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10.15252/embr.201948483
|
MicroRNA-195 controls MICU1 expression and tumor growth in ovarian cancer
|
2020
|
Figure 4
|
<sd-panel> <h2 id="figure-4.-mir-195-regulates-clonal-growth-by-targeting-micu1">Figure 4. miR-195 regulates clonal growth by targeting MICU1</h2> <p><strong>(A&B)</strong> Stable cell lines for CP20 and OVCAR4 expressing GFP-miR-195 or non-target miR-GFP were generated using lentiviral mediated transduction and were selected using puromycin; representative images are shown. Scale bars, 50 µm.</p> <p><strong>(C)</strong> Relative miR-195 expression was measured using RT-qPCR in stable cell lines, normalized with U6. Mean ± SEM; n=3, Biological repeats. *P<0.05, Student's t-test.</p> <p><strong>(D)</strong> CP20 and OVCAR4 stable cell lines were transfected as either empty vector (EV) or pLYS1-MICU1-Flag (MICU1) and relative MICU1 levels were evaluated using immunoblotting.</p> <p><strong>(E, F)</strong> CP20 and OVCAR4 stable cell lines transfected as in (D) were counted and re-plated for anchorage-dependent <strong>(E)</strong> and independent clonal growth <strong>(F).</strong> Quantification compared to the miR-CTL stable cells transfected with EV is shown. Mean ± SD; n=3, Biological repeats. *P<0.05 when comparing with miR-CTL, # P<0.05 when comparing with miR-195 by Student's t-test.</p> </sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=34626
|
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"text": "MICU1",
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"Q9BPX6",
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"Q9BPX6",
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"text": "MICU1",
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"Q9BPX6"
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||
10.15252/embr.201948483
|
MicroRNA-195 controls MICU1 expression and tumor growth in ovarian cancer
|
2020
|
Figure 5
|
<sd-panel> <p><strong>Figure 5. miR-195 expression determines <em>in vivo</em> tumor growth</strong></p> <p><strong>(A)</strong> Female athymic mice were injected subcutaneously with either CP20 GFP-miR-CTL or CP20- GFP-miR-195 cells. Mice injected with the miR-195 expressing cells (miR-195) had significantly smaller tumor volumes than control mice (miR-CTL). Data are mean ± S.D, n=10. *P<0.05, Student's t-test.</p> <p><strong>(B)</strong> Tumor doubling time was significantly longer in the mice injected with miR-195 expressing cells than in control mice. Data are mean ± S.D, n=10. *P<0.05, Student's t-test.</p> <p><strong>(C)</strong> Percent survival based on humane endpoint criteria, was calculated by the Kaplan-Meier method and P values determined by Log Rank Test.</p> <p><strong>(D)</strong> Four tumor samples from each group were analyzed for the expression of MICU1, pPDH, PDH, PARP, and BCL2 using immunoblotting. α tubulin was used as the loading control.</p> <p>(<strong>E, F</strong>) Representative histology images of tumors from mice xenografts of CP20-GPF-miR-CTL (miR-CTL) or CP20-GPF-miR-195 (miR-195) cells with Ki67 expression (Scale Bar = 50 μm) <strong>(E)</strong>, CD31 positive vessels (Scale Bar = 100 μm) and TUNEL staining (Scale Bar = 50 μm) and <strong>(F)</strong> graph showing quantification of each marker in tumors from the experimental mice; values are mean ±SD, n=10, *P<0.05, Student's t-test.</p> <p><strong>(G)</strong> Female athymic mice were injected subcutaneously with either CP20 GFP-miR-CTL or CP20- GFP-miR-195 or CP20- GFP-miR-195 + MICU1 cells and tumor volume was measured, values are mean ±SE, n=10. *P<0.05, Student's t-test.</p> <p><strong><br></strong></p> <p><strong>FIGURE LEGENDS</strong></p> </sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=34628
|
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||
23933751
|
10.1038/nn.3489
|
The Parkinson's disease–linked proteins Fbxo7 and Parkin interact to mediate mitophagy
|
2013
|
figf1
|
<p>(<b>a</b>) Diagram of Fbxo7 isoforms 1 and 2, showing the location of functional domains and the Parkinson's disease–associated mutations. (<b>b</b>) Coimmuno-precipitation (IP) of Fbxo7-HA and Flag-Parkin in whole-cell lysates from U2OS cells over-expressing both proteins. IB, immunoblot. Molecular mass markers are in kilodaltons. (<b>c</b>) Coimmunoprecipitation of endogenous Fbxo7 with Flag-Parkin in HEK293T cells transfected with Flag-Parkin or a control protein (EGFP). (<b>d</b>) Flag immunoprecipitation was repeated in U2OS cells transfected with Flag-Parkin and either full-length (1–522) T7-Fbxo7 or an N-terminal truncation lacking the Ubl domain (89–522). (<b>e</b>) As in <b>d</b>, using lysates from U2OS cells expressing Flag-Parkin and T7-Fbxo7, either full length (1–522) or a C-terminal deletion of the proline-rich region (1–398). * indicates IgG heavy chain. (<b>f</b>) <i>In vitro</i>–translated Flag-Parkin was incubated with bacterially expressed GST or GST fused to the Fbxo7 Ubl domain (1–88) immobilized on glutathione beads. Bead-bound proteins and inputs were analyzed by immunoblotting with anti-Parkin antibodies. (<b>g</b>) The disease-causing mutation T22M interferes with Fbxo7's interaction with Parkin. Coimmunoprecipitation was performed as in <b>b</b> using lysates from U2OS cells expressing Flag-Parkin and WT or T22M Fbxo7-HA. (<b>h</b>) Coimmunoprecipitation of Flag-Parkin and Fbxo7 in the mitochondrial and cytosolic fractions of HEK293T cells overexpressing both proteins. CxVα and GAPDH are markers for mitochondria and cytoplasm, respectively. All western blots are representative of experiments performed at least three times. Full-length blots are presented in <sir rid="S1" refobjid="nn.3489-S1">Supplementary Figure 9</sir>.</p>
|
https://api.sourcedata.io/file.php?figure_id=3709
|
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]
}
] |
|
23933751
|
10.1038/nn.3489
|
The Parkinson's disease–linked proteins Fbxo7 and Parkin interact to mediate mitophagy
|
2013
|
figf2
|
<p>(<b>a</b>) Fbxo7 relocates from the cytosolic to the mitochondrial fractions of HEK293T cells treated with CCCP (10 μM). IB, immunoblot. (<b>b</b>) Fbxo7 levels are increased in Flag-Parkin complexes immunoprecipitated (IP) from the mitochondrial fraction of HEK293T cells transfected with Flag-Parkin and untagged Fbxo7 following 1 or 3 h treatment with CCCP (10 μM). (<b>c</b>) Parkin localization at the mitochondria was assessed by immunocytochemistry in SH-SY5Y cells transfected with Flag-Parkin plus scrambled (scr) or Fbxo7 siRNA, following 1 or 3 h treatment with CCCP (10 μM). Cells were scored visually for the colocalization of Flag-Parkin with HtrA2, a mitochondrial marker. Images are displayed for cells transfected as indicated, following 0 or 3 h CCCP treatment. For corresponding images at 1 h treatment, see <sir rid="S1" refobjid="nn.3489-S1">Supplementary Figure 2c</sir>. Nuclei (blue) were stained with DAPI. Scale bars, 10 μm. (<b>d</b>) Loss of Flag-Parkin translocation upon Fbxo7 silencing is rescued by WT and R378G Fbxo7, but not by T22M Fbxo7, by R498X Fbxo7 or by Fbxo7 in which the mitochondrial targeting sequence is mutated (mt-MTS). For <b>c</b>,<b>d</b>, histograms indicate the percentage of cells in which Parkin localized to the mitochondria. Data are presented as mean of three experiments ± s.e.m. *<i>P</i> 0.05, **<i>P</i> 0.01 compared to cells transfected with Flag-Parkin plus Fbxo7 siRNA. (<b>e</b>) T7-tagged WT Fbxo7 localizes to both cytosolic (C) and mitochondrial (M) fractions of transfected HEK293T cells, but MTS mutant (mt-MTS) Fbxo7 localizes only to the cytosolic fraction. CxVα and PDHE1α are mitochondrial markers; GAPDH is a cytosolic marker. All western blots are representative of experiments performed at least three times. Full-length blots are presented in <sir rid="S1" refobjid="nn.3489-S1">Supplementary Figure 9</sir>.</p>
|
