 2 hours (right panel).</p><p>D The expression of <em>Ifnb1</em> in WT (n=3) and <em>Akt2</em> KO (n=3) primary-MEFs with VSV treatment (MOI, 0.1) for 6 hours was measured by qRT-PCR (left panel). After VSV treatment for 3 hours, the culture suspension was discarded and wash 3 times with PBS, then primary-MEFs was cultured with fresh medium for another 15 hours for analysis of the VSV-infected (GFP) primary-MEFs by fluorescence microscope (middle panel, representative images) and by FACS assay (right panel). Bar, 100 μm.</p><p>E MEF (left panel, n=3) and HEK293T cells (right panel, n=3) were transfected with AKT2 for 24 hours and stimulated with VSV for 6 hours, then cells were harvested for detection the mRNA expression of <em>Ifnb1</em> by qRT-PCR.</p><p>F IFNβ1 luciferase assays of HEK293T cells with transfection of AKT2/AKT2-T309A/S474A and TBK1 (n=3) or infection of VSV (n=3). Protein expression levels are shown in Figure EV2F.</p><p>G Zebrafish larva at 48 hour after fertilization were micro-injected GFP-fused VSV (1 × 10<sup>3</sup> PFU/larvae) for 18 hours, then the representative images of VSV-infected zebrafish larva were collected by fluorescence microscope. The infected area (GFP) and macrophages (Red) are indicated by arrows. Bars, 200 μm.</p><p>H Zebrafish larvae were overexpressed the indicated protein for 48 hours and challenged with VSV for another 6 hours, then the mRNA levels of <em>ifn1</em> in zebrafish larvae were measured by qRT-PCR (left panel). Every dot represents three zebrafish embryos. Horizontal square bracket shows the statistical analysis of the comparison with 'PBS mock', the rest shows the comparison with 'PBS VSV'. PBS mock, n=5; PBS VSV, n=13; AKT2 VSV, n=7; AKT2-T309A/S474A VSV, n=9. H&E staining (middle panel) and survival rates (Kaplan-Meier curve) (right panel) were collected from zebrafish larvae after VSV micro-injection for 18 hours or longer. The arrows indicated the VSV-infected eye and skeletal muscle in zebrafish larvae. Bars, 100 μm.</p><p>Data information: *<em>P</em> < 0.05, **<em>P</em> < 0.01, ***<em>P</em> < 0.001, ****<em>P</em> < 0.0001 and ns, not significant (<em>P</em> > 0.05); using a one-way ANOVA test (E, F, H left panel), or two-way ANOVA test (A-C, D left and right panel), or log-rank (Mantel-Cox) test (H right panel). Data are from three independent experiments (A-C, D left and right panel, E, F) or representative of three independent biological replicates (D middle panel, G, H). Error bars (A-F, mean ± SEM; H, mean ± SD). Source data are available online for this figure.</p>
|
https://api.sourcedata.io/file.php?figure_id=45879
|
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||
10.15252/embj.2021108016
|
AKT2 reduces IFNβ1 production to modulate anti-viral responses and systemic lupus erythematosus
|
2021
|
Figure 3
|
<p><strong>Figure 3. AKT2 restrains IRF3 nuclear translocation via 14-3-3ε</strong></p><p>A and B IFNβ1 luciferase assays (upper panels) in HEK293T (A) and HEK293T-<em>IRF3</em> KO (B) cells transfected with the indicated plasmids or infected with VSV. Immunoblot analysis showed the indicated constructs in HEK293T cells (bottom panels). n=3, respectively.</p><p>C The mRNA levels of <em>Ifnb1</em> were measured by qRT-PCR in WT (n=3) and <em>Akt2</em> KO (n=3) PEMs with <em>Irf3</em> knockdown for 48 hours and VSV treatment for 6 hours.</p><p>D WT and <em>Akt2</em> KO PEMs were infected with or without VSV for 6 hours. Then, cell lysates of WT or Akt2 KO PEMs were prepared for immunoprecipitation using anti-AKT2 antibody, followed by immunoblotting using anti-IRF3 antibody (left panel). Alternatively, cell lysates were prepared for immunoprecipitation using anti-IRF3 antibody, followed by immunoblotting using anti-AKT2 antibody (right panel) to detect the endogenous interaction between AKT2 and IRF3.</p><p>E Immunoblot analysis of GST-AKT2 and His-IRF3 interaction in a GST pull-down assay.</p><p>F Immunoassay of IRF3 in dimer or monomer form by native-gel and p-IRF3 (Ser396), p-TBK1 (Ser172), AKT2 and ACTIN by SDS-gel in WT and <em>Akt2</em> KO PEMs with VSV stimulation for 6 hours.</p><p>G Immunofluorescent microscopic imaging for (left panel) and statistics analysis (right panel) for IRF3 nuclear translocation in WT and <em>Akt2</em> KO PEMs at 6 hour post-VSV infection. IRF3 (red), Nuclei (Hoechst, green). The white arrows indicate the nuclei with IRF3 translocation. Mock, n=2; VSV, n=3. Bar, 20 μm.</p><p>H Immunoassay of IRF3, AKT2, LaminB1 and GAPDH in the nuclear and cytoplasmic fractions from the WT and <em>Akt2</em> KO PEMs after VSV treatment for 6 hours. Tubulin and LaminB1 were used as cytoplasmic and nucleic protein loading control respectively.</p><p>I Immunoassay of IRF3, SP1 and Tubulin in the nuclear and cytoplasmic fractions of the HEK293T cells overexpressed with indicated constructs for 24 hours and stimulated with VSV for 6 hours. Tubulin and SP1 served as cytoplasmic and nucleic protein loading control respectively.</p><p>J IFNβ1 luciferases assays were performed in HEK293T cells transfected with AKT2 and 14-3-3ε followed by VSV treatment. n=3, respectively.</p><p>K qRT-PCR analysis for the <em>Ifnb1</em> mRNA levels in VSV-stimulated WT and <em>Akt2</em> KO PEMs with <em>14-3-3ε</em> siRNA pretreatment. n=3, respectively.</p><p>Data information: *<em>P</em> < 0.05, **<em>P</em> < 0.01, ***<em>P</em> < 0.001, ****<em>P</em> < 0.0001 and ns, not significant (<em>P</em> > 0.05); using a one-way ANOVA (A, B, J), or two-way ANOVA test (C, G right panel, K). Data are from three independent experiments (A-C, J and K), or representative of two or three independent biological replicates (D-I). Error bars (A-C, G, J and K, mean ± SEM). Source data are available online for this figure.</p>
|
https://api.sourcedata.io/file.php?figure_id=45881
|
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||
10.15252/embj.2021108016
|
AKT2 reduces IFNβ1 production to modulate anti-viral responses and systemic lupus erythematosus
|
2021
|
Figure 4
|
<p><strong>Figure 4. AKT2 phosphorylates IRF3 at Thr207 and blocks IRF3 activation</strong></p><p>A Immunoblot analysis of IRF3 in the cytoplasmic and nucleic fractions of HEK293T-<em>IRF3</em> KO cells with overexpression of IRF3 and AKT2 or AKT2-S309A/T474A.</p><p>B Immunoblot analysis of <em>in vitro</em> kinase assay by the phosphorylation-gel. HA-AKT2 was immunoprecipitated from HEK293T cells by anti-HA/IgG antibody and Protein-G beads, and His-IRF3 was purified from <em>E.coli</em> cells by anti-His agarose beads. His-IRF3 alone and anti-IgG-beads added with His-IRF3 served as control. The arrow indicated the phosphorylated IRF3.</p><p>C IFNβ1 luciferase assays and immunoblot analysis showed the HEK293T-<em>IRF3</em> KO cells with overexpression of the indicated plasmids for 24 hours and VSV infection for 6 hours. n=3, respectively.</p><p>D Immunofluorescence microscopy (top panel) of AKT2-, Flag-IRF3- or Flag-IRF3-T207A-overexpressed MEF cells after poly(A:T) stimulation for 6 hours. Flag (IRF3, red) and Hoechst (nuclei, blue). Immunoassay of nuclear-cytoplasm extractions (bottom panel) from HEK293T-<em>IRF3</em> KO cells with overexpression of the indicated plasmids for 24 hours followed by VSV infection for 6 hours. GAPDH and SP1 were used as cytoplasmic and nucleic protein loading control respectively. Bar, 20 μm.</p><p>E HEK293T-IRF3 KO cells were overexpressed with indicated plasmids, and the cell lysate was conducted to immunoblot analysis by phosphorylation-gel for the assay of phosphorylated IRF3 (the upper band) by anti-Flag antibody.</p><p>F Survival rates (left panel) until 72 hours and H&E staining (right panel) at 18 hours of the zebrafish larvae with indicated protein expression and VSV challenge. The arrows indicated the VSV-infected eye and skeletal muscle in zebrafish larvae. Bars, 100 μm.</p><p>G qRT-PCR analysis of the <em>VSV</em> copies in overexpressed zebrafish embryos with the VSV challenge at 18 hours later. Every dot represents three zebrafish embryos. Horizontal vertical square bracket shows the statistical analysis of comparison with 'PBS mock', the rest shows the comparison with 'PBS VSV'. PBS mock, n=15; PBS VSV, n=9; IRF3 VSV, n=16; IRF3-T207A VSV, n=11; AKT2 VSV, n=14; AKT2-T309A/S474A VSV, n=9; IRF3 + AKT2 VSV, n=9; IRF3 + AKT2-T309A/S474A VSV, n=13; IRF3-T207A + AKT2 VSV, n=10.</p><p>H The survival rates of over-expressed zebrafish larvae as long as 72 hours after the VSV challenge.</p><p>Data information: *<em>P</em> < 0.05, **<em>P</em> < 0.01, ***<em>P</em> < 0.001, ****<em>P</em> < 0.0001 and ns, not significant (P > 0.05); using a one-way ANOVA test (G), or two-way ANOVA test (C), or log-rank (Mantel-Cox) test (F left panel and H). Data are from at least three independent experiments (C), or representative of three independent experiments (A, B, D-H). Error bars (C, mean ± SEM; G, mean ± SD). Source data are available online for this figure.</p>
|
https://api.sourcedata.io/file.php?figure_id=45883
|
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10.15252/embj.2021108016
|
AKT2 reduces IFNβ1 production to modulate anti-viral responses and systemic lupus erythematosus
|
2021
|
Figure 5
|
<p><strong>Figure 5. Targeting AKT2 enhances antiviral defense in mice</strong></p><p>A FACS analysis of the percentage of macrophages (CD11b<sup>+</sup> F4/80<sup>+</sup> cells) in WT and <em>Akt2</em> KO BM and spleen.</p><p>B Survival rates of WT and <em>Akt2</em> KO mice after lethal dose injection of VSV during 120 hours (1 × 10<sup>7</sup> PFU/g, i.v.).</p><p>C qRT-PCR analysis of the <em>Ifnb1</em> mRNA expression in the liver (n=8), spleen (n=7) and lung (n=7) of WT or <em>Akt2</em> KO mice 6 hours after the injection of VSV (1 × 10<sup>6</sup> PFU/g, i.v.).</p><p>D IFNβ1 concentrations from WT (n=8) and <em>Akt2</em> KO (n=7) serum were detected by ELISA 3 hours after VSV infection (1 × 10<sup>6</sup> PFU/g, i.v.).</p><p>E WT and <em>Akt2</em> KO mice were injected with VSV for 24 hours (1 × 10<sup>6</sup> PFU/g, i.v.). Representative images of the VSV infected cells (GFP) were collected by fluorescence microscope (left panel) and the <em>VSV</em> copies (WT, n=6; <em>Akt2</em> KO n=7) were measured by qRT-PCR (right panel) in the liver of mice. Bar, 100 μm.</p><p>F-H Bone marrow cells from WT and <em>Akt2</em> KO mice (CD45.2) were adoptively transferred to lethally irradiated CD45.1 mice and infected with VSV. Survival rates (F left panel), serum IFNβ1 concentrations (F right panel, n=5), <em>VSV</em> copies (G, n=9) and representative images (H) were analyzed as Fig 5B, 5D and 5E, respectively. Bar, 100 μm.</p><p>I Survival rates of WT mice that were intraperitoneal injected with CCT128930 (20 mg/kg) twice every other day before VSV infection (1 × 10<sup>7</sup> PFU/g, i.v.).</p><p>Data information: *<em>P</em> < 0.05, **<em>P</em> < 0.01; using a paired <em>t</em>-test (C and F right panel), or unpaired <em>t</em>-test (D, E right panel and G) or log-rank (Mantel-Cox) test (B, F left panel and I). Data are representative of three independent experiments respectively (A-I), in which the different groups of mice were sacrificed and quantified for indicated experimental purposes (C-E, F right panel, G). Error bars (D, E right panel and G, mean ± SD). Source data are available online for this figure.</p>
|
https://api.sourcedata.io/file.php?figure_id=45885
|
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{
"ext_dbs": "NCBI gene",
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] |
||
10.15252/embj.2021108016
|
AKT2 reduces IFNβ1 production to modulate anti-viral responses and systemic lupus erythematosus
|
2021
|
Figure 6
|
<p><strong>Figure 6. <em>Akt2</em> is associated with the pathology of SLE</strong></p><p>A Representative images of lungs and spleens from WT and <em>Akt2</em> KO mice treated with TMPD (500μL per mouse) for 2 weeks, and the corresponding H&E-staining of the tissues. Bar, 200 μm.</p><p>B-C qRT-PCR analysis of the relative <em>Ifnb1</em> and <em>Ifna4</em> mRNA expression levels in PICs (n≥5) and PBMCs (n≥4) (B), and immunoblot analysis of IRF3, LaminB1 and GAPDH in the PIC nuclear and cytoplasmic fractions (C) from WT and <em>Akt2</em> KO mice treated with TMPD for 2 weeks. GAPDH and LaminB1 were used as cytoplasmic and nucleic protein loading control respectively.</p><p>D-E Representative images of lipogranulomas in peritoneal cavity (D), H&E-staining (E left panel) and immunofluorescence of IgG deposits (E right panel) in the kidney sections were collected from WT and <em>Akt2</em> KO bone marrow-reconstituted CD45.1 mice 12 weeks after TMPD treatment. Bar, 50 μm.</p><p>F-H Quantitative analysis of serum anti-dsDNA IgG antibody by ELISA (F, n≥4), mRNA expression levels of PIC <em>Ifnb1</em> and <em>Ifna4</em> by qRT-PCR (G, n≥4) and FACS analysis of the percentages of B220<sup>+</sup> and CD19<sup>+</sup>MHCⅡ<sup>+</sup> cells in PBMC (H, n≥4) from WT and <em>Akt2</em> KO bone marrow-reconstituted CD45.1 mice 12 weeks after TMPD treatment.</p><p>I qRT-PCR analysis of the relative mRNA expression levels of <em>AKT2</em> in PBMC isolated from SLE patients (n=9) or healthy donors (n=9).</p><p>J. qRT-PCR analysis of the relative mRNA expression levels of <em>AKT2</em> (left panel) and <em>IFNA</em> (middle panel) or <em>IFNβ1</em> (right panel) in CD14 positive monocytes isolated from SLE patients (n=9) or healthy donors (n=9).</p><p>K Immunofluorescence of IRF3 (Red), AKT2 (Green), DAPI (Blue, nucleus) in CD14<sup>+</sup> cells from SLE patients followed by analysis of the cells about mean amount of AKT2 in this cell as well as mean amount of IRF3 in the same nucleus with Image J software. Cells (n=39) were collected 3 patients. Bar, 2 μm.</p><p>Data information: *<em>P</em> < 0.05, **<em>P</em> < 0.01 and ****<em>P</em> < 0.0001; using unpaired <em>t</em>-test (B, G-I, J left panel), or two-way ANOVA test (F), or correlation analyses (J middle and right panels, K right panel). Data are pooled from different individuals (I, J, K right panel) or representative of three independent experiments (A-H, K left panel). Error bars (B, F-J, mean ± SD). Source data are available online for this figure.</p><p><strong>Expanded View Figures</strong></p>
|
https://api.sourcedata.io/file.php?figure_id=45887
|
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{
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] |
||
26941261
|
10.15252/emmm.201505714
|
Small molecule inhibitors of the Dishevelled-CXXC5 interaction are new drug candidates for bone anabolic osteoporosis therapy
|
2016
|
Figure 1
|
<p><strong>Fig</strong><strong>ure</strong><strong> 1. </strong><strong>Identification and </strong><strong>characterization</strong><strong> of small molecules competing Dvl-CXXC5 binding </strong><strong><em>in vitro.</em></strong></p>
<p>A. A scheme for <em>in vitro</em> screening method of small molecules competing Dvl-CXXC5 binding. Briefly, purified Dvl PDZ domain was attached to the polystyrene surface of each well of 96-well plates. Then, PolyR-DBM (ployarginine conjugated Dvl binding motif tagged with FITC) (Kim<em> et al</em>, 2015) was added to each well and allowed to bind to the Dvl PDZ domain; 10 µM small molecule compound was added to each well, and the compounds competing with Dvl PZD-PolyR-DBM binding were measured by a microplate reader to screen the compounds reducing fluorescence signal.</p>
<p>B . Screening results of compounds competing Dvl-CXXC5 interaction. Each 2 µM of the compounds was used for competing as described in Fig 1A. [<em>n</em>=3]</p>
<p>C, D<strong>. </strong>Primary calvaria cells were treated with 2 µM of each compound for 2 days. The cells were subjected to immunofluorescence analyses to visualize β-catenin (C; green). The relative numbers of β-catenin-positive nuclei were counted (D). [<em>n</em>=3]</p>
<p>E, F . The calvariae from 4-day-old mice were cultured <em>ex vivo </em>for 7 days with 2 µM of each compound. Representative calvaria sections were visualized by H&E staining (E). The calvaria thicknesses were measured from the images using Image Pro software (<strong>F</strong>). [<em>n</em>=3]</p>
<p>Data Information: For B, D<strong>,</strong> and F, the data are the mean ± s.d. (error bars), and significance was assessed using unpaired Student’s t-test.</p>
|
https://api.sourcedata.io/file.php?figure_id=6826
|
[
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"ext_ids": "Q91WA4",
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"ext_tax_names": "Mus musculus",
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"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "CXXC5",
"type": "geneprod",
"uniprot_ids": [
"Q91WA4"
]
},
{
"ext_dbs": "Uniprot///Uniprot///Uniprot",
"ext_ids": "Q61062///Q60838///P51141",
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"ncbi_gene_id": null,
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},
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"mapping_status": "mapped",
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"original_type": "protein",
"role": "assayed",
"text": "β-catenin",
"type": "geneprod",
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"Q02248"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q02248",
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"ext_tax_names": "Mus musculus",
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"uniprot_ids": [
"Q02248"
]
}
] |
|
26941261
|
10.15252/emmm.201505714
|
Small molecule inhibitors of the Dishevelled-CXXC5 interaction are new drug candidates for bone anabolic osteoporosis therapy
|
2016
|
Figure 2
|
<p><strong>Fig</strong><strong>ure</strong><strong> 2</strong><strong>. </strong><strong>DBM-mimetic binding </strong><strong>of KY-02061 on the Dvl PDZ domain.</strong></p>
<p>A . The chemical structure of KY-02061.</p>
<p>B . A competition curve for the Dvl-CXXC5 interaction by KY-02061.</p>
<p>C<strong>-</strong>E. NMR titration analyses for Dvl PZD domain with KY-02061. <sup>1</sup>H-<sup>15</sup>N-HSQC analyses were performed to analyze the interaction of <sup>15</sup>N-labelled Dvl-PDZ domain with KY-02061. The <sup>1</sup>H-<sup>15</sup>N-HSQC spectrum of different molar ratios (Dvl PDZ domain:KY-02061) are displayed as red (1:0), orange (1:10), purple (1:20), cyan (1:40), green (1:60) and blue (1:80) (C, residues with meaningful chemical shift change are indicated by arrows). Plot of chemical shift changes (Δδ) as a function of residue number in molecular ratio 1:80 (D, a red-colored line indicates the line for Δδ=0.05). The residues with Δδ greater than 0.05 are visualized as a stick model on the ribbon representation of the Dvl PDZ domain structure (E).</p>
<p>F. Molecular docking of Dvl binding motif (DBM) or KY-02061 to Dvl PDZ domain were analyzed by <em>in silico </em>experiments. The superimposed structure of DBM (green) and KY-02061 (yellow) on the surface of Dvl PDZ domain (gray) was visualized.</p>
|
https://api.sourcedata.io/file.php?figure_id=6827
|
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"text": "CXXC5",
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]
},
{
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{
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},
{
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},
{
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"text": "Dvl",
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},
{
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},
{
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"mapping_source": "unknown",
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"text": "Dvl",
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},
{
"ext_dbs": "Uniprot///Uniprot///Uniprot",
"ext_ids": "Q61062///Q60838///P51141",
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"ext_tax_names": "Mus musculus///Mus musculus///Mus musculus",
"mapping_source": "unknown",
"mapping_status": "unmapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "Dvl",
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"uniprot_ids": []
}
] |
|
26941261
|
10.15252/emmm.201505714
|
Small molecule inhibitors of the Dishevelled-CXXC5 interaction are new drug candidates for bone anabolic osteoporosis therapy
|
2016
|
Figure 3
|
<p><strong>Fig</strong><strong>ure</strong><strong> 3</strong><strong>. </strong><strong>Effect of KY-02061 on Wnt/</strong><strong>β</strong><strong>-catenin pathway,</strong><strong> osteoblast differentiation</strong><strong>,</strong><strong> and </strong><strong><em>ex vivo</em></strong><strong>-cultured calvaria growth.</strong></p>
<p>A . MC3T3E1 cells were transfected with pTOPFLASH together with pCMV-β-gal. After 24 h, the cells were treated with DMSO, KY-02061 in DMSO, or 5 µM PolyR-DBM for 2 days. The luciferase activities of whole cell lysates were measured and normalized with β-galactosidase activities. [<em>n</em>=3]</p>
<p>B . Primary calvaria cells were isolated from the calvariae of 4-day-old mice (Manton<em> et al</em>, 2007), and treated with DMSO or KY-02061 in DMSO for 4 days. ALP activity levels were visualized by ALP staining.</p>
<p>C<strong>. </strong>Primary calvaria cells were treated with DMSO or 5 µM KY-02061 in DMSO for 14 days. The cells were subjected to immunofluorescence analyses to visualize Runx2 (green) and β-catenin (red). The cell nuclei were counterstained with DAPI (blue).</p>
<p>D, E<strong>. </strong>Calvariae from 4-day-old mice were cultured <em>ex vivo </em>for 7 days with KY-02061 in DMSO (D). The calvaria thicknesses were measured from the stained sections using Image Pro software (E). [<em>n</em>=3]</p>
<p>Data Information: For <em>A</em> and <em>E</em>, the data are the mean ± s.d. (error bars), and significance was assessed using unpaired Student’s t-test.</p>
|
https://api.sourcedata.io/file.php?figure_id=6828
|
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"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "ALP",
"type": "geneprod",
"uniprot_ids": [
"P09242"
]
},
{
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{
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"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "Runx2",
"type": "geneprod",
"uniprot_ids": [
"Q08775"
]
}
] |
|
26941261
|
10.15252/emmm.201505714
|
Small molecule inhibitors of the Dishevelled-CXXC5 interaction are new drug candidates for bone anabolic osteoporosis therapy
|
2016
|
Figure 4
|
<p><strong>Fig</strong><strong>ure</strong> <strong>4. Binding of </strong><strong>KY-02327</strong><strong>, a KY-02061</strong> <strong>analog, on </strong><strong>Dvl PDZ domain</strong><strong>.</strong></p>
<p>A<strong>. </strong>The chemical structure of KY-02327.</p>
<p>B<strong>. </strong>A competition curve for the Dvl-CXXC5 interaction by KY-02327.</p>
<p>C. Fluorescence quenching plot of Dvl PDZ domain upon addition of different amounts of KY-02327. From top to bottom final moral ratio between Dvl PDZ and KY-02327 was, 1:0, 1:1, 1:2, 1:3, 1:4, 1:5, 1:6, 1:7, 1:8, 1:9, 1:10, 1:15, 1:20 and 1:25, respectively.</p>
<p>D-F<strong>. </strong><sup>1</sup>H-<sup>15</sup>N-HSQC analyses were performed to analyze the interaction of <sup>15</sup>N-labelled Dvl-PDZ domain with KY-02327. The <sup>1</sup>H-<sup>15</sup>N-HSQC spectrum of different molar ratios (Dvl PDZ domain:KY-02327) are displayed as red (1:0), yellow (1:5), green (1:10), and magenta (1:20) (D, residues with meaningful chemical shift change are indicated by arrows). Plot of chemical shift changes (Δδ) as a function of residue number in molecular ratio 1:20 (E, a red-colored line indicates the line for Δδ=0.05). The residues with Δδ greater than 0.05 are visualized as a stick model on the ribbon representation of the Dvl PDZ domain structure (F).</p>
<p>G<strong>. </strong>Molecular docking of KY-02061 or KY-02327 to Dvl PDZ domain were analyzed by <em>in silico </em>experiments. The superimposed structure of KY-02061 (yellow) and KY-02327 (cyan) on the surface of Dvl PDZ domain (gray) was visualized.</p>
|
https://api.sourcedata.io/file.php?figure_id=6829
|
[
{
"ext_dbs": "Uniprot",
"ext_ids": "Q91WA4",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "CXXC5",
"type": "geneprod",
"uniprot_ids": [
"Q91WA4"
]
},
{
"ext_dbs": "Uniprot///Uniprot///Uniprot",
"ext_ids": "Q61062///Q60838///P51141",
"ext_tax_ids": "10090///10090///10090",
"ext_tax_names": "Mus musculus///Mus musculus///Mus musculus",
"mapping_source": "unknown",
"mapping_status": "unmapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "Dvl",
"type": "geneprod",
"uniprot_ids": []
},
{
"ext_dbs": "Uniprot///Uniprot///Uniprot",
"ext_ids": "Q61062///Q60838///P51141",
"ext_tax_ids": "10090///10090///10090",
"ext_tax_names": "Mus musculus///Mus musculus///Mus musculus",
"mapping_source": "unknown",
"mapping_status": "unmapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "Dvl",
"type": "geneprod",
"uniprot_ids": []
},
{
"ext_dbs": "Uniprot///Uniprot///Uniprot",
"ext_ids": "Q61062///Q60838///P51141",
"ext_tax_ids": "10090///10090///10090",
"ext_tax_names": "Mus musculus///Mus musculus///Mus musculus",
"mapping_source": "unknown",
"mapping_status": "unmapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "Dvl",
"type": "geneprod",
"uniprot_ids": []
},
{
"ext_dbs": "Uniprot///Uniprot///Uniprot",
"ext_ids": "Q61062///Q60838///P51141",
"ext_tax_ids": "10090///10090///10090",
"ext_tax_names": "Mus musculus///Mus musculus///Mus musculus",
"mapping_source": "unknown",
"mapping_status": "unmapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "Dvl",
"type": "geneprod",
"uniprot_ids": []
},
{
"ext_dbs": "Uniprot///Uniprot///Uniprot",
"ext_ids": "Q61062///Q60838///P51141",
"ext_tax_ids": "10090///10090///10090",
"ext_tax_names": "Mus musculus///Mus musculus///Mus musculus",
"mapping_source": "unknown",
"mapping_status": "unmapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "Dvl",
"type": "geneprod",
"uniprot_ids": []
},
{
"ext_dbs": "Uniprot///Uniprot///Uniprot",
"ext_ids": "Q61062///Q60838///P51141",
"ext_tax_ids": "10090///10090///10090",
"ext_tax_names": "Mus musculus///Mus musculus///Mus musculus",
"mapping_source": "unknown",
"mapping_status": "unmapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "Dvl",
"type": "geneprod",
"uniprot_ids": []
},
{
"ext_dbs": "Uniprot///Uniprot///Uniprot",
"ext_ids": "Q61062///Q60838///P51141",
"ext_tax_ids": "10090///10090///10090",
"ext_tax_names": "Mus musculus///Mus musculus///Mus musculus",
"mapping_source": "unknown",
"mapping_status": "unmapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "Dvl",
"type": "geneprod",
"uniprot_ids": []
},
{
"ext_dbs": "Uniprot///Uniprot///Uniprot",
"ext_ids": "Q61062///Q60838///P51141",
"ext_tax_ids": "10090///10090///10090",
"ext_tax_names": "Mus musculus///Mus musculus///Mus musculus",
"mapping_source": "unknown",
"mapping_status": "unmapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "Dvl",
"type": "geneprod",
"uniprot_ids": []
}
] |
|
26941261
|
10.15252/emmm.201505714
|
Small molecule inhibitors of the Dishevelled-CXXC5 interaction are new drug candidates for bone anabolic osteoporosis therapy
|
2016
|
Figure 5
|
<p><strong>Fig</strong><strong>ure</strong><strong> 5. </strong><strong>Effects of KY-02327 on Wnt/</strong><strong>β</strong><strong>-catenin pathway and osteoblast differentiation in osteoblasts.</strong></p>
<p>A . MC3T3E1 cells were transfected with pTOPFLASH together with pCMV-β-gal. After 24 h, the cells were treated with indicated dose of KY-02327 for 2 days. The luciferase activities of whole cell lysates were measured and normalized with β-galactosidase activities. [<em>n</em>=3]</p>
<p>B-C . MC3T3E1 cells were treated with indicated concentrations of KY-02327 for 2 days. β-Catenin and α-tubulin were detected by immunoblot (B) or immunofluorescence (C) analyses. Nuclei were counterstained with DAPI (C, blue).</p>
<p>D. MC3T3E1 cells were treated with indicated concentrations of KY-02327 for 14 days. The mRNA level of collagen 1a (Col1a) was measured by quantitative real-time (qRT)-PCR. [<em>n</em>=3]</p>
<p>E. MC3T3E1 cells were treated with indicated concentrations of KY-02327 for 21 days. The mRNA level of osteocalcin (OCN) was measured by qRT-PCR. [<em>n</em>=3]</p>
<p>Data Information: For A, D<strong>,</strong> and E, the data are the mean ± s.d. (error bars), and significance was assessed using unpaired Student’s t-test.</p>
|
https://api.sourcedata.io/file.php?figure_id=6830
|
[
{
"ext_dbs": "Uniprot",
"ext_ids": "Q02248",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "β-Catenin",
"type": "geneprod",
"uniprot_ids": [
"Q02248"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q02248",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "β-Catenin",
"type": "geneprod",
"uniprot_ids": [
"Q02248"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "12842",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "12842",
"original_type": "gene",
"role": "assayed",
"text": "Col1a",
"type": "geneprod",
"uniprot_ids": [
"P11087"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "12842",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "12842",
"original_type": "gene",
"role": "assayed",
"text": "collagen 1a",
"type": "geneprod",
"uniprot_ids": [
"P11087"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "12096",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "12096",
"original_type": "gene",
"role": "assayed",
"text": "OCN",
"type": "geneprod",
"uniprot_ids": [
"P86546"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "12096",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "12096",
"original_type": "gene",
"role": "assayed",
"text": "osteocalcin",
"type": "geneprod",
"uniprot_ids": [
"P86546"
]
}
] |
|
26089099
|
10.15252/emmm.201505245
|
H19 lncRNA alters stromal cell growth via IGF signaling in the endometrium of women with endometriosis.
|
2015
|
Figure 1
|
<p>The expressions of <italic>H19</italic> and <italic>Igf1r</italic> are significantly decreased in the eutopic endometrium of women with endometriosis compared to those without endometriosis</p>
<p><list list-type="simple"><list-item><p>
A–F (A, B, D–F) RNA levels determined by RT–qPCR. Results are presented as mean ± SD,<italic>n</italic> = 10. <italic>P</italic>-values are indicated on the top of each plot. (C) Spearman correlation suggests an <italic>in vivo</italic> positive correlation between the expressions of <italic>H19</italic> and <italic>Igf1r</italic> in a statistically significant manner. Spearman correlation coefficient, <italic>P</italic>-values, and sample numbers are marked on the top left of the plot.
</p></list-item></list></p>
|
https://api.sourcedata.io/file.php?figure_id=6945
|
[
{
"ext_dbs": "NCBI gene",
"ext_ids": "283120",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "unmapped",
"mapping_status": "unmapped",
"ncbi_gene_id": "283120",
"original_type": "gene",
"role": "assayed",
"text": "H19",
"type": "geneprod",
"uniprot_ids": []
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "3480",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "3480",
"original_type": "gene",
"role": "assayed",
"text": "Igf1r",
"type": "geneprod",
"uniprot_ids": [
"P08069",
"C9J5X1"
]
}
] |
|
26089099
|
10.15252/emmm.201505245
|
H19 lncRNA alters stromal cell growth via IGF signaling in the endometrium of women with endometriosis.
|
2015
|
Figure 2
|
<p>H19 promotes <italic>Igf1r</italic> expression in endometrial stromal cells by inhibiting let-7</p>
<p><list list-type="simple"><list-item><p>
A–D Endometrial stromal cells from patients #166 and #80 were each transfected with a mixture of siCon (control siRNA) and microRNA inhibitor control (iCon), siH19 and iCon, or siH19 and iLet7 (let-7-specific inhibitor). RNA and proteins were analyzed at 48 h post-transfection. Combined results from the two patient cells are presented. Western blot gels from #166 cells are shown in (C). Quantitation of Western blots combining both patient cells are shown in (D).
</p></list-item><list-item><p>
E–H Endometrial stromal cells from patients #98 and #212S were each transfected with empty vector or pH19. RNA and proteins were analyzed 48 h post-transfection. Combined results from the two patient cells are presented. Western blot gels from #98 cells are shown in (G). Quantitation of Western blots combining both patient cells are shown in (H).
</p></list-item></list></p>
<p>Data information: Results are presented as mean ± SD, <italic>n</italic> = 6. <italic>P</italic>-values are indicated on the top of each plot.</p>
|
https://api.sourcedata.io/file.php?figure_id=6946
|
[
{
"ext_dbs": "NCBI gene",
"ext_ids": "283120",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "unmapped",
"mapping_status": "unmapped",
"ncbi_gene_id": "283120",
"original_type": "gene",
"role": "intervention",
"text": "H19",
"type": "geneprod",
"uniprot_ids": []
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "283120",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "unmapped",
"mapping_status": "unmapped",
"ncbi_gene_id": "283120",
"original_type": "gene",
"role": "assayed",
"text": "H19",
"type": "geneprod",
"uniprot_ids": []
},
{
"ext_dbs": "Rfam",
"ext_ids": "RF00027",
"ext_tax_ids": "",
"ext_tax_names": "",
"mapping_source": "unknown",
"mapping_status": "unmapped",
"ncbi_gene_id": null,
"original_type": "gene",
"role": "intervention",
"text": "let-7",
"type": "geneprod",
"uniprot_ids": []
},
{
"ext_dbs": "Rfam",
"ext_ids": "RF00027",
"ext_tax_ids": "",
"ext_tax_names": "",
"mapping_source": "unknown",
"mapping_status": "unmapped",
"ncbi_gene_id": null,
"original_type": "gene",
"role": "intervention",
"text": "Let7",
"type": "geneprod",
"uniprot_ids": []
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "283120",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "unmapped",
"mapping_status": "unmapped",
"ncbi_gene_id": "283120",
"original_type": "gene",
"role": "intervention",
"text": "H19",
"type": "geneprod",
"uniprot_ids": []
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "283120",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "unmapped",
"mapping_status": "unmapped",
"ncbi_gene_id": "283120",
"original_type": "gene",
"role": "intervention",
"text": "H19",
"type": "geneprod",
"uniprot_ids": []
},
{
"ext_dbs": "Rfam",
"ext_ids": "RF00027",
"ext_tax_ids": "",
"ext_tax_names": "",
"mapping_source": "unknown",
"mapping_status": "unmapped",
"ncbi_gene_id": null,
"original_type": "gene",
"role": "intervention",
"text": "let-7",
"type": "geneprod",
"uniprot_ids": []
},
{
"ext_dbs": "Rfam",
"ext_ids": "RF00027",
"ext_tax_ids": "",
"ext_tax_names": "",
"mapping_source": "unknown",
"mapping_status": "unmapped",
"ncbi_gene_id": null,
"original_type": "gene",
"role": "intervention",
"text": "Let7",
"type": "geneprod",
"uniprot_ids": []
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "283120",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "unmapped",
"mapping_status": "unmapped",
"ncbi_gene_id": "283120",
"original_type": "gene",
"role": "intervention",
"text": "H19",
"type": "geneprod",
"uniprot_ids": []
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "283120",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "unmapped",
"mapping_status": "unmapped",
"ncbi_gene_id": "283120",
"original_type": "gene",
"role": "intervention",
"text": "H19",
"type": "geneprod",
"uniprot_ids": []
}
] |
|
26089099
|
10.15252/emmm.201505245
|
H19 lncRNA alters stromal cell growth via IGF signaling in the endometrium of women with endometriosis.
|
2015
|
Figure 3
|
<p>H19 stimulates proliferation of endometrial stromal cells</p>
<p><list list-type="simple"><list-item><p>
A–F The indicated cells were transfected with siCon, siH19, empty vector, or pH19. RNA, cell viability (as indicated by viable cell numbers), and caspase activity (as a readout for apoptosis) were analyzed 48 h post-transfection. Combined results from two patient cells in each group are presented.