https://api.sourcedata.io/file.php?figure_id=3710
|
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] |
|
23933751
|
10.1038/nn.3489
|
The Parkinson's disease–linked proteins Fbxo7 and Parkin interact to mediate mitophagy
|
2013
|
figf3
|
<p>(<b>a</b>,<b>b</b>) Overexpression of Fbxo7 by <i>da-GAL4</i> (<i>da>Fbxo7</i>) suppresses climbing (<b>a</b>) and flight (<b>b</b>) defects of <i>parkin</i> mutants. (<b>c</b>) Overexpression of Fbxo7 also suppresses dopaminergic (DA) neurodegeneration <i>parkin</i> mutants. (<b>d</b>–<b>f</b>) Top and middle panels, toluidine blue–stained sections of adult thorax. Bottom panels, transmission electron micrographs of muscle. Fbxo7 overexpression suppresses muscle degeneration and mitochondrial disruption in <i>parkin</i> mutants. Scale bars: 200 μm (top), 20 μm (middle), 2 μm (bottom). Images are representative of three animals per genotype. (<b>g</b>,<b>h</b>) Overexpression of Fbxo7 pathogenic mutants, mt-MTS or isoform 2 by <i>da-GAL4</i> fails to rescue climbing (<b>g</b>) and flight (<b>h</b>) deficits in <i>parkin</i> mutants. Control genotype is <i>park</i><super><i>25</i></super>/+<i>; da-GAL4</i>/+. All transgenic lines are site-directed integration except WT(4), which is random integration line 4 (see <sir rid="S1" refobjid="nn.3489-S1">Supplementary Fig. 3</sir> and Online Methods). Histograms indicate mean ± s.e.m. One-way ANOVA with Bonferroni correction (***<i>P</i> 0.001, **<i>P</i> 0.01). For climbing and flight assays, at least 50 flies were assessed; number of flies is shown for each bar.</p>
|
https://api.sourcedata.io/file.php?figure_id=3711
|
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] |
|
23933751
|
10.1038/nn.3489
|
The Parkinson's disease–linked proteins Fbxo7 and Parkin interact to mediate mitophagy
|
2013
|
figf4
|
<p>(<b>a</b>) Coimmunoprecipitation (IP) of PINK1-Myc and Flag-Fbxo7 in whole-cell lysates from U2OS cells overexpressing both proteins. IB, immunoblot. (<b>b</b>) Coimmunoprecipitation of PINK1-Myc with full-length and two N-terminally deleted Flag-Fbxo7 forms. PINK1-Myc is detected at low levels in complex with Flag-Fbxo7(89–522) but not with Flag-Fbxo7(129–522). (<b>c</b>) As in <b>b</b>, using lysates from U2OS cells expressing PINK1-Myc, and Flag-Fbxo7 containing either N- or C-terminal truncations. (<b>d</b>) <i>In vitro</i> coprecipitation experiments were performed using <i>in vitro</i>–translated (IVT) PINK1-Myc and either GST or GST fusions of Fbxo7(1–398) or Fbxo7(129–398) immobilized on glutathione beads. (<b>e</b>) Competitive binding assays using immobilized GST-Fbxo7(1–398) incubated with IVT Flag-Parkin and/or full length (top panel) or N-terminally truncated (bottom panel) PINK1-Myc. Input and bead-bound proteins were analyzed by immunoblotting as indicated. (<b>f</b>) As in <b>e</b>, immobilized GST-ΔN-PINK1 (top panel), GST-Parkin (middle panel) and immobilized GST alone (bottom panel) were incubated with combinations of IVT Flag-Parkin, T7-ΔN-PINK1 and Fbxo7-HA as indicated. Input and bead-bound proteins were analyzed by immunoblotting with the indicated antibodies. All western blots were performed a minimum of three times. Full-length blots are presented in <sir rid="S1" refobjid="nn.3489-S1">Supplementary Figure 9</sir>.</p>
|
https://api.sourcedata.io/file.php?figure_id=3712
|
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"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "Parkin",
"type": "geneprod",
"uniprot_ids": [
"O60260"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q9BXM7",
"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": "PINK1",
"type": "geneprod",
"uniprot_ids": [
"Q9BXM7"
]
}
] |
|
23933751
|
10.1038/nn.3489
|
The Parkinson's disease–linked proteins Fbxo7 and Parkin interact to mediate mitophagy
|
2013
|
figf5
|
<p>(<b>a</b>) PINK1 localization at the mitochondria was assessed by immunocytochemistry in SH-SY5Y cells transfected with PINK1-HA plus scrambled (scr) or Fbxo7 siRNA following 1 or 3 h treatment with CCCP (10 μM). Cells were scored visually for the colocalization of PINK1-HA with complex Vβ subunit (CxVβ), a mitochondrial marker. Nuclei (blue) are stained with DAPI. Histograms indicate the percentage of cells in which PINK1-HA accumulated at the mitochondria. Data are presented as mean ± s.e.m.; *<i>P</i> 0.05. Representative images are displayed for cells transfected as indicated, following 0 or 3 h CCCP treatment. For corresponding images at 0 h and 1 h treatment, see <sir rid="S1" refobjid="nn.3489-S1">Supplementary Figure 5a</sir>. Scale bars, 10 μm. (<b>b</b>) Fbxo7 accumulation in the mitochondrial fraction following treatment with CCCP (10 μM) is impaired in SH-SY5Y cells transfected with PINK1 siRNA compared to scrambled siRNA (scr). IB, immunoblot. Full-length blots are presented in <sir rid="S1" refobjid="nn.3489-S1">Supplementary Figure 9</sir>. (<b>c</b>–<b>f</b>) Overexpression of Fbxo7 does not rescue climbing (<b>c</b>,<b>e</b>) or flight (<b>d</b>,<b>f</b>) defects in <i>PINK1</i> male mutants (<i>PINK1</i><super><i>B9</i></super>) or <i>PINK1:parkin</i> double mutants (<i>PINK1</i><super><i>B9</i></super><i>;park</i><super><i>25</i></super><i>, daG4</i>). Control genotypes are <i>PINK1</i><super><i>B9</i></super>/+<i>; da-GAL4</i>/+ (<b>c</b>,<b>d</b>) and <i>da-GAL4</i>/+ (<b>e</b>,<b>f</b>). Histograms indicate mean ± s.e.m. One-way ANOVA with Bonferroni correction (***<i>P</i> 0.001). For climbing and flight assays, at least 50 flies were assessed; number of flies is shown for each bar for <b>c</b>–<b>f</b>.</p>
|
https://api.sourcedata.io/file.php?figure_id=3713
|
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{
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},
{
"ext_dbs": "NCBI gene",
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]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "50873",
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"ext_tax_names": "Mus musculus",
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"ncbi_gene_id": "50873",
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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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"uniprot_ids": [
"Q9BXM7"
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},
{
"ext_dbs": "NCBI gene",
"ext_ids": "65018",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "65018",
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"role": "intervention",
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"uniprot_ids": [
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]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "65018",
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"ext_tax_names": "Homo sapiens",
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"mapping_status": "mapped",
"ncbi_gene_id": "65018",
"original_type": "gene",
"role": "intervention",
"text": "PINK1",
"type": "geneprod",
"uniprot_ids": [
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]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "65018",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "65018",
"original_type": "gene",
"role": "intervention",
"text": "PINK1",
"type": "geneprod",
"uniprot_ids": [
"Q9BXM7"
]
}
] |
|
23933751
|
10.1038/nn.3489
|
The Parkinson's disease–linked proteins Fbxo7 and Parkin interact to mediate mitophagy
|
2013
|
figf6
|
<p>(<b>a</b>,<b>b</b>) Ubiquitination of Mfn1 following treatment with CCCP (10 μM) is reduced in the mitochondrial fraction of both SH-SY5Y cells stably expressing <i>Fbxo7</i> short hairpin RNA (Fbxo7 KD) compared to an empty vector control line (<b>a</b>) and in patient fibroblasts with homozygous R378G mutation compared to fibroblasts from healthy controls (<b>b</b>). Arrowheads indicate ubiquitinated Mfn1. IB, immunoblot. (<b>c</b>,<b>d</b>) Fbxo7 expression restores elevated Mfn steady-state levels in <i>parkin</i> (<b>c</b>) but not <i>PINK1</i> (<b>d</b>) mutant <i>Drosophila</i>. Histograms show mean ± s.e.m. of densitometry analysis of Mfn immunoblots above, normalized to complex Vα (CxVα). Control genotypes are <i>park</i><super><i>25</i></super>/+<i>; da-GAL4</i>/+ (<b>c</b>) and <i>PINK1</i><super><i>B9</i></super>/+<i>; da-GAL4</i>/+ (<b>d</b>). (<b>e</b>) Mitochondria in control <i>Drosophila</i> S2R+ cells stained with MitoTracker Red show a heterogeneous morphology, with a mixture of tubules and fragmented mitochondria. RNAi knockdown of <i>parkin</i> or <i>PINK1</i> causes excessive fusion and elongated mitochondria compared to control double-stranded RNA (<i>Caenorhabditis elegans</i> gene <i>ZK686.3</i>). Expression of Fbxo7 restores <i>parkin</i> but not <i>PINK1</i> knockdown phenotype to WT appearance. Scale bar shows 5 μm. (<b>f</b>) Quantification of mitochondrial morphology in dsRNA treated cells. Scoring system: 1, fragmented; 2, WT; 3, tubular; 4, hyper-fused (clumped). Histograms indicate mean ± s.e.m. Two-tailed Student <i>t-</i>tests (***<i>P</i> 0.001, *<i>P</i> 0.05). All western blots were performed a minimum of three times and images are representative of 100 cells scored per condition. Full-length blots are presented in <sir rid="S1" refobjid="nn.3489-S1">Supplementary Figure 9</sir>.</p>
|
https://api.sourcedata.io/file.php?figure_id=3714
|
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]
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]
},
{
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"text": "Mfn",
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]
},
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},
{
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{
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},
{
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"ext_ids": "40336",
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"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "40336",
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"role": "intervention",
"text": "parkin",
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"uniprot_ids": [
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]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "31607",
"ext_tax_ids": "7227",
"ext_tax_names": "Drosophila melanogaster",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "31607",
"original_type": "gene",
"role": "intervention",
"text": "PINK1",
"type": "geneprod",
"uniprot_ids": [
"Q0KHV6"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "31607",
"ext_tax_ids": "7227",
"ext_tax_names": "Drosophila melanogaster",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "31607",
"original_type": "gene",
"role": "intervention",
"text": "PINK1",
"type": "geneprod",
"uniprot_ids": [
"Q0KHV6"
]
}
] |
|
23933751
|
10.1038/nn.3489
|
The Parkinson's disease–linked proteins Fbxo7 and Parkin interact to mediate mitophagy
|
2013
|
figf7
|
<p>(<b>a</b>) Treatment with CCCP (10 μM) results in an increase in LC3-II in the mitochondrial but not the cytosolic fraction of cells stably expressing the empty shRNA vector (control), and this is delayed in stable Fbxo7 knockdown (KD) SH-SY5Y cells. (<b>b</b>) As in <b>a</b>, an accumulation of LC3-II was observed in the mitochondrial fraction of healthy control fibroblasts following 1 and 5 h CCCP treatment, but this was reduced in fibroblasts from a patient carrying the R378G mutation. Western blots were performed a minimum of three times. (<b>c</b>) Mitochondrial accumulation of p62 following CCCP treatment is inhibited by Fbxo7 siRNA. Flag-Parkin overexpressing SH-SY5Y cells were transfected with scrambled (scr) or Fbxo7 siRNA as indicated and treated with either DMSO or CCCP (10 μM) for 6 h. Colocalization of p62 with HtrA2, a mitochondrial marker, was assessed by Pearson's correlation coefficient (<i>R</i><sub>r</sub>) on a cell-by-cell basis. Histogram shows the percentage of cells in which <i>R</i><sub>r</sub> was greater than 0.5. Data are represented as mean ± s.e.m., *<i>P</i> 0.05. Scale bars, 10 μm. (<b>d</b>) Mitophagy was analyzed in untransfected (UT) SH-SY5Y cells or in stable Flag-Parkin overexpressing SH-SY5Y cells transfected with either scrambled (scr) or Fbxo7 siRNA. Histogram indicates the percentage of cells with no remaining mitochondria following 24 h treatment with CCCP (10 μM) for each condition. Complex Vβ subunit (CxVβ) was used as a mitochondrial marker. Data are presented as mean ± s.e.m., **<i>P</i> 0.01. Scale bars, 10 μm. (<b>e</b>) Mitochondrial mass was measured in Flag-Parkin overexpressing SH-SY5Y cells transfected with scrambled (scr) or Fbxo7 siRNA and treated for 24 h with either dimethylsulfoxide (DMSO) vehicle or CCCP (10 μM). For representative images, see <sir rid="S1" refobjid="nn.3489-S1">Supplementary Figure 8d</sir>. Full-length blots are presented in <sir rid="S1" refobjid="nn.3489-S1">Supplementary Figure 9</sir>.</p>
|
https://api.sourcedata.io/file.php?figure_id=3715
|
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"role": "intervention",
"text": "Fbxo7",
"type": "geneprod",
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]
},
{
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"mapping_status": "mapped",
"ncbi_gene_id": "25793",
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"role": "intervention",
"text": "Fbxo7",
"type": "geneprod",
"uniprot_ids": [
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},
{
"ext_dbs": "Uniprot",
"ext_ids": "O43464",
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"text": "Parkin",
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"O60260"
]
},
{
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"ext_ids": "25793",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "25793",
"original_type": "gene",
"role": "intervention",
"text": "Fbxo7",
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"uniprot_ids": [
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}
] |
|
10.15252/embj.2020107485
|
Regulated splicing of large exons is linked to phase-separation of vertebrate transcription factors
|
2021
|
Figure 2
|
<h2 id="figure-2.-srsf3-overrides-splicing-suppressive-activity-of-hnrnp-k">Figure 2. SRSF3 overrides splicing-suppressive activity of hnRNP K</h2><ol type="A"> <li> <p>Enrichment of RBP-RNA interaction sites in the SRSF3-dependent large constitutive exons (S3-LCEs). Fraction of S3-LCEs in exons having eCLIP peaks in 334 eCLIP data in ENCODE. hnRNP K-eCLIPs are indicated in red.</p> </li> <li> <p>Sashimi plots of representative SRSF3-dependent exons. C2C12 cells were treated with control siRNA (siCont), <em>Srsf3</em> siRNA (siSrsf3), <em>Hnrnpk</em> siRNA (siHnrnpk), or both <em>Srsf3</em> and <em>Hnrnpk</em> siRNAs (siSrsf3+siHnrnpk), and RNA-seq was performed. Lines indicate junction-spanning reads. Gene structures are shown below the Sashimi plots.</p> </li> <li> <p>Scatter plots showing PSI values of control cells (siCont), <em>Srsf3</em>-silenced cells (siSrsf3; left panel), and both <em>Srsf3</em>- and <em>Hnrnpk</em>-silenced cells (siSrsf3 + siHnrnpk; right panel). The PSI values of all internal exons are plotted. Yellow dotted lines indicate ΔPSI = 0.2 and -0.2. Skipped and included exons (|ΔPSI| > 0.2 and Bayes factor > 10) by siSrsf3 are indicated in red and blue, respectively. Note that exon skipping and inclusion are partly mitigated by an additional knockdown of hnRNP K (right panel).</p> </li> <li> <p>PSI values of the exons skipped by <em>Srsf3</em> silencing (red circles in Fig 2C) in cells treated with the control siRNA (C), <em>Srsf3</em> siRNA (S), <em>Hnrnpk</em> siRNA (K), or both <em>Srsf3</em> and <em>Hnrnpk</em> siRNAs (S+K). The box plot shows the interquartile range (boxes), the median (central band) and the minimum and maximum except for the outliers at the ends of whiskers (<em>n</em> = 344).