</p></list-item><list-item><p>
G E2 stimulates <italic>H19</italic> expression in endometrial stromal cells. Endometrial stromal cells #166 and #98 were stimulated with E2 (+) or vehicle (−) for 48 h, followed by RT–qPCR analysis of RNA extracted from the cells. Results combining two patient cells are shown.
</p></list-item><list-item><p>
H A proposed model of the H19/let-7/IGF1R-mediated regulation of endometrial stromal cell proliferation. During the proliferative phase of the endometrium, E2 stimulates the expression of <italic>H19</italic>. As its level rises, H19 acts as a sponge to sequester let-7 and prevent it from inhibiting its target gene <italic>Igf1r</italic>. Increased IGF1R protein level leads to increased IGF1 signaling with a biological endpoint of increased proliferation of endometrial stromal cells.
</p></list-item></list></p>
<p>Data information: Results are presented as mean ± SD, <italic>n</italic> = 6. <italic>P</italic>-values are indicated on the top of each plot.</p>
|
https://api.sourcedata.io/file.php?figure_id=6947
|
[
{
"ext_dbs": "NCBI gene",
"ext_ids": "283120",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "unmapped",
"mapping_status": "unmapped",
"ncbi_gene_id": "283120",
"original_type": "gene",
"role": "intervention",
"text": "H19",
"type": "geneprod",
"uniprot_ids": []
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "283120",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "unmapped",
"mapping_status": "unmapped",
"ncbi_gene_id": "283120",
"original_type": "gene",
"role": "assayed",
"text": "H19",
"type": "geneprod",
"uniprot_ids": []
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "283120",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "unmapped",
"mapping_status": "unmapped",
"ncbi_gene_id": "283120",
"original_type": "gene",
"role": "assayed",
"text": "H19",
"type": "geneprod",
"uniprot_ids": []
}
] |
|
30737259
|
10.15252/embj.2018100492
|
Length-independent telomere damage drives cardiomyocyte senescence
|
2019
|
Figure 1
|
<p><strong>Figure 1 Telomere dysfunction increases with age in mouse cardiomyocytes.</strong></p><p><strong>A)</strong> Representative images of γH2AX immuno-FISH in troponin-C/α-actinin (top left and bottom left panels, respectively) positive mouse CMs (white - troponin-C/α-actinin; red - telo-FISH; green - γH2AX). Images are Z-projections of 0.1μm stacks taken with a 100x oil objective. Scale bar: 20μm. Right panels represent a single Z-plane where co-localisation between a γH2AX foci and telomere was observed, Scale bars 1μm. (Below) 3D reconstruction of Immuno-FISH using STED microscopy for γH2A.X and telomeres in a CM from 30 month old mice. Scale bars as indicated and scale the same for both individual TAF examples using STED.</p><p><strong>B, C)</strong> Mean number of TAF (B) and % of TAF positive (C) α-actinin positive CMs from C57BL/6 mice. Data are mean ± SEM of n=4-7 mice per age group. 100 α-actinin positive CMs were quantified per mouse.</p><p><strong>D, E)</strong> Mean number of total γH2A.X foci (D) and % of γH2A.X foci -positive nuclei (E) in α-actinin positive CMs from C57BL/6 mice. Data are mean ± SEM of <em>n</em>=4-7 mice per age group. 100 α-actinin positive CMs were quantified per mouse.</p><p><strong>F)</strong> Fold enrichment of γH2AX at telomere repeats by real-time PCR. Graph represents fold enrichment of γH2AX at telomeric repeats between IgG control, 3 and 30 month old whole mouse hearts. Data are mean ± SEM of n=3 mice per age group.</p><p><strong>G)</strong> Quantitative PCR-ELISA TRAP assay comparing telomerase activity of 3 and 30 month old C57BL/6 mice whole heart lysates. Data are mean ± SEM of n=4 mice per age group.</p><p><strong>H)</strong> Histograms displaying distributions of telomere intensity in CMs analysed by 3D Q-FISH in young (4 months) and old (30 months) wild-type mice. Data are from n=3 mice. > 100 CMs were analysed per mouse.</p><p><strong>I)</strong> % of telomere FISH signal loss in 30 months old wild-type mice and late generation Terc<sup>-/-</sup> mice (6 months old) in comparison to 4 months old wild-type mice. Data are from n=3 mice. >100 CMs were analysed per mouse.</p><p>Data information: Statistical analysis was performed using one-way ANOVA (Holm-Sidak method) for multiple comparisons and Mann-Whitney test and two-tailed t-test for single comparisons. ***P<0.001; **P<0.01.</p>
|
https://api.sourcedata.io/file.php?figure_id=24494
|
[
{
"ext_dbs": "Uniprot",
"ext_ids": "P27661",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "γH2A.X",
"type": "geneprod",
"uniprot_ids": [
"P27661"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P27661",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "γH2AX",
"type": "geneprod",
"uniprot_ids": [
"P27661"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P27661",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "γH2AX",
"type": "geneprod",
"uniprot_ids": [
"P27661"
]
},
{
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|
30737259
|
10.15252/embj.2018100492
|
Length-independent telomere damage drives cardiomyocyte senescence
|
2019
|
Figure 2
|
<p><strong>Figure 2 Stress-induced telomere-associated DNA damage is persistent in mouse embryonic cardiomyocytes, rat neonatal cardiomyocytes and H9C2 myoblasts</strong></p><p><strong>A)</strong> Representative images of mouse embryonic cardiomyocytes at days 0, 3, 5 and 10 days following 10Gy X-irradiation. Left panels represent troponin C-positive embryonic cardiomyocytes (troponin C - magenta; DAPI - light blue). Middle panels display γH2AX foci (green) and telomeres (red) in Z projections of 0.1µm slices, with white arrows indicating co-localisation. Co-localising foci are amplified in the right-hand panels (amplified images represent a single Z-plane where co-localisation was observed). Scale bars represent 10μm. Scale bars in single plane images 500nm.</p><p><strong>B)</strong> (Left) Mean number of both TAF and non-TAF in troponin I-positive mouse embryonic cardiomyocytes at days 0, 3, 5 and 10 following 10Gy X-irradiation. Data are mean ±S.E.M of <em>n</em>=3 independent experiments; 30-50 troponin positive cardiomyocytes were analysed per experiment. (Right) Mean percentage of γH2AX foci co-localising with telomeres (% TAF) in troponin C-positive mouse embryonic cardiomyocytes at days 0, 3, 5 and 10 following 10Gy X-irradiation. Statistical analysis performed using one-way ANOVA (Holm-Sidak method); * P<0.05. Significant differences were found for mean number of non-TAF, but not for mean number of TAF.</p><p><strong>C)</strong> Mean number of both TAF and non-TAF in neonatal rat cardiomyocytes at days 0, 3, 5, 10 days following treatment for 24h with H<sub>2</sub>O<sub>2</sub>. Data are mean ±S.E.M of <em>n</em>=3. >50 cells were quantified per condition. Statistical analysis performed using one-way ANOVA (Holm-Sidak method); **P<0.01.</p><p><strong>D)</strong> (Left) <strong>Representative images of γH2AX immuno-FISH in H9C2 myoblasts 3 days 10Gy X-irradiation (red - telo-FISH; green - γH2AX). White arrows identify areas shown in higher magnification panels. (Right)</strong> Mean number of both TAF and non-TAF in H9C2 myoblasts at days 3 and 5 following 10Gy X-irradiation. Data are mean ±S.E.M of <em>n</em>=3. >50 cells were quantified per condition. Statistical analysis performed using one-way ANOVA (Holm-Sidak method); ***P<0.001. Scale bars represent 1μm. Scale bars in single plane images 500nm.</p><p><strong>E)</strong> Representative time-lapse images of H9C2 rat cardiomyoblasts expressing AcGFP-53BP1 from 3 days after 10Gy irradiation at the indicated times (mins). Images are maximum intensity projections with a 6.7µm focal depth. Scale bar represents 1μm.</p><p><strong>F)</strong> Kaplan-Meyer survival curves for AcGFP-53BP1c DDR foci in H9C2 cells 3 days after 10Gy irradiation at 10 minute intervals for 24 hours. >500 foci from 10 cells were tracked per condition. Gehan-Breslow Test was used, P<0.001.</p><p><strong>G)</strong> Schematic illustration showing 1 month old C57BL/6 mice treated with 2Gy whole body X-irradiation, followed by a recovery period of 11 months before culling at 12 months of age. Mean number of TAF in α-actinin positive cardiomyocytes. Data are mean ± SEM of <em>n</em>=3 mice per group. 90 α-actinin positive cardiomyocytes were quantified per condition. Statistical analysis performed using two-tailed t test; *P<0.05.</p>
|
https://api.sourcedata.io/file.php?figure_id=24495
|
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"text": "γH2AX",
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]
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"role": "assayed",
"text": "troponin C",
"type": "geneprod",
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]
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{
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"mapping_source": "direct",
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"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "troponin C",
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"P19123"
]
},
{
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"ext_tax_names": "Rattus norvegicus",
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"text": "γH2AX",
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]
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|
30737259
|
10.15252/embj.2018100492
|
Length-independent telomere damage drives cardiomyocyte senescence
|
2019
|
Figure 3
|
<p><strong>Figure 3 TRF1-FokI fusion protein induces telomere-specific double strand breaks, senescence, and hypertrophy in rat neonatal cardiomyocytes.</strong></p><p><strong>A)</strong> Representative images of rat neonatal CMs 4 days following transfection with a FLAG-tagged TRF1-FokI-D450A (top row) or TRF1-FokI (middle and bottom row) fusion protein (cell treatments the same for all subsequent panels in Figure) (red - telo-FISH; green - γH2A.X). Images are z-projections of 0.1µm stacks taken with 100X objective. White arrows indicate co-localisation between telomeres and γH2A.X, with co-localising foci amplified in the right panels (taken from single z-planes where co-localisation was found). Scale bar represents 3.5μm. Scale bar in magnified images showing individual co-localisation 500nm.</p><p><strong>B, C)</strong> % of γH2A.X foci co-localising with telomeres (B) and mean number of Telomere-associated Foci (TAF) (C) in FLAG-tagged TRF1-FokI-D450A- and TRF1-FokI-expressing CMs. Data are mean ± SEM of n=4 independent experiments. >50 cells were analysed per condition. Statistical analysis was performed by two-tailed t-test ***P<0.001.</p><p><strong>D)</strong> Histograms displaying telomere intensity for telomeres co-localising or not co-localising with γH2AX foci. Red dotted lines represent median. Mann-Whitney test show no significant difference in telomere intensity between TAF and non-TAF.</p><p><strong>E)</strong> Mean % of FLAG-labelled CMs positive for SA-β-Gal activity. Data are mean ± SEM of n=3 independent experiments. >100 cells were quantified per condition. Statistical analysis performed using two tailed t test; **P<0.01.</p><p><strong>F)</strong> Expression of p21 mRNA (as a function of β-actin and Gapdh) by real-time PCR in TRF1-FokI-D450A and TRF1-FokI expressing CMs. Data are mean ± SEM of n=6 independent experiments. Statistical analysis performed using two tailed t test; ***P<0.001.</p><p><strong>G)</strong> Mean± SEM cell surface area (μm<sup>2</sup>) of FLAG-labelled CMs expressing TRF1-FokI-D450A and TRF1-FokI. Statistical analysis performed using two tailed t test; ***P<0.001. Scale bar represents 50μm.</p>
|
https://api.sourcedata.io/file.php?figure_id=24497
|
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"ncbi_gene_id": null,
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"text": "γH2A.X",
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"text": "γH2AX",
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},
{
"ext_dbs": "NCBI gene",
"ext_ids": "114851",
"ext_tax_ids": "10116",
"ext_tax_names": "Rattus norvegicus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "114851",
"original_type": "gene",
"role": "assayed",
"text": "p21",
"type": "geneprod",
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"A0A0G2K2H2",
"Q64315"
]
}
] |
|
30737259
|
10.15252/embj.2018100492
|
Length-independent telomere damage drives cardiomyocyte senescence
|
2019
|
Figure 4
|
<p><strong>Figure 4 Aged cardiomyocytes activate senescence pathways but not a typical SASP.</strong></p><p><strong>A)</strong> Schematic illustrating CM isolation procedure.</p><p><strong>B)</strong> Real-time PCR gene expression analysis in isolated mouse CMs from C57BL/6 mice. Data are mean ± SEM of <em>n</em>=3-4 per age group. Statistical analysis performed by one-Way ANOVA (Holm-Sidak method); *P<0.05.</p><p><strong>C)</strong> Mean % of p21-positive CM nuclei from 3, 15, and 30 month old C57BL/6 mice by immunohistochemistry (IHC). Data are mean ± SEM of <em>n</em>=4 per age group. >100 CMs were quantified per age group. Statistical analysis performed using one-way ANOVA (Holm-Sidak method); *P<0.05.</p><p><strong>D)</strong> Mean % of 3 and 24 month old mouse CMs staining positive for SA-β-Gal <em>in vivo</em> with representative images above (blue - SA-β-Gal; green - troponin C; red - WGA). Black arrows indicate SA-β-Gal expression in a troponin C expressing CM. Statistical analysis performed using two-tailed t-test; *P<0.05. Data are mean ± SEM from the analysis of >500 CMs per mouse, 4 mice per age group. Scale bar 20µm.</p><p><strong>E)</strong> Mean % of SADS-positive CM nuclei from 3 and 30 month old mouse CMs positive for SADS <em>in vivo</em>, as detected by centromere-FISH. Data are mean ± SEM of <em>n</em>=4 per age group. >200 CMs per mouse were quantified. Statistical analysis performed using two-tailed t-test; *P<0.05.</p><p><strong>F)</strong> SASP heatmap: Pearson correlation clustered heatmap showing a curated list of known SASP genes (top panel) or a selection of secreted SASP proteins (bottom panel) in young (3 months) and old (20 months) mouse CMs (n=5 per age group). The colour intensity represents column Z-score, where red indicates highly and blue lowly expressed.</p>
|
https://api.sourcedata.io/file.php?figure_id=24499
|
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"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "p21",
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"uniprot_ids": [
"P39689"
]
},
{
"ext_dbs": "Uniprot",
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"mapping_status": "mapped",
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"role": "assayed",
"text": "troponin C",
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"P19123"
]
},
{
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"ext_tax_names": "Mus musculus",
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"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "troponin C",
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]
}
] |
|
30737259
|
10.15252/embj.2018100492
|
Length-independent telomere damage drives cardiomyocyte senescence
|
2019
|
Figure 5
|
<p><strong>Figure 5 Cardiomyocyte SASP induces fibrosis and reduces proliferation in fibroblasts and induces hypertrophy in cardiomyocytes.</strong></p><p><strong>A)</strong> (Above) RNA-sequencing of purified CMs from 4 mice per age group reveal age-dependent increased expression of 3 secreted proteins Edn3, Tgfb2, and Gdf15; the colour intensity represents column Z-score, where red indicates highly and blue lowly expressed. (Below) mRNA expression of Edn3, Tgfb2, and Gdf15 was independently validated by RT-PCR in young and old isolated adult CMs. Data are mean ±S.E.M of n=8 mice per group.</p><p><strong>B)</strong> CMs were isolated by <em>Langendorff</em> heart perfusion, purified and cultured for 48h. Conditioned medium (CM) was collected and added to cultures of neonatal fibroblasts in the presence of 10μM EdU.</p><p><strong>C)</strong> Representative images of immunofluorescent staining against α-SMA and EdU in neonatal fibroblasts cultured in the presence of CM from young and old CMs.</p><p><strong>D, E)</strong> Quantification of % of EdU incorporation (D) and % of a-SMA positive cells (E) in neonatal fibroblasts after treatment for 48h with CM from young and old CM. Data are mean ±S.E.M of n=3-4 mice per age group; >200 cells were quantified per condition.</p><p><strong>F)</strong> Representative micrographs of neonatal fibroblasts and CMs treated with recombinant proteins: Tgfb2, Edn3, and Gdf15 for 48h and immunostained against α-SMA and EdU (fibroblasts) and α-actinin (CMs).</p><p><strong>G-I)</strong> Quantification of α-SMA (G) and EdU positive neonatal fibroblasts (H) and surface area (μm<sup>2</sup>) (I) in neonatal CMs following treatment with the indicated recombinant proteins. Data are mean ±S.E.M of n=3-4 independent experiments.</p><p>Data information: Asterisks denote statistical significance with one-way ANOVA (multiple comparisons) (G, H, I) or two-tailed t-test (A, D, E). ***P<0.001; **P<0.01; *P<0.05. For all panels scale bars represent 50μm.</p>
|
https://api.sourcedata.io/file.php?figure_id=24501
|
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"P48299"
]
},
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"Q9Z0J7"
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"P62737"
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] |
|
30737259
|
10.15252/embj.2018100492
|
Length-independent telomere damage drives cardiomyocyte senescence
|
2019
|
Figure 6
|
<p><strong>Figure 6 Mitochondrial dysfunction is a feature of cardiomyocyte senescence and drives TAF in mouse cardiomyocytes <em>in vivo</em>.</strong></p><p><strong>A)</strong> Mito and ETC genes with GSEA analysis: Clustered heatmap showing all genes associated with the "Mitochondrion" GO term in young and old, mouse CMs as observed by the GSEA pre-ranked list enrichment analysis (normalised enrichment score: -1.70; FDR q-value < 0.05). Alongside this is a column clustered heatmap displaying a list of genes from the electron transport chain (ETC) GO ontology. In both instances, genes are by column and samples by row with the colour intensity representing column Z-score, where red indicates highly and blue lowly expressed.</p><p><strong>B)</strong> Real-time PCR gene expression analysis of MAO-A, MnSOD and catalase in isolated mouse CMs from young (3 months) and old (20 months) mice. Data are mean ± SEM of n=4-5 per age group. Asterisks denote a statistical significance at P<0.05 using two-tailed t-test.</p><p><strong>C)</strong> Mean % of 4-HNE- (top) or 8oxodG- (bottom) positive CMs from 3 month (young) or 30 month (old) aged mice. Data are mean ± SEM of n=4 per age group. 100 CMs were quantified per age group. Asterisks denote a statistical significance at P<0.05 using two-tailed t-test.</p><p><strong>D-G)</strong> Mean % of TAF-positive nuclei (left graphs) or mean % of TAF (right graphs) in wild-type (control) compared to MAO-A transgenic mice with or without drinking water supplemented with 1.5g/kg/day NAC from the age of 4 to 24 weeks, MnSOD<sup>+/+</sup> vs MnSOD<sup>-/+</sup>, Catalase<sup>+/+</sup> <em>vs</em>. Catalase<sup>-/-</sup>, WT <em>vs</em>. POLG double mutant mice. Data are mean ±S.E.M of n=3-4 per group. >100 CMs were quantified per age group. Statistical analysis was performed using two-tailed t test (E-G) or one-way ANOVA (for multiple comparisons) (D); *P<0.05.</p><p><strong>H)</strong> Schematic depicting isolated mouse adult CMs isolated from 4 animals were treated with or without 100nM rotenone either in the presence of 5mM NAC or vehicle control (pre-treated for 30 minutes before rotenone treatment), for 24 h before fixation. Mean number of TAF (top graph) and mean % of TAF-positive nuclei (bottom graph). Data are mean ± SEM from 4 separate CM cultures isolated from 3 month-old mice. 50 CMs were quantified per condition. Asterisks denote a statistical significance at P<0.05 using one-way ANOVA (Holm-Sidak method).</p>
|
https://api.sourcedata.io/file.php?figure_id=24503
|
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"Q64133",
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"ext_dbs": "NCBI gene",
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"P24270"
]
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"ext_dbs": "NCBI gene",
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"role": "intervention",
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"Q3UG70",
"Q3UZX3",
"Q75WC0"
]
}
] |
|
30737259
|
10.15252/embj.2018100492
|
Length-independent telomere damage drives cardiomyocyte senescence
|
2019
|
Figure 7
|
<p><strong>Figure 7 Genetic clearance of p16 positive cells in aged mice reduces cardiomyocyte senescence, cardiac hypertrophy and fibrosis.</strong></p><p><strong>A)</strong> Examples of individual short axis cine-MR images of 3 or 20 month old mouse hearts. Ejection fraction and LV thickness was calculated based on manual measurements of Left ventricle epicardial and endocardial borders. % change in wall thickening calculation based on wall thickness at the 4 points indicated. Measurements were made in all cine slices at end diastole and end systole. Graphs representing data obtained from MRI analysis of >7 animals per age group. Data are mean ± S.E.M. Asterisks denote a statistical significance at P<0.05 using Mann Whitney U-test. Scale bars represent 5mm.</p><p><strong>B)</strong> Comparison between mean number of TAF per CM and CM area in 22 month old animals. Data are mean ± S.E.M. of n=4. >100 CMs were quantified per mouse. Statistical analysis performed using one-way ANOVA (Holm-Sidak method); *P<0.05.</p><p><strong>C)</strong> Schematic depicting experimental design for Figures d-f: 27 month old INK-ATTAC mice were treated 4 times with AP20187 (or Vehicle), 3 days in a row, every 2 weeks (2-month-long treatment in total) and were sacrificed afterwards for analysis.</p><p><strong>D)</strong> Comparison between the % of p16- or eGFP-positive CMs by RNA-<em>in situ</em> hybridization per plane in INK-ATTAC mice (28-29 month old) treated with vehicle or AP20187. Data are mean ± SEM of <em>n</em>=5 per age group. 100 CMs were analysed per mouse. Asterisks denote a statistical significance at *P<0.05 or ***P<0.001 using two-tailed t-test.</p><p><strong>E)</strong> Mean number of TAF (left graph) and mean % of TAF-positive nuclei (right graph) in CMs. Data are mean ± S.E.M. of n=6 per age group. 100 CMs were analysed per mouse. ***P<0.001; **P<0.01; *P<0.05.</p><p><strong>F)</strong> Mean CM area μm<sup>2</sup>. Data are mean ±S.E.M. of <em>n</em>=6 per age group, >150 CMs analysed per mouse. Asterisks denote a statistical significance at *P<0.05 using two-tailed t-test.</p><p><strong>G)</strong> % of fibrotic area evaluated by Sirius Red staining. Data are mean ±S.E.M. of n=6 per age group. Asterisks denote a statistical significance using Mann Whitney test. ***P<0.001.</p>
|
https://api.sourcedata.io/file.php?figure_id=24504
|
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"ext_dbs": "NCBI gene",
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"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "12578",
"original_type": "gene",
"role": "assayed",
"text": "p16",
"type": "geneprod",
"uniprot_ids": [
"P51480",
"Q64364"
]
}
] |
|
30737259
|
10.15252/embj.2018100492
|
Length-independent telomere damage drives cardiomyocyte senescence
|
2019
|
Figure 8
|
<p><strong>Figure 8 Pharmacological clearance of senescent cells with Navitoclax (ABT 263) reduces cardiomyocyte senescence and stimulates cardiomyocyte regeneration.</strong></p><p><strong>A)</strong> Schematic depicting experimental design. Mice at 100 weeks (23-months) of age were treated with vehicle (Veh) or navitoclax (Nav) intermittently for 2 weeks. At 104 weeks mice were injected every day with EdU for 1 week.</p><p><strong>B)</strong> Quantification of mean number of TAF and % of TAF-positive CMs in 24 months old wild-type mice treated with vehicle or navitoclax (50mg/kg/day). Data are mean± SEM of <em>n</em>=5-8 mice per group. More than 100 CMs were quantified per animal.</p><p><strong>C)</strong> CM cross-sectional area in 24 months old wild-type mice treated with vehicle or navitoclax. Data are mean± SEM of <em>n</em>=8 mice per group.</p><p><strong>D)</strong> (Left) Representative images of Sirius red staining and (right) % of fibrosis area in 24 month-old mice treated or not with navitoclax. Data are mean mean±S.E.M of n=3 per group. Scale bar represents 50µm.</p><p><strong>(E-G)</strong> MRI analysis of ejection fraction (EF%), left ventricle mass (LVmass) index and % of ventricle wall thickness (%WTC) in 24 month-old mice treated or not with navitoclax. Data are mean±S.E.M of n=6 mice per treatment group.</p><p><strong>H)</strong> Examples of confocal microscopy images of CMs positive for CM marker troponin C (TropC), EdU, Ki67 and Aurora B from navitoclax treated animals. (Upper Right panel) white arrows identify two nuclei in the same CM that have incorporated EdU. (Lower Right panel) white arrow identify EdU expressing Aurora B symmetrically between two nuclei. Scale bars represent 20µm.</p><p><strong>I)</strong> Table summarising numbers of CMs quantified in (J).</p><p><strong>J)</strong> Quantification of EdU positive CMs (mono- or multi-nucleated) in vehicle and navitoclax treated animals. Data are mean±S.E.M of n=5-6 mice per group.</p><p><strong>K)</strong> % of Ki67 positive CMs in 29 month old INK-ATTAC mice treated with vehicle or AP20187. Data are mean±S.E.M of n=4-6 mice per group.</p><p>Data information: Asterisks denote a statistical significance using two-tailed t test (B, C, K) or Mann Whitney test (D, J). ***P<0.001; **P<0.01; *P<0.05.</p><p><strong>Expanded View Figure legends</strong></p>
|
https://api.sourcedata.io/file.php?figure_id=24505
|
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"ncbi_gene_id": null,
"original_type": "protein",
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"text": "Aurora B",
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]
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{
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"text": "Ki67",
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"E9PVX6"
]
},
{
"ext_dbs": "Uniprot",
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"mapping_source": "direct",
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"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "TropC",
"type": "geneprod",
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"P19123"
]
},
{
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"ext_ids": "P19123",
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"text": "troponin C",
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]
},
{
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] |
|
10.15252/emmm.202216225
|
Targeting gut dysbiosis against inflammation and impaired autophagy in Duchenne muscular dystrophy
|
2022
|
Figure 4
|
<p><strong>Figure 4. Expression of autophagy and inflammatory genes in wt and mdx mice treated with NaB or DFZ.</strong></p><p>A-I Bar chart with individual points showing the mRNA expression levels of the indicated genes measured in the gastrocnemius of control and mdx mice treated with or without NaB and DFZ.</p><p>J-K Representative blotting and bar chart with individual points showing the expression and/or phosphorylation of pAKT/AKT and COX2 in the gastrocnemius of the indicated six groups of mice.</p><p>Data Information: Each bar is the mean ± S.E.M. from 5 independent biological replicates. **** = <em>p</em>≤0.0001; *** = <em>p</em>≤0.0003; ** = <em>p</em>≤0.005; * = <em>p</em>≤0.05 versus the indicated experimental group calculated using ANOVA.</p>
|
https://api.sourcedata.io/file.php?figure_id=51595
|
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"P31750"
]
},
{
"ext_dbs": "Uniprot",
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"text": "AKT",
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]
},
{
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"ext_tax_names": "Mus musculus",
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"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "COX2",
"type": "geneprod",
"uniprot_ids": [
"P00405"
]
}
] |
||
10.15252/emmm.202216225
|
Targeting gut dysbiosis against inflammation and impaired autophagy in Duchenne muscular dystrophy
|
2022
|
Figure 5
|
<p><strong>Figure 5. Measurement of endocannabinoid system activity in the plasma and skeletal muscle of wt and mdx mice treated with NaB and DFZ.</strong></p><p>A-B Levels of AEA and 2-AG in plasma samples of wt and mdx mice expressed as pmol mg−1 of wet tissue weight.</p><p>C-D Bar charts with individual points showing the mRNA expression levels of CB1 and CB2 measured in the gastrocnemius of the indicated groups of mice.</p><p>E Representative blots showing the expression levels of CB1 and CB2 proteins in the gastrocnemius of the indicated groups of mice.</p><p>F Quantification of CB1 and CB2 proteins to the housekeeping protein GAPDH.</p><p>Data Information: Each bar is the mean ± S.E.M. of 4-5 independent biological samples. *** = p≤0.0003; ** = p≤0.003; * = p≤0.05 versus the indicated experimental group calculated using ANOVA.</p>
|
https://api.sourcedata.io/file.php?figure_id=51596
|
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"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "12801",
"original_type": "gene",
"role": "assayed",
"text": "CB1",
"type": "geneprod",
"uniprot_ids": [
"P47746",
"A0A385KNU8"
]
},
{
"ext_dbs": "NCBI gene",
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"original_type": "gene",
"role": "assayed",
"text": "CB2",
"type": "geneprod",
"uniprot_ids": [
"P47936"
]
},
{
"ext_dbs": "Uniprot",
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"P47746"
]
},
{
"ext_dbs": "Uniprot",
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"ext_tax_names": "Mus musculus",
"mapping_source": "direct",
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"ncbi_gene_id": null,
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"text": "CB1",
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},
{
"ext_dbs": "Uniprot",
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"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "CB2",
"type": "geneprod",
"uniprot_ids": [
"P47936"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P47936",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "direct",
"mapping_status": "mapped",
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"role": "assayed",
"text": "CB2",
"type": "geneprod",
"uniprot_ids": [
"P47936"
]
}
] |
||
10.15252/emmm.202216225
|
Targeting gut dysbiosis against inflammation and impaired autophagy in Duchenne muscular dystrophy
|
2022
|
Figure 6
|
<p><strong>Figure 6. Effect of rimonabant on autophagy in mdx mice.</strong></p><p>A-C Bar charts with individual points showing the mRNA expression levels of <em>Ulk</em>, <em>Pink</em> and <em>Becn1</em> measured in control and mdx mice treated with rimonabant (0.5 mg kg-1).</p><p>D Representative blots showing the expression levels of LC3I and LC3II proteins in the gastrocnemius of the indicated groups of mice.</p><p>E, F Quantification of LC3I and LC3II proteins to the housekeeping protein GAPDH.</p><p>Data Information: Each bar is the mean ± S.E.M. from 3 independent biological samples. ** = p≤0.005 * = p≤0.05 versus the indicated experimental group calculated using ANOVA.</p>
|
https://api.sourcedata.io/file.php?figure_id=51597
|
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"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "56208",
"original_type": "gene",
"role": "assayed",
"text": "Becn1",
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"E9QAM0"
]
},
{
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"mapping_source": "ncbi_gene",
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"ncbi_gene_id": "18431",
"original_type": "gene",
"role": "assayed",
"text": "Pink",
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]
},
{
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"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "22241",
"original_type": "gene",
"role": "assayed",
"text": "Ulk",
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"uniprot_ids": [
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]
},
{
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},
{
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"ext_ids": "Q9CQV6",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "LC3I",
"type": "geneprod",
"uniprot_ids": [
"Q9CQV6"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q9CQV6",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "LC3II",
"type": "geneprod",
"uniprot_ids": [
"Q9CQV6"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q9CQV6",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "LC3II",
"type": "geneprod",
"uniprot_ids": [
"Q9CQV6"
]
}
] |
||
10.15252/emmm.202216225
|
Targeting gut dysbiosis against inflammation and impaired autophagy in Duchenne muscular dystrophy
|
2022
|
Figure 7
|
<p><strong>Figure 7. Effect of NaB on LPS-stimulated C2C12 cells.</strong></p><p>A-B Bar chart with individual points showing the mRNA expression levels of <em>Il6</em> and <em>Cox2</em> in control (vehicle, DMSO) and/or GPR109A-silenced C2C12 myoblasts exposed to LPS (1 μg/ml) in the presence or absence of either MK1903 (1 μM), rosiglitazone (1 μM) or T007 (1 μM).</p><p>C Time-dependent effect of NaB (3 mM), MK1903 (1 μM) and rosiglitazone (1 μM) on autophagosome formation measured in C2C12 myoblasts. Data are expressed as fluorescence intensity normalized to controls (%).</p><p>Data Information: Each bar is the mean ± S.E.M. of at least 3 independent replicates. * = p≤0.05 versus the veh group. ± = p≤0.05 versus the LPS group; # = p≤0.05 versus the other experimental groups (A) or the veh group (B) calculated using ANOVA.</p>
|
https://api.sourcedata.io/file.php?figure_id=51598
|
[
{
"ext_dbs": "NCBI gene",
"ext_ids": "17709",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "17709",
"original_type": "gene",
"role": "assayed",
"text": "Cox2",
"type": "geneprod",
"uniprot_ids": [
"P00405",
"Q7JCZ1"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "80885",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "80885",
"original_type": "gene",
"role": "intervention",
"text": "GPR109A",
"type": "geneprod",
"uniprot_ids": [
"Q9EP66",
"Q0VBA6"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "16193",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "16193",
"original_type": "gene",
"role": "assayed",
"text": "Il6",
"type": "geneprod",
"uniprot_ids": [
"P08505",
"A0A0G2JGF4",
"A2RTD1"
]
}
] |
||
10.15252/emmm.202216225
|
Targeting gut dysbiosis against inflammation and impaired autophagy in Duchenne muscular dystrophy
|
2022
|
Figure 8
|
<p><strong>Figure 8. Effect of LPS on the endocannabinoid system activity in C2C12 cells.</strong></p><p>A-F Bar chart with individual points showing the mRNA expression levels of <em>Cb1</em><strong>,</strong> <em>Daglα</em><strong>,</strong> <em>Daglβ</em><strong>,</strong> <em>Magl</em>, <em>Napepld</em>, and <em>Faah</em> in control (vehicle, DMSO) and/or GPR109A-silenced C2C12 myoblasts exposed to LPS (1 μg/ml) in the presence or absence of either MK1903 (1 μM), rosiglitazone (1 μM) or T007 (1 μM).</p><p>G-H Levels of AEA and 2-AG were measured in C2C12 cells exposed to LPS (1 μg/ml) or NaB (3 mM) for 24 h.</p><p>I Effect of ACEA (1 μM) and rimonabant (1 μM) on autophagosome formation measured in C2C12 cells.</p><p>Data Information: Each bar is the mean ± S.E.M. from 3 independent biological replicates. ** p≤ 0.005; * = p≤0.05 versus the veh group; ± = p≤0.05 versus the LPS group calculated using ANOVA.</p>
|
https://api.sourcedata.io/file.php?figure_id=51599
|
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{
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"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "12801",
"original_type": "gene",
"role": "assayed",
"text": "Cb1",
"type": "geneprod",
"uniprot_ids": [
"P47746",
"A0A385KNU8"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "269060",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "269060",
"original_type": "gene",
"role": "assayed",
"text": "Daglα",
"type": "geneprod",
"uniprot_ids": [
"Q6WQJ1",
"A4FU75"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "231871",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "231871",
"original_type": "gene",
"role": "assayed",
"text": "Daglβ",
"type": "geneprod",
"uniprot_ids": [
"Q91WC9"
]
},
{
"ext_dbs": "NCBI gene",
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"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "14073",
"original_type": "gene",
"role": "assayed",
"text": "Faah",
"type": "geneprod",
"uniprot_ids": [
"O08914"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "80885",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "80885",
"original_type": "gene",
"role": "intervention",
"text": "GPR109A",
"type": "geneprod",
"uniprot_ids": [
"Q9EP66",
"Q0VBA6"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "23945",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "23945",
"original_type": "gene",
"role": "assayed",
"text": "Magl",
"type": "geneprod",
"uniprot_ids": [
"O35678",
"D3YYS6",
"E9Q3B9",
"Q3UFN1"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "242864",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "242864",
"original_type": "gene",
"role": "assayed",
"text": "Napepld",
"type": "geneprod",
"uniprot_ids": [
"Q8BH82"
]
}
] |
||
10.15252/emmm.202216225
|
Targeting gut dysbiosis against inflammation and impaired autophagy in Duchenne muscular dystrophy
|
2022
|
Figure 9
|
<p><strong>Figure 9. Effect of LPS on the expression of miRNAs targeting the <em>Cnr1</em> gene.</strong></p><p>A Schematic representation of miRNAs targeting the 3′-UTR region of both murine and human CB1 gene.</p><p>B Heatmap representation of the expression of selected miRNAs in the indicated biological replicates. Red, upregulated; green, downregulated.</p><p>C-J Bar chart with individual points showing the expression of selected miRNAs in control and Gpr109A-silenced C2C12 myoblasts exposed to LPS (1 μg/ml) in the presence or absence of either NaB (3 mM), MK1903 (1 μM), rosiglitazone (1 μM). NaB was also tested in the presence or absence of either rosiglitazone (1 μM) or T007 (1 μM).</p><p>Data Information: Each bar is the mean ± S.E.M. from 3 independent biological replicates. ± = p≤0.05 vs veh group; ** = p≤0.03 vs LPS group; # = p≤0.05 versus the other experimental groups calculated using ANOVA.</p>
|
https://api.sourcedata.io/file.php?figure_id=51600
|
[
{
"ext_dbs": "NCBI gene",
"ext_ids": "80885",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "80885",
"original_type": "gene",
"role": "intervention",
"text": "Gpr109A",
"type": "geneprod",
"uniprot_ids": [
"Q9EP66",
"Q0VBA6"
]
}
] |
||
10.15252/emmm.202216225
|
Targeting gut dysbiosis against inflammation and impaired autophagy in Duchenne muscular dystrophy
|
2022
|
Figure 10
|
<p><strong>Figure 10. Effect of NaB, MK1903 and Rosiglitazone in primary myoblasts isolated from DMD</strong></p><p><strong>donors.</strong></p><p>A-E Bar chart showing the mRNA expression levels of IL6, COX2, ULK 1, ATG13 and ATG4 mRNA in primary human myoblasts isolated from one healthy donor (HD) and five DMD donors (D1- D5).</p><p>Data Information: The quantification of transcripts by quantitative real-time PCR was measured twice for each sample.</p>
|
https://api.sourcedata.io/file.php?figure_id=51601
|
[
{
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"ext_ids": "9776",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "9776",
"original_type": "gene",
"role": "assayed",
"text": "ATG13",
"type": "geneprod",
"uniprot_ids": [
"O75143",
"A8K0S6"
]
},
{
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"ext_tax_names": "Homo sapiens",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "23192",
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"text": "ATG4",
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"B3KVU2",
"B7ZA52"
]
},
{
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"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "4513",
"original_type": "gene",
"role": "assayed",
"text": "COX2",
"type": "geneprod",
"uniprot_ids": [
"P00403",
"U5Z487"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "3569",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "3569",
"original_type": "gene",
"role": "assayed",
"text": "IL6",
"type": "geneprod",
"uniprot_ids": [
"P05231",
"B4DNQ5",
"B4DVM1",
"B5MC21",
"B5MCZ3",
"Q75MH2"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "8408",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "8408",
"original_type": "gene",
"role": "assayed",
"text": "ULK 1",
"type": "geneprod",
"uniprot_ids": [
"O75385"
]
}
] |
||
10.15252/msb.202110824
|
Molecular profiling reveals features of clinical immunity and immunosuppression in asymptomatic P. falciparum malaria
|
2022
|
Figure 2
|
<sd-panel><p><strong>Figure 2. Identification of MBC and <sd-pretag id="sdPretag652542221sm" type="cell" role="component">memory CD4<sup>+</sup> T cell sub</sd-pretag>-populations induced by <em>P<sd-pretag id="sdPretag386434833sm" type="organism" role="component">. falciparum</sd-pretag></em> symptomatic and <sd-pretag id="sdPretag134716359sm" category="disease">asymptomatic infection</sd-pretag>.</strong></p> <p><sd-pretag id="sdPretag254824454sm" type="cell" role="component">PBMCs</sd-pretag> from <em>P. <sd-pretag id="sdPretag414899409sm" type="organism" role="component">falciparum</sd-pretag></em> symptomatic (n=16) and asymptomatic (n=24) infected <sd-pretag id="sdPretag227549637sm" type="organism" role="component">individuals</sd-pretag> as well as healthy immune controls (n=24) were stained with a panel of metal-labelled antibodies and analysed by <sd-pretag id="sdPretag1673537457sm" category="assay">CyTOF</sd-pretag>. <sd-pretag id="sdPretag481677502sm" category="assay">tSNE</sd-pretag> analysis was performed and <sd-pretag id="sdPretag85912677sm" type="small" role="assayed">FlowSOM</sd-pretag> clustering was used to identify individual cell sub-populations within gated:</p> <p>A. T<sub>H1</sub>-like <sd-pretag id="sdPretag172313888sm" type="cell" role="component">memory CD4<sup>+</sup> T cells</sd-pretag> (<sd-pretag id="sdPretag268525313sm" type="geneprod" role="assayed">CD19</sd-pretag><sup>-</sup><sd-pretag id="sdPretag1175400617sm" type="geneprod" role="assayed">CD3<sup>+</sup>CD4<sup>+</sup>CD45RA</sd-pretag><sup>-</sup><sd-pretag id="sdPretag2022482914sm" type="geneprod" role="assayed">CCR6</sd-pretag><sup>-</sup><sd-pretag id="sdPretag1768885352sm" type="geneprod" role="assayed">CXCR3<sup>+</sup></sd-pretag>)</p> <p>B. <sd-pretag id="sdPretag727426903sm" type="geneprod" role="assayed">T<sub>H2</sub></sd-pretag>-like <sd-pretag id="sdPretag1341903601sm" type="cell" role="component">memory CD4<sup>+</sup> T cells</sd-pretag> (<sd-pretag id="sdPretag1487878762sm" type="geneprod" role="assayed">CD19</sd-pretag><sup>-</sup><sd-pretag id="sdPretag562625268sm" type="geneprod" role="assayed">CD3<sup>+</sup>CD4<sup>+</sup>CD45RA</sd-pretag><sup>-</sup><sd-pretag id="sdPretag765864047sm" type="geneprod" role="assayed">CCR6</sd-pretag><sup>-</sup><sd-pretag id="sdPretag57710035sm" type="geneprod" role="assayed">CXCR3</sd-pretag><sup>-</sup>)</p> <p>C. Circulating <sd-pretag id="sdPretag1982702415sm" type="cell" role="component">memory T<sub>FH</sub> cells</sd-pretag> (<sd-pretag id="sdPretag668414143sm" type="geneprod" role="assayed">CD19</sd-pretag><sup>-</sup><sd-pretag id="sdPretag1415112429sm" type="geneprod" role="assayed">CD3<sup>+</sup>CD4<sup>+</sup>CD45RA</sd-pretag><sup>-</sup><sd-pretag id="sdPretag648604143sm" type="geneprod" role="assayed">CXCR5<sup>+</sup></sd-pretag>)</p> <p>D. Classical <sd-pretag id="sdPretag736645068sm" type="cell" role="component">MBCs</sd-pretag> (<sd-pretag id="sdPretag2046334500sm" type="geneprod" role="assayed">CD3</sd-pretag><sup>-</sup><sd-pretag id="sdPretag1937002491sm" type="geneprod" role="assayed">CD19<sup>+</sup>CD20<sup>+</sup>CD10</sd-pretag><sup>-</sup><sd-pretag id="sdPretag962541132sm" type="geneprod" role="assayed">CD27<sup>+</sup>CD21<sup>+</sup></sd-pretag>)</p> <p>E. Atypical <sd-pretag id="sdPretag275411870sm" type="cell" role="component">MBCs</sd-pretag> (<sd-pretag id="sdPretag975815660sm" type="geneprod" role="assayed">CD3</sd-pretag><sup>-</sup><sd-pretag id="sdPretag2110194444sm" type="geneprod" role="assayed">CD19<sup>+</sup>CD20<sup>+</sup>CD10</sd-pretag><sup>-</sup><sd-pretag id="sdPretag1052532724sm" type="geneprod" role="intervention">CD27</sd-pretag><sup>-</sup><sd-pretag id="sdPretag1216861419sm" type="geneprod" role="intervention">CD21</sd-pretag><sup>-</sup>)</p> <p>F. Activated <sd-pretag id="sdPretag516878223sm" type="cell" role="component">MBCs</sd-pretag> (<sd-pretag id="sdPretag1102962090sm" type="geneprod" role="assayed">CD3</sd-pretag><sup>-</sup><sd-pretag id="sdPretag1487475073sm" type="geneprod" role="assayed">CD19<sup>+</sup>CD20<sup>+</sup>CD10</sd-pretag><sup>-</sup><sd-pretag id="sdPretag1054665601sm" type="geneprod" role="assayed">CD27<sup>+</sup>CD21</sd-pretag><sup>-</sup>)</p> <p>The tSNE plots in the top panel display cell density and represent the pooled data for each group, while the lower panel shows a projection of the FlowSOM clusters on a tSNE plot. Heatmaps show the median marker expression for each FlowSOM cluster.</p></sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=46996
|
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"type": "geneprod",
"uniprot_ids": [
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]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P08575",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "direct",
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"ncbi_gene_id": null,
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"role": "assayed",
"text": "CD45RA",
"type": "geneprod",
"uniprot_ids": [
"P08575"
]
},
{
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"ext_ids": "P08575",
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"uniprot_ids": [
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]
},
{
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"ext_ids": "P08575",
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"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
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] |
||
10.15252/msb.202110824
|
Molecular profiling reveals features of clinical immunity and immunosuppression in asymptomatic P. falciparum malaria
|
2022
|
Figure 8
|
<sd-panel><p><strong>Figure 8. Asymptomatic <em>P. falciparum</em> malaria supports humoral responses to infection but drives immunosuppressive responses.</strong></p> <p><strong>A. Volcano plot showing genes upregulated in symptomatic individuals that were significantly correlated with IgM<sup>+</sup> activated MBCs.</strong></p> <p><strong>B. Volcano plot showing genes upregulated in symptomatic individuals that were significantly correlated with T-bet<sup>+</sup> CD4<sup>+</sup> T cells.</strong></p> <p><strong>C. Chord diagram integrating associations between symptomatic malaria signature genes, immune cell populations and antibody responses. Blue lines within the chord diagram represent positive correlations between two variables, while red lines represent negative correlations. (Benjamini-Hochberg adjusted Spearman's Rho, FDR<5%).</strong></p> <p><strong>D. Chord diagram integrating associations between asymptomatic malaria signature genes, immune cell populations and antibody responses. Blue lines within the chord diagram represent positive correlations between two variables, while red lines represent negative correlations. (Benjamini-Hochberg adjusted Spearman's Rho, FDR<5%).</strong></p></sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=47005
|
[
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"ext_ids": "Q9UL17",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "T-bet",
"type": "geneprod",
"uniprot_ids": [
"Q9UL17"
]
}
] |
||
10.15252/msb.202110824
|
Molecular profiling reveals features of clinical immunity and immunosuppression in asymptomatic P. falciparum malaria
|
2022
|
Figure 9
|
<sd-panel><p><strong>Figure 9. CTLA-4 is upregulated in memory CD4<sup>+</sup> T cells in asymptomatic malaria and contributes to the development of clinically-silent parasitemia.</strong></p> <p><strong>A.</strong> Estimated proportions of PBMC subpopulations determined from cell-type deconvolution featuring transcriptional profiles upregulated in asymptomatic individuals.</p> <p>B-G. <strong>PBMCs from</strong> <em>P. falciparum</em> symptomatic (n=6) and asymptomatic (n=6) infected individuals as well as healthy immune controls (n=6) were stained with a panel of antibodies and analyzed by flow cytometry. tSNE plots (B) display cell density of the pooled data for each group, (C) shows a projection of the FlowSOM clusters on a tSNE plot, and (D) is a heatmap depicting the celluar phenotype of clusters of CTLA-4<sup>+</sup>CD3<sup>+</sup>CD19<sup>-</sup> cells. Bar plots representing mean relative abundance of biological replicates <span class="underline">+</span> SEM of relevant clusters among clinical groups (E), Mann-Whitney test, *p<0.05. The panel on the left shows the average CTLA-4 mean fluorescent intensity (MFI) or 6 biological replicates in cluster 4 <span class="underline">+</span> SEM, Mann-Whitney test, **p<0.01, while representative histograms of CTLA-4 expression in cluster 4 are shown on the right (F). Marker intensity within clusters 1 and 6 (G).</p> <p>H. C57BL/6 mice (n=10) were infected with <em>P. chabaudi chabaudi.</em> Percentage parasitemia of infected mice was determined every 2-3 days. Symbols represent average parasitemia <span class="underline">+ SEM.</span></p> <p>I-Q. Splenocytes from <em>P. chabaudi chabaudi</em> infected mice were stained with fluorescent antibodies and analyzed by flow cytometry. (I) Representative contour plots showing CTLA-4-expressing cells among T<sub>REG</sub> and CD44<sup>+</sup> CD4<sup>+</sup> T cells. (J, K) Percentage of CTLA-4<sup>+</sup> cells among CD4<sup>+</sup>FoxP3<sup>+</sup> T<sub>reg</sub> cells (J) and CD44<sup>+</sup> activated CD4<sup>+</sup> T cells (K) at peak (day 8 p.i) and recrudescent (day 20 p.i) parasitemia and after infection resolution (day 40 p.i). Bar plots represent mean percentage of 6 biological replicates <span class="underline">+</span> SEM (unpaired t-test, ***p<0.005, *p<0.05). (L-N) tSNE plots (L) display cell density of the pooled data for each group, (M) shows a projection of the FlowSOM clusters on a tSNE plot, and (N) is a heatmap depicting the celluar phenotype of CTLA-4<sup>+</sup> conventional CD4<sup>+</sup> T cells during peak and recrudescent parasitemia. (O) Bar plots represent the average relative abundance of 6 biological replicates in relevant clusters <span class="underline">+</span> SEM (unpaired t-test, **p<0.01). (P-Q) Representative contour plots (P) and absolute number (Q) of CTLA-4-expressing CD4<sup>+</sup>CD44<sup>+</sup>CCR7<sup>+</sup>CD62L<sup>high</sup> central memory (CM) and CD4<sup>+</sup>CD44<sup>+</sup>CCR7<sup>-</sup>CD62L<sup>low</sup> effector memory (EM) cells during peak and recrudescent parasitemia. Symbols represent the mean cell number of 6 biological replicates <span class="underline">+</span> SEM (unpaired t-test, ***p<0.05).</p> <p>R. C57BL/6 mice (n=6) were infected with <em>P. chabaudi chabaudi</em> and treated with anti-CTLA-4 or isotype control every 3 days from day 13 p.i as indicated by the red arrows. Parasitemia was determined every 2-3 days. Bar plots represent mean parasitemia of biological replicates <span class="underline">+</span> SEM (unpaired t-test, **p<0.01, *p<0.05).</p> <p><strong>Expanded View Figure Legends</strong></p></sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=47006
|
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] |
||
10.15252/emmm.202216987
|
sTREM2 is associated with amyloid-related p-tau increases and glucose hypermetabolism in Alzheimer's
|
2022
|
Figure 1
|
<p><strong>Figure 1.</strong> Cross-sectional and longitudinal analysis of the association between amyloid-PET (in centiloid), CSF p-tau<sub>181</sub>, and CSF sTREM2 in early Aβ-accumulators (i.e. Aβ CSF+/PET−; n=70) and late Aβ-accumulators (i.e. Aβ CSF+/PET+; n=201). Cross-sectional linear regressions between <strong>A)</strong> centiloid and p-tau<sub>181</sub> and <strong>B)</strong> centiloid and sTREM2. Longitudinal linear regressions between <strong>C)</strong> centiloid and change in p-tau<sub>181</sub> and <strong>D)</strong> centiloid and change in sTREM2. Standardized beta-estimates (β), T-values, and p-values were derived from linear regressions controlling for age, sex, education, and clinical status. <strong>E)</strong> Cross-sectional mediation analyses with centiloid as predictor, sTREM2 as mediator, and p-tau<sub>181</sub> as dependent variable. <strong>F)</strong> Longitudinal mediation analyses with centiloid as predictor, sTREM2 as mediator, and change in p-tau<sub>181</sub> as dependent variable. Early Aβ-accumulators are displayed in green, and late Aβ-accumulators in orange. Beta-estimates (B) and p-values for each path are displayed on the respective arrow. The average causal mediation effect [ACME] and the average direct effect [ADE] are displayed under each mediation triangle.</p><p>Data information: All models are controlled for age, sex, education, and clinical status.</p>
|
https://api.sourcedata.io/file.php?figure_id=51894
|
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] |
||
10.15252/emmm.202216987
|
sTREM2 is associated with amyloid-related p-tau increases and glucose hypermetabolism in Alzheimer's
|
2022
|
Figure 2
|
<p><strong>Figure 2.</strong> Association between CSF sTREM2 and FDG-PET in early Aβ-accumulators (i.e. Aβ CSF+/PET−; n=70) and late Aβ-accumulators (i.e. Aβ CSF+/PET+; n=201). <strong>A)</strong> Plot shows significant (p<0.05) sTREM2 by group interaction on FDG-PET z-scores within an FDG-PET meta-ROI (Landau & Jagust, 2011) using a linear regression. <strong>B)</strong> T-value projection of the association between sTREM2 on FDG-PET, stratified by group. FDG-PET z-scores were derived by referencing FDG-PET SUVRs to cognitively normal controls (i.e. <em>n</em>=131; Aβ CSF−/PET−).</p><p>Data information: The models are controlled for age, sex, education, and clinical status. Boxplots are displayed as median (center line) ± inter-quartile range (box boundaries) with whiskers including observations falling within the 1.5 interquartile range. 200 Regions of interest are displayed per group.</p>
|
https://api.sourcedata.io/file.php?figure_id=51896
|
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] |
||
26783363
|
10.15252/embj.201593477
|
Identification and function of conformational dynamics in the multidomain GTPase dynamin
|
2015
|
Figure 3
|
<p><strong>Figure </strong><strong>3</strong><strong>:</strong> <strong>Large conformational changes of the PHD identified by FRET</strong>.</p>
<p>(<strong>A</strong>) Design of a functional dynamin mutant to probe PHD stalk interactions. Minimal structure of the PHD and the PHD-Stalk interface showing the location of important residues discussed in this study. The unresolved loop L1N<sup>S</sup> in the stalk hosts the IAEDANS label and is sensitive to the two tryptophans (W525 and W542) in the PHD. The distance between two introduced cysteines (S357C and native C602) used to construct a double cysteine Dyn1 is also shown. (<strong>B</strong>) Comparison of emission spectra of various IAEDANS-labeled Dyn1 RCL variants (D352C, Y354C, S357C, I365C, H367C), upon Trp excitation at 295 nm. (<strong>C</strong>) FRET transfer upon excitation is contributed by two neighboring Trps (W525 and W542); Substitution by Phe resulted in significant loss of FRET. (<strong>D</strong>) IAEDANS emission kinetics upon addition of lipid nanotubes with or without PI4,5P<sub>2</sub> (ex=295). The arrow indicates addition of lipids.</p>
|
https://api.sourcedata.io/file.php?figure_id=5989
|
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] |
|
26783363
|
10.15252/embj.201593477
|
Identification and function of conformational dynamics in the multidomain GTPase dynamin
|
2015
|
Figure 4
|
<p><strong>Figure </strong><strong>4</strong><strong>: </strong><strong>Biochemical properties of PHD ‘closed’</strong> <strong>and</strong> <strong>‘open’ </strong><strong>states.</strong></p>
<p>(<strong>A</strong>) Design of dynamin mutants to restrict the PHD in the closed (Dyn1<sup>Closed</sup>) or open (Dyn1ΔΔ) state. (<strong>B</strong>) Histogram shows basal and assembly-stimulated GTPase activities of non-crosslinked Dyn1<sup>CC</sup> vs crosslinked Dyn1<sup>Closed </sup>and Dyn1<sup>WT</sup>. Inset shows crosslinking of the PHD and stalk domains in Dyn1<sup>Y354C</sup><sup>/</sup><sup>S607C</sup> (Dyn1<sup>CC</sup>) with the bifunctional crosslinker, MTS-2-MTS, to yield Dyn1<sup>Closed</sup>, which migrates more slowly on SDS-PAGE, as well as liposome binding of Dyn1<sup>CC </sup>compared to Dyn1<sup>Closed</sup> (Bound, B; Unbound, UB). (<strong>C</strong>) Ability of Dyn1<sup>WT</sup>, Dyn1<sup>CC</sup> and Dyn1<sup>Closed</sup> to catalyze membrane fission and vesicle release from SUPER templates. (<strong>D</strong>) Size exclusion chromatographic profiles of Dyn1<sup>CC</sup>, Dyn1<sup>Closed</sup> at room temperature or after incubation for 10 min at 37°C. (<strong>E</strong>) Oligomeric state of Dyn1ΔΔ at room temperature. (<strong>F</strong>) Negative-stain electron micrographs of Dyn1<sup>WT</sup>, Dyn1ΔΔ and Dyn1<sup>C</sup><sup>losed</sup> assembled onto lipid nanotubes. Scale bar = 200 nm (<strong>G</strong>) Curvature dependent liposome-stimulated GTPase activity of Dyn1<sup>WT</sup> and Dyn1ΔΔ<strong>. </strong>(<strong>H)</strong> Ability of Dyn1<sup>WT</sup> and Dyn1ΔΔ to catalyze membrane fission and vesicle release from SUPER templates.</p>
|
https://api.sourcedata.io/file.php?figure_id=5990
|
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] |
|
26783363
|
10.15252/embj.201593477
|
Identification and function of conformational dynamics in the multidomain GTPase dynamin
|
2015
|
Figure 5
|
<p><strong>Figure </strong><strong>5</strong><strong>: </strong><strong>Biochemical properties and PHD conformational dynamics of Dyn2, disease-associated S619L mutant</strong></p>
<p>(<strong>A</strong>) Temperature dependence of basal and lipid stimulated GTPase activity of Dyn1<sup>WT</sup> and Dyn2<sup>S619L</sup>. (<strong>B</strong>) Temperature sensitive membrane fission activity of Dyn1<sup>WT</sup>, Dyn2<sup>WT</sup> and Dyn2<sup>S619L</sup> measured using SUPER templates. (<strong>C</strong>) Detection of Dyn2 PHD-stalk interactions by FRET using IAEDANS-labeled Dyn2<sup>L354C</sup>. (<strong>D</strong>) Curvature dependent membrane binding and consequent opening of PHD in Dyn1<sup>Y354C-IAEDANS</sup> and Dyn2<sup>L354C-IAEDANS</sup><strong>. </strong>(<strong>E</strong>) Differential temperature dependence of PHD-stalk FRET for WT and S619L mutant Dyn2<sup>IAEDANS</sup>. Data are presented as relative FRET distances assuming a single donor/acceptor pair. (<strong>F</strong>) Differential solvent exchange kinetics of Dyn1<sup>S619L</sup> at ambient temperature compared to Dyn1<sup>WT</sup> under identical conditions. Yellow coloring indicates a significant increase in HDX. Quantitative data on the individual peptides used to generate this map are provided in (Appendix Fig. S5).</p>
|
https://api.sourcedata.io/file.php?figure_id=5991
|
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] |
|
26783363
|
10.15252/embj.201593477
|
Identification and function of conformational dynamics in the multidomain GTPase dynamin
|
2015
|
Figure 6
|
<p><strong>Figure 6: </strong><strong>In vivo function of </strong><strong>CNM</strong><strong>-causing Dyn2</strong><strong> mutant S619L</strong></p>
<p>(<strong>A,B</strong>) Transferrin receptor (TfnR) uptake, a measure of CME, shown as % uptake of total steady-state surface TfnR for control H1299 cells, and H1299 cells stabily expressing low amounts of siRNA-resistant Dyn2<sup>WT</sup>-EGFP (<strong>A) </strong>or Dyn2<sup>S619L</sup>-EGFP (<strong>B</strong>) with or without treatment of siRNA-directed towards endogenous Dyn2. (<strong>C</strong>) Fixed cell TIRF-M images of Dyn2<sup>WT</sup>-EGFP or Dyn2<sup>S619L</sup>-EGFP expressing H1299 cells with or without Dyn2-siRNA treatment showing co-localization with clathrin light chain immunostained rabbit anti-CLC and Alexa 547-conjugated secondary antibodies. (<strong>D</strong>) Percentage of Dyn2-EGFP positive clathrin coated pits detected by live cell TIRF-M and automated master/slave image analysis (Aguet et al, 2013). (<strong>E</strong>) Lifetime analysis of CCPs which are positive for EGFP-Dyn2<sup>WT</sup> or EGFP-Dyn2<sup>S619L</sup> with or without siRNA-mediated specific knockdown of endogenous Dyn2.</p>
|
https://api.sourcedata.io/file.php?figure_id=5992
|
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] |
|
10.15252/emmm.202114759
|
GENETICALLY-MODIFIED MACROPHAGES ACCELERATE MYELIN REPAIR
|
2022
|
Figure 1
|
<sd-panel><p><strong>Figure 1. Graft-derived macrophages in demyelinating lesions</strong></p> <p><strong>A</strong>. Bone marrow isolated from actin-GFP mice was transplanted into pre-conditioned recipients.</p> <p><strong>B</strong>. Flow cytometry analyses of recipient blood 2 months post-transplant. Bi. Transplanted cells detected by GFP fluorescence. Bii. CD11b lebelling shows a large proportion of monocytes expressing GFP.</p> <p><strong>C</strong>. Demyelinating lesions in chimeric mice at 3 dpl. Ci. Demyelination was induced by injecting LPC in the spinal cord white matter. Cii-Civ. Co-immunolabeling for GFP, MBP, and a mixture of CD11b/CD68, showing graft-derived macrophages in the lesion (identified by lack of MBP staining). White lines indicate lesion borders. Scale bar 20 µm. MBP-myelin basic protein; GFP-green fluorescent protein.</p></sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=48222
|
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"ext_tax_names": "Mus musculus",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "CD11b",
"type": "geneprod",
"uniprot_ids": [
"P05555"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P31996",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "direct",
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"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "CD68",
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"uniprot_ids": [
"P31996"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P05555",
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"ext_tax_names": "Mus musculus",
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"mapping_status": "mapped",
"ncbi_gene_id": null,
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"role": "assayed",
"text": "CD11b",
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"P05555"
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},
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"ext_dbs": "Uniprot",
"ext_ids": "P04370",
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"ext_tax_names": "Mus musculus",
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]
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"original_type": "protein",
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"text": "MBP",
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"P04370"
]
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"text": "MBP",
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"P04370"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P04370",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "myelin basic protein",
"type": "geneprod",
"uniprot_ids": [
"P04370"
]
}
] |
||
10.15252/emmm.202114759
|
GENETICALLY-MODIFIED MACROPHAGES ACCELERATE MYELIN REPAIR
|
2022
|
Figure 2
|
<sd-panel><p><strong>Figure 2</strong>. <strong>Genetically engineered HSCs secrete Sema3F that attracts OPCs in vitro.</strong></p> <p><strong>A-C</strong>. Transduction of HSCs. <strong>A</strong>. Mouse bone marrow was isolated and differentiated cells (Lin+) were removed using MACS. Non-differentiated cells were transduced and expanded for 5 days. <strong>B</strong>. Lower numbers of GFP+ cells, verified using flow cytometry, after transduction with Sema3F vector, ***p<0.0001, Student t test, n=8 independent experiments. Mean±SEM. <strong>C</strong>. Western blot showing GFP expression in cells transduced with both vectors and Sema3F expression in the supernatant of Sema3F-transduced cells only.</p> <p><strong>D</strong>. OPCs isolated from adult PDGFRα-GFP mice using FACS were subjected to transwell-chamber migration assay in response to supernatants from non-transduced (NT), GFP-transduced (gfp), or Sema3F -transduced (sema3F-gfp) HSCs.</p> <p><strong>E</strong>. Fold increase in cells that crossed the membrane insert compared to NT. ***p‹0.0001. One-way ANOVA followed by Bonferroni's Multiple Comparison test. n= 1-2 normalized replicates from 3-5 independent experiments. Mean±SEM. ***p<0.0001. R.=recombinant. Super=supernatant. Anti-Nrp2=Neuropilin2 function blocking antibody.</p></sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=48223
|
[
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"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "6405",
"original_type": "gene",
"role": "intervention",
"text": "Sema3F",
"type": "geneprod",
"uniprot_ids": [
"Q13275",
"C9JPG5",
"Q59G50"
]
},
{
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"ncbi_gene_id": "6405",
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"Q13275",
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"Q59G50"
]
},
{
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"text": "Sema3F",
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"Q13275"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "O35375",
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"ext_tax_names": "Mus musculus",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "intervention",
"text": "Neuropilin2",
"type": "geneprod",
"uniprot_ids": [
"O35375"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "O35375",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "intervention",
"text": "Nrp2",
"type": "geneprod",
"uniprot_ids": [
"O35375"
]
}
] |
||
10.15252/emmm.202114759
|
GENETICALLY-MODIFIED MACROPHAGES ACCELERATE MYELIN REPAIR
|
2022
|
Figure 3
|
<sd-panel><p><strong>Figure 3. Middle-age OPCs maintain Nrp2 expression and responsiveness to Sema3F.</strong></p> <p><strong>A-B.</strong> Expression of Nrp2 gene by OPCs is maintained in middle-age (12 month (m) old) mice. A. Microarray analyses results for Nrp2 expression by OPCs purified using FACS from the brains of 2 months versus 12 months old PDGFR<span class="math inline"><em>α</em>−</span>GFP mice (n=3-4 independent experiments). B. RNA sequencing results for Nrp2 expression by oligodendroglia-enriched preparations isolated from the spinal cords of 2 month versus 12 month old mice. (n=3-4 independent experiments). Mean±SEM</p> <p><strong>C-G</strong>. Sema 3F expression in demyelinating lesions at 4 dpl (onset of OPC recruitment) is decreased in middle-aged (12 m old) and old (18m old) mice compared to young mice (2m old). C-E. Colabellings for Sema3F and Iba1 (macrophage marker) in demyelinating lesions at 4 dpl in 2m (C), 12m (D),and 18m old mice (E). Arrowheads point to double-labelled cells. F. Quantification of Sema3F expressing cells in the lesion. G. Percentage of Iba1+ cells positive for Sema3F. NWM-normal white matter. dpl-days post lesion. n=4-8 mice/group. Mean±SEM Two-way ANOVA followed by Tukey's Multiple Comparison test. *p<0.05, **p<0.01, ***p<0.0001.</p> <p><strong>H</strong>. Transwell chamber assay was used to evaluate migration of young versus middle-age OPCs in response to recombinant Sema3F and supernatant from PGK-GFP-T2A-Sema3F transduced cells. OPCs of both ages migrate in response to recombinant Sema3F and PGK-GFP-T2A-Sema3F-transduced cell supernatant. n= 1-2 normalized replicates from 2-5 independent experiments. Mean±SEM. One-way ANOVA followed by Bonferroni's Multiple Comparison test. *p<0.05, ** p<0.01. Scale bar 50 µm.</p></sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=48224
|
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"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "18187",
"original_type": "gene",
"role": "assayed",
"text": "Nrp2",
"type": "geneprod",
"uniprot_ids": [
"O35375",
"Q3U5I8",
"Q8QZY7"
]
},
{
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"Q3U5I8",
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{
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"mapping_source": "direct",
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"ncbi_gene_id": null,
"original_type": "protein",
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"text": "Iba1",
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"uniprot_ids": [
"Q9EQW9"
]
},
{
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},
{
"ext_dbs": "Uniprot",
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"text": "Sema 3F",
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]
},
{
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"text": "Sema3F",
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"uniprot_ids": [
"O88632"
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},
{
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},
{
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"type": "geneprod",
"uniprot_ids": [
"Q13275"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q13275",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "direct",
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"ncbi_gene_id": null,
"original_type": "protein",
"role": "intervention",
"text": "Sema3F",
"type": "geneprod",
"uniprot_ids": [
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]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q13275",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "intervention",
"text": "Sema3F",
"type": "geneprod",
"uniprot_ids": [
"Q13275"
]
}
] |
||
10.15252/emmm.202114759
|
GENETICALLY-MODIFIED MACROPHAGES ACCELERATE MYELIN REPAIR
|
2022
|
Figure 4
|
<sd-panel><p><strong>Figure 4</strong>. <strong>Generation of Sema3F chimeras.</strong></p> <p><strong>A</strong>. Transduced female HSCs were injected retro-orbitally into pre-conditioned male mice. Blood was analyzed 2 months post-transplant.</p> <p><strong>B</strong>. Percentage of transplanted (female) cells in the blood. n=18-19 mice/group. Mean±SEM</p> <p><strong>C</strong>. Percentage of transduced (GFP+) cells in the blood . Mean±SEM. ***p<0.0001. n=22-25 mice/group.</p> <p><strong>D</strong>. Percentages of GFP+ cells labeled with CD11b, CD19, and CD3. The proportion of GFP+ cells labeled with CD11b is increased in Sema3F mice (p=0.01), while that of CD19-labeled cells is decreased (p=0.0003). Mean±SEM. Unpaired Student t-test. n=9 mice/group. *p<0.05,***p<0.001.</p> <p><strong>E</strong>. Percentages of total blood cells expressing CD11b, CD19, and CD3. Red dashed lines indicate the percentage expression of these antigens in blood cells of control mice. n=9 mice/group. Mean±SEM.</p></sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=48225