</p> </li> <li> <p>Relationship between exon lengths and recovery of exon skipping in <em>Srsf3</em>-silenced cells by additional <em>Hnrnpk</em> silencing. The exons skipped by <em>Srsf3</em> silencing (red circles in Fig 2C) are classified into four groups according to the degree of recovery by the additional <em>Hnrnpk</em> silencing [ΔPSI (PSI<sub>siSrsf3+siHnrnpk</sub> - PSI<sub>siSrsf3</sub>)]. The box plot shows the interquartile range (boxes), the median (central band) and the minimum and maximum except for the outliers at the ends of whiskers (<em>n =</em> 60 for "ΔPSI ≤ 0", <em>n =</em> 131 for "ΔPSI 0 to 0.2", <em>n =</em> 95 for "ΔPSI 0.2 to 0.4", and <em>n =</em> 57 for "ΔPSI > 0.4").</p> </li> <li> <p>Relationship between the number of CCC motifs in exons and recovery of exon skipping in <em>Srsf3</em>-silenced cells by the additional <em>Hnrnpk</em> silencing. The exons skipped by <em>Srsf3</em> silencing (red circles in Fig 2C) are classified as in (E). The box plot shows the interquartile range (boxes), the median (central band) and the minimum and maximum except for the outliers at the ends of whiskers (<em>n =</em> 60 for "ΔPSI ≤ 0", <em>n =</em> 131 for "ΔPSI 0 to 0.2", <em>n =</em> 95 for "ΔPSI 0.2 to 0.4", and <em>n =</em> 57 for "ΔPSI > 0.4").</p> </li> <li> <p>Distributions of hnRNP K-RNA interactions around 3′ (left) or 5′ (right) splice sites (SS) of the SRSF3-dependent exons in control cells (black) and <em>Srsf3</em>-silenced cells (red). The standard error of the average density of hnRNP K-tRIP reads is shown as a semi-transparent shade around the average curve.</p> </li> </ol><p>Data information: *<em>p</em> < 0.05, ***<em>p</em> < 0.001, ****<em>p</em> < 0.0001 by Steel-Dwass test.</p>
|
https://api.sourcedata.io/file.php?figure_id=43326
|
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"P61979",
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},
{
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"P61979",
"B2M1R6",
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{
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"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
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"mapping_status": "mapped",
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"P61979",
"B2M1R6",
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"Q5FWJ5"
]
},
{
"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": "15387",
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"text": "Hnrnpk",
"type": "geneprod",
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"P61979",
"B2M1R6",
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]
},
{
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"ext_tax_names": "Mus musculus",
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"text": "Srsf3",
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{
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{
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"text": "SRSF3",
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"P84104"
]
},
{
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]
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{
"ext_dbs": "NCBI gene",
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"mapping_status": "mapped",
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"original_type": "gene",
"role": "intervention",
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"P84104"
]
}
] |
||
10.15252/embj.2020107485
|
Regulated splicing of large exons is linked to phase-separation of vertebrate transcription factors
|
2021
|
Figure 3
|
<h2 id="figure-3.-interactome-analysis-for-srsf3-and-hnrnp-k">Figure 3. Interactome analysis for SRSF3 and hnRNP K</h2><ol type="A"> <li> <p>Schematic diagram of the identification of protein complexes associated with SRSF3 and hnRNP K. Nuclei were extracted from HEK 293 cells overexpressing FLAG-tagged SRSF3 (3XFLAG-SRSF3-IP) or FLAG-tagged hnRNP K (3XFLAG-HNRNPK-IP), followed by isolation of the high molecular weight (HMW) fraction (Damianov <em>et al</em>., 2016). After mild treatment with MNase to release proteins from chromatin, immunoprecipitation (IP) was performed using anti-FLAG antibody and mass spectrometry analysis was performed. Naïve cells not expressing a FLAG-tagged protein were used for control IP (Cont-IP).</p> </li> <li> <p>Volcano plot showing fold changes versus <em>P</em>-values of the normalized MASCOT scores (see Materials and Methods) of identified proteins between 3XFLAG-SRSF3-IP and Cont-IP. Each experiment was triplicated. The members of the representative families of splicing factors are highlighted by colors (right upper box).</p> </li> <li> <p>Volcano plot showing fold changes versus <em>P</em>-values of the normalized MASCOT scores of identified proteins between 3XFLAG-HNRNPK-IP and Cont-IP. Each experiment was triplicated. The members of the representative families of splicing factors are highlighted by colors (right upper box).</p> </li> <li> <p>Bubble plot of MASCOT scores of representative proteins identified in 3XFLAG-SRSF3-IP (red) and 3XFLAG-HNRNPK-IP (green). <em>P</em>-values by paired <em>t</em>-test are indicated by bubble sizes.</p> </li> </ol>
|
https://api.sourcedata.io/file.php?figure_id=43328
|
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{
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"ext_ids": "P61978",
"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": "HNRNPK",
"type": "geneprod",
"uniprot_ids": [
"P61978"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P84103",
"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": "SRSF3",
"type": "geneprod",
"uniprot_ids": [
"P84103"
]
}
] |
||
10.15252/embj.2020107485
|
Regulated splicing of large exons is linked to phase-separation of vertebrate transcription factors
|
2021
|
Figure 4
|
<h2 id="figure-4.-the-srsf3hnrnp-k-axis-regulates-global-selection-of-polyadenylation-sites">Figure 4. The SRSF3-hnRNP K axis regulates global selection of polyadenylation sites</h2><ol type="A"> <li> <p>Scatter plots of percent distal polyA site usage indices (PDUIs) in control cells (siCont), <em>Srsf3</em>-silenced cells (siSrsf3; left panel), and both <em>Srsf3</em>- and <em>Hnrnpk</em>-silenced cells (siSrsf3 + siHnrnpk; right panel). PDUIs of all 3′ UTRs are plotted. The 3′ UTRs shortened and extended by siSrsf3 exceeding the thresholds of |ΔPDUI| > 0.2 and <em>p</em> < 0.01 are indicated in red and blue, respectively.</p> </li> <li> <p>3′ UTRs that were shortened by <em>Srsf3</em> silencing were first selected. PDUIs of these 3′ UTRs in C2C12 cells treated with control siRNA (C), <em>Srsf3</em> siRNA (S), <em>Hnrnpk</em> siRNA (K), or both <em>Srsf3</em> and <em>Hnrnpk</em> siRNAs (S+K) are plotted. ****<em>p</em> < 0.0001 by Steel-Dwass test. The box plot shows the interquartile range (boxes), the median (central band) and the minimum and maximum except for the outliers at the ends of whiskers (<em>n =</em> 965).</p> </li> <li> <p>mRNA expression levels of seven CPSF factors in C2C12 cells treated with the indicated siRNA normalized for those treated with the control siRNA. **<em>p</em> < 0.01 by CuffDiff (Trapnell <em>et all.,</em> 2010).</p> </li> <li> <p>Western blots showing protein expression levels of CPSF6 and β-actin (ACTB). Whole cell lysates were harvested 42 h after siRNA transfection.</p> </li> <li> <p>Distributions of interactions between RNA and CPSF6 (red), hnRNP K (black), or SRSF3 (blue) around the distal polyA sites that are downregulated in <em>Srsf3</em>-silenced cells. The standard error of the average density of tRIP reads is shown as a semi-transparent shade around the average curve.</p> </li> </ol>
|
https://api.sourcedata.io/file.php?figure_id=43330
|
[
{
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"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "94230",
"original_type": "gene",
"role": "assayed",