|
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] |
||
10.15252/emmm.202114759
|
GENETICALLY-MODIFIED MACROPHAGES ACCELERATE MYELIN REPAIR
|
2022
|
Figure 5
|
<sd-panel><p><strong>Figure 5. Transgene-carrying macrophages in demyelinating lesions.</strong></p> <p><strong>A-F.</strong> Co-labeling for GFP and MBP on spinal cord sections of GFP (A-C) and Sema3F-GFP chimeras (D-F) sacrificed at 7 (A,D), 10 (B,E), and 60 (C,F) days post lesion (dpl). Absence of MBP labeling in A-B,D-E indicates the lesion (delimited by yellow lines). Areas faintly labeled with MBP in C-F likely represent remyelinated areas.</p> <p><strong>G</strong>. Quantification of GFP+ cells. Kruskal-Wallis test p=0.02. No significant differences between GFP and Sema3F at any of the time points (Dunn's post test; Mann-Whitney test). Decrease in GFP+ cells between 7 and 60 dpl for both GFP and Sema3F mice 2m.</p> <p><strong>H-M</strong>. Co-labeling for GFP/MBP/Iba1 (macrophage/microglia marker) shows colocalization of GFP with Iba1. Arrows indicate double-labeled cells.</p> <p><strong>N-P</strong> Co-labeling for GFP and T cell marker CD3. Arrows indicate CD3-labeled cells.</p> <p><strong>Q-S</strong>. Co-labeling for GFP and B cell marker CD45R/B220. Arrows indicate CD45R/B220-labeled cells.</p> <p><strong>T</strong>. Percentages of GFP+ cells that are Iba1+, CD3+, and CD45R/B220+. The absolute majority of GFP+ cells are Iba1+.</p> <p><strong>U</strong>. Quantification of Iba1+, CD3+, and B220+ cells. For all 3 populations, no significant differences in cell numbers were observed between GFP and Sema3F mice, and a general decrease was observed at 60 dpl compared to earlier time points.</p> <p><strong>V-Aa</strong>. Co-labeling for GFP and microglial marker P2Y12. Purple arrows indicate P2Y12+ cells. Exclusion between the two markers is obvious in both groups.</p> <p><strong>Ab</strong>. Quantification of P2Y12+ cells. No significant changes are observed between the groups or across the time.</p> <p>Data information: For all figure panels, n=6-7 mice/group for 7 and 10 dpl, n=2-3 mice/group for 60 dpl. Mean±SEM. Scale bars 20 μm, except for S (10 μm).</p></sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=48226
|
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] |
||
10.15252/emmm.202114759
|
GENETICALLY-MODIFIED MACROPHAGES ACCELERATE MYELIN REPAIR
|
2022
|
Figure 6
|
<sd-panel><p><strong>Figure 6. OPC recruitment is increased in Sema3F chimeras.</strong></p> <p><strong>A</strong>. Temporal sequence of events in LPC lesion. dpl-days post lesion. Red inverted triangles indicate sacrifice.</p> <p><strong>B-G</strong>. Lesions at 7 dpl in GFP (B,E) and Sema3F (C,F) mice. B-C. Co-labeling for PDGFRα, MBP, and DAPI. Arrows indicate OPCs in the lesion. Bi and Ci-insets of white dotted squares in B and C. <strong>D</strong>. Higher numbers of PDGFRα+ (OPCs) cells in Sema3F mice at 7 dpl (Mann Whitney test: p=0.0031, n=6-8 mice/group). E-F. Co-labeling for Olig2 and MBP. E'-F'. Co-labeling for Olig2 and GFP of the lesions shown in E-F. 3D reconstructions. Proximity of OPCs and Sema 3F-carrying cells. E'i-E'iii and F'i-F'iii-insets of E'-F'. <strong>G</strong>. Higher numbers of Olig2+ (oligodendroglial) cells in Sema3F-GFP mice at 7 dpl (Mann Whitney test: p=0.0047, n=5-8 mice/group). ** p<0.01.</p> <p><strong>H-I</strong>. Immunolabelling for activated OPC marker Nkx2.2.</p> <p><strong>J</strong>. Numbers of Nkx2.2+ cells are increased in lesions of Sema3F-GFP mice at 7dpl (Mann Whitney test: p=0.014, n=6-7 mice/group). Arrows indicate Nkx2.2+ cells in close proximity of GFP+ cells. Mean±SEM. *p<0.05.</p> <p><strong>K-P</strong>. colabelling for Nkx2.2 and proliferation marker Ki67. Arrows indicate double labeled cells. <strong>Q</strong>. Numbers of Nkx2.2+Ki67+ cells are increased at 7 dpl in Sema3F-GFP mice. Mean±SEM. n=6-7 mice/group.</p> <p><strong>R</strong>. The proportion of Nkx2.2+ cells co-expressing Ki67 is unchanged. Mean±SEM. n=6-7 mice/group.</p> <p><strong>S-X</strong>. Colabelling for Olig2 and cleaved caspase 3, marker of apoptosis indicates occasional apoptotic cells in both groups of mice that are Olig2-. Arrows indicate cleaved caspase 3+ cells.<strong>Y</strong>. Numbers of cleaved caspase 3+ cells are the same in two groups. Mean±SEM. n=6 mice/group.</p> <p>Data information: Scale bars 20 μm (B,C,E,F), 10 μm (H,I,M,P,U,X), 5 μm (Bi, Ci).</p></sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=48227
|
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"ncbi_gene_id": null,
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"role": "assayed",
"text": "Olig2",
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"uniprot_ids": [
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] |
||
10.15252/emmm.202114759
|
GENETICALLY-MODIFIED MACROPHAGES ACCELERATE MYELIN REPAIR
|
2022
|
Figure 7
|
<sd-panel><p><strong>Figure 7. Oligodendrogenesis and remyelination are accelerated in Sema 3F chimeras.</strong></p> <p><strong>A-B</strong>. Labelling for APC/CC1, a marker of oligodendrocytes. Dotted lines indicate the lesion border. APC+ cells are scarce in the lesions of GFP mice (A). B. APC+ cells in the lesion of Sema3F mice.</p> <p><strong>C</strong>. Quantification of APC+ cells (Mann Whitney test; p=0.0061 for 7 dpl, p=0.0081 for 10 dpl; n= 6-7 mice/group). *p<0.01.</p> <p><strong>D-E</strong>. EM images of the lesion in GFP (D) and Sema3F (E) chimeras at 14 dpl. Thin myelin sheaths in Sema 3F mice (yellow arrows).</p> <p><strong>F</strong>. Higher power image of a new myelin sheath in a Sema3F mouse. <strong>Fi</strong>. Inset of yellow square in F.</p> <p><strong>G</strong>. Quantification of remyelinated axons (Mann Whitney test: p=0.03, n=6 mice/group). *p<0.05.</p> <p><strong>H.</strong> In Sema3F mice, oligodendroglial cells (O) and early remyelination (*) are frequently observed in macrophage (M) vicinity. <strong>Hi</strong>. Inset of yellow dashed square in H.</p> <p>Data information: Scale bars 20 μm (A,B), 1 μm (D,E), 500 nm (F).</p></sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=48228
|
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] |
||
10.15252/embj.2018101397
|
NLRC3 expression in dendritic cells attenuates CD4+ T cell response and autoimmunity
|
2019
|
Figure 1
|
<sd-panel> <p><strong>Figure 1. <sd-pretag id="sdPretag1211623972sm" type="geneprod" role="intervention">NLRC3</sd-pretag> deficiency promoted antigen-presenting function of DCs.</strong></p> <p><strong>A.</strong> Representative <sd-pretag id="sdPretag995375132sm" category="assay">flow cytometry</sd-pretag> data showing surface phenotypes of <sd-pretag id="sdPretag431974568sm" type="cell" role="component">DCs</sd-pretag> sorted from <sd-pretag id="sdPretag4525811sm" type="tissue" role="component">spleens</sd-pretag> of wild type (WT) or <sd-pretag id="sdPretag493462119sm" type="geneprod" role="intervention"><em>Nlrc3</em></sd-pretag><sup>-/-</sup> <sd-pretag id="sdPretag1699871138sm" type="organism" role="component">mice</sd-pretag> and treated with <sd-pretag id="sdPretag154963376sm" type="molecule" role="intervention">LPS</sd-pretag> (100 ng/ml) for 48 hours.</p> <p><strong>B.</strong> <sd-pretag id="sdPretag601705471sm" category="assay">ELISA</sd-pretag> of cytokines in culture supernatants of <sd-pretag id="sdPretag1787068995sm" type="cell" role="component">DCs</sd-pretag> treated as in <strong>A</strong>.</p> <p><strong>C-F.</strong> The intracellular production of <sd-pretag id="sdPretag1070377965sm" type="geneprod" role="intervention">IFN-γ</sd-pretag> and <sd-pretag id="sdPretag590398938sm" type="geneprod" role="intervention">IL-17</sd-pretag> by <sd-pretag id="sdPretag280820836sm" type="geneprod" role="intervention">CD4</sd-pretag><sup>+</sup> <sd-pretag id="sdPretag2110601724sm" type="cell" role="component">T cells</sd-pretag> <strong>(C)</strong>, cytokines in culture supernatants <strong>(D)</strong>, <sd-pretag id="sdPretag1772511621sm" type="molecule" role="component">thymidine</sd-pretag> <sd-pretag id="sdPretag1554397645sm" category="assay">incorporation proliferation assay</sd-pretag> <strong>(E)</strong> and <sd-pretag id="sdPretag1638992297sm" type="geneprod" role="intervention">CFSE</sd-pretag> <sd-pretag id="sdPretag1730722441sm" category="assay">proliferation assay</sd-pretag> <strong>(F)</strong> among naive 2D2 CD4<sup>+</sup> <sd-pretag id="sdPretag797006441sm" type="cell" role="component">T cells</sd-pretag> stimulated with <sd-pretag id="sdPretag34819023sm" type="molecule" role="intervention">MOG</sd-pretag>(35-55) plus DCs treated as in <strong>A</strong>.</p> <p>Data information: Data (n=5 in B, D and E) shown are the mean ±SD. **<em>P</em> < 0.01 and ***<em>P</em> < 0.001 by an unpaired <em>t</em>-test. Data are representative of three independent experiments with similar results.</p> </sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=26889
|
[
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"mapping_status": "mapped",
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"original_type": "gene",
"role": "intervention",
"text": "Nlrc3",
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"ext_tax_names": "Mus musculus",
"mapping_source": "direct",
"mapping_status": "mapped",
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"role": "assayed",
"text": "IL-17",
"type": "geneprod",
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] |
||
10.15252/embj.2018101397
|
NLRC3 expression in dendritic cells attenuates CD4+ T cell response and autoimmunity
|
2019
|
Figure 2
|
<sd-panel> <p><strong>Figure 2. <sd-pretag id="sdPretag37445962sm" type="geneprod" role="intervention">NLRC3</sd-pretag> deficiency promoted EAE development.</strong></p> <p>WT and <sd-pretag id="sdPretag1778181205sm" type="geneprod" role="intervention"><em>Nlrc3</em></sd-pretag><sup>-/-</sup> <sd-pretag id="sdPretag1883508229sm" type="organism" role="component">mice</sd-pretag> were immunized with MOG(35-55) peptide in CFA adjuvant and <sd-pretag id="sdPretag249839245sm" type="geneprod" role="intervention">pertussis toxin</sd-pretag> to induce EAE.</p> <p><strong>A.</strong> Mean clinical scores of EAE in immunized WT (n= 10) and <sd-pretag id="sdPretag1312649317sm" type="geneprod" role="intervention"><em>Nlrc3</em></sd-pretag><sup>-/-</sup> <sd-pretag id="sdPretag1383467358sm" type="organism" role="component">mice</sd-pretag> (n= 10).</p> <p><strong>B.</strong> Representative <sd-pretag id="sdPretag46071991sm" category="assay">flow cytometry</sd-pretag> data showing intracellular production of <sd-pretag id="sdPretag1653330058sm" type="geneprod" role="assayed">IFN-γ</sd-pretag> and <sd-pretag id="sdPretag1615271398sm" type="geneprod" role="assayed">IL-17A</sd-pretag> by <sd-pretag id="sdPretag1140014574sm" type="cell" role="component">CD4</sd-pretag><sup>+</sup> <sd-pretag id="sdPretag723773872sm" type="cell" role="component">T cells</sd-pretag> from the <sd-pretag id="sdPretag1463055008sm" type="tissue" role="component">spinal cord</sd-pretag> and <sd-pretag id="sdPretag856257338sm" type="tissue" role="component">brain</sd-pretag> of WT or <sd-pretag id="sdPretag863285268sm" type="geneprod" role="intervention"><em>Nlrc3</em></sd-pretag><sup>-/-</sup> <sd-pretag id="sdPretag2038553172sm" type="organism" role="component">mice</sd-pretag> 26 d after EAE induction after restimulation with <sd-pretag id="sdPretag26854417sm" type="molecule" role="intervention">MOG</sd-pretag>(35-55) peptide. Pooled data are presented in the right panel.</p> <p><strong>C.</strong> Representative <sd-pretag id="sdPretag261556079sm" category="assay">flow cytometry</sd-pretag> data showing surface phenotypes of <sd-pretag id="sdPretag1620378772sm" type="cell" role="component">DCs</sd-pretag> from <sd-pretag id="sdPretag1749778625sm" type="tissue" role="component">spleens</sd-pretag> of WT or <sd-pretag id="sdPretag1078329982sm" type="geneprod" role="intervention"><em>Nlrc3</em></sd-pretag><sup>-/-</sup> <sd-pretag id="sdPretag426965722sm" type="organism" role="component">mice</sd-pretag> 26 d after EAE induction.</p> <p><strong>D.</strong> Expression of <em><sd-pretag id="sdPretag1315716133sm" type="geneprod" role="assayed">Nlrc3</sd-pretag>, <sd-pretag id="sdPretag802450306sm" type="geneprod" role="assayed">Il12</sd-pretag></em>, <sd-pretag id="sdPretag1235607303sm" type="geneprod" role="assayed"><em>Il6</em></sd-pretag>, <sd-pretag id="sdPretag326752327sm" type="geneprod" role="assayed"><em>Il23</em></sd-pretag> and <sd-pretag id="sdPretag1330924861sm" type="geneprod" role="assayed"><em>Il27</em></sd-pretag> mRNA in <sd-pretag id="sdPretag933365042sm" type="cell" role="component">DCs</sd-pretag> sorted from WT and <sd-pretag id="sdPretag1106112508sm" type="geneprod" role="intervention"><em>Nlrc3</em></sd-pretag><sup>-/-</sup> <sd-pretag id="sdPretag943570368sm" type="organism" role="component">mice</sd-pretag> 26 d after EAE induction, presented relative to that of <sd-pretag id="sdPretag491571127sm" type="geneprod" role="assayed"><em>Gapdh</em></sd-pretag>.</p> <p>Data information: Data (n=5 in B right and D) shown are the mean ±SD. *<em>P</em> < 0.05, **<em>P</em> < 0.01and ***<em>P</em> < 0.001 by an unpaired <em>t</em>-test. Data are representative of three independent experiments with similar results.</p> </sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=26890
|
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"ext_ids": "Q62386",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "IL-17A",
"type": "geneprod",
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]
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{
"ext_dbs": "NCBI gene",
"ext_ids": "268857",
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"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "268857",
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"role": "intervention",
"text": "Nlrc3",
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"Q5DU56",
"J3QQ49"
]
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"ext_dbs": "NCBI gene///NCBI gene",
"ext_ids": "16160///16159",
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"ext_tax_names": "Mus musculus///Mus musculus",
"mapping_source": "unknown",
"mapping_status": "unmapped",
"ncbi_gene_id": null,
"original_type": "gene",
"role": "assayed",
"text": "Il12",
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},
{
"ext_dbs": "NCBI gene",
"ext_ids": "83430",
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"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
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"text": "Il23",
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"Q9EQ14"
]
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"Q8K3I6"
]
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{
"ext_dbs": "NCBI gene",
"ext_ids": "16193",
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"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "16193",
"original_type": "gene",
"role": "assayed",
"text": "Il6",
"type": "geneprod",
"uniprot_ids": [
"P08505",
"A0A0G2JGF4",
"A2RTD1"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "268857",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "268857",
"original_type": "gene",
"role": "intervention",
"text": "Nlrc3",
"type": "geneprod",
"uniprot_ids": [
"Q5DU56",
"J3QQ49"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "268857",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "268857",
"original_type": "gene",
"role": "assayed",
"text": "Nlrc3",
"type": "geneprod",
"uniprot_ids": [
"Q5DU56",
"J3QQ49"
]
}
] |
||
10.15252/embj.2018101397
|
NLRC3 expression in dendritic cells attenuates CD4+ T cell response and autoimmunity
|
2019
|
Figure 3
|
<sd-panel> <p><strong>Figure 3. <sd-pretag id="sdPretag1337359199sm" type="geneprod" role="intervention">NLRC3</sd-pretag> deficiency in DC promoted EAE development.</strong></p> <p>DC(WT) and DC(<sd-pretag id="sdPretag2130942000sm" type="geneprod" role="intervention">NLRC3</sd-pretag>-KO) <sd-pretag id="sdPretag1317687797sm" type="organism" role="component">mice</sd-pretag> were immunized with MOG(35-55) peptide in CFA adjuvant and <sd-pretag id="sdPretag119638196sm" type="geneprod" role="intervention">pertussis toxin</sd-pretag> to induce EAE.</p> <p><strong>A.</strong> Mean clinical scores of EAE in immunized DC(WT) (n= 5) and DC(<sd-pretag id="sdPretag2099887677sm" type="geneprod" role="intervention">NLRC3</sd-pretag>-KO) <sd-pretag id="sdPretag20854542sm" type="organism" role="component">mice</sd-pretag> (n= 5).</p> <p><strong>B.</strong> Representative <sd-pretag id="sdPretag1111889077sm" category="assay">flow cytometry</sd-pretag> data showing intracellular production of <sd-pretag id="sdPretag271524074sm" type="geneprod" role="assayed">IFN-γ</sd-pretag> and <sd-pretag id="sdPretag409561277sm" type="geneprod" role="assayed">IL-17A</sd-pretag> by <sd-pretag id="sdPretag1677657788sm" type="cell" role="component">CD4</sd-pretag><sup>+</sup> <sd-pretag id="sdPretag188958940sm" type="cell" role="component">T cells</sd-pretag> in the <sd-pretag id="sdPretag2086655974sm" type="subcellular" role="component">spinal</sd-pretag><sd-pretag id="sdPretag1879456093sm" type="tissue" role="component"> cord</sd-pretag> and <sd-pretag id="sdPretag752022134sm" type="tissue" role="component">brain</sd-pretag> from DC(WT) and DC(<sd-pretag id="sdPretag1596038088sm" type="geneprod" role="intervention">NLRC3</sd-pretag>-KO) <sd-pretag id="sdPretag1059420361sm" type="organism" role="component">mice</sd-pretag> 26 d after EAE induction after restimulation with MOG(35-55) peptide.</p> <p><strong>C.</strong> Recall response to <sd-pretag id="sdPretag1375788233sm" type="cell" role="component">MOG</sd-pretag>(<sd-pretag id="sdPretag305655973sm" type="cell" role="component">35-55</sd-pretag>) by <sd-pretag id="sdPretag1179297397sm" type="cell" role="component">splenocytes</sd-pretag> isolated from DC(WT) and DC(<sd-pretag id="sdPretag1495064891sm" type="geneprod" role="intervention">NLRC3</sd-pretag>-KO) <sd-pretag id="sdPretag1851056993sm" type="organism" role="component">mice</sd-pretag> 26 d after EAE induction.</p> <p><strong>D.</strong> Expression of <sd-pretag id="sdPretag1767736015sm" type="geneprod" role="assayed"><em>Il12</em></sd-pretag>, <sd-pretag id="sdPretag1292480482sm" type="geneprod" role="assayed"><em>Il6</em></sd-pretag>, <sd-pretag id="sdPretag376942751sm" type="geneprod" role="assayed"><em>Il23</em></sd-pretag> and <sd-pretag id="sdPretag22199857sm" type="geneprod" role="assayed"><em>Il27</em></sd-pretag> mRNA in <sd-pretag id="sdPretag1924885108sm" type="cell" role="component">DCs</sd-pretag> sorted from DC(WT) and DC(<sd-pretag id="sdPretag1139932337sm" type="geneprod" role="intervention">NLRC3</sd-pretag>-KO) <sd-pretag id="sdPretag833064525sm" type="organism" role="component">mice</sd-pretag> 26 d after EAE induction, presented relative to that of <sd-pretag id="sdPretag1641797874sm" type="geneprod" role="component"><em>Gapdh</em></sd-pretag>.</p> <p><strong>E-F.</strong> CFSE <sd-pretag id="sdPretag1915584847sm" category="assay">proliferation assay</sd-pretag> <strong>(E)</strong> and cytokine secretion <strong>(F)</strong> of naive 2D2 CD4<sup>+</sup> <sd-pretag id="sdPretag574194190sm" type="cell" role="component">T cells</sd-pretag> stimulated with MOG(35-55) plus DCs sorted from DC(WT) and DC(<sd-pretag id="sdPretag1217721003sm" type="geneprod" role="intervention">NLRC3</sd-pretag>-KO) <sd-pretag id="sdPretag31054323sm" type="organism" role="component">mice</sd-pretag> 26 d after EAE induction.</p> <p>Data information: Data (n=5 in C, D and F) shown are the mean ±SD. *<em>P</em> < 0.05, **<em>P</em> < 0.01and ***<em>P</em> < 0.001 by an unpaired <em>t</em>-test. Data are representative of three independent experiments with similar results.</p> </sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=26891
|
[
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"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "268857",
"original_type": "gene",
"role": "intervention",
"text": "NLRC3",
"type": "geneprod",
"uniprot_ids": [
"Q5DU56",
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]
},
{
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"Q5DU56",
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]
},
{
"ext_dbs": "NCBI gene",
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"mapping_source": "ncbi_gene",
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"ncbi_gene_id": "268857",
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"text": "NLRC3",
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},
{
"ext_dbs": "NCBI gene",
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{
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{
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"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
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{
"ext_dbs": "NCBI gene///NCBI gene",
"ext_ids": "16159///16160",
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"ext_tax_names": "Mus musculus///Mus musculus",
"mapping_source": "unknown",
"mapping_status": "unmapped",
"ncbi_gene_id": null,
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"text": "Il12",
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},
{
"ext_dbs": "NCBI gene",
"ext_ids": "83430",
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"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "83430",
"original_type": "gene",
"role": "assayed",
"text": "Il23",
"type": "geneprod",
"uniprot_ids": [
"Q9EQ14"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "246779",
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"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
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"role": "assayed",
"text": "Il27",
"type": "geneprod",
"uniprot_ids": [
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},
{
"ext_dbs": "NCBI gene",
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"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "16193",
"original_type": "gene",
"role": "assayed",
"text": "Il6",
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"P08505",
"A0A0G2JGF4",
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]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "268857",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "268857",
"original_type": "gene",
"role": "intervention",
"text": "NLRC3",
"type": "geneprod",
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"Q5DU56",
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]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "268857",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "268857",
"original_type": "gene",
"role": "intervention",
"text": "NLRC3",
"type": "geneprod",
"uniprot_ids": [
"Q5DU56",
"J3QQ49"
]
},
{
"ext_dbs": "NCBI gene",
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"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "268857",
"original_type": "gene",
"role": "intervention",
"text": "NLRC3",
"type": "geneprod",
"uniprot_ids": [
"Q5DU56",
"J3QQ49"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "268857",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "268857",
"original_type": "gene",
"role": "intervention",
"text": "NLRC3",
"type": "geneprod",
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"Q5DU56",
"J3QQ49"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "268857",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "268857",
"original_type": "gene",
"role": "intervention",
"text": "NLRC3",
"type": "geneprod",
"uniprot_ids": [
"Q5DU56",
"J3QQ49"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "268857",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "268857",
"original_type": "gene",
"role": "intervention",
"text": "NLRC3",
"type": "geneprod",
"uniprot_ids": [
"Q5DU56",
"J3QQ49"
]
}
] |
||
10.15252/embj.2018101397
|
NLRC3 expression in dendritic cells attenuates CD4+ T cell response and autoimmunity
|
2019
|
Figure 4
|
<sd-panel> <p><strong>Figure 4 <sd-pretag id="sdPretag1750570231sm" type="geneprod" role="assayed">NLRC3</sd-pretag> negatively regulated <sd-pretag id="sdPretag465651527sm" type="geneprod" role="assayed">p38</sd-pretag> signaling pathway in DC.</strong></p> <p><sd-pretag id="sdPretag1556565204sm" type="cell" role="component">DCs</sd-pretag> were sorted from <sd-pretag id="sdPretag1514866168sm" type="tissue" role="component">spleens</sd-pretag> of WT or <sd-pretag id="sdPretag269233468sm" type="geneprod" role="intervention"><em>Nlrc3</em></sd-pretag><sup>-/-</sup> <sd-pretag id="sdPretag16355746sm" type="organism" role="component">mice</sd-pretag>.</p> <p><strong>A.</strong> Purified <sd-pretag id="sdPretag1662532592sm" type="cell" role="component">DCs</sd-pretag> were treated with <sd-pretag id="sdPretag1535870875sm" type="molecule" role="intervention">LPS</sd-pretag> (100 ng/ml) for specified time. DC lysates were probed for phosphorylated <sd-pretag id="sdPretag1677688375sm" type="geneprod" role="assayed">p65</sd-pretag> (p-p65), total p65, p-AKT, AKT, p-<sd-pretag id="sdPretag832294864sm" type="geneprod" role="component">p38</sd-pretag>, p38, p-ERK, ERK, p-<sd-pretag id="sdPretag752637141sm" type="geneprod" role="intervention">JNK</sd-pretag>, JNK and <sd-pretag id="sdPretag910992376sm" type="geneprod" role="component">GAPDH</sd-pretag>.</p> <p><strong>B-D.</strong> Purified <sd-pretag id="sdPretag1523652639sm" type="cell" role="component">DCs</sd-pretag> were treated for 48 hours with <sd-pretag id="sdPretag1728980485sm" type="molecule" role="intervention">LPS</sd-pretag> (100 ng/ml) in the presence or absence of the <sd-pretag id="sdPretag1217264443sm" type="geneprod" role="intervention">p38</sd-pretag> inhibitor <sd-pretag id="sdPretag1440175715sm" type="molecule" role="intervention">SB203580</sd-pretag> (10 μM or indicated concentrations). (<strong>B</strong>) Concentrations of <sd-pretag id="sdPretag1855273865sm" type="geneprod" role="assayed">IL-12</sd-pretag>, <sd-pretag id="sdPretag1770165006sm" type="geneprod" role="assayed">IL-6</sd-pretag>, <sd-pretag id="sdPretag1751796594sm" type="geneprod" role="assayed">IL-23</sd-pretag> and <sd-pretag id="sdPretag1935755119sm" type="geneprod" role="assayed">IL-27</sd-pretag> in supernatants were detected by <sd-pretag id="sdPretag9379076sm" category="assay">ELISA</sd-pretag>. Cytokines in culture supernatants (<strong>C</strong>) and <sd-pretag id="sdPretag1471701612sm" type="geneprod" role="intervention">CFSE</sd-pretag> <sd-pretag id="sdPretag1557890206sm" category="assay">proliferation assay</sd-pretag> (<strong>D</strong>) among naive 2D2 CD4+ <sd-pretag id="sdPretag1684569008sm" type="cell" role="component">T cells</sd-pretag> stimulated with MOG(35-55) plus DCs. NC: negative control.</p> <p>Data information: Data (n=5 in B and C) shown are the mean ±SD. *<em>P</em> < 0.05, **<em>P</em> < 0.01and ***<em>P</em> < 0.001 by an unpaired <em>t</em>-test. Data are representative of three independent experiments with similar results.</p> </sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=26892
|
[
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"mapping_source": "ncbi_gene",
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"role": "intervention",
"text": "Nlrc3",
"type": "geneprod",
"uniprot_ids": [
"Q5DU56",
"J3QQ49"
]
},
{
"ext_dbs": "Uniprot///Uniprot///Uniprot",
"ext_ids": "Q9WUA6///Q60823///P31750",
"ext_tax_ids": "10090///10090///10090",
"ext_tax_names": "Mus musculus///Mus musculus///Mus musculus",
"mapping_source": "unknown",
"mapping_status": "unmapped",
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"text": "AKT",
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{
"ext_dbs": "Uniprot///Uniprot///Uniprot",
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"ext_tax_names": "Mus musculus///Mus musculus///Mus musculus",
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},
{
"ext_dbs": "Uniprot///Uniprot",
"ext_ids": "P63085///Q63844",
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"ext_tax_names": "Mus musculus///Mus musculus",
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"text": "ERK",
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},
{
"ext_dbs": "Uniprot///Uniprot",
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},
{
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{
"ext_dbs": "Uniprot",
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"role": "intervention",
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"type": "geneprod",
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]
}
] |
||
10.15252/embj.2018101397
|
NLRC3 expression in dendritic cells attenuates CD4+ T cell response and autoimmunity
|
2019
|
Figure 5
|
<sd-panel> <p><strong>Figure 5. <sd-pretag id="sdPretag222661892sm" type="geneprod" role="intervention">NLRC3</sd-pretag> deficiency in DC promoted EAE development via <sd-pretag id="sdPretag1085689213sm" type="geneprod" role="assayed">p38</sd-pretag> signaling pathway.</strong></p> <p><strong>A.</strong> Activity phosphorylation of <sd-pretag id="sdPretag1677411210sm" type="geneprod" role="assayed">p38</sd-pretag> were detected in <sd-pretag id="sdPretag342335837sm" type="cell" role="component">DCs</sd-pretag> in the <sd-pretag id="sdPretag561402887sm" type="tissue" role="component">spleens</sd-pretag> from DC(WT) and DC(<sd-pretag id="sdPretag667877704sm" type="geneprod" role="intervention">NLRC3</sd-pretag>-KO) <sd-pretag id="sdPretag10943054sm" type="organism" role="component">mice</sd-pretag> 26 d after EAE induction. Pooled data are presented in the right panel.</p> <p><strong>B-D.</strong> DC(<sd-pretag id="sdPretag961576392sm" type="geneprod" role="intervention">p38</sd-pretag>-KO) and DC(<sd-pretag id="sdPretag150244387sm" type="geneprod" role="intervention">p38</sd-pretag>+<sd-pretag id="sdPretag417158017sm" type="geneprod" role="intervention">NLRC3</sd-pretag>-KO) <sd-pretag id="sdPretag931509130sm" type="organism" role="component">mice</sd-pretag> were immunized with MOG(35-55) peptide in CFA adjuvant and <sd-pretag id="sdPretag1090784674sm" type="geneprod" role="intervention">pertussis toxin</sd-pretag> to induce EAE. (<strong>B</strong>) Mean <sd-pretag id="sdPretag1087783668sm" category="assay">clinical scores</sd-pretag> of EAE in immunized DC(WT) (n= 5) and DC(<sd-pretag id="sdPretag958643952sm" type="geneprod" role="intervention">NLRC3</sd-pretag>-KO) <sd-pretag id="sdPretag1283292006sm" type="organism" role="component">mice</sd-pretag> (n= 5). (<strong>C</strong>) Frequencies of <sd-pretag id="sdPretag199394617sm" type="geneprod" role="intervention">CD4</sd-pretag><sup>+</sup> <sd-pretag id="sdPretag96304192sm" type="cell" role="component">T cells</sd-pretag> that express <sd-pretag id="sdPretag755637233sm" type="geneprod" role="component">IFN-γ</sd-pretag> and <sd-pretag id="sdPretag1502297308sm" type="geneprod" role="assayed">IL-17A</sd-pretag> in the <sd-pretag id="sdPretag1890573819sm" type="subcellular" role="component">spinal</sd-pretag><sd-pretag id="sdPretag236875377sm" role="component"> cord</sd-pretag> and <sd-pretag id="sdPretag1256896683sm" type="tissue" role="component">brain</sd-pretag> from DC(WT) and DC(<sd-pretag id="sdPretag470824130sm" type="geneprod" role="intervention">NLRC3</sd-pretag>-KO) <sd-pretag id="sdPretag1497979123sm" type="organism" role="component">mice</sd-pretag> 26 d after EAE induction after restimulation with MOG(35-55) peptide. Pooled data are presented in the right panel. (<strong>D</strong>) Expression of <sd-pretag id="sdPretag866645296sm" type="geneprod" role="assayed"><em>Il12</em></sd-pretag>, <sd-pretag id="sdPretag1462165661sm" type="geneprod" role="assayed"><em>Il6</em></sd-pretag> and <sd-pretag id="sdPretag1637603915sm" type="geneprod" role="assayed"><em>Il23</em></sd-pretag> mRNA in <sd-pretag id="sdPretag56083278sm" type="cell" role="component">DCs</sd-pretag> sorted from <sd-pretag id="sdPretag409498923sm" type="tissue" role="component">spleens</sd-pretag> of DC(WT), DC(<sd-pretag id="sdPretag1346749593sm" type="geneprod" role="intervention">NLRC3</sd-pretag>-KO), <sd-pretag id="sdPretag224780657sm" type="geneprod" role="intervention">DC</sd-pretag>(<sd-pretag id="sdPretag2027809702sm" type="geneprod" role="intervention">p38</sd-pretag>-KO) and <sd-pretag id="sdPretag524286325sm" type="geneprod" role="intervention">DC</sd-pretag>(<sd-pretag id="sdPretag1009533506sm" type="geneprod" role="intervention">p38</sd-pretag>+<sd-pretag id="sdPretag331392783sm" type="geneprod" role="intervention">NLRC3</sd-pretag>-KO) <sd-pretag id="sdPretag1747310143sm" type="organism" role="component">mice</sd-pretag> 26 d after EAE induction, presented relative to that of <sd-pretag id="sdPretag517633317sm" type="geneprod" role="assayed"><em>Gapdh</em></sd-pretag>.</p> <p>Data information: Data (n=5 in A, B, C right and D) shown are the mean ±SD. **<em>P</em> < 0.01 and ***<em>P</em> < 0.001 by one-way ANOVA test. Data are representative of three independent experiments with similar results.</p> </sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=26893
|
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"text": "NLRC3",
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"mapping_status": "mapped",
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"text": "NLRC3",
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]
}
] |
||
10.15252/embj.2018101397
|
NLRC3 expression in dendritic cells attenuates CD4+ T cell response and autoimmunity
|
2019
|
Figure 6
|
<sd-panel> <p><strong>Figure 6. <sd-pretag id="sdPretag1380060263sm" type="geneprod" role="intervention">NLRC3</sd-pretag>-overexpression attenuated antigen-presenting function of <sd-pretag id="sdPretag1678835690sm" type="geneprod" role="component">DCs</sd-pretag>.</strong></p> <p>DC(Ctrl) and DC(<sd-pretag id="sdPretag1041938629sm" type="geneprod" role="intervention">NLRC3</sd-pretag>-OE) were stimulated with <sd-pretag id="sdPretag449261566sm" type="molecule" role="intervention">LPS</sd-pretag> (100 ng/ml) for specified time.</p> <p><strong>A.</strong> DC lysates were probed for p-<sd-pretag id="sdPretag1451611339sm" type="geneprod" role="assayed">p38</sd-pretag>, <sd-pretag id="sdPretag1982392412sm" type="geneprod" role="assayed">p38</sd-pretag>, <sd-pretag id="sdPretag966666058sm" type="geneprod" role="assayed">NLRC3</sd-pretag> and <sd-pretag id="sdPretag2132443068sm" type="geneprod" role="assayed">GAPDH</sd-pretag>. Densitometry quantification of band intensity were presented in the right panel.</p> <p><strong>B.</strong> <sd-pretag id="sdPretag1767611645sm" category="assay">Enzyme</sd-pretag>-<sd-pretag id="sdPretag1084705523sm" category="assay">linked immunosorbent assay</sd-pretag> of cytokines in culture supernatants of <sd-pretag id="sdPretag2025570236sm" type="cell" role="component">DCs</sd-pretag> treated with <sd-pretag id="sdPretag1923380143sm" type="molecule" role="intervention">LPS</sd-pretag> for 48 hours.</p> <p><strong>C-D.</strong> Cytokines in culture supernatants <strong>(C)</strong>, and <sd-pretag id="sdPretag551834493sm" type="geneprod" role="intervention">CFSE</sd-pretag> <sd-pretag id="sdPretag1176714939sm" category="assay">proliferation assay</sd-pretag> <strong>(D)</strong> among naive 2D2 CD4<sup>+</sup> <sd-pretag id="sdPretag1760002467sm" type="cell" role="component">T cells</sd-pretag> stimulated with MOG(35-55) plus DCs treated with <sd-pretag id="sdPretag1126297112sm" type="molecule" role="intervention">LPS</sd-pretag> for 48 hours.</p> <p>Data information: Data (n=3 in A right; n=5 in B and C) shown are the mean ±SD. *<em>P</em> < 0.05, **<em>P</em> < 0.01 and ***<em>P</em> < 0.001 by an unpaired <em>t</em>-test. Data are representative of three independent experiments with similar results.</p> </sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=26894