"text": "CPSF",
"type": "geneprod",
"uniprot_ids": [
"Q9EPU4",
"A0A2R8VK76"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q6NVF9",
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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": "CPSF6",
"type": "geneprod",
"uniprot_ids": [
"Q6NVF9"
]
}
] |
||
10.15252/embj.2020107485
|
Regulated splicing of large exons is linked to phase-separation of vertebrate transcription factors
|
2021
|
Figure 6
|
<h2 id="figure-6.-srsf3-silencing-disrupts-transcription-assemblies">Figure 6. <em>Srsf3</em> silencing disrupts transcription assemblies</h2><ol type="A"> <li> <p>Representative transcriptional factor genes containing the SRSF3-dependent exons. Edges show protein-protein interaction (PPI) as annotated within the STRING database (Szklarczyk <em>et al</em>., 2019). Solid lines and dotted lines indicate PPIs within a cluster and over a cluster, respectively. Genes are clustered by the Markov cluster algorithm.</p> </li> <li> <p>SRSF3-responsive alternative 3′ ends of the <em>Med1</em> gene. (Top panel) Disorder analysis for MED1 using PONDR VL-XT (deep blue) and IUPred2 (light blue). The scores in the ordinate indicate disordered tendencies between 0 and 1 (a score of more than 0.5 indicates disordered). (Middle panel) Protein and gene structures of MED1. The protein structure was segmented into individual exonic regions. The SRSF3-responsive last exon is indicated in pink. (Bottom panel) Sashimi plots of RNA-seqs from <em>Srsf3</em>- and/or <em>Hnrnpk</em>-silenced cells.</p> </li> <li> <p>Immunofluorescence images of MED1 in C2C12 cells treated with siCont (C), siSrsf3 (S), siHnrnpk (K), or siSrsf3+siHnrnpk (S+K). A white dotted contour outlines the nucleus. Box plots (right) show quantification of nuclear (NUC) and cytoplasmic (CYT) localization of MED1. The average intensity of one nucleus or a cytoplasmic segment is individually plotted.</p> </li> <li> <p>The intrinsically disordered region (IDR) in MED4. Disorder analysis, protein and gene structures, and Sashimi plots are shown in (B). Splicing of these genes was not affected by the siRNA treatment.</p> </li> <li> <p>Immunofluorescence images of MED4 in C2C12 cells treated with the indicated siRNAs. Box plots show quantification of nuclear localization of MED4. Each dot represents one nucleus.</p> </li> <li> <p>Immunofluorescence images of MED1 and MED4 in C2C12 cells The arrows denote representative puncta, including both MED1 and MED4.</p> </li> <li> <p>The number of MED1 puncta (left) and MED4 puncta (right) per nucleus in cells treated with the indicated siRNA.</p> </li> <li> <p>MED1 signals on MED4 puncta normalized to nuclear MED1 signals. MED1 signal intensity on each MED4 punctum was individually plotted.</p> </li> </ol><p>Data information: *<em>p</em> < 0.01, **<em>p</em> < 0.01, ***<em>p</em> < 0.001, ****<em>p</em> < 0.0001 by Steel-Dwass test. In (C, D, G, and H), box plots show the interquartile range (boxes), the median (central band) and the minimum and maximum except for the outliers at the ends of whiskers. More than 50 nuclei in more than five randomly selected visual fields of at least two independent immunostainings were analyzed in each experiment.</p>
|
https://api.sourcedata.io/file.php?figure_id=43334
|
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{
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] |
||
10.15252/embj.2019103420
|
Re-equilibration of imbalanced NAD metabolism ameliorates the impact of telomere dysfunction
|
2020
|
Figure 2
|
<sd-panel> <p><strong>Figure 2. CD38 depletion ameliorates dysregulated NAD metabolism in DC cells.</strong></p> <ol type="A"> <li> <p>Quantitative RT-PCR and immunoblots of the expression of CD38 and SARM1 in DC and age-matched health control fibroblasts. All values are presented as mean ± SD of three replicates in quantitative RT-PCR. Protein levels are normalized to GAPDH, and mean (± SD) quantification values of 4 controls vs 5 DC samples are shown. Student's <em>t</em> test was performed on DC cells vs controls. Irrelevant intervening lanes have been removed for clarity (full blots are available online as Source Data).</p> </li> <li> <p>Immunoblots and quantification of indicated proteins in DC fibroblasts treated with DMSO and with 2 μM ATM inhibitor, KU-55933 for 48 hours. Mean (± SD) quantification values of three DC lines with and without ATMi treatment are shown. P values on the basis of Student's <em>t</em> test.</p> </li> <li> <p>The efficacy of CD38 shRNA (sh-1 and sh-2) was verified by quantitative RT-PCR in DC fibroblasts and by RT-PCR and immunoblots in A549 cells. The relative CD38 mRNA values in the CD38 knockdown cells were normalized to the scrambled shRNA. All values are presented as mean ± SD of three replicates. Student's <em>t</em> test was performed on DC and A549 cells in indicated conditions.</p> </li> </ol> <p>D, E Intracellular NAD levels and immunoblots of the expression of indicated proteins in the scramble and CD38 knockdown DC fibroblasts. The CD38 knockdown DC fibroblasts were treated with the PARP1 inhibitor Olaparib (400nM) and the SIRT1 inhibitor EX 527 (1 μM) for 24 hours. Data are representative four replicates. All values are presented as mean ± SD of four replicates. One-way ANOVA was performed on DC cells in indicated conditions.</p> </sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=34896
|
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{
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"P28907",
"B4E006"
]
},
{
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"mapping_source": "direct",
"mapping_status": "mapped",
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"text": "PARP1",
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"P09874"
]
},
{
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]
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{
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]
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},
{
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"ext_tax_names": "Homo sapiens",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
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"uniprot_ids": [
"Q96EB6"
]
}
] |
||
10.15252/embj.2019103420
|
Re-equilibration of imbalanced NAD metabolism ameliorates the impact of telomere dysfunction
|
2020
|
Figure 3
|
<sd-panel> <p><strong>Figure 3. G3 <em>Tert</em><sup>-/-</sup> mice display defects in the NAD metabolism.</strong></p> <p>A, B Intracellular NAD levels and immunoblots of the expression of NAD consuming related proteins and their activities in brain tissues from 6-month- old G1 and G3 <em>Tert<sup>-/-</sup></em> female mice. The CD38 antibody was validated using the <em>CD38<sup>-/-</sup></em> mouse brain tissues.</p> <p>C Quantification of immunoblots from the indicated proteins in B.</p> <p>D NADase activity in G1 and G3 <em>Tert<sup>-/-</sup></em> mouse brain lysate was determined at various time points during the reaction. NADase activity was not detectable in the extracts treated with the CD38 inhibitor, 78c, at a concentration of 50nM.</p> <p>Data information: All values are presented as mean ± SD of G1 <em>Tert-/-</em> mouse brain tissues versus G3 <em>Tert-/-</em> mouse brain tissues. n=4 in each group. P values on the basis of Student's <em>t</em> test.</p> </sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=34897
|
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{
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"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "12494",
"original_type": "gene",
"role": "intervention",
"text": "CD38",
"type": "geneprod",
"uniprot_ids": [
"P56528",
"Q3UCS6",
"Q4FJL8"
]
},
{
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"ext_tax_names": "Mus musculus",
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"mapping_status": "mapped",
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"original_type": "protein",
"role": "assayed",
"text": "CD38",
"type": "geneprod",
"uniprot_ids": [
"P56528"
]
},
{
"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": "CD38",
"type": "geneprod",
"uniprot_ids": [
"P56528"
]
}
] |
||
10.15252/embj.2019103420
|
Re-equilibration of imbalanced NAD metabolism ameliorates the impact of telomere dysfunction
|
2020
|
Figure 4
|
<sd-panel> <p><strong>Figure 4. NAD intervention impacts mitochondrial parameters of DC fibroblasts.</strong></p> <p>A Representative immunoblots of the expression of PGC1-1α in DC cells treated with vehicle or 3 mM NR. Quantification of the indicated proteins is from three immunoblots.</p> <p>B-D Cellular and mitochondrial ROS in DC and age-matched healthy control cells supplemented with vehicle and NR (B and C) and in the scramble and CD38 knockdown DC cells (D) were measured by flow cytometry from three replicates.</p> <p>E Representative images captured by transmission electron microscopy of DC1 cells treated with vehicle or NR. White arrows: mitochondria. Yellow arrow: autophagosome-like structures with engulfed mitochondria. Enlarged image within white frame is shown.</p> <p>F-H Quantifications of percentage of damaged mitochondria per cell (F), mitochondrial length (G), and mitochondrial diameter (H). A minimum of 200 mitochondria counted per group.</p> <p>Data information: All data are represented as mean ± SD. Student's <em>t</em> test was performed for individual pairs in indicated conditions. Con: control.</p> </sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=34898
|
[
{
"ext_dbs": "Uniprot",
"ext_ids": "Q9UBK2",
"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": "PGC1-1α",
"type": "geneprod",
"uniprot_ids": [
"Q9UBK2"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "952",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "952",
"original_type": "gene",
"role": "intervention",
"text": "CD38",
"type": "geneprod",
"uniprot_ids": [
"P28907",
"B4E006"
]
}
] |
||
10.15252/embj.2019103420
|
Re-equilibration of imbalanced NAD metabolism ameliorates the impact of telomere dysfunction
|
2020
|
Figure 5
|
<sd-panel> <p><strong>Figure 5. Impaired mitophagy process in DC fibroblasts is improved by NR supplementation.</strong></p> <ol type="A"> <li> <p>Representative images of mitophagy showing co-localization between the mitophagy dye (red) and the lysosome dye (green) in DC and control fibroblasts treated with vehicle or 3 mM NR. White arrows: mitophagy.</p> </li> </ol> <p>B The mean value of fluorescence intensity/cells in each image was scored. At least 15 images (~ 200 cells) were counted per group. <strong>The relative values in each group was normalized to Con1.</strong></p> <p>C Representative immunoblots of the expression of PINK1 and PARKIN in DC cells treated with vehicle or 3 mM NR. Quantification of immunoblots from the indicated proteins is from three replicates.</p> <p>Data information: All values are represented as mean ± SD. One-way ANOVA (B) and Student's <em>t</em> test (C) were performed for each individual pair. Con: age-matched healthy controls.</p> </sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=34899
|
[
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"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "PINK1",
"type": "geneprod",
"uniprot_ids": [
"Q9BXM7"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "O60260",
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"ext_tax_names": "Homo sapiens",
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"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "PARKIN",
"type": "geneprod",
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"O60260"
]
}
] |
||
10.15252/embj.2019103420
|
Re-equilibration of imbalanced NAD metabolism ameliorates the impact of telomere dysfunction
|
2020
|
Figure 6
|
<sd-panel> <p><strong>Figure 6. NR supplementation reduces telomeric oxidative DNA lesions and TIF formation in DC cells.</strong></p> <p>A PCR amplification efficiency at the telomere in the mock- and FPG-treated DC and age-matched healthy control fibroblasts supplemented with vehicle or 3 mM NR. All values are presented as mean ± SD of three replicates. <strong>The relative telomere PCR amplification in each sample was normalized to the <em>36B4</em> reference gene</strong>.</p> <p>B Telomere restriction fragment analysis in DC and control fibroblasts treated with vehicle or 3 mM NR. Genomic DNA was isolated from the indicated cell lines at 0 d or 14 d, with or without 3 mM NR treatment. At left, DNA molecular mass markers, in kilobase pairs (Kb).</p> <p>C, D Representative images of γH2AX (green), telomere immuno-FISH (red) in DC cells treated with vehicle or 3 mM NR. White arrows: co-localization of γH2AX foci and telomeric DNA (or TIF). Enlarged views of co-localizing foci are shown at the right panel and in Figure EV1. Percentage of DC and control cells with indicated TIFs per nuclei. ~ 100 cells per condition were scored.</p> <p>Data information: All values are represented as mean ± SD. P values were calculated using One-way ANOVA (A and D). Con: age-matched healthy controls.</p> </sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=34900
|
[
{
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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": "γH2AX",
"type": "geneprod",
"uniprot_ids": [
"P16104"
]
},
{
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"ext_ids": "P16104",
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"role": "assayed",
"text": "γH2AX",
"type": "geneprod",
"uniprot_ids": [
"P16104"
]
}
] |
||
10.15252/embj.2019103420
|
Re-equilibration of imbalanced NAD metabolism ameliorates the impact of telomere dysfunction
|
2020
|
Figure 7
|
<sd-panel> <p><strong>Figure 7. NAD intervention improves the proliferative capacity and suppresses cellular senescence and SASP in DC fibroblasts.</strong></p> <p>A Cumulative population doubling analysis of the proliferation of representative scramble and CD38 knockdown DC fibroblasts or DC fibroblasts treated with vehicle or 3 mM NR. Each data point is represented as mean ± SD of three replicates.</p> <p>B, C Representative images of BrdU (red) and DAPI (blue) staining of DC and age-matched healthy control fibroblasts treated with vehicle or NR. Percentage of BrdU -positive cells per condition<strong>.</strong> Each dot represents the percentage of cells with BrdU staining per image. <strong>~400 cells were counted per condition.</strong> All values are presented as mean ± SD.</p> <p>D, E Representative images of SPiDER-β-gal (green) and DAPI (blue) staining of DC and age-matched healthy control cells treated with vehicle or 3 mM NR. Percentage of SA-β-gal-positive cells per condition<strong>.</strong> Each dot represents the percentage of cells with SA-β-gal staining per image. <strong>~</strong>400 cells <strong>were counted per condition</strong>. All values are presented as mean ± SD.</p> <p>F The levels of IL-6, IL-8, and MCP-1 in both supernatant and cell lysate of indicated DC fibroblasts treated with vehicle or 3 mM NR. All values are represented as mean ± SD of three replicates.</p> <p>G, H Representative immunoblots of p21 and p16 in DC fibroblasts treated with vehicle or 3 mM NR. Quantification of the indicated proteins are presented as mean ± SD from three immunoblots.</p> <p>Data information: P values were calculated using one-way ANOVA for multiple comparisons (C) and Student's <em>t</em> test between two groups (C, E, F and H). Con: control.</p> </sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=34901
|
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{
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25837623
|
10.1371/journal.pbio.1002114
|
Regulation of protein quality control by UBE4B and LSD1 through p53-mediated transcription.