|
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"text": "NLRC3",
"type": "geneprod",
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] |
||
10.15252/embj.2018101397
|
NLRC3 expression in dendritic cells attenuates CD4+ T cell response and autoimmunity
|
2019
|
Figure 7
|
<sd-panel> <p><strong>Figure 7. Vaccination with <sd-pretag id="sdPretag1313104421sm" type="geneprod" role="intervention">NLRC3</sd-pretag>-overexpression <sd-pretag id="sdPretag1047717715sm" type="cell" role="component">DCs</sd-pretag> suppressed EAE.</strong></p> <p>EAE was induced by immunization of naive B6 <sd-pretag id="sdPretag1638098182sm" type="organism" role="component">mice</sd-pretag> with MOG (35-55), and the <sd-pretag id="sdPretag796249283sm" type="organism" role="component">mice</sd-pretag> were randomly divided into five groups. <sd-pretag id="sdPretag1983338452sm" type="cell" role="component">BMDCs</sd-pretag> transduced with either <sd-pretag id="sdPretag1691834812sm" type="organism" role="component">lentiviral</sd-pretag> vector encoding <sd-pretag id="sdPretag1366845404sm" type="geneprod" role="reporter">GFP</sd-pretag> and <sd-pretag id="sdPretag1669474867sm" type="geneprod" role="intervention">NLRC3</sd-pretag> (LV-<sd-pretag id="sdPretag1660842306sm" type="geneprod" role="intervention">NLRC3</sd-pretag>) or only <sd-pretag id="sdPretag2090810043sm" type="geneprod" role="reporter">GFP</sd-pretag> (LV-Ctrl) were administered i.v. 4 times, once every 4 days, starting at day 10 after EAE induction.</p> <p><strong>A.</strong> Mean clinical scores of EAE (n= 5 <sd-pretag id="sdPretag1227006353sm" type="organism" role="component">mice</sd-pretag> per group ). Arrows indicate DC vaccine administration.</p> <p><strong>B.</strong> Effects of therapeutic <sd-pretag id="sdPretag1223184139sm" type="tissue" role="component">DC</sd-pretag> vaccination on B6 EAE. The maximum score: Mean of the maximum scores per <sd-pretag id="sdPretag1676170997sm" type="organism" role="component">mouse</sd-pretag> in each group. Data shown are the mean ±SD. Determination of statistical differences was performed using by an one-way ANOVA test.</p> <p><strong>C-D.</strong> Recall proliferative <strong>(C)</strong> and cytokine response <strong>(D)</strong> to <sd-pretag id="sdPretag676357843sm" type="cell" role="component">MOG</sd-pretag> (35-55) in <sd-pretag id="sdPretag1777584696sm" type="cell" role="component">splenocytes</sd-pretag> taken from <sd-pretag id="sdPretag1385446500sm" type="molecule" role="intervention">DCs</sd-pretag>-treated <sd-pretag id="sdPretag1396169683sm" type="organism" role="component">mice</sd-pretag> 26 days after EAE induction.</p> <p>Data information: Data shown (n=5 in A, C and D) are the mean ±SD. **<em>P</em> < 0.01 and ***<em>P</em> < 0.001 by an one-way ANOVA test. Data are representative of three independent experiments with similar results.</p> </sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=26895
|
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||
10.15252/embr.202154147
|
Developmental arsenic exposure impairs cognition, directly targets DNMT3A and reduces DNA methylation
|
2022
|
Figure 2
|
<sd-panel><p><strong>Figure 2 - Arsenic directly binds to DNMT3A.</strong></p> <p><strong>A</strong> LC-ESI-MS/MS spectrum of Dnmt3a pulled down by Biotin-As in NIH3T3 cells. NIH3T3 cells were treated with 10 μg/mL Biotin-As for 2 hours, followed by pull-down assay and determination using LC-ESI-MS/MS.</p> <p><strong>B-D</strong> Validation of the binding between DNMT3A and Biotin-As at 5 μg/mL in NIH3T3 (B), MEFs (C) and CCRF-CEM (D) cells in the Biotin-As pull-down assay.</p> <p><strong>E</strong> Schematic diagram of the structure of human DNMT3A. Upper panel: All cysteines in DNMT3A are shown. Lower panel: Structure of DNMT3A-ADD (PDB: 3A1A) and the four interested cysteine triads.</p> <p><strong>F</strong> Measurement of DNMT3A-ADD thermodynamic stability upon ATO treatment. Purified DNMT3A-ADD was mixed with ATO at the indicated ratios in 20 mM HEPES (pH 7.5) for 1 hour. Melting curves were measured by DSF (left panel), and the calculated Δ<em>Tm</em> values are shown (right panel). Data are presented as mean ± SD of <em>n</em> = 4 technical replicates. ****<em>p</em> < 0.0001 by unpaired two-tailed Student's t test.</p> <p><strong>G</strong> LC-MS spectra of purified DNMT3A-ADD before and after ATO incubation at 1:5 molar ratio for 16 hours.</p> <p><strong>H, I</strong> Biotin-As pull-down assays for the transfected DNMTs (H) and DNMT3A-C520A/C524A mutation (I) in 293T cells treated with 5 μg/mL Biotin-As.</p></sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=46831
|
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||
10.15252/embr.202154147
|
Developmental arsenic exposure impairs cognition, directly targets DNMT3A and reduces DNA methylation
|
2022
|
Figure 3
|
<sd-panel><p><strong>Figure 3 - Arsenic induces DNMT3A degradation via the ubiquitin-proteasome pathway.</strong></p> <p><strong>A</strong> Immunoblotting of DNMT3A protein levels in MEFs (upper panel) and CCRF-CEM cells (lower panel) treated with ATO in the indicated conditions.</p> <p><strong>B</strong> MEFs (upper panel) and CCRF-CEM cells (lower panel) were pretreated with 20 μM DMSO, 1 μM MG132, 0.02 μM Concanamycin A (Conc A), 20 μM Calpeptin (Calp), or 20 μM Z-VAD-FMK (Z-VAD) for 2 hours, followed by 16-hour ATO co-treatment at 1 μg/mL for MEFs or 0.3 μg/mL for CCRF-CEM cells. Immunoblotting of DNMT3A in whole cell lysate is shown.</p> <p><strong>C</strong> HCT116 cells were pretreated with 3 μM MG132 for 2 hours, followed by ATO co-treatment for 16 hours at the indicated concentrations. Immunoblotting of DNMT3A in whole cell lysate is shown.</p> <p><strong>D</strong> <em>In vivo</em> ubiquitination assay. 293T cells were transiently transfected with HA-ubiquitin and Myc-DNMT3A. After 24 hours, cells were treated with or without MG132 for 2 hours at the indicated concentrations, followed by ATO co-treatment for 6 hours at the indicated concentrations. Myc-DNMT3A was immunoprecipitated (IP) with anti-Myc antibody, followed by immunoblotting (IB) as indicated.</p> <p><strong>E</strong> Immunoblotting of the transfected wild-type DNMT3A, C520A/C524A and C541A mutants in 293T cells upon 1 μg/mL ATO treatment for the indicated durations.</p> <p><strong>F</strong> Measurement of DNMT3A-ADD thermodynamic stability upon ATO or AsPh<sub>3</sub> treatment. Purified DNMT3A-ADD was mixed with ATO or AsPh<sub>3</sub> at the indicated ratios in 20 mM HEPES (pH 7.5) for 1 hour. Chemical structure of AsPh<sub>3</sub> is shown. Melting curves were measured by DSF (upper panel), and the calculated Δ<em>Tm</em> values are shown (lower panel). Data are presented as mean ± SD of <em>n</em> = 4 technical replicates. ns, not significant; ****<em>p</em> < 0.0001 by unpaired two-tailed Student's t test.</p> <p><strong>G</strong> Immunoblotting of DNMT3A in MEFs (upper panel) and CCRF-CEM cells (lower panel) treated with ATO or AsPh<sub>3</sub> in the indicated conditions.</p> <p><strong>H, I</strong> Immunoblotting of endogenous DNMT3A, DNMT3B and DNMT1 protein levels in CCRF-CEM (H) and THP-1 (I) cells treated with DAC or ATO in the indicated conditions. DAC: +, 0.2 μM. ATO: +, 0.06 μg/mL; ++, 0.2 μg/mL; +++, 0.6 μg/mL. Red asterisk indicates the specific band.</p></sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=46833
|
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||
10.15252/embr.202154147
|
Developmental arsenic exposure impairs cognition, directly targets DNMT3A and reduces DNA methylation
|
2022
|
Figure 4
|
<sd-panel><p><strong>Figure 4 - Arsenic induces genome-wide DNA hypomethylation in MEFs.</strong></p> <p><strong>A</strong> Dot blot analysis of global DNA methylation levels in MEFs upon ATO or DAC treatment at the indicated concentrations for 7 days. The relative 5meC levels were quantified by ImageJ. The full blotting image of Fig 4A is shown in Fig EV4D, the treatment is the same.</p> <p><strong>B</strong> COBRA-<em>IAP</em> of global DNA methylation levels in MEFs upon ATO or DAC treatment at the indicated concentrations for 7 days. The signal density of unmethylated and methylated DNA were quantified by ImageJ.</p> <p><strong>C</strong> 5meC enrichment analysis of the <em>IAP</em>, <em>Xist, H19</em> loci in MEFs upon ATO treatment at 0.3 μg/mL for 4 or 7 days as measured by MeDIP-qPCR. Data are presented as mean ± SD of <em>n</em> = 3 technical replicates. *<em>p</em> < 0.05; **<em>p</em> < 0.01; ***<em>p</em> < 0.001 by unpaired two-tailed Student's t test.</p> <p><strong>D</strong> Dot blot analysis of global DNA methylation levels in CCRF-CEM cells upon ATO or DAC treatment at the indicated concentrations for 7 days. The relative 5meC levels were quantified by ImageJ.</p> <p><strong>E</strong> COBRA-<em>LINE-1</em> of global DNA methylation levels in CCRF-CEM cells upon ATO or DAC treatment in the indicated conditions. The signal density of unmethylated and methylated DNA were quantified by ImageJ.</p> <p><strong>F</strong> 5meC enrichment analysis of the <em>XIST, H19</em> loci in CCRF-CEM cells upon ATO treatment at the indicated concentrations for 63 days as measured by MeDIP-qPCR. Data are presented as mean ± SD of <em>n</em> = 3 technical replicates. ns, not significant by unpaired two-tailed Student's t test.</p></sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=46835
|
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"role": "assayed",
"text": "LINE-1",
"type": "geneprod",
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"Q5T7N2"
]
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{
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] |
||
10.15252/emmm.202216554
|
β-catenin activity induces an RNA biosynthesis program promoting therapy resistance in T Acute Lymphoblastic Leukemia
|
2022
|
Figure 1
|
<p><strong>Figure 1</strong>. <strong>β-catenin chromatin binding in T-ALL cell lines.</strong> </p><p>a) Representative density plot (upper panels) and heatmaps (bottom panels) showing β-catenin chromatin binding centered at TSS ± 10 Kb in RPMI8402 or Jurkat cells after precipitation in the indicated conditions with two different antibodies (R&D or SC). The order in the y-axis represents the closest gene annotated to the β-catenin peak obtained in the basal condition with R&D antibody and confirmed in at least another condition (for the RPMI8402 cell line: n=5 for R&D antibody in basal conditions, n =2 for R&D antibody upon LiCl treatment, n=2 for SC antibody in basal conditions, n=2 for SC antibody upon LiCl treatment. For Jurkat cell line: n=3 for R&D antibody in basal conditions in the Jurkat cell line).</p><p>b) Genomic distribution of β-catenin ChIPseq peaks shown in a).</p><p>c) DNA motifs enriched in the β-catenin binding regions using as an input the peaks obtained in the basal condition with R&D antibody and confirmed in at least another condition.</p><p>d) Representative heatmap showing the enrichment of 10Kb upstream and downstream of the identified β-catenin peaks obtained by precipitating TCF1 (n=3), LEF1 (n=3) and Kaiso (n=3) (from left to right).</p><p>e) Venn diagram (left panel) representing the number of β-catenin, TCF1/LEF1 and Kaiso targets obtained from ChIPSeq. Each gene dataset is formed by the genes obtained in at least two different replicates for TCF1, LEF1 and Kaiso. Summary of number of peaks and their corresponding annotated genes (right panel) obtained from ChIPSeq of β-catenin, TCF1, LEF1 and Kaiso.</p><p>f) Integrative genomic viewer snapshot showing the position of β-catenin, TCF1, LEF1 and Kaiso peaks near the TSS of the indicated genes.</p><p>g-h) Representative β-catenin ChIP-qPCR of indicated target genes in wt and TCF1/LEF1 long isoform double KO (DLKO) clones (g) and Kaiso KO clones (h) in RPMI8402 cells. Enrichment of each ChIP is normalized to its respective negative IgG control, indicated by a red-dashed line. DLKO1, DLKO2, KKO1 and KKO2 designate independent single-cell derived clones. Graph represents the mean and sd of 3 technical replicates.</p>
|
https://api.sourcedata.io/file.php?figure_id=51786
|
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"text": "TCF1",
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"P36402",
"B3KQ75"
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{
"ext_dbs": "NCBI gene",
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"ext_tax_names": "Homo sapiens",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "10009",
"original_type": "gene",
"role": "intervention",
"text": "Kaiso",
"type": "geneprod",
"uniprot_ids": [
"Q86T24"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P35222",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "β-catenin",
"type": "geneprod",
"uniprot_ids": [
"P35222"
]
}
] |
||
10.15252/emmm.202216554
|
β-catenin activity induces an RNA biosynthesis program promoting therapy resistance in T Acute Lymphoblastic Leukemia
|
2022
|
Figure 2
|
<p><strong>Figure 2</strong>. <strong>β-catenin-regulated transcriptional program in T-ALL cell lines.</strong></p><p>a) MA plot showing the log2 fold changes for each gene over the mean of normalized counts obtained in the RNAseq analysis of sh-β-catenin vs sh-control (n=3 for each condition). Dots in blue are those genes differentially expressed with an adjusted p-value<0.05.</p><p>b) Heatmap showing the differentially expressed genes (adjusted p-value<0.05) for each condition.</p><p>c) Biological functions significantly enriched (adjusted p-value < 0.05) in groups of genes downregulated (Down) or upregulated (Up) in the RNAseq analysis.</p><p>d) Venn diagram with differentially expressed genes downregulated (DEGs Down) or upregulated (DEGs UP) in the RNAseq analysis compared to the genes obtained in the β-catenin ChIPseq analysis obtained in the basal condition with R&D antibody and confirmed in at least another condition (ChIP targets).</p><p>e) Relative mRNA expression of β-catenin target genes in the RPMI8402 cell line (right panel) after knockdown of β-catenin (left panel) compared to control. Graph represents the mean and sd of 6 independent experiments.</p><p>f) Relative mRNA expression of β-catenin target genes in the RPMI8402 cell line after treatment with the β-catenin inhibitor ICG-001 (10µM, overnight). Graph represents the mean and sd of 3 independent experiments.</p><p>g) Relative mRNA expression of β-catenin target genes in the RPMI8402 cell lines (right panel) after knockdown of ZBTB33/Kaiso (left panel) compared to control. Graph represents the mean and sd of 3 independent experiments.</p><p>h-i) Representative flow cytometry histograms of EU incorporation into RNA (h) or OPP incorporation into nascent peptides (i) in the indicated conditions (upper panels). Quantification of relative EU or OPP incorporation. Graph represents the mean and sd of 3 independent experiments (bottom panels). Cells were pre-treated with FH353 30µM or ICG-001 10µM (or DMSO) overnight prior to EU or OPP incubation.</p><p>Data information: Statistical significance was determined by two-sided Student's <em>t</em> test.</p>
|
https://api.sourcedata.io/file.php?figure_id=51787
|
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"original_type": "gene",
"role": "assayed",
"text": "β-catenin",
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"uniprot_ids": [
"P35222",
"B4DGU4"
]
},
{
"ext_dbs": "NCBI gene",
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"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "1499",
"original_type": "gene",
"role": "intervention",
"text": "β-catenin",
"type": "geneprod",
"uniprot_ids": [
"P35222",
"B4DGU4"
]
},
{
"ext_dbs": "NCBI gene",
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"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "ncbi_gene",
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"text": "β-catenin",
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"P35222",
"B4DGU4"
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{
"ext_dbs": "NCBI gene",
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"ext_tax_names": "Homo sapiens",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
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"original_type": "gene",
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"text": "β-catenin",
"type": "geneprod",
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"P35222",
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{
"ext_dbs": "NCBI gene",
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"ext_tax_names": "Homo sapiens",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "10009",
"original_type": "gene",
"role": "intervention",
"text": "Kaiso",
"type": "geneprod",
"uniprot_ids": [
"Q86T24"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "10009",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "10009",
"original_type": "gene",
"role": "intervention",
"text": "ZBTB33",
"type": "geneprod",
"uniprot_ids": [
"Q86T24"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P35222",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "intervention",
"text": "β-catenin",
"type": "geneprod",
"uniprot_ids": [
"P35222"
]
}
] |
||
10.15252/emmm.202216554
|
β-catenin activity induces an RNA biosynthesis program promoting therapy resistance in T Acute Lymphoblastic Leukemia
|
2022
|
Figure 5
|
<p><strong>Figure 5. β-catenin activity determines cell recovery after chemotherapy treatment in T-ALL cells.</strong></p><p>a) Effect of Vincristine (VCR) treatment on cell viability of RPMI8402 cells transduced with sh β-catenin or sh-control. Dose-response curves represent the logistic fitting and individual points correspond to mean ± SD of three independent experiments. *** p ≤ 0.001 of IC50 comparison with respect to sh control</p><p>b-c) Effect of VCR (b), Methotrexate (MTX) (c left), L-Asparaginase (L-ASP) (c central) or Cytarabine (Ara-C) (c right) treatment in the presence or absence of increasing doses of the β-catenin inhibitor ICG-001. Dose-response curves represent the logistic fitting and individual points correspond to mean ± SD of three independent experiments. **** p ≤ 0.0001, *** p ≤ 0.001, ** p ≤ 0.01, * p ≤ 0.05 of IC50 comparison with respect VCR-treated cells.</p><p>d) Schematic diagram of the experimental approach used for the drug recovery experiments in e) and f). Figure partially created with Biorender.com</p><p>e) Cell viability of RPMI8402 cells as fold change relative to day 0 (n = 3). VCR, 15nM; ICG-001, 10 µM. **** p ≤ 0.0001 with respect to control; ### p ≤ 0.001 with respect to VCR-treated cells.</p><p>f) Percentage of viability of RPMI8402 cells after drug wash-out during recovery in the presence or absence of ICG-001 10 µM at the indicated time points. **** p ≤ 0.0001, *** p ≤ 0.001, ** p ≤ 0.01, * p ≤ 0.05 with respect to recovery in complete medium.</p><p>g) Schematic diagram of the experimental approach used for the drug recovery experiments in h) and i). Figure partially created with Biorender.com</p><p>h) Cell viability of RPMI8402 cells transduced with sh β-catenin or sh-control as fold change relative to day 0 (n = 3). **** p ≤ 0.0001 untreated sh β-catenin with respect to untreated sh control; #### p ≤ 0.0001, VCR 1nM sh β-catenin with respect to VCR 1nM sh control; ++++ p ≤ 0.0001 , VCR15nM sh β-catenin with respect to VCR 15nM sh control.</p><p>i) Percentage of viability of RPMI8402 cells upon β-catenin knockdown after drug wash-out as compared to control at the indicated time points. **** p ≤ 0.0001, *** p ≤ 0.001, ** p ≤ 0.01, with respect to sh control.</p><p>Data information: For all applicable figure panels, data represent mean ± SD of three independent experiments. Statistical significance was determined by two-sided Student's t test for a, b, c, f. i, and h (at day 0), or by one-way ANOVA with Tukey's correction for multiple comparison testing for e and h (at day 2). Exact p-values are disclosed in the Source data file.</p>
|
https://api.sourcedata.io/file.php?figure_id=51793
|
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"ext_tax_names": "Homo sapiens",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "1499",
"original_type": "gene",
"role": "intervention",
"text": "β-catenin",
"type": "geneprod",
"uniprot_ids": [
"P35222",
"B4DGU4"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P35222",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "intervention",
"text": "β-catenin",
"type": "geneprod",
"uniprot_ids": [
"P35222"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P35222",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
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"role": "intervention",
"text": "β-catenin",
"type": "geneprod",
"uniprot_ids": [
"P35222"
]
}
] |
||
10.15252/emmm.202216554
|
β-catenin activity induces an RNA biosynthesis program promoting therapy resistance in T Acute Lymphoblastic Leukemia
|
2022
|
Figure 6
|
<p><strong>Figure 6. β-catenin inhibition enhances chemotherapy response in a mouse model of T-ALL.</strong></p><p>a) Experimental design of in vivo treatment of NSG mice transplanted with RPMI8402 cells. Induction-like chemotherapy: V (vincristine, 0.15 mg·kg<sup>-1</sup>·day<sup>-1</sup>), D (dexamethasone, 5 mg·kg<sup>-1</sup>·day<sup>-1</sup>), L (L-Asparaginase, 1,000 IU·kg<sup>-1</sup>·day<sup>-1</sup>). ICG-001: 10 mg kg<sup>-1</sup>·day<sup>-1</sup>.</p><p>b) Percentage of RPMI8402 cells in PB at the indicated time points monitoring leukemic progression in the mouse model. RPMI8402 cells identified as human CD45<sup>+</sup>HLA-ABC<sup>+</sup>CD5<sup>+</sup> by flow cytometry and gated on DAPI negative cells.</p><p>c) Percentage of RPMI8402 cells PB, BM, spleen and liver at sacrifice. RPMI8402 cells identified as human CD45<sup>+</sup>HLA-ABC<sup>+</sup>CD5<sup>+</sup> by flow cytometry and gated on DAPI negative cells.</p><p>d-e) Photograph of the livers (d) and spleen (e) collected at sacrifice with the indicated treatments. One control (liver #1 in Fig. 6g) and one Chemo + DMSO (liver #4 in Fig. 6g) mice were sacrificed 2 days before the end of the experiment following humane endpoint criteria.</p><p>f) Quantification of spleen (left panel) and liver (right panel) weight normalized to the mouse body weight at sacrifice.</p><p>g) H&E staining of representative images per each mouse treated as indicated.</p><p>h) Percentage of liver area covered by cellular colonies per 10X micrograph. 4 different images were quantified per animal and mean values per animal are represented by dots.</p><p>Control: animals left untreated (n = 2); Chemo + DMSO: animals receiving chemotherapy and vehicle (n = 4); Chemo + ICG-001: animals receiving chemotherapy and the β-catenin inhibitor ICG-001 (n = 4), following scheme and doses depicted in Fig. 6a and methods.</p><p>Data information: For all applicable figure panels, data from Chemo + DMSO and Chemo + ICG-001 groups are mean ± SD and dots represent individual values per animal. Control group data is only represented by individual values per animal. Statistical significance between Chemo + DMSO and Chemo + ICG-001 groups was determined by two-sided Student's <em>t</em> test.</p><p><strong>EXPANDED VIEW FIGURE LEGENDS</strong></p>
|
https://api.sourcedata.io/file.php?figure_id=51795
|
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"role": "assayed",
"text": "CD5",
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"P06127"
]
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{
"ext_dbs": "Uniprot",
"ext_ids": "Q02248",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
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"text": "β-catenin",
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"Q02248"
]
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{
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"ext_ids": "P04439",
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"ext_tax_names": "Homo sapiens",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "HLA-A",
"type": "geneprod",
"uniprot_ids": [
"P04439"
]
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{
"ext_dbs": "Uniprot",
"ext_ids": "P08575",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "CD45",
"type": "geneprod",
"uniprot_ids": [
"P08575"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q02248",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
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"uniprot_ids": [
"Q02248"
]
}
] |
||
10.15252/embj.2019103649
|
CALCOCO1 acts with VAMP-Associated Proteins to mediate ER-phagy.
|
2020
|
Figure 1
|
<sd-panel> <p><strong>Figure 1. CALCOCO1 is degraded by macroautophagy.</strong></p> <p>A Domain architecture of CALCOCO paralogs showing the SKICH domain, a conserved LIR motif (LVV), coiled-coli regions (CC) and zinc finger domains (ZF).</p> <p>B-E Immunoblot analysis of indicated cell lines, starved for 6 hours (HBSS) as indicated, and treated with 25 μM MG132 or 200 ng/ml of bafilomycin A1 (Baf A1) for the indicated times. In C and E, endogenous CALCOCO1 is analysed and the bars represent the mean±sd of band intensities relative to the actin loading control, as quantified using ImageJ of three independent experiments. Statistical comparison was analyzed by one-way ANOVA followed by Tukey multiple comparison test and significance displayed as ***p ˂ 0.001, **p ˂ 0.005, *p ˂ 0.01; ns is not significant.</p> <p>F A representative micrograph using widefield and deconvolution microscopy of HeLa CALCOCO1 KO cells stably expressing EGFP-CALCOCO1 and immunostained for endogenous GM130. Scale bars are 5 μm and 2 μm (zoomed inset).</p> <p>G Same cells as in E were left untreated or treated with Baf A1 for 6 hours, and then immunostained for endogenous p62 and LC3B. Scale bars are 5 μm for the confocal microscopy images and 2 μm for the airyscans.</p> <p>H CALCOCO1, p62 and LC3B puncta in in the indicated conditions, counted using an automated system. The error bars represent mean±SEM of puncta per cell of three independent experiments per condition and 250 cells per experiment. Statistical comparison was analyzed by one-way ANOVA followed by Tukey multiple comparison test. Significance is displayed as ***p<0.001.</p> <p>I Percentage of co-localization of CALCOCO1 puncta with p62 and/or LC3B in cells treated as indicated. The error bars represent mean±SEM of three independent experiments per condition and over 250 cells per experiment. Statistical comparison was analyzed by one-way ANOVA followed by Tukey multiple comparison test. Significance is displayed as ***p<0.001.</p> <p>J HeLa CALCOCO1 KO cells stably expressing EGFP-CALCOCO1 were treated with Baf A1 for 6 hours and immunostained for endogenous LAMP1. Scale bars are 5 μm for the confocal microscopy images and 2 μm for the airyscans.</p> </sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=33147
|
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"text": "p62",
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"ext_ids": "Q9P1Z2",
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||
10.15252/embj.2019103649
|
CALCOCO1 acts with VAMP-Associated Proteins to mediate ER-phagy.
|
2020
|
Figure 2
|
<sd-panel> <p><strong>Figure 2. CALCOCO1 binds directly to ATG8 family proteins with preference for the GABARAP subfamily.</strong></p> <p>A GST pulldown binding assay of <em>in vitro</em> transcribed/translated <sup>35</sup>S-Myc-CALCOCO1 with recombinant GST-tagged ATG8 family proteins. GST and GST fusion proteins were visualized by coomassie brilliant blue staining (bottom panel), and the co-precipitated Myc-CALCOCO1 was detected by autoradiography (upper panel). The numbers below the AR represent % binding in the shown AR .</p> <p>B GST pulldown assay of transiently transfected Myc-CALCOCO1 from HEK293 cell extracts with recombinant GST-tagged ATG8 family proteins. GST and GST fusions were visualized by Ponceau S staining (bottom panel), and co-precipitated Myc-CALCOCO1 detected by immunoblotting with anti-Myc antibody (upper panel).</p> <p>C CALCOCO1 deletion constructs used to map the ATG8 interactions. The red X indicate a point mutation or deletion of the LIR motif. Constructs with no or very weak interaction are indicated in orange.</p> <p>D-H GST pulldown assays of indicated <em>in vitro</em> transcribed/translated <sup>35</sup>S-Myc-CALCOCO1 constructs with indicated recombinant GST-tagged ATG8 family proteins. Precipitated GST and GST fusions and co-precipitated Myc-CALCOCO1 constructs were analyzed as in A.</p> <p>I GST pulldown assay of endogenous GABARAP from HEK293 cell extracts with recombinant GST-tagged CALCOCO1 constructs. GST and GST fusions were visualized as in A, and co-precipitated GABARAP with anti-GABARAP antibody (upper panel).</p> </sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=33148
|
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||
10.15252/embj.2019103649
|
CALCOCO1 acts with VAMP-Associated Proteins to mediate ER-phagy.
|
2020
|
Figure 3
|
<sd-panel> <p><strong>Figure 3. CALCOCO1 binds both to LDS and UDS of ATG8 family proteins.</strong></p> <p>A, B GST pulldowns testing binding of indicated in vitro transcribed/translated <sup>35</sup>S-Myc-CALCOCO1 constructs with indicated recombinant GST-tagged ATG8 family proteins (left). Cartoon of CALCOCO1 with domain organization indicated and the location of LIR and UIR motifs. The presence of two well separated binding surfaces on ATG8 proteins binding to LIR (LDS) and UIR (UDS) is indicated (right).</p> <p>C GST pulldown assays of <em>in vitro</em> transcribed/translated <sup>35</sup>S-Myc-CALCOCO1 and <sup>35</sup>S-Myc-p62 with recombinant GST-GABARAPL2 (WT and indicated mutants).</p> <p>D GST pulldown assays of <em>in vitro</em> transcribed/translated <sup>35</sup>S-Myc-TAX1BP1 (WT and indicated mutants) with recombinant GST-GABARAP (WT and indicated mutants).</p> <p>E, F Immunoblot analysis of HeLa CALCOCO1 KO cell lines stably transfected with WT EGFP-CALCOCO1 or EGFP-CALCOCO1 mLIR+∆623-691. Cells were induced with tetracycline for 24 hours and then starved or treated with MG132 or Baf A1 as indicated. The blot panels are from more than one western blot experiment but for clarity, only a single actin/GAPDH loading control is shown. In F, the bars represent the mean±sd of band intensities relative to the actin or GAPDH loading controls of three independent experiments quantified using ImageJ. Statistical comparison was analyzed by one-way ANOVA followed by Tukey multiple comparison test and significance displayed as ***p ˂ 0.001, *p ˂ 0.01; ns is not significant.</p> <p>G HeLa CALCOCO1 KO cells stably expressing EGFP-CALCOCO1 or EGFP-CALCOCO1 mLIR+∆623-691 grown in full medium and treated with Baf A1 as indicated were immunostained for endogenous p62 and LC3B. Scale bars, 5 μm.</p> </sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=33150
|
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||
10.15252/embj.2019103649
|
CALCOCO1 acts with VAMP-Associated Proteins to mediate ER-phagy.
|
2020
|
Figure 4
|
<sd-panel> <p><strong>Figure 4. CALCOCO1 promotes basal autophagic flux but not bulk autophagy.</strong></p> <p>A, B HeLa CALCOCO1 KO cells stably expressing EGFP-CALCOCO1 were starved for 4 hours and then immunostained with anti-ATG13 and anti-WIPI2 antibodies. Scale bars in A are 5 μm for the confocal microscopy images and 2 μm for the airyscans. In B, the error bars represent mean±sd of puncta per cell from three independent experiments and100-200 cells per each experiment.</p> <p>C-L Immunoblot analysis of indicated cell lines treated as indicated. Numbers below the blots represent relative intensity of the bands in the shown blots normalized against the loading control (GAPDH or actin). The asterisk in K indicates that endogenous CALCOCO1 is detected in WT and KO cell extracts and EGFP-CALCOCO1 in cells extracts from the rescued cells. In D, F, H, I and L, the bars represent the mean±sd of band intensities relative to the actin or GAPDH loading control as quantified using ImageJ, n=5 in I, n=3 in others. Statistical comparison was analyzed by one-way ANOVA and significance displayed as ***p ˂ 0.001, **p ˂ 0.005, *p ˂ 0.01; ns is not significant.</p> </sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=33152
|
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||
10.15252/embj.2019103649
|
CALCOCO1 acts with VAMP-Associated Proteins to mediate ER-phagy.
|
2020
|
Figure 5
|
<sd-panel> <p><strong>Figure 5. CALCOCO1 interacts with VAP-A/B via a FFAT-like motif.</strong></p> <p>A Stably expressed EGFP or EGFP-CALCOCO1 in HEK293 cells were immunoprecipitated from the cell lysates followed by mass spectrometry identification of interacting proteins. Only some of the identified proteins are shown.</p> <p>B Co- IP of Myc-VAPA or Myc-VAPB with EGFP-CALCOCO1 from transiently transfected HEK293 cells. The asterisks (*) indicate Myc-VAP previously detected on the same membrane</p> <p>C, D GST pulldown assays of <em>in vitro</em> transcribed/translated <sup>35</sup>S-Myc-CALCOCO1 constructs with indicated recombinant GST-VAPA or GST-VAPB constructs.The scheme is a representation of CALCOCO1 domains and motifs.</p> <p>E HeLa cells transiently co-transfected with EGFP-CALCOCO1 and Myc-VAPA or -VAPB were immunostained with anti-Myc antibody. Scale bars, 5 μm.</p> </sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=33154
|
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"ext_tax_names": "Homo sapiens",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "VAPB",
"type": "geneprod",
"uniprot_ids": [
"O95292"
]
}
] |
||
10.15252/embj.2019103649
|
CALCOCO1 acts with VAMP-Associated Proteins to mediate ER-phagy.
|
2020
|
Figure 6
|
<sd-panel> <p><strong>Figure 6. VAP proteins promote autophagy and starvation-induced degradation of tubular ER.</strong></p> <p>A, B Immunoblot analysis of indicated cell lines, starved for 6 hours (HBSS) as indicated, and treated with MG132 or Baf A1 as indicated. Numbers below the blots in A represent relative intensity of the bands in the shown blots normalized against GAPDH loading control. In B, the bars represent the mean±sd of band intensities of three independent experiments as quantified using ImageJ. Statistical comparison was analyzed by one-way ANOVA and significance displayed as **p ˂ 0.005, *p ˂ 0.01; ns is not significant.</p> <p>C Immunoblot analysis of HeLa cells transfected with the indicated siRNAs.</p> <p>D, E Immunoblot analysis of HeLa cells transfected with the indicated siRNAs and treated with Baf A1 as indicated. In D, the panels are from more than one western blot experiment but only a single GAPDH loading control is shown. In E, the bars represent the mean±sd of band intensities of three independent experiments as quantified using ImageJ. Statistical comparison was analyzed by one-way ANOVA followed by Tukey multiple comparison test and significance displayed as ***p ˂ 0.001, **p ˂ 0.005; ns is not significant.</p> <p>F HeLa KO CALCOCO1 cells were transiently co-transfected with EGFP-CALCOCO1 and Myc-VAPA or Myc-VAPB, and then immunostained with anti-Myc and anti-LC3B antibodies. Arrows indicate dots of co-localization of all three proteins. Scale bars, 5 μm for large merged images and 1 μm for zoomed images.</p> </sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=33156
|
[
{
"ext_dbs": "Uniprot",
"ext_ids": "Q9GZQ8",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "LC3B",
"type": "geneprod",
"uniprot_ids": [
"Q9GZQ8"
]
}
] |
||
10.15252/embj.2019103649
|
CALCOCO1 acts with VAMP-Associated Proteins to mediate ER-phagy.
|
2020
|
Figure 7
|
<sd-panel> <p><strong>Figure 7. CALCOCO1 is a soluble ER-phagy receptor.</strong></p> <p>A, B Immunoblot analysis of HeLa WT and HeLa CALCOCO1 KO cells. The cells were starved for 6 hours (HBSS) as indicated and treated with Baf A1 as indicated. Numbers below the blots in A represent relative intensity of the bands in the shown blots normalized against GAPDH loading control. In A, the panels are collected from more than one western blot experiment but for clarity, only a single GAPDH loading control is shown. In B, the bars represent the mean±sd of band intensities of three independent experiments as quantified using ImageJ. Statistical comparison was analyzed by one-way ANOVA followed by Tukey multiple comparison test and significance displayed as **p ˂ 0.005, *p ˂ 0.01; ns is not significant.</p> <p>C, D Immunoblot analysis of HeLa CALCOCO1 KO cell lines reconstituted with EGFP-CALCOCO1. Expression of EGFP-CALCOCO1 was induced or not with tetracycline and the cells were treated with MG132 or Baf A1 as indicated. Numbers below the blots in C represent relative intensity of the bands in the shown blots normalized against actin loading control. In C, the panels are collected from more than one western blot experiment but only a single actin loading control is shown. In D, the bars represent the mean±sd of band intensities of three independent experiments as quantified using ImageJ. Statistical comparison was analyzed as in B and significance displayed as **p ˂ 0.005, *p ˂ 0.01; ns is not significant.</p> <p>E HeLa CALCOCO1 KO cell lines reconstituted with EGFP-CALCOCO1 were treated with tetracycline or not to induce expression of EGFP-CALCOCO1. Abundance of the ER was quantified from widefield fluorescence images of endogenous RTN3 staining (see Materials and methods). Data are presented as mean ± sd of three independent experiments. Statistical comparison was analyzed as in B and significance displayed as ***p ˂ 0.001, **p ˂ 0.005, *p ˂ 0.01; ns is not significant.</p> <p>F, G Immunoblot analysis of cells analyzed in C. The bars in G represent the mean±sd of band intensities relative to the loading control from three independent experiments quantified using ImageJ. Statistical comparison was analyzed by one-way ANOVA followed by Tukey multiple comparison test. Significance is displayed as **p ˂ 0.005, *p ˂ 0.01; ns is not significant.</p> <p>H, I Immunoblot analysis of HeLa CALCOCO1 KO cells stably expressing EGFP-CALCOCO1 in fed or starved conditions and transfected with the indicated VAPA/B siRNAs.</p> </sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=33157
|
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"mapping_status": "mapped",
"ncbi_gene_id": "57658",
"original_type": "gene",
"role": "intervention",
"text": "CALCOCO1",
"type": "geneprod",
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"Q9P1Z2"
]
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{
"ext_dbs": "NCBI gene",
"ext_ids": "57658",
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"ext_tax_names": "Homo sapiens",
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"mapping_status": "mapped",
"ncbi_gene_id": "57658",
"original_type": "gene",
"role": "intervention",
"text": "CALCOCO1",
"type": "geneprod",
"uniprot_ids": [
"Q9P1Z2"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q9P1Z2",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
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"role": "assayed",
"text": "CALCOCO1",
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"Q9P1Z2"
]
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{
"ext_dbs": "NCBI gene",
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"role": "intervention",
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"ext_tax_names": "Homo sapiens",
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"mapping_status": "mapped",
"ncbi_gene_id": "57658",
"original_type": "gene",
"role": "intervention",
"text": "CALCOCO1",
"type": "geneprod",
"uniprot_ids": [
"Q9P1Z2"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "O95197",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "RTN3",
"type": "geneprod",
"uniprot_ids": [
"O95197"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "57658",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "57658",
"original_type": "gene",
"role": "intervention",
"text": "CALCOCO1",
"type": "geneprod",
"uniprot_ids": [
"Q9P1Z2"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "9218",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "9218",
"original_type": "gene",
"role": "intervention",
"text": "VAPA",
"type": "geneprod",
"uniprot_ids": [
"Q9P0L0"
]
}
] |
||
10.15252/embj.2019103649
|
CALCOCO1 acts with VAMP-Associated Proteins to mediate ER-phagy.
|
2020
|
Figure 8
|
<sd-panel> <p><strong>Figure 8. Interaction with ATG8 proteins is required for CALCOCO1-mediated ER-phagy.</strong></p> <p>A Immunoblot analysis of HeLa CALCOCO1 KO cells stably expressing EGFP-CALCOCO1 in fed or starved conditions and treated as indicated with Baf A1 or PI3KC3 inhibitor SAR405.</p> <p>B Immunoblot analysis of HeLa CALCOCO1 KO cells stably expressing EGFP-CALCOCO1 mLIR+∆623-691 for 24 hours or not, and then treated as indicated.</p> <p>C, D Representative confocal images of HeLa CALCOCO1 KO cells transiently co-transfected with mCherry-CALCOCO1, Myc-VAPA and EGFP-LAMP1, and then treated as indicated before immunostaining with anti-Myc anti-body. Arrows indicate co-localization. Scale bars in C, 5 μm for large merged images and 1 μm for zoomed images. In D, data are presented as mean ± sd. Statistical comparison was analyzed by one-way ANOVA followed by Tukey multiple comparison test and significance displayed as ***p ˂ 0.001; ns is not significant, n=3.</p> <p>E Model of ER-phagy mediated by CALCOCO1 dimers illustrating the dual LIR-LDS and UIR-UDS interaction with lipidated GABARAP subfamily proteins on the phagophore, and the FFAT-like motif mediated interaction with MSP domains of VAP proteins on tubular ER.</p> </sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=33158
|
[
{
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"ext_ids": "Q8NEB9",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "intervention",
"text": "PI3KC3",
"type": "geneprod",
"uniprot_ids": [
"Q8NEB9"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "57658",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "57658",
"original_type": "gene",
"role": "intervention",
"text": "CALCOCO1",
"type": "geneprod",
"uniprot_ids": [
"Q9P1Z2"
]
}
] |
||
20098416
|
10.1038/ncb2012
|
PINK1/Parkin-mediated mitophagy is dependent on VDAC1 and p62/SQSTM1
|
2010
|
figf1
|
<p>(<b>a</b>) Schematic view of human Parkin structure (UBL, ubiquitin-like domain; R0, RING0/unique Parkin domain; R1/2, RING finger domains; IBR, in-between-ring domain). Parkinson's disease-associated mutations and the Parkin fragments used are indicated. (<b>b</b>) Parkin is recruited selectively to depolarized mitochondria and directs mitophagy. HeLa cells transfected with HA–Parkin were treated with CCCP for the indicated times. Mitochondria were stained by anti-TOM20 (pseudo coloured; blue) and a Δ&PSgr;m-dependent MitoTracker (red). Parkin was stained with anti-HA (green). Without treatment, mitochondria are intact and stained by both mitochondrial markers, whereas Parkin is equally distributed in the cytoplasm. After 2 h of CCCP treatment, mitochondria are depolarized as shown by the loss of MitoTracker staining. Parkin completely translocates to mitochondria clustering at perinuclear regions. After 24 h of CCCP treatment, massive loss of mitochondria is observed as shown by the disappearance of the mitochondrial marker. Only Parkin-positive cells show mitochondrial clustering and clearance, in contrast to adjacent untransfected cells. Scale bars, 10 μm. (<b>c</b>) Pathogenic Parkin mutations abrogate mitochondrial translocation and/or clearance. HeLa cells transfected with Flag–Parkin wild-type or pathogenic mutants were treated with CCCP and stained with anti-Flag (green), anti-TOM20 (red) and Hoechst33342 (blue). Representative merged images are shown. Scale bars, 10 μm. Immunostaining of cells transfected with non-functional cysteine mutants and functional Parkin variants is shown in <sir rid="s1">Supplementary Information, Fig. S1a</sir> and <sir rid="s1">S1b</sir>, respectively. (<b>d</b>, <b>e</b>) Based on the mitochondrial effects, Parkin mutants can be classified into functional and non-functional classes. (<b>d</b>) Quantification of Parkin translocation to damaged mitochondria after 2 h of CCCP treatment, as defined by complete colocalization of Parkin with the mitochondrial marker (<i>n</i> = 3). (<b>e</b>) Quantification of cells with uncleared mitochondria after 24 h of CCCP treatment, as shown by complete loss of mitochondrial staining (<i>n</i> = 3). Data represent the mean ± s.d., <super>*</super><i>P</i> ≤ 0.05, <super>**</super><i>P</i> ≤ 0.005, <super>***</super><i>P</i> ≤ 0.0005 compared with wild-type. WT, wild-type.</p>
|
https://api.sourcedata.io/file.php?figure_id=2938
|
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"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "Parkin",
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"uniprot_ids": [
"O60260"
]
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{
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"original_type": "protein",
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"text": "Parkin",
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"O60260"
]
},
{
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"text": "Parkin",
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"O60260"
]
},
{
"ext_dbs": "Uniprot",
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{
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"original_type": "protein",
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"text": "Parkin",
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"uniprot_ids": [
"O60260"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "O60260",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
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"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
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"text": "Parkin",
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]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q15388",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "TOM20",
"type": "geneprod",
"uniprot_ids": [
"Q15388"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "5071",
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"ext_tax_names": "Homo sapiens",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "5071",
"original_type": "gene",
"role": "intervention",
"text": "Parkin",
"type": "geneprod",
"uniprot_ids": [
"O60260",
"X5DR79"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "O60260",
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"ext_tax_names": "Homo sapiens",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "Parkin",
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"uniprot_ids": [
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]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "O60260",
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"mapping_source": "direct",
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"ncbi_gene_id": null,
"original_type": "protein",
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"text": "Parkin",
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]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q15388",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "TOM20",
"type": "geneprod",
"uniprot_ids": [
"Q15388"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "5071",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "5071",
"original_type": "gene",
"role": "intervention",
"text": "Parkin",
"type": "geneprod",
"uniprot_ids": [
"O60260",
"X5DR79"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "O60260",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "Parkin",
"type": "geneprod",
"uniprot_ids": [
"O60260"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "O60260",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "Parkin",
"type": "geneprod",
"uniprot_ids": [
"O60260"
]
}
] |
|
20098416
|
10.1038/ncb2012
|
PINK1/Parkin-mediated mitophagy is dependent on VDAC1 and p62/SQSTM1
|
2010
|
figf2
|
<p>Stable Parkin wild-type or pathogenic mutants expressing SH-SY5Y cell lines were induced with doxycycline (DOX) for 72 h and treated with CCCP for the indicated times. Cells were stained with anti-Parkin (green), anti-TOM20 (red) and Hoechst33342 (blue). (<b>a</b>–<b>b</b>) CCCP treatment of stable SH-SY5Y cells for 0 h. Unstimulated control cells (– DOX) show relatively low levels of endogenous Parkin, compared to cells with induced expression of Parkin wild-type or K161N, R275W and G430D mutants (+ DOX). Immunostaining (<b>a</b>) and western blot analysis (<b>b</b>) of the induced cells demonstrate comparable levels of Parkin expression in the selected clones. β-Actin served as a loading control. (<b>c</b>, <b>d</b>) After 2 h of CCCP treatment, massive colocalization of wild-type Parkin and mitochondrial clusters can be observed in the induced cells when compared with unstimulated controls. Similarly, Parkin K161N and R275W mutants translocate to mitochondria, whereas G430D does not. (<b>e</b>, <b>f</b>) After 24 h of CCCP treatment, induced wild-type Parkin-expressing cells show full clearance of damaged mitochondria. In contrast, the pathogenic mutants analysed fail to execute mitophagy and, therefore, damaged mitochondria remain uncleared. Representative images of three independent experiments are shown. Scale bars, 10 μm (<b>a</b>, <b>c</b> and <b>e</b>). (<b>d</b>, <b>f</b>) Quantifications of the observed mitochondrial effects in Parkin-expressing SH-SY5Y cells (<i>n</i> = 3). Data represent the mean ± s.d., <super>***</super><i>P</i> ≤ 0.0005 compared with induced wild-type Parkin. WT, wild-type.</p>
|
https://api.sourcedata.io/file.php?figure_id=2939
|
[
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"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "5071",
"original_type": "gene",
"role": "intervention",
"text": "Parkin",
"type": "geneprod",
"uniprot_ids": [
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"X5DR79"
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},
{
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"ext_tax_names": "Homo sapiens",
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"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
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"text": "Parkin",
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]
},
{
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"ncbi_gene_id": null,
"original_type": "protein",
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"text": "Parkin",
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},
{
"ext_dbs": "Uniprot",
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{
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},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q15388",
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"ext_tax_names": "Homo sapiens",
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"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "TOM20",
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"uniprot_ids": [
"Q15388"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "5071",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "5071",
"original_type": "gene",
"role": "intervention",
"text": "Parkin",
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"uniprot_ids": [
"O60260",
"X5DR79"
]
},
{
"ext_dbs": "Uniprot",
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},
{
"ext_dbs": "NCBI gene",
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] |
|
20098416
|
10.1038/ncb2012
|
PINK1/Parkin-mediated mitophagy is dependent on VDAC1 and p62/SQSTM1
|
2010
|
figf3
|
<p>(<b>a</b>) Schematic representation of human PINK1 (MTS, mitochondrial targeting sequence; TM, transmembrane domain; Ser/Thr-Kinase, Serine/threonine kinase domain). Mutations of an artificial triple kinase-dead (3×KD)<bibr rid="b24"></bibr> PINK1 variant are indicated. (<b>b</b>) Co-immunoprecipitations of Parkin and PINK1 after mitochondrial depolarization. Endogenous Parkin and PINK1 were co-immunoprecipitated from neuronal SH-SY5Y cells after CCCP treatment with specific antibodies. (<b>c</b>) Western blot of <i>PINK1</i> siRNA-transfected HeLa cells used in <b>d</b>–<b>h</b> demonstrates the knockdown efficiency and specificity of <i>PINK1</i> silencing. (<b>d</b>–<b>h</b>) <i>PINK1</i>-specific siRNA abrogates Parkin translocation to mitochondria after 2 h, and mitochondrial clearance after 24 h, of CCCP treatment. This can be rescued by re-transfection with wild-type PINK1, but not with a kinase-dead mutant or a PINK1 variant lacking the MTS. Control siRNA- or <i>PINK1</i> siRNA-silenced HeLa cells were transfected with EGFP–Parkin wild-type and PINK1–V5 wild-type, 3×KD or ΔMTS mutants. Use of appropriate empty vector controls is depicted. Cells were treated with CCCP and stained with anti-TOM20 (pseudo coloured; blue) and anti-V5 (red) to visualize mitochondrial morphology and re-transfected PINK1, respectively. Wild-type Parkin was visualized by EGFP epifluorescence (green). Parkin-positive cells are surrounded by a line. Representative images of four independent experiments are shown. Scale bars, 10 μm. (<b>e</b>) Wild-type Parkin colocalization with impaired mitochondria after 2 h of CCCP treatment was analysed (<i>n</i> = 4). (<b>f</b>) Uncleared mitochondria were analysed after 24 h of CCCP treatment (<i>n</i> = 4). (<b>g</b>) Quantification of results from cells in <b>e</b>. (<b>h</b>) Quantification of results from cells in <b>f</b>. Data represent the mean ± s.d., <super>**</super><i>P</i> ≤ 0.005, <super>***</super><i>P</i> ≤ 0.0005 compared with control siRNA-transfected cells. Immunostaining of control siRNA-transfected cells at all analysed time points is shown in <sir rid="s1">Supplementary Information, Fig. S2</sir>. WT, wild-type.</p>
|
https://api.sourcedata.io/file.php?figure_id=2940
|
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"ext_ids": "O60260",
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] |
|
20098416
|
10.1038/ncb2012
|
PINK1/Parkin-mediated mitophagy is dependent on VDAC1 and p62/SQSTM1
|
2010
|
figf4
|
<p>(<b>a</b>, <b>b</b>) Stable Mito-DsRed (pseudo coloured; blue)-expressing HeLa cells were transfected with Flag–Parkin wild-type or pathogenic mutants. Cells were treated with CCCP before immunostaining of Parkin with anti-Flag (green) and endogenous poly-ubiquitin with a specific antibody FK1 (red). (<b>a</b>) In contrast to pathogenic mutations, wild-type Parkin shows colocalization with poly-ubiquitin after 6 h of CCCP treatment at the site of condensed mitochondria. (<b>b</b>) After 24 h of CCCP treatment, K161N and R275W Parkin mutants colocalize with both poly-ubiquitin and mitochondria. In contrast, translocation-deficient Parkin mutants K211N, T240R and G430D lack the mitochondria-associated poly-ubiquitin signal. Representative images are shown. Scale bars, 10 μm. Complementary immunostaining of untreated cells and quantification of colocalization of Parkin, mitochondria and poly-ubiquitin upon CCCP treatment are shown in <sir rid="s1">Supplementary Information, Fig. S3a, b and c</sir>, respectively. (<b>c</b>, <b>d</b>) Parkin-directed mitophagy specifically involves linkage of ubiquitin through lysines 27 and 63. HeLa cells were transfected with EGFP–Parkin wild-type and ubiquitin lysine variants and treated with CCCP before immunostaining with anti-HtrA2/Omi, as a mitochondrial marker (pseudo coloured; blue) and anti-His (red) to detect ectopic ubiquitin. Parkin was visualized by its fusion to EGFP (green). (<b>c</b>) Note that only wild-type, K27 and K63 6×His-tagged ubiquitin variants are colocalized with condensed mitochondria and EGFP–Parkin after 6 h of CCCP treatment. All other ubiquitin mutants interfere with Parkin translocation to mitochondria. (<b>d</b>) Only co-expression of K27 or K63 ubiquitin recapitulates mitochondrial clearance similarly to 6×His-tagged wild-type ubiquitin after 24 h of CCCP treatment. Representative images are shown. Scale bars, 10 μm. Immunostaining of untreated cells and all other ubiquitin variant combinations tested are shown in <sir rid="s1">Supplementary Information, Fig. S4a and b, c</sir>, respectively. WT, wild-type; PolyUb, poly-ubiquitin.</p>
|
https://api.sourcedata.io/file.php?figure_id=2941
|
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}
] |
|
20098416
|
10.1038/ncb2012
|
PINK1/Parkin-mediated mitophagy is dependent on VDAC1 and p62/SQSTM1
|
2010
|
figf5
|
<p>(<b>a</b>, <b>b</b>) Stable Mito-DsRed (pseudo coloured; blue)-expressing HeLa cells were transfected with Flag–Parkin wild-type or pathogenic mutants. Cells were treated with CCCP for the indicated times before immunostaining with anti-Flag (green) and anti-p62 (red). (<b>a</b>) In contrast to the pathogenic mutants, wild-type Parkin colocalizes with p62 at the site of clustered mitochondria, after 6 h of CCCP treatment. (<b>b</b>) After 24 h of CCCP treatment, wild-type Parkin-transfected cells show complete loss of mitochondria, whereas K161N and R275W Parkin mutants colocalize with both p62 and mitochondria. In contrast, translocation-compromised mutants K211N, T240R and G430D, lacking the mitochondria-associated poly-ubiquitin signal (<figr rid="f4">Fig. 4b</figr>), did not colocalize with p62. Representative images of four independent experiments are shown. Data from untreated control cells and quantification of colocalization of Parkin, mitochondria and p62 upon CCCP treatment are shown in <sir rid="s1">Supplementary Information, Fig. 5a and b, c</sir>, respectively. (<b>c</b>, <b>d</b>) Control siRNA- or <i>p62</i> siRNA-silenced HeLa cells were transfected with EGFP–Parkin wild-type. Cells were treated with CCCP for the indicated times and stained with anti-TOM20 (pseudo coloured; blue) to visualize mitochondrial morphology and anti-p62 (red) to monitor silencing efficiency. Parkin wild-type was visualized by EGFP epifluorescence (green). Parkin-positive cells with cleared mitochondria are surrounded by a line. (<b>c</b>–<b>f</b>) Knockdown of <i>p62</i> has no influence on Parkin translocation to mitochondria after 6 h of CCCP treatment (<b>c</b>–<b>e</b>), but completely blocks final clearance after 24 h (<b>c</b>, <b>d</b>, <b>f</b>). (<b>e</b>, <b>f</b>) Relative parkin translocation (<b>e</b>) and mitochondrial clearance (<b>f</b>) after <i>p62</i> knockdown and CCCP treatment (<i>n</i> = 4). Data represent the mean ± s.d., <super>***</super><i>P</i> ≤ 0.0005 compared with control siRNA-transfected cells. Representative images of four independent experiments are shown. Scale bars, 10 μm. Immunostainings of control cells are shown in <sir rid="s1">Supplementary Information, Fig. S5d, e</sir>. (<b>g</b>) Western blot of siRNA-transfected HeLa cells used in <b>c</b>–<b>f</b> demonstrates the efficiency of <i>p62</i> silencing. β-Actin probing served as a loading control. WT, wild-type.</p>
|
https://api.sourcedata.io/file.php?figure_id=2942
|
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{
"ext_dbs": "NCBI gene",
"ext_ids": "8878",
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"ext_tax_names": "Homo sapiens",
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"ncbi_gene_id": "8878",
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}
] |
|
20098416
|
10.1038/ncb2012
|
PINK1/Parkin-mediated mitophagy is dependent on VDAC1 and p62/SQSTM1
|
2010
|
figf6
|
<p>(<b>a</b>) Time-course experiment of HeLa cells transfected with Flag–Parkin wild-type and treated with CCCP for the indicated periods. Total lysates were prepared, and western blots were probed with specific anti-Parkin, anti-PINK1, anti-TOM20 and anti-VDAC1 antibodies. β-Actin probing served as a loading control. All of the proteins detected are endogenously expressed, except Flag–Parkin. (<b>b</b>) Pathogenic Parkin mutants fail to poly-ubiquitylate endogenous VDAC1 in response to CCCP treatment. HeLa cells were transfected with empty vector (-), Flag–Parkin wild-type or pathogenic mutants along with 6×His-tagged ubiquitin wild-type for 24 h. Cells were treated with CCCP for 6 h and subsequently protein lysates were prepared in urea buffer. Denaturing conditions of Ni-NTA affinity purifications were used to specifically pulldown only proteins covalently modified with 6xHis-tagged ubiquitin. Western blots of protein lysates and purified Ni-NTA agarose elutions were probed with anti-VDAC1, anti-TOM20 and anti-Parkin antibodies. Modification of VDAC1 was observed in cells expressing Parkin wild-type and the functional mutant G328E, whereas non-functional mutants did not have this effect. (<b>c</b>) In response to CCCP treatment, Parkin catalyses predominantly K27-linked poly-ubiquitin chains on endogenous VDAC1 and is itself strongly poly-ubiquitylated. HeLa cells were transfected with an empty vector (-) or Flag–Parkin wild-type along with 6×His-tagged ubiquitin variants for 24 h. Treatment of cells, preparation of lysates and Ni-NTA purification were performed as described in <b>c</b> and probed for Parkin, VDAC1 and β-actin. WT, wild-type; Ub, ubiquitin.</p>
|
https://api.sourcedata.io/file.php?figure_id=2943
|
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"text": "Parkin",
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]
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},
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"ext_dbs": "Uniprot///Uniprot",
"ext_ids": "P0CG48///P0CG47",
"ext_tax_ids": "9606///9606",
"ext_tax_names": "Homo sapiens///Homo sapiens",
"mapping_source": "unknown",
"mapping_status": "unmapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "poly-ubiquitin",
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"ext_dbs": "Uniprot",
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"text": "VDAC1",
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]
},
{
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"ext_ids": "P21796",
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"ncbi_gene_id": null,
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"role": "assayed",
"text": "VDAC1",
"type": "geneprod",
"uniprot_ids": [
"P21796"
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}
] |
|
20098416
|
10.1038/ncb2012
|
PINK1/Parkin-mediated mitophagy is dependent on VDAC1 and p62/SQSTM1
|
2010
|
figf7
|
<p>(<b>a</b>) Western blot analysis of parental SH-SY5Y cells treated with CCCP for the indicated times. Time-course experiments of CCCP-treated neuronal cells reveal increasing modifications of VDAC1 over time. Total lysates were prepared, and western blots were probed with specific anti-Parkin, anti-PINK1, anti-TOM20 and anti-VDAC1 antibodies. All proteins represent endogenous levels. (<b>b</b>) Immunoprecipitations of Parkin and VDAC1 from parental SH-SY5Y cells confirm ubiquitylation of both proteins. CCCP treatment of neuronal cells increases ubiquitylated species of endogenous Parkin and VDAC1 over time. Using specific antibodies, Parkin and VDAC1 were immunoprecipitated from lysates of parental SH-SY5Y cells at different time points, western blotted and probed with anti-ubiquitin, anti-Parkin and anti-VDAC1 antibodies. (<b>c</b>) Pathogenic Parkin mutations fail to poly-ubiquitylate endogenous VDAC1 in response to CCCP treatment. Western blot analysis of a time-course experiment with inducible Parkin SH-SY5Y cells after CCCP treatment. Total lysates were prepared, and western blots were probed with specific anti-Parkin and anti-VDAC1 antibodies. β-Actin probing served as a loading control in <b>a</b>–<b>c</b>. WT, wild-type; Ub, ubiquitin.</p>
|
https://api.sourcedata.io/file.php?figure_id=2944
|
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}
] |
|
20098416
|
10.1038/ncb2012
|
PINK1/Parkin-mediated mitophagy is dependent on VDAC1 and p62/SQSTM1
|
2010
|
figf8
|
<p><i>VDAC1</i>-specific siRNA abrogates Parkin translocation to mitochondria after 2 h, and mitochondrial clearance after 24 h, of CCCP treatment. Both effects can be rescued by re-transfection with wild-type VDAC1. (<b>a</b>) Immunofluorescence and (<b>b</b>) western blot of siRNA-transfected HeLa cells used in <b>c</b>–<b>g</b> demonstrate partial silencing of endogenous VDAC1. (<b>a</b>) Silenced cells were stained with anti-HtrA2/Omi, a mitochondrial marker (pseudo coloured; blue), and anti-VDAC1 (red) antibodies. (<b>b</b>) Lysates from silenced cells were subjected to western blot analysis and probed with an anti-VDAC1 antibody, while TOM20 and β-actin probing served as loading controls. (<b>c</b>–<b>e</b>) Control siRNA- or <i>VDAC1</i> siRNA-silenced HeLa cells were transfected with the indicated combinations of EGFP–Parkin wild-type, VDAC1–Flag wild-type or appropriate empty vector controls. Cells were treated with CCCP for 2 h and 24 h and stained with anti-HtrA2/Omi (pseudo coloured; blue) and anti-Flag (red) to visualize mitochondrial morphology and re-transfected VDAC1, respectively. Wild-type Parkin was visualized by EGFP epifluorescence (green). Parkin-positive cells are surrounded by a line. Representative pictures of three independent experiments are shown. Scale bars, 10 μm. (<b>f</b>, <b>g</b>) Quantification of <b>d</b> (<b>f</b>) and <b>e</b> (<b>g</b>). Parkin wild-type colocalization with impaired mitochondria after 2 h (<b>f</b>) and uncleared mitochondria after 24 h (<b>g</b>) of CCCP treatment (<i>n</i> = 3). Data represent the mean ± s.d., <super>*</super><i>P</i> ≤ 0.05 compared with control siRNA-transfected or with VDAC1–Flag wild-type-transfected cells.</p>
|
https://api.sourcedata.io/file.php?figure_id=2945
|
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"ncbi_gene_id": "7416",
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] |
|
10.15252/embr.202154322
|
Evolutionary remodelling of N-terminal domain loops fine-tunes SARS-CoV-2 spike.
|
2022
|
Figure 2
|
<sd-panel><p><strong>Figure 2. NTD deletions are necessary for efficient entry by Alpha and Omicron spike.</strong> Lentiviral pseudovirus (PV), encoding a luciferase reporter gene, were used to evaluate spike-mediated entry by Wu-Hu-1 (Wuhan-Hu-1 reference strain) and Alpha.</p> <p><strong>A.</strong> Cellular expression and PV incorporation of spike were assessed by Western blotting using an anti-S2 mAb. Lentiviral capsid components were detected using anti-p24/55.</p> <p><strong>B.</strong> Representative raw luciferase activity upon PV infection of the stated cell lines, annotated values represent fold enhancement of Alpha entry compared to Wu-Hu-1, n=4 technical repeats.</p> <p><strong>C.</strong> Alpha infection of HeLa ACE2 and HEK 293T cells relative to Wu-Hu-1 control. Data points represent the mean of independent experiments, n=8 biological repeats.</p> <p><strong>D.</strong> Surface expression of ACE2 (goat anti-ACE2) in HeLa ACE2 and HEK 293T cells was assessed by flow cytometry, negative control represents cells incubated with secondary antibody only.</p> <p><strong>E.</strong> ACE2 RNA transcripts were assessed by qPCR, abundance is expressed relative to negative control (no-RT). Representative data, n=2 technical repeats.</p> <p><strong>F.</strong> Western blot detection of ACE2 (rabbit anti-ACE2) in cell lysates of the stated cells. ACE2 was detected in HEK 293T samples after loading 3X more lysate and increasing signal exposure time (labelled in boldface).</p> <p><strong>G.</strong> Representative raw luciferase activity after PV infection of HEK 293T cells preincubated with 20µg/ml goat anti-ACE2, n=4 technical repeats.</p> <p><strong>H.</strong> Alpha and Middle Eastern respiratory syndrome-CoV PV infection of HEK 293T cells treated with a serial dilution of anti-ACE2, data points are expressed relative to untreated control cells and represent the mean of n=3 biological repeats.</p> <p><strong>I.</strong> Raw luciferase values after Wu-Hu-1 and Alpha PV infection of HEK 293T cells transfected to over-express ACE2 or TMPRSS2, annotated values represent fold enhancement compared to Wu-Hu-1, n=8 technical repeats.</p> <p><strong>J.</strong> Over-expression confirmed by Western blotting, actin and CD81 were used as loading controls for ACE2 and TMPRSS2 respectively.</p> <p><strong>K.</strong> Entry of PV bearing the stated spike proteins into HeLa ACE2 and HEK 293T. Infection is expressed relative to Wu-Hu-1, data points represent mean values from n=8 (HeLa ACE2) and 4 (HEK 293T) biological repeats.</p> <p><strong>L.</strong> Cellular expression and PV incorporation of the stated spike proteins were assessed by Western blotting. The displayed samples are taken from the same image and have been cropped to remove irrelevant lanes/bands.</p> <p><strong>M.</strong> Entry of PV bearing the stated spike proteins into HeLa ACE2 and HEK 293T. Infection is expressed relative to Wu-Hu-1, data points represent mean values from n=5 biological repeats.</p> <p><strong>N.</strong> Cellular expression and PV incorporation of the stated spike proteins were assessed by Western blotting, note the change in sample order relative to panel M.</p> <p>Data information: In all plots, error bars indicate standard error of the mean, statistical analysis (T-test and ANOVA) performed in GraphPad Prism. Fitted curves were determined to be statistically different using an F-test. * P ≤ 0.05, ** P ≤ 0.01, *** P ≤ 0.001, ns = not significant. Comparisons performed against control Wu-Hu-1 apart from in (K and M) where statistical analyses are performed relative to respective parental spike i.e. Wu-Hu-1 Δ69/70 Δ144 vs Wu-Hu-1 and Alpha +H69 +V70 +Y144 vs Alpha.</p></sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=49263
|
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"ext_tax_names": "Severe acute respiratory syndrome coronavirus 2",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "43740568",
"original_type": "gene",
"role": "intervention",
"text": "spike",
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"P0DTC2",
"A0A679G9E9",
"A0A6G7K2L4"
]
},
{
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"mapping_source": "direct",
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"original_type": "protein",
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"text": "S2",
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"uniprot_ids": [
"P0DTC2"
]
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{
"ext_dbs": "Uniprot",
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"ext_tax_names": "Homo sapiens",
"mapping_source": "direct",
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"original_type": "protein",
"role": "assayed",
"text": "ACE2",
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"uniprot_ids": [
"Q9BYF1"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q9BYF1",
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"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "ACE2",
"type": "geneprod",
"uniprot_ids": [
"Q9BYF1"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q9BYF1",
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"ext_tax_names": "Homo sapiens",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "ACE2",
"type": "geneprod",
"uniprot_ids": [
"Q9BYF1"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q9BYF1",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "ACE2",
"type": "geneprod",
"uniprot_ids": [
"Q9BYF1"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "O15393",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "TMPRSS2",
"type": "geneprod",
"uniprot_ids": [
"O15393"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P0DTC2",
"ext_tax_ids": "2697049",
"ext_tax_names": "Severe acute respiratory syndrome coronavirus 2",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "spike",
"type": "geneprod",
"uniprot_ids": [
"P0DTC2"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P0DTC2",
"ext_tax_ids": "2697049",
"ext_tax_names": "Severe acute respiratory syndrome coronavirus 2",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "spike",
"type": "geneprod",
"uniprot_ids": [
"P0DTC2"
]
}
] |
||
10.15252/embr.202154322
|
Evolutionary remodelling of N-terminal domain loops fine-tunes SARS-CoV-2 spike.
|
2022
|
Figure 3
|
<sd-panel><p><strong>Figure 3. Length polymorphism of the <sd-pretag id="sdPretag442742789sm" category="disease">NTD</sd-pretag> loops across the sarbecoviruses.</strong></p> <p><strong>A.</strong> Surface representation of spike colour-coded for conservation across the <sd-pretag id="sdPretag1417672637sm" type="organism" role="component">sarbecoviruses</sd-pretag> (as shown in the key), spike is shown from the side and from above. NTD, annotated, is a hotspot of diversity.</p> <p><strong>B.</strong> Maximum likelihood phylogeny of the Spike NTD nucleotide <sd-pretag id="sdPretag1890238374sm" category="assay">sequences</sd-pretag> (without loops) for 86 <sd-pretag id="sdPretag1251134316sm" type="organism" role="component">sarbecoviruses</sd-pretag>. Nodes with bootstrap support below 70 have been dropped. Clades containing nearly identical <sd-pretag id="sdPretag781831109sm" type="geneprod" role="assayed">HKU-3</sd-pretag>-like and <sd-pretag id="sdPretag696091905sm" type="geneprod" role="assayed">RaTG15</sd-pretag>-like <sd-pretag id="sdPretag1670948926sm" type="organism" role="component">viruses</sd-pretag> (see Dataset EV1) have been collapsed for clarity. Branches are coloured based on clade groupings.</p> <p><strong>C.</strong> NTD loop lengths were quantified across the sarbecoviruses; data points are colour-coded as in 3B, SARS-<sd-pretag id="sdPretag1935346040sm" type="organism" role="component">CoV-2</sd-pretag> is represented as a star. In each column, the bar represents mean loop length.</p> <p><strong>D.</strong> Example protein alignments for each loop displaying SARS<sd-pretag id="sdPretag100607736sm" type="organism" role="component">-CoV-2</sd-pretag> (Wu-<sd-pretag id="sdPretag169189525sm" type="geneprod" role="intervention">Hu-1</sd-pretag>), <sd-pretag id="sdPretag346934903sm" type="small" role="intervention">Pangolin</sd-pretag> CoV (Guangdong <sd-pretag id="sdPretag1397925873sm" type="small" role="assayed">isolate</sd-pretag>, GD) and SARS<sd-pretag id="sdPretag2051467324sm" type="organism" role="component">-CoV</sd-pretag>. The length of each loop is provided with each label. Lentiviral <sd-pretag id="sdPretag349711626sm" type="organism" role="component">PV</sd-pretag> encoding a <sd-pretag id="sdPretag600325543sm" type="geneprod" role="assayed">luciferase</sd-pretag> reporter gene were used to evaluate spike-mediated entry by <sd-pretag id="sdPretag811137018sm" type="small" role="intervention">Pangolin</sd-pretag> CoV GD.</p> <p><strong>E.</strong> Cellular expression and <sd-pretag id="sdPretag702406392sm" type="organism" role="component">PV</sd-pretag> incorporation of the stated spike proteins were assessed by <sd-pretag id="sdPretag371323729sm" category="assay">Western blotting</sd-pretag>.</p> <p><strong>F.</strong> Representative raw <sd-pretag id="sdPretag233591026sm" category="assay">luciferase</sd-pretag> activity upon <sd-pretag id="sdPretag47801584sm" type="organism" role="component">PV</sd-pretag> infection of the <sd-pretag id="sdPretag1505289919sm" type="cell" role="component">HeLa</sd-pretag> <sd-pretag id="sdPretag1622114463sm" type="geneprod" role="intervention">ACE2</sd-pretag> and <sd-pretag id="sdPretag1511259658sm" type="cell" role="component">HEK 293T</sd-pretag> cells by the stated <sd-pretag id="sdPretag736581840sm" type="organism" role="component">PV</sd-pretag>, annotated values represent fold enhancement in entry compared to Wu-<sd-pretag id="sdPretag2081662668sm" type="geneprod" role="assayed">Hu-1</sd-pretag>, n=3 technical repeats.</p> <p><strong>G.</strong> Pangolin CoV entry into <sd-pretag id="sdPretag734219695sm" type="cell" role="component">HeLa</sd-pretag> <sd-pretag id="sdPretag255094747sm" type="geneprod" role="intervention">ACE2</sd-pretag> and <sd-pretag id="sdPretag932137141sm" type="cell" role="component">HEK 293T</sd-pretag> cells relative to Wu-<sd-pretag id="sdPretag1622656601sm" type="geneprod" role="assayed">Hu-1</sd-pretag> control. Data points represent the mean of independent experiments, n=8 biological repeats.</p> <p><strong>H.</strong> Surface representation of spike protein illustrating the NTD swaps between Wu-<sd-pretag id="sdPretag405685612sm" type="geneprod" role="assayed">Hu-1</sd-pretag> and <sd-pretag id="sdPretag950988373sm" type="geneprod" role="assayed">Pangolin CoV</sd-pretag>.</p> <p><strong>I.</strong> Entry of PV bearing the stated spike proteins into <sd-pretag id="sdPretag2000544445sm" type="cell" role="component">HeLa</sd-pretag> <sd-pretag id="sdPretag1441754859sm" type="geneprod" role="assayed">ACE2</sd-pretag> and <sd-pretag id="sdPretag1864409935sm" type="cell" role="component">HEK 293T</sd-pretag>. Infection is expressed relative to Wu-<sd-pretag id="sdPretag1976327855sm" type="geneprod" role="intervention">Hu-1</sd-pretag>. Data points represent the mean of independent experiments, n=10 biological repeats.</p> <p><strong>J.</strong> Cellular Expression and <sd-pretag id="sdPretag1483253529sm" type="organism" role="component">PV</sd-pretag> incorporation of the stated spike proteins were assessed by <sd-pretag id="sdPretag884973893sm" category="assay">Western blotting</sd-pretag>.</p> <p>Data information: In all plots, error bars indicate standard error of the mean, statistical analysis (T-test and ANOVA, compared to control Wu-<sd-pretag id="sdPretag1445177443sm" type="geneprod" role="intervention">Hu-1</sd-pretag>) performed in GraphPad Prism. * P ≤ 0.05, ** P ≤ 0.01, *** P ≤ 0.001, ns = not significant.</p></sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=49265
|
[
{
"ext_dbs": "Uniprot",
"ext_ids": "P0DTC2",
"ext_tax_ids": "2697049",
"ext_tax_names": "Severe acute respiratory syndrome coronavirus 2",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "spike",
"type": "geneprod",
"uniprot_ids": [
"P0DTC2"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P0DTC2",
"ext_tax_ids": "2697049",
"ext_tax_names": "Severe acute respiratory syndrome coronavirus 2",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "spike",
"type": "geneprod",
"uniprot_ids": [
"P0DTC2"
]
}
] |
||
10.15252/embr.202154322
|
Evolutionary remodelling of N-terminal domain loops fine-tunes SARS-CoV-2 spike.