|
2015
|
Fig 1
|
<title>Identification and characterization of a robust suppressor that ameliorates the locomotion defects in the <italic>C</italic>. <italic>elegans</italic> model of SOD1-associated ALS.</title>
<p>(<bold>A</bold>) Workflow of the suppressor screen identifying mutant <italic>C</italic>. <italic>elegans</italic> (red) with saliently improved movement. (<bold>B</bold>) Locomotor behavior, measured by thrashing rates in liquid medium, in the <italic>C</italic>. <italic>elegans</italic> strains with neuronal expression of human WT SOD1 or ALS-linked mutant SOD1<sup>G85R</sup>, in the presence (M1/M1) or absence (+/+) of the suppressor mutation (<italic>n</italic> = 16). (<bold>C</bold>) Northern (top panel) and western (middle, bottom panels) blot analyses of total RNA and protein from SOD1<sup>G85R</sup> strains, with (M1/M1) or without (+/+) suppressor mutations, demonstrating that the levels of SOD1<sup>G85R</sup> mRNA and total protein are not changed by the suppressor mutation (M1/M1). The western blot lanes are from the same gel and exposure. (<bold>D</bold>) Sequence analysis of the M1 strain, revealing that independent mutations in two genes, a lysine-specific demethylase, <italic>spr-5 (R646Q)</italic>, and a ubiquitin ligase, <italic>ufd-2 (W824X)</italic>, are required for the full suppressor phenotype. (<bold>E</bold>) <italic>C</italic>. <italic>elegans</italic> SPR-5 and UFD-2 and their mammalian homologs lysine-specific demethylase 1 (LSD1) and ubiquitination factor E4 B (UBE4B) share all major protein domains. These include the Swi3-Rsc8-Moira (SWIRM), amine oxidase-like (AOL), and TOWER domains in LSD1/SPR-5 and the Ufd2 Core and U-box domains in UBE4B/UFD-2. Positions of the missense, nonsense, and deletion mutations in mutant <italic>C</italic>. <italic>elegans</italic> are indicated. (<bold>F</bold>) Locomotor behavior, measured by thrashing rates, of the <italic>C</italic>. <italic>elegans</italic> carrying the SOD1<sup>G85R</sup> transgene on the normal background (WT), with the null mutation of either <italic>ufd-2(tm1380)</italic> or <italic>spr-5(by134)</italic>, the double mutation <italic>ufd-2(tm1380);spr-5(by134)</italic>, or the M1 suppressor <italic>ufd-2(W824X);spr-5(R646Q</italic>) (<italic>n</italic> = 16). (<bold>G</bold>) Western blotting of the supernatant (S) and pellet (P) protein fractions from the <italic>C</italic>. <italic>elegans</italic> carrying the SOD1<sup>G85R</sup> transgene with the double mutation <italic>ufd-2(tm1380);spr-5(by134)</italic> compared with controls. While SOD1<sup>G85R</sup> protein levels are unchanged in the S fraction, those in the P fraction are decreased in the double suppressor mutant. The P fraction represents only about 1.7% of total SOD1<sup>G85R</sup> in the WT sample; therefore, a higher ratio of the P fraction relative to the S fraction (approximately 2:1) is used for the western analysis. (<bold>H</bold>) The overexpression (OE) of WT UFD-2 or SPR-5 in the <italic>C</italic>. <italic>elegans</italic> nervous system blocks the protection conferred by the double mutation <italic>ufd-2(tm1380);spr-5(by134)</italic> (<italic>n</italic> = 16). Data represent means ± SEM. The numerical data used to make this figure can be found in <xref rid="pbio.1002114.s001" ref-type="supplementary-material">S1 Data</xref>.</p>
|
https://api.sourcedata.io/file.php?figure_id=4336
|
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|
25837623
|
10.1371/journal.pbio.1002114
|
Regulation of protein quality control by UBE4B and LSD1 through p53-mediated transcription.
|
2015
|
Fig 2
|
<title>Suppression of neurodegeneration associated with diverse misfolded proteins in invertebrate models by <italic>ufd-2</italic> and <italic>spr-5</italic> loss-of-function mutations.</title>
<p>(<bold>A</bold>) Top: schematic drawing depicts pan-neuronal expression of YFP in head and ventral neurons in the context of the <italic>C</italic>. <italic>elegans</italic> body plan. Left: micrographs show the SOD1<sup>G85R</sup>-YFP proteins expressed in WT or the <italic>spr-5(by134);ufd-2(tm1380)</italic> mutant background. The double-mutant worms show a marked decrease in protein aggregation in neurons. Enlarged sections of head neurons (red framed) and ventral cord neurons (white framed) are shown. Middle: quantification of locomotion in the <italic>spr-5(by134);ufd-2(tm1380)</italic> and the WT <italic>C</italic>. <italic>elegans</italic> with neuronal expression of SOD1<sup>G85R</sup>-YFP (<italic>n</italic> = 30). Right: a decrease in the protein levels of SOD1<sup>G85R</sup>-YFP in the presence of <italic>spr-5(by134);ufd-2(tm1380)</italic> is shown by western blots of the supernatant (S) and the pellet (P) fractions. (<bold>B and C</bold>) Analyses of the <italic>spr-5(by134);ufd-2(tm1380)</italic> and the WT <italic>C</italic>. <italic>elegans</italic> with neuronal expression of TDP-43-c25-YFP (<italic>n</italic> = 30) or PolyQ-YFP (<italic>n</italic> = 12) as in (A). (<bold>D</bold>) Neurodegenerative rough-eye phenotype in adults is alleviated by the knockdown of the <italic>Drosophila</italic> homologs of <italic>ufd-2</italic>/UBE4B and <italic>spr-5</italic>/LSD1—CG9934 and Su(Var)3-3, respectively, compared to the control (CTRL). Eye-specific expression of TDP-43<sup>M337V</sup>, FUS<sup>R521C</sup>, and RNA interference (RNAi) was driven by GMR-Gal4. (<bold>E</bold>) <italic>Drosophila</italic> eye pigment quantitation. Data represent means ± SEM. The numerical data used to make this figure can be found in <xref rid="pbio.1002114.s001" ref-type="supplementary-material">S1 Data</xref>.</p>
|
https://api.sourcedata.io/file.php?figure_id=4337
|
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|
25837623
|
10.1371/journal.pbio.1002114
|
Regulation of protein quality control by UBE4B and LSD1 through p53-mediated transcription.
|
2015
|
Fig 3
|
<title>UBE4B and LSD1 double-knockdown accelerates SOD1<sup>G85R</sup> protein degradation.</title>
<p>(<bold>A</bold>) Western blots of cell lysates derived from mock (CTRL), single UBE4B or LSD1, or double UBE4B and LSD1 knockdowns. Supernatant (S) and pellet (P) fractions were probed with indicated antibodies. While the LSD1 or UBE4B single-knockdown reduces the SOD1<sup>G85R</sup> aggregates in both supernatant and pellet fractions, the combined knockdown produces the strongest reduction in the aggregates. (<bold>B</bold>) Quantification of SOD1<sup>G85R</sup> protein levels by western blotting (A). <italic>n</italic> = 3 (supernatant); <italic>n</italic> = 8 (pellet). (<bold>C</bold>) Western blots of a representative cycloheximide chase experiment to determine SOD1 protein half-lives in the double UBE4B and LSD1 knockdown cells versus controls. (<bold>D</bold>) Quantification of SOD1<sup>G85R</sup> clearance, as analyzed by western blotting in (C). The graph indicates the relative band intensity of SOD1<sup>G85R</sup> at each chase time point. <italic>n</italic> = 5; Overall <italic>p</italic> = 0.02 (paired <italic>t</italic> test, CTRL versus UBE4B and LSD1 double knockdown). Individual <italic>p</italic> = 0.03 (3 h), <italic>p</italic> = 0.003 (6 h), <italic>p</italic> = 0.06 (9 h), and <italic>p</italic> = 0.004 (12–21 h). (<bold>E</bold>) The half-life of SOD1<sup>G85R</sup> is reduced from 8.5 h to 5 h upon knockdown of UBE4B and LSD1. Data represent means ± SEM. The numerical data used to make this figure can be found in <xref rid="pbio.1002114.s001" ref-type="supplementary-material">S1 Data</xref>.</p>
|
https://api.sourcedata.io/file.php?figure_id=4338
|
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|
25837623
|
10.1371/journal.pbio.1002114
|
Regulation of protein quality control by UBE4B and LSD1 through p53-mediated transcription.