|
2022
|
Figure 4
|
<sd-panel><p><strong>Figure 4. Length polymorphism of the N2 loop alters <sd-pretag id="sdPretag1587075742sm" type="organism" role="component">SARS-CoV-2</sd-pretag> spike function independent of immune evasion</strong></p> <p><strong>A.</strong> Protein alignment illustrating the N2 loop variants designed for this study; loops of equivalent length to Wu-<sd-pretag id="sdPretag673876571sm" type="geneprod" role="assayed">Hu1</sd-pretag> and <sd-pretag id="sdPretag1926768300sm" type="geneprod" role="assayed">Alpha</sd-pretag> are annotated. The location of the N74 glycosylation site, and N74K mutation, is highlighted in bold.</p> <p><strong>B.</strong> Molecular models to illustrate the N2 loop lengths (generated using AlphaFold/ColabFold); shorter loops tend to adopt a <sd-pretag id="sdPretag151598480sm" type="geneprod" role="assayed">β-hairpin</sd-pretag>. N74 is annotated.</p> <p><strong>C.</strong> N2 loop variant spike <sd-pretag id="sdPretag1967864430sm" type="organism" role="component">PV</sd-pretag> infection of the stated cell lines, expressed relative to Wu-<sd-pretag id="sdPretag1857914828sm" type="geneprod" role="assayed">Hu-1</sd-pretag> (15 residue loop, coloured grey), n=3 biological repeats.</p> <p><strong>D.</strong> Cellular Expression and <sd-pretag id="sdPretag532376875sm" type="organism" role="component">PV</sd-pretag> incorporation of the stated spike proteins were assessed by <sd-pretag id="sdPretag1299903288sm" category="assay">Western blotting</sd-pretag>.</p> <p><strong>E.</strong> Experiments performed with authentic Public Health England strain <sd-pretag id="sdPretag701135560sm" type="organism" role="component">SARS-CoV-2</sd-pretag> without the polybasic cleavage site (PHE ΔPBCS), compared to an N2 loop deleted mutant that emerged spontaneously in cell culture (Δ67-76). AlphaFold/ColabFold molecular models illustrate the N2 loop in either <sd-pretag id="sdPretag558046748sm" type="organism" role="component">virus</sd-pretag>.</p> <p><strong>F.</strong> Three-day Vero cell <sd-pretag id="sdPretag109629918sm" category="assay">growth</sd-pretag> curves. One representative experiment is shown, n=4 technical repeats.</p> <p><strong>G.</strong> and <strong>H.</strong> Single round titres and <sd-pretag id="sdPretag723280266sm" category="assay">qPCR</sd-pretag> Ct values in cell culture supernatant from either <sd-pretag id="sdPretag1806630940sm" type="organism" role="component">virus</sd-pretag>, values represent the mean of n=4 biological repeats.</p> <p><strong>I.</strong> Representative inverted greyscale images of <sd-pretag id="sdPretag1871317896sm" type="small" role="assayed">crystal</sd-pretag> <sd-pretag id="sdPretag685294282sm" type="small" role="intervention">violet</sd-pretag>-stained cells in a plaque <sd-pretag id="sdPretag1573581786sm" category="assay">assay</sd-pretag>, lighter areas represent areas of cell death. <sd-pretag id="sdPretag460505308sm" type="geneprod" role="assayed">PHE</sd-pretag> ΔPBCS Δ67-76 exhibits larger plaques. Note, the white squares in the corners of each micrograph are a feature of the imaging system and cannot be removed.</p> <p>Data information: In all plots, error bars indicate standard error of the mean, statistical analysis performed in GraphPad Prism. (ANOVA and T-test, compared to controls N2 loop=15 residues (C), <sd-pretag id="sdPretag782056637sm" type="geneprod" role="assayed">PHE</sd-pretag> ΔPBCS (G and H)) * P ≤ 0.05, ** P ≤ 0.01, *** P ≤ 0.001, ns = not significant.</p> <h1 id="expanded-view-figure-legends">Expanded View Figure Legends</h1></sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=49267
|
[
{
"ext_dbs": "Uniprot",
"ext_ids": "P0DTC2",
"ext_tax_ids": "2697049",
"ext_tax_names": "Severe acute respiratory syndrome coronavirus 2",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "spike",
"type": "geneprod",
"uniprot_ids": [
"P0DTC2"
]
}
] |
||
23917356
|
10.1038/ncomms3308
|
Cytosolic p53 inhibits Parkin-mediated mitophagy and promotes mitochondrial dysfunction in the mouse heart
|
2013
|
f1
|
<p>(<b>a</b>) Ten-month-old adult mice and 20-month-old aged mice were treated with an intraperitoneal injection of 5 mg kg<super>−1</super> <named-entity id="named-entity-429">CCCP</named-entity> and their hearts were collected 12 h later. Representative electron micrographs of hearts from <named-entity id="named-entity-430">CCCP</named-entity>-treated adult and aged mice; original magnification × 5,000; scale bar, 2 μm. The magnified photograph represents an autophagic vacuole containing mitochondria; original magnification × 12,000; scale bar, 500 nm. Mitochondria incorporated into an autophagic vacuole in baseline and <named-entity id="named-entity-431">CCCP</named-entity>-treated conditions were quantified blindly from 8–10 images from different fields (original magnification × 5,000) (<i>n</i>=3 per group). (<b>b</b>,<b>c</b>) <named-entity id="named-entity-432">CCCP</named-entity>-induced recruitment of <named-entity id="named-entity-433">Parkin</named-entity> and <named-entity id="named-entity-434">p62</named-entity> to mitochondria was determined by immunoblotting of the heart mitochondria-rich fraction in adult and aged mice (<b>b</b>), and <named-entity id="named-entity-435">DOX</named-entity>-treated mice (<b>c</b>). Representative immunoblots are shown from four independent experiments. (<b>d</b>) <named-entity id="named-entity-436">Parkin</named-entity> was overexpressed in young and senescent MEFs using adenovirus-mediated transduction for the <i>in vitro</i> cell-based bioassay to assess the ability to clear damaged mitochondria. Mitochondrial content after 24 h of treatment with 20 μM <named-entity id="named-entity-437">CCCP</named-entity> was assessed by flow cytometry for <named-entity id="named-entity-438">MitoTracker Green FM</named-entity>. Results from four independent experiments performed in duplicate are shown. MEFs at passage 3 and passage 9 were used as young and senescent MEFs, respectively. (<b>e</b>) Mitochondrial DNA content was assessed by real-time PCR. Results are shown from six-independent experiments. (<b>f</b>) Mitochondrial content was assessed by immunoblotting for the mitochondrial chaperone, <named-entity id="named-entity-439">GRP75</named-entity> (matrix protein) and complex I subunit, <named-entity id="named-entity-440">NDUFA9</named-entity> (inner membrane protein). MEFs were treated with 100 nM <named-entity id="named-entity-441">bafilomycin-A1</named-entity>, (<named-entity id="named-entity-442">Baf-A1</named-entity>, an inhibitor of the vacuolar-type proton ATPase) to inhibit autophagy. Representative immunoblots are shown from three independent experiments. (<b>g</b>) Representative images of GFP-LC3 expressing MEFs treated with 20 μM <named-entity id="named-entity-443">CCCP</named-entity> for 10 h before the immunostaining of mitochondria with anti-<named-entity id="named-entity-444">TOM20</named-entity> (red); original magnification, × 400 and × 1,000; scale bar, 100 μm and scale bar, 15 μm. Line scans below the images indicate colocalization between LC3 (green) and mitochondria (red) and correlate to the arrows drawn in the images. WHL indicates whole-heart lysate. Data are shown as the means±s.d. *<i>P</i>0.05; **<i>P</i>0.01 (two-tailed unpaired Student’s <i>t</i>-test).</p>
|
https://api.sourcedata.io/file.php?figure_id=3336
|
[
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"text": "Parkin",
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]
},
{
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"text": "p62",
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{
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"ext_tax_names": "Mus musculus",
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"original_type": "protein",
"role": "assayed",
"text": "Parkin",
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},
{
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"ext_ids": "Q64337",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
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"text": "p62",
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{
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"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "50873",
"original_type": "gene",
"role": "intervention",
"text": "Parkin",
"type": "geneprod",
"uniprot_ids": [
"Q9WVS6",
"A0A3B2W489"
]
},
{
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"ext_ids": "P38647",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "GRP75",
"type": "geneprod",
"uniprot_ids": [
"P38647"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q9DC69",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "NDUFA9",
"type": "geneprod",
"uniprot_ids": [
"Q9DC69"
]
},
{
"ext_dbs": "Uniprot///Uniprot",
"ext_ids": "Q9CQV6///Q91VR7",
"ext_tax_ids": "10090///10090",
"ext_tax_names": "Mus musculus///Mus musculus",
"mapping_source": "unknown",
"mapping_status": "unmapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "LC3",
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{
"ext_dbs": "Uniprot",
"ext_ids": "Q9DCC8",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "TOM20",
"type": "geneprod",
"uniprot_ids": [
"Q9DCC8"
]
}
] |
|
23917356
|
10.1038/ncomms3308
|
Cytosolic p53 inhibits Parkin-mediated mitophagy and promotes mitochondrial dysfunction in the mouse heart
|
2013
|
f2
|
<p>(<b>a</b>) The senescence-associated molecules <named-entity id="named-entity-447">p53</named-entity>, <named-entity id="named-entity-448">p21</named-entity>, <named-entity id="named-entity-449">p16</named-entity>, <named-entity id="named-entity-450">H-Ras</named-entity> 12V and <named-entity id="named-entity-451">Rb</named-entity> were overexpressed in MEFs by retrovirus-mediated transduction. After <named-entity id="named-entity-452">puromycin</named-entity> selection, mitophagy induction was performed with treatment of 20 μM <named-entity id="named-entity-453">CCCP</named-entity> 24 h after adenovirus-mediated <named-entity id="named-entity-454">Parkin</named-entity> expression. Mitochondrial content 24 h after mitophagy induction was assessed by flow cytometry for <named-entity id="named-entity-455">MitoTracker Green FM</named-entity>. Results are shown from four independent experiments performed in duplicate. (<b>b</b>) Representative images of MEFs infected with the GFP-LC3 adenovirus and stained with anti-<named-entity id="named-entity-456">TOM20</named-entity> (red) to visualize mitochondria 10 h after mitophagy induction; original magnification, × 400 and × 1,000; scale bar, 100 μm and scale bar, 15 μm. (<b>c</b>) Mitochondrial content of <named-entity id="named-entity-457">H-Ras</named-entity> 12 V expressing WT, <i><named-entity id="named-entity-458">p53</named-entity></i><super>−/−</super> and <i><named-entity id="named-entity-459">p21</named-entity></i><super>−/−</super> MEFs was assessed by flow cytometry 24 h after mitophagy induction. Results are shown from four independent experiments performed in duplicate. (<b>d</b>) Mitochondrial content of WT and <i><named-entity id="named-entity-460">p53</named-entity></i><super>−/−</super> MEFs was assessed by flow cytometry 24 h after mitophagy induction. WT and <i><named-entity id="named-entity-461">p53</named-entity></i><super>−/−</super> MEFs were transfected with control or <named-entity id="named-entity-462">p53</named-entity>-specific siRNAs or cultured in complete medium for 24 h in the presence or absence of 20 μM <named-entity id="named-entity-463">pifithrin-α</named-entity> before mitophagy induction. Results are shown from four independent experiments performed in duplicate. (<b>e</b>) Murine HL-1 cardiac myocytes were infected with retrovirus vectors encoding <named-entity id="named-entity-464">p53</named-entity>, <named-entity id="named-entity-465">p21</named-entity> or <named-entity id="named-entity-466">p16</named-entity> and after <named-entity id="named-entity-467">puromycin</named-entity> selection, underwent mitophagy induction. Mitochondrial content is assessed by flow cytometry from four independent experiments performed in duplicate are shown. (<b>f</b>) HL-1 cells were transfected with control, <named-entity id="named-entity-468">p53</named-entity>, <named-entity id="named-entity-469">p21</named-entity> or <named-entity id="named-entity-470">p16</named-entity>-specific siRNAs, followed by treatment with 0.02 μM <named-entity id="named-entity-471">DOX</named-entity> and mitophagy induction. Mitochondrial content is assessed by flow cytometry from four independent experiments performed in duplicate. (<b>g</b>) <named-entity id="named-entity-472">CCCP</named-entity>-induced recruitment of <named-entity id="named-entity-473">Parkin</named-entity> and expression of <named-entity id="named-entity-474">Mfn1</named-entity> and <named-entity id="named-entity-475">Drp1</named-entity> in <named-entity id="named-entity-476">DOX</named-entity>-treated WT, <i><named-entity id="named-entity-477">p53</named-entity></i><super>−/−</super> and <i><named-entity id="named-entity-478">p21</named-entity></i><super>−/−</super> mice were determined by immunoblotting of the heart mitochondria-rich fraction. Representative immunoblots are shown from four independent experiments. Data are shown as the means±s.d. *<i>P</i>0.05; **<i>P</i>0.01 (two-tailed unpaired Student’s <i>t</i>-test).</p>
|
https://api.sourcedata.io/file.php?figure_id=3337
|
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"P02340",
"Q3UGQ1",
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"ext_dbs": "Uniprot///Uniprot",
"ext_ids": "Q9CQV6///Q91VR7",
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"mapping_source": "unknown",
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"ext_dbs": "Uniprot",
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"Q549C9",
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{
"ext_dbs": "NCBI gene",
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"ext_tax_names": "Mus musculus",
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{
"ext_dbs": "NCBI gene",
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"ext_tax_names": "Mus musculus",
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{
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]
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"text": "p53",
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"uniprot_ids": [
"P02340",
"Q3UGQ1",
"Q549C9",
"Q80ZA1"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "12575",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "12575",
"original_type": "gene",
"role": "intervention",
"text": "p21",
"type": "geneprod",
"uniprot_ids": [
"P39689",
"Q564P6"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "12578",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "12578",
"original_type": "gene",
"role": "intervention",
"text": "p16",
"type": "geneprod",
"uniprot_ids": [
"P51480",
"Q64364"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "22059",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "22059",
"original_type": "gene",
"role": "intervention",
"text": "p53",
"type": "geneprod",
"uniprot_ids": [
"P02340",
"Q3UGQ1",
"Q549C9",
"Q80ZA1"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "12575",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "12575",
"original_type": "gene",
"role": "intervention",
"text": "p21",
"type": "geneprod",
"uniprot_ids": [
"P39689",
"Q564P6"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "22059",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "22059",
"original_type": "gene",
"role": "intervention",
"text": "p53",
"type": "geneprod",
"uniprot_ids": [
"P02340",
"Q3UGQ1",
"Q549C9",
"Q80ZA1"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q8K1M6",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "Drp1",
"type": "geneprod",
"uniprot_ids": [
"Q8K1M6"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q811U4",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "Mfn1",
"type": "geneprod",
"uniprot_ids": [
"Q811U4"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q9WVS6",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "Parkin",
"type": "geneprod",
"uniprot_ids": [
"Q9WVS6"
]
}
] |
|
23917356
|
10.1038/ncomms3308
|
Cytosolic p53 inhibits Parkin-mediated mitophagy and promotes mitochondrial dysfunction in the mouse heart
|
2013
|
f3
|
<p>(<b>a</b>) Whole-cell lysates of HL-1 cells treated with 0.02 μM <named-entity id="named-entity-481">DOX</named-entity> and transfected with <named-entity id="named-entity-482">FLAG</named-entity>-tagged <named-entity id="named-entity-483">Parkin</named-entity> or the <named-entity id="named-entity-484">FLAG</named-entity>-empty vector were immunoprecipitated with the anti-Flag-M2 antibody and blotted with anti-<named-entity id="named-entity-485">p53</named-entity> and Flag antibodies. (<b>b</b>) Whole-cell lysates of rat neonatal cardiomyocytes treated with the indicated concentrations of <named-entity id="named-entity-486">H<sub>2</sub>O<sub>2</sub></named-entity> and <named-entity id="named-entity-487">DOX</named-entity> for 24 h were immunoprecipitated with the anti-<named-entity id="named-entity-488">Parkin</named-entity> antibody. (<b>c</b>) Cytosolic heart lysates of adult and aged mice were immunoprecipitated with anti-<named-entity id="named-entity-489">Parkin</named-entity>, <named-entity id="named-entity-490">p53</named-entity> and control IgG antibodies. (<b>d</b>) Schematic representation of N-terminally <named-entity id="named-entity-491">FLAG</named-entity>-tagged WT <named-entity id="named-entity-492">Parkin</named-entity> and various mutants of <named-entity id="named-entity-493">Parkin</named-entity>. (<b>e</b>) The association of endogenous <named-entity id="named-entity-494">p53</named-entity> with various <named-entity id="named-entity-495">Parkin</named-entity> mutants in <named-entity id="named-entity-496">DOX</named-entity>-treated HeLa cells. The immunoprecipitation assay revealed that the RING0 domain was essential for the interaction with <named-entity id="named-entity-497">p53</named-entity>. (<b>f</b>) Schematic representation of the GST–<named-entity id="named-entity-498">p53</named-entity> fusion proteins. (<b>g</b>) GST pull-down assays using GST–<named-entity id="named-entity-499">p53</named-entity> fusion proteins and <i>in vitro</i> transcribed/translated <named-entity id="named-entity-500">FLAG</named-entity>-<named-entity id="named-entity-501">Parkin</named-entity>. Residues 81–160 of <named-entity id="named-entity-502">p53</named-entity> were sufficient to bind <named-entity id="named-entity-503">Parkin</named-entity>.</p>
|
https://api.sourcedata.io/file.php?figure_id=3338
|
[
{
"ext_dbs": "NCBI gene",
"ext_ids": "50873",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "50873",
"original_type": "gene",
"role": "intervention",
"text": "Parkin",
"type": "geneprod",
"uniprot_ids": [
"Q9WVS6",
"A0A3B2W489"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "22059",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "22059",
"original_type": "gene",
"role": "intervention",
"text": "p53",
"type": "geneprod",
"uniprot_ids": [
"P02340",
"Q3UGQ1",
"Q549C9",
"Q80ZA1"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q9JK66",
"ext_tax_ids": "10116",
"ext_tax_names": "Rattus norvegicus",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "Parkin",
"type": "geneprod",
"uniprot_ids": [
"Q9JK66"
]
},
{
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"ext_ids": "Q9WVS6",
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"ext_tax_names": "Mus musculus",
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"role": "assayed",
"text": "Parkin",
"type": "geneprod",
"uniprot_ids": [
"Q9WVS6"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P02340",
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"ext_tax_names": "Mus musculus",
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"mapping_status": "mapped",
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"text": "p53",
"type": "geneprod",
"uniprot_ids": [
"P02340"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "5071",
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"ext_tax_names": "Homo sapiens",
"mapping_source": "ncbi_gene",
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"text": "Parkin",
"type": "geneprod",
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"X5DR79"
]
},
{
"ext_dbs": "Uniprot",
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"ext_tax_names": "Homo sapiens",
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"text": "Parkin",
"type": "geneprod",
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]
},
{
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"ext_ids": "O60260",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "direct",
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"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "Parkin",
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]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P04637",
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"ext_tax_names": "Homo sapiens",
"mapping_source": "direct",
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},
{
"ext_dbs": "Uniprot",
"ext_ids": "P04637",
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]
},
{
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"ncbi_gene_id": "7157",
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"text": "p53",
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"uniprot_ids": [
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"A0A087WT22",
"A0A087WXZ1",
"A0A087X1Q1",
"H2EHT1",
"K7PPA8",
"Q53GA5"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "7157",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "7157",
"original_type": "gene",
"role": "intervention",
"text": "p53",
"type": "geneprod",
"uniprot_ids": [
"P04637",
"A0A087WT22",
"A0A087WXZ1",
"A0A087X1Q1",
"H2EHT1",
"K7PPA8",
"Q53GA5"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "O60260",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
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"role": "assayed",
"text": "Parkin",
"type": "geneprod",
"uniprot_ids": [
"O60260"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "O60260",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "Parkin",
"type": "geneprod",
"uniprot_ids": [
"O60260"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P04637",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "p53",
"type": "geneprod",
"uniprot_ids": [
"P04637"
]
}
] |
|
23917356
|
10.1038/ncomms3308
|
Cytosolic p53 inhibits Parkin-mediated mitophagy and promotes mitochondrial dysfunction in the mouse heart
|
2013
|
f4
|
<p>(<b>a</b>) HL-1 cells transfected with control or <named-entity id="named-entity-506">p53</named-entity>-specific siRNAs no.1 and cultured in complete medium for 24 h in the presence or absence of 0.02 μM <named-entity id="named-entity-507">DOX</named-entity>. After treatment with 20 μM <named-entity id="named-entity-508">CCCP</named-entity> for 6 h, the fractionation experiment was performed. Endogenous <named-entity id="named-entity-509">Parkin</named-entity> translocation to mitochondria and ubiquitination were assessed by immunoblotting. Representative immunoblots are shown from three independent experiments. (<b>b</b>) These samples were subjected to immunoprecipitation with the anti-VDAC antibody to evaluate ubiquitination. Representative immunoblots are shown from three independent experiments. (<b>c</b>,<b>d</b>) Representative images of YFP-<named-entity id="named-entity-510">Parkin</named-entity> overexpressing <i><named-entity id="named-entity-511">p53</named-entity></i><super>−/−</super> HCT116 cells re-transfected with WT <named-entity id="named-entity-512">p53</named-entity> and various mutants of <named-entity id="named-entity-513">p53</named-entity> and treated with 60 μM <named-entity id="named-entity-514">CCCP</named-entity> for 8 (<b>c</b>) and 36 h (<b>d</b>) before the immunostaining of mitochondria with anti-<named-entity id="named-entity-515">TOM20</named-entity> (red) and endogenous poly-ubiquitin with a specific antibody FK-2 (white); original magnification, × 630; scale bar, 20 μm. (<b>e–g</b>) <named-entity id="named-entity-516">Parkin</named-entity> mitochondrial translocation (<b>e</b>) and ubiquitination (<b>f</b>) 8 h after <named-entity id="named-entity-517">CCCP</named-entity> treatment and mitochondrial clearance (<b>g</b>) 36 h after <named-entity id="named-entity-518">CCCP</named-entity> treatment were quantified. A minimum of 300–400 YFP-positive cells were scored in three independent experiments. The single-letter amino-acid code is used. NES indicates nuclear export signal; NLS, nuclear localization signal; ER, endoplasmic reticulum; Ub, ubiquitin. Data are shown as the means±s.d. *<i>P</i>0.05, compared with the corresponding control (two-tailed unpaired Student’s <i>t</i>-test).</p>
|
https://api.sourcedata.io/file.php?figure_id=3339
|
[
{
"ext_dbs": "NCBI gene",
"ext_ids": "22059",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "22059",
"original_type": "gene",
"role": "intervention",
"text": "p53",
"type": "geneprod",
"uniprot_ids": [
"P02340",
"Q3UGQ1",
"Q549C9",
"Q80ZA1"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q9WVS6",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "Parkin",
"type": "geneprod",
"uniprot_ids": [
"Q9WVS6"
]
},
{
"ext_dbs": "Uniprot///Uniprot///Uniprot",
"ext_ids": "Q60931///Q60930///Q60932",
"ext_tax_ids": "10090///10090///10090",
"ext_tax_names": "Mus musculus///Mus musculus///Mus musculus",
"mapping_source": "unknown",
"mapping_status": "unmapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "VDAC",
"type": "geneprod",
"uniprot_ids": []
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "7157",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "7157",
"original_type": "gene",
"role": "intervention",
"text": "p53",
"type": "geneprod",
"uniprot_ids": [
"P04637",
"A0A087WT22",
"A0A087WXZ1",
"A0A087X1Q1",
"H2EHT1",
"K7PPA8",
"Q53GA5"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "7157",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "7157",
"original_type": "gene",
"role": "intervention",
"text": "p53",
"type": "geneprod",
"uniprot_ids": [
"P04637",
"A0A087WT22",
"A0A087WXZ1",
"A0A087X1Q1",
"H2EHT1",
"K7PPA8",
"Q53GA5"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "7157",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "7157",
"original_type": "gene",
"role": "intervention",
"text": "p53",
"type": "geneprod",
"uniprot_ids": [
"P04637",
"A0A087WT22",
"A0A087WXZ1",
"A0A087X1Q1",
"H2EHT1",
"K7PPA8",
"Q53GA5"
]
},
{
"ext_dbs": "Uniprot///Uniprot///Uniprot///Uniprot",
"ext_ids": "P42677///P62987///P0CG48///P0CG47",
"ext_tax_ids": "9606///9606///9606///9606",
"ext_tax_names": "Homo sapiens///Homo sapiens///Homo sapiens///Homo sapiens",
"mapping_source": "unknown",
"mapping_status": "unmapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "poly-ubiquitin",
"type": "geneprod",
"uniprot_ids": []
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q15388",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "TOM20",
"type": "geneprod",
"uniprot_ids": [
"Q15388"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "O60260",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "Parkin",
"type": "geneprod",
"uniprot_ids": [
"O60260"
]
}
] |
|
23917356
|
10.1038/ncomms3308
|
Cytosolic p53 inhibits Parkin-mediated mitophagy and promotes mitochondrial dysfunction in the mouse heart
|
2013
|
f7
|
<p>(<b>a</b>) Representative electron micrographs of the heats of 20-month-old aged mice; original magnification × 5,000; scale bar, 2 μm. The magnified photograph shows an autophagic vacuole containing mitochondria; original magnification, × 12,000; scale bar, 500 nm. (<b>b</b>,<b>c</b>) Mitochondria incorporated into an autophagic vacuole (<b>b</b>) and abnormal mitochondria (<b>c</b>) were quantified blindly from 8–10 images from different fields (original magnification × 5,000) (<i>n</i>=3 per group). (<b>d</b>,<b>e</b>) The sequential state III <named-entity id="named-entity-554">oxygen</named-entity> consumption rate of heart isolated mitochondria was assessed using the Seahorse XF24 Analyser. With the initial presence of 5 μg mitochondria per well, 0.5 mM <named-entity id="named-entity-555">NADH</named-entity> and 4 μM <named-entity id="named-entity-556">FCCP</named-entity>, injections were performed as follows: port A, 50 μl of 20 μM <named-entity id="named-entity-557">rotenone</named-entity> (2 μM final); port B, 55 μl of 100 mM <named-entity id="named-entity-558">succinate</named-entity> (10 mM final); port C, 60 μl of 40 μM <named-entity id="named-entity-559">antimycin A</named-entity> (4 μM final); port D, 65 μl of 100 mM <named-entity id="named-entity-560">ascorbate</named-entity> plus 1 mM <named-entity id="named-entity-561">TMPD</named-entity> (10 μM and 100 μM final, respectively). Representative results of aged littermates are shown (<b>d</b>) and <named-entity id="named-entity-562">oxygen</named-entity> consumption by each complex was calculated from four independent experiments, five replicates per sample, and four samples per experiment (<i>n</i>=8 per group, <b>e</b>). (<b>f</b>) <named-entity id="named-entity-563">NADH</named-entity>-driven <named-entity id="named-entity-564">H<sub>2</sub>O<sub>2</sub></named-entity> production was determined using Amplex Red. Results are shown from five hearts analysed in duplicate. (<b>g</b>) Maximum dP/dt was examined using cardiac catheterization with graded <named-entity id="named-entity-565">dobutamine</named-entity> infusion in WT and <named-entity id="named-entity-566">Parkin</named-entity> Tg aged littermates (<i>n</i>=8 per group). (<b>h</b>) Photographs showing heart sections after SA-<named-entity id="named-entity-567">β-gal</named-entity> staining; original magnification, × 200; scale bar, 40 μm. SA-<named-entity id="named-entity-568">β-gal</named-entity>-positive cells were quantified (<i>n</i>=4 per group). Five images per mouse were taken on brightfield and DAPI staining was used to count the total cell number per section. (<b>i</b>) Real-time PCR assessing the expression of cell cycle inhibitors and proinflammatory cytokines (<i>n</i>=8 per group). (<b>j</b>) Representative immunoblots assessing the expression of cell cycle inhibitors are shown; Data are shown as the means±s.d. *<i>P</i>0.05; **<i>P</i>0.01 (two-tailed unpaired Student’s <i>t</i>-test). (<b>k</b>) Proposed model for mitochondrial compromise in heart failure.</p>
|
https://api.sourcedata.io/file.php?figure_id=3342
|
[
{
"ext_dbs": "NCBI gene",
"ext_ids": "50873",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "50873",
"original_type": "gene",
"role": "intervention",
"text": "Parkin",
"type": "geneprod",
"uniprot_ids": [
"Q9WVS6",
"A0A3B2W489"
]
}
] |
|
10.15252/emmm.201911793
|
Antagonism of interferon signaling by fibroblast growth factors promotes viral replication
|
2020
|
Figure 1
|
<sd-panel> <p><strong>Fig 1: Inhibition of FGFR signaling in keratinocytes promotes IFN and ISG expression</strong></p> <p>(<strong>A,B</strong>) qRT-PCR for different ISGs relative to <em>Rps29</em> using epidermal RNA from 8 week-old (A) or 5 day- or 9 day-old (B) K5-R1/R2 and control (CTRL) mice.</p> <p>(<strong>C</strong>) Confocal microscopy images of epidermal sheets from back skin of K5-R1/R2 and CTRL mice stained for IRF7 and K14, counterstained with DAPI. Arrows denote nuclear IRF7 (red) in basal and suprabasal keratinocytes of K5-R1/R2 mice. The strong red staining of the <em>stratum corneum</em> (sc) is unspecific background and is more pronounced in K5-R1/R2 mice due to the increased thickness of this layer.</p> <p><strong>(D)</strong> qRT-PCR for different ISGs, <em>Ifnb,</em> and <em>Ifnl3</em> relative to <em>Rps29</em> using RNA from freshly isolated, non-cultured keratinocytes of K5-R1/R2 and control (CTRL) mice at P7.</p> <p>(<strong>E</strong>) qRT-PCR for ISGs relative to <em>Rps29</em> using RNA from primary keratinocytes of neonatal CTRL and K5-R1/R2 mice.</p> <p><strong>(F)</strong> qRT-PCR for ISGs and Cre relative to <em>Rps29</em> using RNA from primary keratinocytes of neonatal K5-Cre and wild-type (WT) mice.</p> <p>(<strong>G</strong>) Western blot analysis of total (L) and nuclear (N) lysates from immortalized (imm.) keratinocytes of CTRL and K5-R1/R2 mice for IRF1, IRF7, IRF9, Lamin A/C (nuclear marker, loading control) and GAPDH (cytosolic marker, loading control).</p> <p>(<strong>H</strong>) qRT-PCR for <em>RSAD2</em> and <em>ISG15</em> relative to <em>RPLP0</em> using RNA from HaCaT keratinocytes treated for 48 h with the FGFR inhibitor BGJ398 (3.5 μM) or vehicle in the presence of serum.</p> <p>Data information: Scatter plots show mean +/- S.E.M. Mean expression levels in CTRL mice or cell cultures were set to 1, and mRNA levels relative to this value are shown. In (F) expression levels in K5-Cre mice were set to 1. A: N=10 mice per genotype, B: N=6-14 mice per genotype. C: Representative images of two experiments. Magnification bar: 20 μm. D: N=5 mice per genotype. E, F: N=4-7 cultures (each from a different mouse) per genotype. G: Representative of three experiments. H: N=6-9 per treatment group. *<em>P</em>≤0.05, **<em>P</em>≤0.01, ***<em>P</em>≤0.001, ****<em>P</em>≤0.0001 (Mann-Whitney U test). Exact P-values are provided in Dataset EV2.</p> </sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=34137
|
[
{
"ext_dbs": "Uniprot",
"ext_ids": "P70434",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "IRF7",
"type": "geneprod",
"uniprot_ids": [
"P70434"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P70434",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "IRF7",
"type": "geneprod",
"uniprot_ids": [
"P70434"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q61781",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "K14",
"type": "geneprod",
"uniprot_ids": [
"Q61781"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "15977",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "15977",
"original_type": "gene",
"role": "assayed",
"text": "Ifnb",
"type": "geneprod",
"uniprot_ids": [
"P01575",
"Q0VE17"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "338374",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "338374",
"original_type": "gene",
"role": "assayed",
"text": "Ifnl3",
"type": "geneprod",
"uniprot_ids": [
"Q8CGK6"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "2777477",
"ext_tax_ids": "10678",
"ext_tax_names": "Escherichia virus P1",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "2777477",
"original_type": "gene",
"role": "intervention",
"text": "Cre",
"type": "geneprod",
"uniprot_ids": [
"Q71TG5",
"P06956",
"B3Y8R6"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "2777477",
"ext_tax_ids": "10678",
"ext_tax_names": "Escherichia virus P1",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "2777477",
"original_type": "gene",
"role": "assayed",
"text": "Cre",
"type": "geneprod",
"uniprot_ids": [
"Q71TG5",
"P06956",
"B3Y8R6"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P15314",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "IRF1",
"type": "geneprod",
"uniprot_ids": [
"P15314"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P70434",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "IRF7",
"type": "geneprod",
"uniprot_ids": [
"P70434"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q61179",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "IRF9",
"type": "geneprod",
"uniprot_ids": [
"Q61179"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "9636",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "9636",
"original_type": "gene",
"role": "assayed",
"text": "ISG15",
"type": "geneprod",
"uniprot_ids": [
"P05161"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "91543",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "91543",
"original_type": "gene",
"role": "assayed",
"text": "RSAD2",
"type": "geneprod",
"uniprot_ids": [
"Q8WXG1",
"C9J674"
]
},
{
"ext_dbs": "Uniprot///Uniprot///Uniprot///Uniprot",
"ext_ids": "P22455///P22607///P21802///P11362",
"ext_tax_ids": "9606///9606///9606///9606",
"ext_tax_names": "Homo sapiens///Homo sapiens///Homo sapiens///Homo sapiens",
"mapping_source": "unknown",
"mapping_status": "unmapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "intervention",
"text": "FGFR",
"type": "geneprod",
"uniprot_ids": []
}
] |
||
10.15252/emmm.201911793
|
Antagonism of interferon signaling by fibroblast growth factors promotes viral replication
|
2020
|
Figure 2
|
<sd-panel> <p><strong>Fig 2: FGF7 and FGF10 suppress the IFN response in keratinocytes</strong></p> <p>(<strong>A</strong>) Growth factor-starved primary keratinocytes from WT mice were treated for 3 or 6 h with FGF7 (10 ng/ml) or vehicle (CTRL). RNA samples were analyzed by qRT-PCR for the indicated ISGs relative to <em>Rps29</em>.</p> <p>(<strong>B</strong>) Serum-starved HaCaT keratinocytes were treated for 6 h with FGF7 or FGF10 (each 10 ng/ml). RNA samples were analyzed by qRT-PCR for <em>IRF7 and RSAD2</em> relative to <em>RPLP0</em>.</p> <p>(C) Serum-starved HaCaT keratinocytes were treated for 16 h with FGF7 (10 ng/ml). Protein lysates were analyzed by Western blot for IRF1, IRF3, IRF9 and GAPDH.</p> <p>(<strong>D</strong>) RNA samples from untreated, serum-starved primary keratinocytes from WT and <em>Ifnar1</em>-KO mice were analyzed by qRT-PCR for <em>Irf7</em>, <em>Rsad2</em>, <em>Oasl2</em> and <em>Ifnar1 relative to Rps29.</em></p> <p>(<strong>E</strong>) Growth factor-starved primary keratinocytes from neonatal WT, <em>Ifnar1</em>-KO or <em>Ifnar1</em>/<em>Ifnlr1</em>-KO mice were treated for 24 h with FGF7 (10 ng/ml). RNA samples were analyzed by qRT-PCR for <em>Irf7 relative to Rps29.</em></p> <p>(<strong>F</strong>) HaCaT keratinocytes were transiently transfected with an ISRE-Luciferase reporter construct and starved 24 h after transfection for 9 h. They were then incubated in the presence or absence of FGF7 (10 ng/ml) for 20 h. Lysates were analyzed using a DualGlo Luciferase Assay.</p> <p><strong>(G, H) HaCaT keratinocytes were pre-treated for 2 h with the proteasome inhibitors MG132 (10 μm (G) or epoxomicin (100 nM) (H), followed by a 20h treatment with FGF7</strong> (10 ng/ml) <strong>or vehicle. RNA samples were analyzed by qRT-PCR for <em>IRF7</em> and <em>IRF1</em></strong> relative to <em>RPLP0.</em></p> <p>Data information: Scatter plots show mean +/- S.E.M. Mean expression levels in CTRL cell cultures (not treated with FGF7 or any inhibitor) were set to 1. In (D) and in the left panel of (E) expression levels in wt cells were set to 1, while expression levels in untreated IFN receptor knockout cells were set to 1 in the middle and right panel of (E). A: N=8-11 cultures (each from a different mouse) from four experiments. B: N=3-5 from one experiment. C: Representative of 3 experiments. D, E: N=5-11 cultures (each from a different mouse) from two experiments. The results with <em>Ifnar1</em>-KO mice were reproduced in two additional experiments. F: N=16-18 from 4 experiments. G: Representative of four experiments, N=3 per treatment group for each experiment. H: N=6 per treatment group from two experiments. ns: non-significant, *<em>P</em>≤0.05, **<em>P</em>≤0.01, ***<em>P</em>≤0.001, ****P<0.0001 (Mann-Whitney U test (A, B, D, E, F, H) or t-test for assessment of FGF7 effect (G), with Welch correction for <em>IRF1</em>. Exact P-values are shown in Dataset EV2.</p> </sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=34139
|
[
{
"ext_dbs": "Uniprot",
"ext_ids": "P21781",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "intervention",
"text": "FGF7",
"type": "geneprod",
"uniprot_ids": [
"P21781"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "3665",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "3665",
"original_type": "gene",
"role": "assayed",
"text": "IRF7",
"type": "geneprod",
"uniprot_ids": [
"Q92985",
"B4E1B1",
"M9RSF4"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "91543",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "ncbi_gene",
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||
10.15252/emmm.201911793
|
Antagonism of interferon signaling by fibroblast growth factors promotes viral replication
|
2020
|
Figure 3
|
<sd-panel> <p><strong>Fig 3: FGF7 suppresses IFN-induced ISG expression</strong></p> <p><strong>(A-C)</strong> Serum-starved HaCaT keratinocytes were treated with FGF7 (10 ng/ml (A, C) or different concentrations as indicated (B)) and/or IFN-α (500-1000 U/ml) for 12-16 h. RNA was analyzed by qRT-PCR for ISGs relative to <em>RPLP0</em> (A, B) and protein samples by Western blot for total and pSTAT1 (Y701 and S727), IRF1, IRF9 and RSAD2 and GAPDH (C). The vertical line in the RSAD2 blot indicates a place where the gel was broken. Densitometric quantification of the different blots (N=3) is shown on the right.</p> <p>(<strong>D</strong>) Human primary keratinocytes were starved and treated for 12 h with FGF7 (10 ng/ml) and/or IFN-α (1000 U/ml). RNA samples were analyzed by qRT-PCR for ISGs relative to <em>RPLP0</em>.</p> <p>Data information: Scatter plots show mean +/- S.E.M. Mean expression levels in CTRL cell cultures were set to 1. A: N=5-6 from two independent experiments. B: N=2-3 from one experiment. C: Representative blot from two experiments. The intensities of the bands were used for the quantification (N=3). D: N=6 replicates from two experiments with cells from two donors. ns: non-significant, *<em>P</em>≤0.05, **<em>P</em>≤0.01, ***<em>P</em>≤0.001, ****P<0.0001 (2-way ANOVA with Tukey's multiple comparisons test (A, D) or t test with Welch correction for assessment of FGF7 effect (C)). Exact P-values are shown in Dataset EV2.</p> </sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=34141
|
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||
10.15252/emmm.201911793
|
Antagonism of interferon signaling by fibroblast growth factors promotes viral replication
|
2020
|
Figure 4
|
<sd-panel> <p><strong>Fig 4: FGF7 suppresses poly(I:C)-induced IFN and ISG expression</strong></p> <p>(<strong>A</strong>) Serum-starved HaCaT cells were treated for 24 h with poly(I:C) (5 μg/ml) in the presence or absence of FGF7 (10 ng/ml). RNA samples were analyzed by qRT-PCR for <em>IFNL1</em>, <em>IFNB</em>, <em>RSAD2</em>, <em>IRF1</em>, <em>IRF7</em>, <em>CGAS, TLR3 or DDX58,</em> relative to <em>RPLP0.</em></p> <p>(<strong>B</strong>) Serum-starved HaCaT cells were treated for 18 h with poly(I:C) (5 μg/ml) in the presence or absence of FGF7 (10 ng/ml). Protein lysates were analyzed by Western blot for total and pSTAT1 (Y701 and S727), total and pSTAT2 (Y690), IRF1, IRF3, pIRF3 (S396), IRF9, RIG-1, RSAD2 and GAPDH.</p> <p>Data information: Scatter plots show mean +/- S.E.M. Mean expression levels in cell cultures treated with poly(I:C) only were set to 1, since IFN mRNA levels in non-treated cells are hardly detectable. A: N=6-9 from two experiments. B: Representative blot from two experiments. Quantification of the bands is shown in Figure EV3. **<em>P</em>≤0.01, ***<em>P</em>≤0.001 (2-way ANOVA with Tukey's multiple comparisons test). Exact P-values are shown in Dataset EV2.</p> </sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=34143
|
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] |
||
10.15252/emmm.201911793
|
Antagonism of interferon signaling by fibroblast growth factors promotes viral replication
|
2020
|
Figure 5
|
<sd-panel> <p><strong>Fig 5: FGF7 promotes HSV-1 replication in human keratinocytes</strong></p> <p>(<strong>A-C</strong>) Serum-starved HaCaT cells were infected with HSV-1 (MOI=0.5) in the presence or absence of FGF7 (10 ng/ml) or IFN-α (1000 U/ml). Viral load was determined 24 h post infection (hpi) by qPCR for the HSV-1 <em>Glyc-B</em> gene relative to the human β-actin gene (<em>ACTB</em>) (A) or by HSV-1 Glyc-D immunofluorescence (red) and DAPI counterstaining (blue) (B). (C) Transmission microscopy images of HaCaT cells 48 h post infection (hpi).</p> <p>(<strong>D, E</strong>) Serum-starved HaCaT cells (D) or human primary keratinocytes (HPK, from two donors) (E) were infected with HSV-1 (MOI=0.5) in the presence or absence of FGF7 at the indicated concentrations. Virus load was determined by qPCR for HSV-1 <em>Glyc-B</em> relative to <em>ACTB</em> 24 hpi.</p> <p>(<strong>F</strong>) Serum-starved HaCaT cells were infected with HSV-1 (MOI=0.5) in the presence or absence of FGF7, FGF10 or FGF2 (10 ng/ml). DNA samples were analyzed by qPCR for <em>Glyc-D</em> DNA relative to <em>ACTB</em> and protein lysates were analyzed by Western blot for Glyc-D and vinculin 10 hpi.</p> <p>(<strong>G</strong>) Epidermal sheets from tail skin, infected <em>ex vivo</em> with HSV-1 (MOI = 2) +/- FGF7 (10 ng/ml), were stained 48 hpi for Glyc-D (red) using DAPI as counterstain (blue). The infected area (red staining) was measured using Image J software. Data are expressed as A.U. = arbitrary unit. Background staining of hairs was subtracted manually.</p> <p>(<strong>H</strong>) Serum-starved HaCaT cells were infected with HSV-1 in the presence or absence of FGF7 (10 ng/ml) or IFN-α (1000 U/ml). Viral load was determined 24 hpi by qPCR for the HSV-1 <em>Glyc-B</em> gene relative to <em>ACTB</em> or by Western blot for the viral protein Glyc-D and GAPDH.</p> <p>(<strong>I</strong>) Serum-starved HaCaT cells were infected with HSV-1 (MOI = 0.5). Four hours hpi, infected cells were washed and incubated in fresh serum-free medium containing FGF7 (10 ng/ml). Viral load was measured 8 h later by qPCR for <em>Glyc-B</em> relative to <em>ACTB</em>.</p> <p>(<strong>J</strong>) Serum-starved HaCaT keratinocytes were treated for 6 h with FGF7 (10 ng/ml). RNA samples were analyzed by qRT-PCR for <em>NECT1</em> (encoding nectin-1) relative to <em>RPLP0</em>.</p> <p>Data information: Scatter plots show mean +/- S.E.M. In (A), and (D-I) mean viral DNA levels or stained area in HSV-1-infected, but non-treated cells were set to 1. In (J) mean expression levels in CTRL cell cultures were set to 1. A: N=16-24 from four independent experiments. B, C: Representative pictures are shown. D: N=6 from one experiment. E: N=6 from two experiments and two donors. F: N=4 from two experiments. The Western blot is a representative of two experiments. G: N=16-24 measured areas from 8 mice from 4 experiments. H (scatter plot): N=6 from two experiments. The Western blot is a representative of two experiments. I: N=8 mice from two experiments. J: N=6 from 2 experiments. *<em>P</em>≤0.05, **<em>P</em>≤0.01, ****<em>P</em>≤0.0001 (Mann-Whitney U test). Exact P-values are shown in Dataset EV2. Magnification bars: 200 μm (B) or 80 μm (C) and 800 µm (G).</p> </sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=34144
|
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||
10.15252/emmm.201911793
|
Antagonism of interferon signaling by fibroblast growth factors promotes viral replication
|
2020
|
Figure 6
|
<sd-panel> <p><strong>Fig 6: FGF7 suppresses virus-induced ISG expression and stimulates replication of different viruses in keratinocytes</strong></p> <p>(<strong>A-E</strong>) Serum-starved HaCaT cells were infected with HSV-1 (MOI=0.5) +/- FGF7 (10 ng/ml), added at the indicated time points (A). 12 h after infection, RNA samples were analyzed by qRT-PCR for <em>RSAD2</em>, <em>IRF7</em> and <em>IFNL2</em> relative to <em>RPLP0</em> (B), DNA samples were analyzed by qPCR for <em>Glyc-B</em> DNA relative to <em>ACTB</em> (C), and protein lysates were analyzed by Western blot for Glyc-D, total and phosphorylated STAT1 (Y701), STAT2 and IRF3, for IRF1, IRF7, IRF9 and RSAD2 and for GAPDH or vinculin (loading controls) (E). Quantification of the Glyc-D, RSAD2, IRF1, IRF7, IRF9 and STAT2 band intensity relative to GAPDH is shown on the right hand side. (D) shows mean <em>Glyc-B</em> DNA and RSAD2, IRF7 and IFNL2 mRNA levels (based on results shown in Fig. 6B and C) in virus-infected cells treated for different periods with FGF7.</p> <p>(<strong>F</strong>) HaCaT cells were infected with LCMV in the presence or absence of FGF7 (10 ng/ml) or IFN-α (1000 U/ml) and analyzed for LCMV nucleoprotein (NP) by flow cytometry 24 hpi. Arbitrary units are shown.</p> <p>(<strong>G, H</strong>) HaCaT cells were infected with ZIKV strains 976 (Uganda isolate) (MOI = 0.1) or PF13/251013-18 (French Polynesia isolate) (MOI = 20) and treated 2 hpi with FGF7 (20 ng/ml) or vehicle (CTRL). Immunofluorescence staining for the ZIKV envelope protein and quantification of the percentage of cells expressing the ZIKV envelope protein (G) and qRT-PCR analysis of RNA samples for ZIKV RNA (H) 48 hpi is shown.</p> <p>(<strong>I, J</strong>) HaCaT cells were infected with the ZIKV PF13/251013-18 (MOI = 20) in the presence or absence of FGF7 (20 ng/ml). RNA samples were analyzed by qRT-PCR for <em>OAS1</em> and <em>MxA</em> relative to <em>RPLP0</em> 72 hpi.</p> <p>Data information: Scatter plots show mean +/- S.E.M. In (B-H and J) results obtained with virus-infected, but non-treated cells were set to 1; in (I) mean expression levels in non-infected cell cultures were set to 1. B: N=4-5 from 2 experiments. C: N=4 from 2 experiments. E: Representative blots of two experiments. F: N=5-6 from two experiments. G, H: N=4 from one experiment. I, J: N=4-8 from two experiments. Magnification bar in (G): 40 μm. *<em>P</em>≤0.05, **<em>P</em>≤0.01, ***<em>P</em>≤0.001 (Mann-Whitney U test). Exact P-values are provided in Dataset EV2.</p> </sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=34145
|
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},
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]
},
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},
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},
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]
},
{
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},
{
"ext_dbs": "Uniprot",
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]
},
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},
{
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},
{
"ext_dbs": "Uniprot",
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]
},
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"ext_ids": "Q91KX7",
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]
},
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"ext_ids": "P21781",
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},
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},
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"ext_ids": "4599",
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"ext_tax_names": "Homo sapiens",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "4599",
"original_type": "gene",
"role": "assayed",
"text": "MxA",
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"uniprot_ids": [
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"H9KVC7"
]
},
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"ext_ids": "4938",
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"uniprot_ids": [
"P00973",
"A0A6Q8PHR1",
"A0A7P0T8F9",
"A0A7P0T9Q4",
"A0A7P0Z4N8",
"H0YIB8"
]
},
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"ext_ids": "P21781",
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"ext_tax_names": "Homo sapiens",
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]
}
] |
||
10.15252/emmm.201911793
|
Antagonism of interferon signaling by fibroblast growth factors promotes viral replication
|
2020
|
Figure 7
|
<sd-panel> <p><strong>Fig 7: Inhibition of FGFR signaling blocks HSV-1 replication</strong></p> <p>(<strong>A</strong>) Serum-starved HaCaT cells were infected with HSV-1 (MOI = 0.5) in the presence or absence of FGF7 (10 ng/ml) and the FGFR kinase inhibitors AZD4547 (1 μM) or BGJ398 (3.5 μM). DNA and protein lysates were analyzed by qPCR for <em>Glyc-B</em> relative to <em>ACTB</em> or by Western blot for Glyc-D and GAPDH, respectively, 16 hpi.</p> <p>(<strong>B, C</strong>) HaCaT cells were cultured in DMEM/10% FCS (B) or DMEM/5% FCS (C) and infected with HSV-1 (MOI=0.5) in the presence or absence of AZD45347 (1 μM) and/or BGJ398 (3.5 μM). Viral load was determined by qPCR for <em>Glyc-D</em> relative to <em>ACTB</em> (B) or by measurement of viral titers (plaque forming units (PFU)) 14 hpi (C).</p> <p>(<strong>D, E</strong>) Adult C57BL/6 wild-type (D) or K5-R1/R2 mice and respective controls (E) were infected subcutaneously with HSV-1 (MOI = 10). RNA from infected skin was analyzed by qRT-PCR for <em>Fgf7</em> relative to <em>Rps29</em> (D) and DNA was analyzed by qPCR for <em>ICP0</em>, normalized to the host gene <em>Tbx15</em> 48 hpi (E).</p> <p>Data information: Scatter plots show mean +/- S.E.M. In (A, B) mean viral DNA levels in HSV-1-infected, but non-treated cells were set to 1. In (C) absolute PFU/ml cell lysate is shown. In (D) mean expression in non-infected mice (vehicle-injected) were set to 1, and in (E) mean <em>ICP0</em> DNA levels in Ctrl mice were set to 1. A: N=5-6 from two experiments. B: N=12-13 from 4 experiments. C: N=6 from two experiments. D: N=9-10 infected mouse skin spots from two experiments. F: N=20-24 infected mouse skin spots from two experiments. *<em>P</em>≤0.05, **<em>P</em>≤0.01, ****<em>P</em><0.0001 (Mann-Whitney U test). Exact P-values are provided in Dataset EV2.</p> </sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=34146
|
[
{
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"ext_ids": "24271469",
"ext_tax_ids": "10298",
"ext_tax_names": "Human alphaherpesvirus 1",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "24271469",
"original_type": "gene",
"role": "assayed",
"text": "Glyc-B",
"type": "geneprod",
"uniprot_ids": [
"F8RFB2",
"P10211",
"A0A181ZGI5"
]
},
{
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"ext_ids": "P21781",
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"ext_tax_names": "Homo sapiens",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "intervention",
"text": "FGF7",
"type": "geneprod",
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"P21781"
]
},
{
"ext_dbs": "Uniprot///Uniprot///Uniprot///Uniprot",
"ext_ids": "P22455///P22607///P21802///P11362",
"ext_tax_ids": "9606///9606///9606///9606",
"ext_tax_names": "Homo sapiens///Homo sapiens///Homo sapiens///Homo sapiens",
"mapping_source": "unknown",
"mapping_status": "unmapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "intervention",
"text": "FGFR",
"type": "geneprod",
"uniprot_ids": []
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "14178",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
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"mapping_status": "mapped",
"ncbi_gene_id": "14178",
"original_type": "gene",
"role": "assayed",
"text": "Fgf7",
"type": "geneprod",
"uniprot_ids": [
"P36363",
"Q544I6"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "2703389",
"ext_tax_ids": "10298",
"ext_tax_names": "Human alphaherpesvirus 1",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "2703389",
"original_type": "gene",
"role": "assayed",
"text": "ICP0",
"type": "geneprod",
"uniprot_ids": [
"A0A7S4U4A1",
"G8HBH2"
]
}
] |
||
10.15252/emmm.202012497
|
Mycobacterium tuberculosis Rv2626c-derived peptide as a therapeutic agent for sepsis
|
2020
|
Figure 1
|
<sd-panel> <p><strong>Figure 1. Effects of rRv2626c on inflammatory response in macrophages.</strong></p> <p>(<strong>A</strong>) Bacterially purified 6xHis-rRv2626c and analyzed by Coomassie blue staining (left) or immuno blotting (IB) with αHis (right). (<strong>B</strong>) BMDMs were incubated with rRv2626c for the indicated times and then cell viability measured with MTT assay. (<strong>C</strong>) Fluorescence confocal images showing in BMDMs treated with Rv2626c (2.5 μg/ml) for 30 min, fixed, immunostained with antibodies for His (Alexa 488) and DAPI. Scale bar, 10 μm. (<strong>D</strong> and <strong>E</strong>) BMDMs from WT mice were treated with LPS (100 ng/ml) or rRv2626c for indicated times (<strong>D</strong>). BMDMs from WT, TLR2<sup>-/-</sup>, TLR4<sup>-/-</sup>, MyD88<sup>-/-</sup>, TRIF<sup>-/-</sup>, IRAK1<sup>-/-</sup>, TRAF6<sup>-/-</sup>, TBK1<sup>-/-</sup> mice were treated with 2.5 μg/ml rRv2626c or rVector for 18 h (<strong>E</strong>). Culture supernatants were harvested, and the levels of TNF-α, IL-6, IL-12p40, and IL-10 were measured by ELISA. (<strong>F</strong>) BMDMs were treated with 2.5 μg/ml rRv2626c for 1 h, harvested and then subjected to IB for αIκBα and His. αActin was used as a loading control. Data shown are representative of three independent experiments with similar results (<strong>A, C, E</strong>). Data shown are the means ± SD of five experiments (<strong>B, D, E</strong>). Statistical significance was determined by Student's <em>t</em>-test with Bonferroni adjustment (***P < 0.001) compared with rVector.</p> </sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=36905
|
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"text": "TRAF6",
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"mapping_source": "direct",
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"role": "assayed",
"text": "IL-10",
"type": "geneprod",
"uniprot_ids": [
"P18893"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P43432",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "IL-12p40",
"type": "geneprod",
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"P43432"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P08505",
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"ext_tax_names": "Mus musculus",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "IL-6",
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"uniprot_ids": [
"P08505"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P06804",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "TNF-α",
"type": "geneprod",
"uniprot_ids": [
"P06804"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P9WJA3",
"ext_tax_ids": "83332",
"ext_tax_names": "Mycobacterium tuberculosis H37Rv",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "intervention",
"text": "Rv2626c",
"type": "geneprod",
"uniprot_ids": [
"P9WJA3"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q9Z1E3",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "IκBα",
"type": "geneprod",
"uniprot_ids": [
"Q9Z1E3"
]
}
] |
||
10.15252/emmm.202012497
|
Mycobacterium tuberculosis Rv2626c-derived peptide as a therapeutic agent for sepsis
|
2020
|
Figure 2
|
<sd-panel> <p><strong>Figure 2. TLR-mediated inflammatory responses in macrophages are negatively regulated by rRv2626c.</strong></p> <p>BMDMs were pretreated with 2.5 μg/ml rRv2626c or rVector for 1 h, and stimulated with 100 ng/ml LPS (<strong>A</strong> and <strong>C</strong>) or Pam<sub>2</sub>CSK<sub>4</sub> (<strong>B</strong>) for indicated times. (<strong>A</strong> and <strong>B</strong>) Culture supernatants were harvested, and the levels of TNF-α, IL-6, IL-12p40, and IL-10 were measured by ELISA. (<strong>C</strong>) Cells were harvested and then subjected to IB for the phosphorylated forms of AKT, MAPK (ERK, p38, JNK), IκBα, total forms of IκBα. αActin was used as a loading control (left). The densitometric values were calculated from the ratios of protein levels relative to actin (right). Data shown are the means ± SD of three experiments (<strong>A</strong> and <strong>B</strong>). Data shown are representative of five independent experiments with similar results (<strong>C</strong>). Statistical significance was determined by Student's <em>t</em>-test with Bonferroni adjustment (*, P < 0.05; **, P < 0.01; ***, P < 0.001) compared with rVector.</p> </sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=36906
|
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"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "intervention",
"text": "Rv2626c",
"type": "geneprod",
"uniprot_ids": [
"P9WJA3"
]
},
{
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"ext_tax_names": "Mus musculus",
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"ncbi_gene_id": null,
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"text": "IL-10",
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},
{
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"P43432"
]
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"mapping_source": "direct",
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"P9WJA3"
]
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"ext_ids": "P18893",
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"ext_tax_names": "Mus musculus",
"mapping_source": "direct",
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"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "IL-10",
"type": "geneprod",
"uniprot_ids": [
"P18893"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P43432",
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"ext_tax_names": "Mus musculus",
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"mapping_status": "mapped",
"ncbi_gene_id": null,
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"P43432"
]
},
{
"ext_dbs": "Uniprot",
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"ext_tax_names": "Mus musculus",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "IL-6",
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"uniprot_ids": [
"P08505"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P06804",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "TNF-α",
"type": "geneprod",
"uniprot_ids": [
"P06804"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P31749",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "AKT",
"type": "geneprod",
"uniprot_ids": [
"P31749"
]
},
{
"ext_dbs": "Uniprot///Uniprot///Uniprot",
"ext_ids": "Q61831///Q9WTU6///Q91Y86",
"ext_tax_ids": "10090///10090///10090",
"ext_tax_names": "Mus musculus///Mus musculus///Mus musculus",
"mapping_source": "unknown",
"mapping_status": "unmapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "JNK",
"type": "geneprod",
"uniprot_ids": []
},
{
"ext_dbs": "Uniprot///Uniprot///Uniprot///Uniprot",
"ext_ids": "P47811///Q9Z1B7///O08911///Q9WUI1",
"ext_tax_ids": "10090///10090///10090///10090",
"ext_tax_names": "Mus musculus///Mus musculus///Mus musculus///Mus musculus",
"mapping_source": "unknown",
"mapping_status": "unmapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "p38",
"type": "geneprod",
"uniprot_ids": []
},
{
"ext_dbs": "Uniprot///Uniprot",
"ext_ids": "Q63844///P63085",
"ext_tax_ids": "10090///10090",
"ext_tax_names": "Mus musculus///Mus musculus",
"mapping_source": "unknown",
"mapping_status": "unmapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "ERK",
"type": "geneprod",
"uniprot_ids": []
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q9Z1E3",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "IκBα",
"type": "geneprod",
"uniprot_ids": [
"Q9Z1E3"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q9Z1E3",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "IκBα",
"type": "geneprod",
"uniprot_ids": [
"Q9Z1E3"
]
}
] |
||
10.15252/emmm.202012497
|
Mycobacterium tuberculosis Rv2626c-derived peptide as a therapeutic agent for sepsis
|
2020
|
Figure 3
|
<sd-panel> <p><strong>Figure 3. TRAF6 interacts with Rv2626c.</strong></p> <p>(<strong>A</strong>) Identification of TLR2, IRAK1, RIP1, TRAF6, MAPK11 and TOLLIP as endogenous binding partners of rRv2626c. THP-1 cell lysates were incubated with His tagged-rRv2626c or rVector and then IP with His-agarose beads. Binding partners were confirmed by silver staining and mass spectrometric analysis. The red-colored letters indicate the peptides identified from mass spectrometry analysis. (<strong>B</strong>) 293T cells were co-transfected with Flag-TRAF6 and Myc-Rv2626c and IP with αFlag or αMyc. WCLs were used for IB with αFlag, αMyc or αActin. (<strong>C</strong>) THP-1 and BMDMs were stimulated with rRv2626c (2.5 μg/ml) for the indicated times, followed by IP with αHis (up) or αTRAF6 (down) and IB with αTRAF6, αHis, and αActin. (<strong>D</strong>) Immunostaining of BMDMs treated with 2.5 μg/ml rRv2626c for 30 min. and then immunolabeled with antibody to His-rRv2626c (Alexa Fluor 488) or TRAF6 (Alexa Fluor 568). DAPI (blue) stained nuclei. Scale bar, 10 μm. The data are representative of five independent experiments with similar results (<strong>A</strong>-<strong>D</strong>).</p> </sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=36907
|
[
{
"ext_dbs": "Uniprot",
"ext_ids": "P9WJA3",
"ext_tax_ids": "83332",
"ext_tax_names": "Mycobacterium tuberculosis H37Rv",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "Rv2626c",
"type": "geneprod",
"uniprot_ids": [
"P9WJA3"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P9WJA3",
"ext_tax_ids": "83332",
"ext_tax_names": "Mycobacterium tuberculosis H37Rv",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "intervention",
"text": "Rv2626c",
"type": "geneprod",
"uniprot_ids": [
"P9WJA3"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P51617",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "IRAK1",
"type": "geneprod",
"uniprot_ids": [
"P51617"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q15759",
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"ext_tax_names": "Homo sapiens",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "MAPK11",
"type": "geneprod",
"uniprot_ids": [
"Q15759"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q13546",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "RIP1",
"type": "geneprod",
"uniprot_ids": [
"Q13546"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "O60603",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "TLR2",
"type": "geneprod",
"uniprot_ids": [
"O60603"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q9H0E2",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "TOLLIP",
"type": "geneprod",
"uniprot_ids": [
"Q9H0E2"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P70196",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "TRAF6",
"type": "geneprod",
"uniprot_ids": [
"P70196"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "22034",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "22034",
"original_type": "gene",
"role": "intervention",
"text": "TRAF6",
"type": "geneprod",
"uniprot_ids": [
"P70196"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P9WJA3",
"ext_tax_ids": "83332",
"ext_tax_names": "Mycobacterium tuberculosis H37Rv",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "intervention",
"text": "Rv2626c",
"type": "geneprod",
"uniprot_ids": [
"P9WJA3"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P70196",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "TRAF6",
"type": "geneprod",
"uniprot_ids": [
"P70196"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P70196",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "TRAF6",
"type": "geneprod",
"uniprot_ids": [
"P70196"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P9WJA3",
"ext_tax_ids": "83332",
"ext_tax_names": "Mycobacterium tuberculosis H37Rv",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "Rv2626c",
"type": "geneprod",
"uniprot_ids": [
"P9WJA3"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P70196",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "TRAF6",
"type": "geneprod",
"uniprot_ids": [
"P70196"
]
}
] |
||
10.15252/emmm.202012497
|
Mycobacterium tuberculosis Rv2626c-derived peptide as a therapeutic agent for sepsis
|
2020
|
Figure 4
|
<sd-panel> <p><strong>Figure 4. Rv2626c associates with N-terminal region of TRAF6 through CBS2 domain and attenuates E3 ubiquitin ligase activity of TRAF6.</strong></p> <p>(<strong>A</strong>) Schematic diagram of the structures of Rv2626c (up). 293T cells were co-transfected with Flag-TRAF6 together with GST-vector or GST-Rv2626c and its mutant constructs, subjected to GST pulldown, followed by IB with αFlag. WCLs were used for IB with αGST, αFlag or αActin (down). (<strong>B</strong>) At 12 hr post-transfection with mammalian Myc-Rv2626c constructs together with Flag-TRAF6 and 293T cells treated with several Tat-CBS2 peptide for 12 h (10 µM) for 6h, subjected to IP with αMyc, followed by IB with αFlag. WCLs were used for IB with αMyc, αFlag or αActin. (<strong>C</strong>) Schematic diagram of the structures of TRAF6 (up). 293T cells were co-transfected with Myc-Rv2626c together with GST-vector or GST-TRAF6 and its mutant constructs, subjected to GST pulldown, followed by IB with αMyc. WCLs were used for IB with αGST, αMyc or αActin (down). (<strong>D</strong>) 293T cells were co-transfected with Flag-TRAF6, Myc-Rv2626c as indicated doses and HA-ubiquitin (left), HA-K48-linked ubiquitin (middle), HA-K63-linked ubiquitin (right)</p> <p>and then IP with αFlag, followed by IB with αHA. WCLs were used for IB with αFlag, αMyc, or αActin. (<strong>E</strong>) BMDMs were pretreated with 2.5 μg/ml rRv2626c for 1 h, and stimulated with 100 ng/ml LPS for 30 min, followed by IP with αTRAF6, IB with ubiquitin, K48-linked ubiquitin, or K63-linked ubiquitin. WCLs were used for IB with αHis, αTRAF6, or αActin. The data are representative of five independent experiments with similar results (<strong>A</strong>-<strong>E</strong>).</p> </sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=36908
|
[
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"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "22034",
"original_type": "gene",
"role": "intervention",
"text": "TRAF6",
"type": "geneprod",
"uniprot_ids": [
"P70196"
]
},
{
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"ext_ids": "P9WJA3",
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"ext_tax_names": "Mycobacterium tuberculosis H37Rv",
"mapping_source": "direct",
"mapping_status": "mapped",
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]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "A6MI22",
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"ext_tax_names": "Human immunodeficiency virus 1",
"mapping_source": "direct",
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"text": "Tat",
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{
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"text": "TRAF6",
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]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P9WJA3",
"ext_tax_ids": "83332",
"ext_tax_names": "Mycobacterium tuberculosis H37Rv",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "intervention",
"text": "Rv2626c",
"type": "geneprod",
"uniprot_ids": [
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]
},
{
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},
{
"ext_dbs": "Uniprot",
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"ncbi_gene_id": null,
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] |
||
10.15252/emmm.202012497
|
Mycobacterium tuberculosis Rv2626c-derived peptide as a therapeutic agent for sepsis
|
2020
|
Figure 5
|
<sd-panel> <p><strong>Figure 5. Design and expression of Tuftsin-conjugated Rv2626c peptide-based protein.</strong></p> <p>(<strong>A</strong>) Schematic in design of rRv2626c and its mutants. (<strong>B</strong>) Bacterially purified 6xHis-rRv2626c and analyzed by Coomassie blue staining (left) or immuno blotting (IB) with αHis (right). (<strong>C</strong>) BMDMs were incubated with rRv2626c-CA, rRv2626c-DN, or rVehicle for the indicated times and then cell viability measured with MTT assay. (<strong>D</strong>) BMDMs were pretreated with rRv2626c-WT, rRv2626c-CA, or rRv2626c-DN for 1 h, and stimulated with 100 ng/ml LPS for 18 h. Culture supernatants were harvested, and the levels of TNF-α, IL-6, IL-12p40, and IL-10 were measured by ELISA. (<strong>E</strong>) Myc-Rv2626c-expressing Raw264.7 or THP-1 cells were pretreated with rRv2626c-WT (2.5 μg/ml), rRv2626c-CA (10 ng/ml), rRv2626c-DN (2.5 μg/ml), for 1 h, and stimulated with 100 ng/ml LPS for 30 min, followed by IP with αMyc or αTRAF6, IB with αMyc and ubiquitin. WCLs were used for IB with αMyc, αTRAF6, αHis or αActin. The data are representative of five independent experiments with similar results (<strong>B</strong> and <strong>E</strong>). Data shown are the means ± SD of three experiments (<strong>C</strong> and <strong>D</strong>). SC, solvent control (PBS).</p> </sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=36909
|
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] |
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