|
2015
|
Fig 4
|
<title>UBE4B and LSD1 knockdown activates transcription mediated by p53.</title>
<p>(<bold>A</bold>) Venn diagram of upstream activators (z-score ≥ 2) that are differentially activated in single—UBE4B or LSD1—knockdowns and double UBE4B and LSD1 knockdowns, compared with the control. Activation state of an upstream regulator is predicted from differential mRNA levels of its downstream target genes. (<bold>B</bold>) The volcano scatter plot indicates fold changes in the levels of gene transcripts affected differentially by the UBE4B and LSD1 double knockdown versus control shRNA. Gray spots represent 22,148 annotated transcripts. Red spots are predicted p53-activated targets, and blue spots are predicted p53-inhibited targets. The enrichment of red spots in the up-regulated genes (right upper quadrant, >1.2-fold change, <italic>p</italic> ≤ 0.04) and blue spots in the down-regulated genes (left upper quadrant) indicates that the p53-mediated transcription is activated by the UBE4B and LSD1 double knockdown. (<bold>C</bold>) RT-qPCR validation of the expression levels of representative p53 target genes in the UBE4B and LSD1 double-knockdown samples. <italic>n</italic> = (2 to 6), <italic>p</italic> ≤ 0.04. (<bold>D</bold>) The p53 protein level is significantly increased by UBE4B and LSD1 double knockdown. Left: representative western blots showing p53 levels, the knockdown of UBE4B and LSD1, and the actin control in HEK293T cells. Right: quantification of the p53 protein levels normalized against actin (<italic>n</italic> = 3). (<bold>E</bold>) The p53-mediated transcriptional activity is measured by a luciferase reporter under the control of a p53-response element promoter, which was transfected into HEK293T cells 72–96 h after the initiation of the UBE4B and LSD1 single or double knockdowns (<italic>n</italic> = 6). (<bold>F</bold>) Increased interaction of p53 with its activating partner 53BP1 in response to UBE4B and LSD1 knockdown. Left: representative western blots of 53BP1 co-immunoprecipitation. Right: quantification of the 53BP1 co-immunoprecipitation (<italic>n</italic> = 2). Data represent means ± SEM. (<bold>G</bold>) RT-qPCR validation of the expression levels of FOXO3a, FOXO4, and PSMD11 (<italic>n</italic> = 6). (<bold>H</bold>) The FOXO3a-mediated transcriptional activity was measured with a luciferase reporter under the control of a FOXO-response element promoter. HEK293T cells were transfected with shRNAs for control, LSD1, UBE4B, or both LSD1 and UBE4B, followed by transfection of the luciferase reporter together with a constitutively active form of FOXO3a (TM) 72–96 h later (<italic>n</italic> = 6). Data represent means ± SEM. The numerical data used to make this figure can be found in <xref rid="pbio.1002114.s001" ref-type="supplementary-material">S1 Data</xref>.</p>
|
https://api.sourcedata.io/file.php?figure_id=4339
|
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] |
|
25837623
|
10.1371/journal.pbio.1002114
|
Regulation of protein quality control by UBE4B and LSD1 through p53-mediated transcription.
|
2015
|
Fig 5
|
<title>UBE4B and LSD1 double knockdown activates both proteasomes and autophagy.</title>
<p>(<bold>A</bold>) Increased protein levels of proteasome subunits upon the UBE4B and LSD1 double knockdown in HEK293T cells. (<bold>B</bold>) The UBE4B and LSD1 single or double knockdowns increase the proteasomal degradation of a reporter substrate, Suc-LLVY-Luciferin, whose degradation is measured in a luciferase release assay. The double knockdown shows synergistic proteasomal activation when compared with the individual knockdowns (<italic>n</italic> = 6). (<bold>C</bold>) The autophagy activity is significantly increased in cells with the UBE4B and LSD1 double knockdown. The in vivo activity of the ATG4B protease, which cleaves LC3 precursors, was quantified via a <italic>Gaussia</italic> luciferase release assay (see <xref rid="pbio.1002114.s006" ref-type="supplementary-material">S5D Fig., S5E Fig</xref>., and <xref rid="sec012" ref-type="sec">Materials and Methods</xref> for details). The HCT116 cells were analyzed 48 h after the initiation of the knockdown. (<bold>D</bold>) Quantification of LC3-II levels in HEK293T cells with the UBE4B and LSD1 double knockdown or the mock control. The cells were treated with or without 10 mM 3-methyladenine (3-MA) for 48h before lysis. Western blots indicate an increase in LC3 levels (top panels) in the double UBE4B and LSD1 knockdown cells (middle panels), while the actin control is unchanged (bottom panels). The graph shows the quantification of LC3-II levels as normalized to actin levels (<italic>n</italic> = 3). A one-way ANOVA test with matched multiple comparisons and Tukey correction was used for statistics. Data represent means ± SEM. The numerical data used to make this figure can be found in <xref rid="pbio.1002114.s001" ref-type="supplementary-material">S1 Data</xref>.</p>
|
https://api.sourcedata.io/file.php?figure_id=4340
|
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] |
|
25837623
|
10.1371/journal.pbio.1002114
|
Regulation of protein quality control by UBE4B and LSD1 through p53-mediated transcription.
|
2015
|
Fig 6
|
<title>p53 promotes the clearance of misfolded SOD1 mutant proteins.</title>
<p>(<bold>A</bold>) p53 small molecule activators Tenovin-1 and CP-31398 reduce the levels of misfolded SOD1 proteins, as determined by the SOD1<sup>G85R</sup> solubility assay in HEK293 cells. Increasing concentrations of the p53 activators significantly decrease the levels of SOD1<sup>G85R</sup> but not the endogenous WT SOD1 proteins in western blots of both supernatant and pellet fractions. (<bold>B</bold>) A decrease in p53 as the result of shRNA knockdown increases the levels of SOD1<sup>G85R</sup> but not WT SOD1 proteins in the SOD1<sup>G85R</sup> aggregation assay, as shown by western blots of both supernatant (S) (<italic>n</italic> = 2) and pellet (P) (<italic>n</italic> = 3) fractions. (<bold>C</bold>) A complete absence of p53 increases the accumulation of SOD1<sup>G85R</sup> mutant proteins in p53–/– HCT116 cells when compared with controls. Representative western blots (left panels) and quantification of SOD1<sup>G85R</sup> levels in the supernatant lysates are shown. The middle graph indicates the ratio of G85R to WT SOD1 proteins in the presence or absence of p53 with varying amounts of transfected mutant SOD1. The right graph panel shows the same data as shown in the middle panel, but normalized to the average SOD1<sup>G85R</sup> level for each amount of the transfected plasmid. Data represent means ± SEM. The numerical data used to make this figure can be found in <xref rid="pbio.1002114.s001" ref-type="supplementary-material">S1 Data</xref>.</p>
|
https://api.sourcedata.io/file.php?figure_id=4341
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"text": "SOD1",
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"uniprot_ids": [
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]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P00441",
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"ext_tax_names": "Homo sapiens",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
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"uniprot_ids": [
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}
] |
|
25837623
|
10.1371/journal.pbio.1002114
|
Regulation of protein quality control by UBE4B and LSD1 through p53-mediated transcription.
|
2015
|
Fig 7
|
<title>Enhanced protein quality control by the knockdown of UBE4B and LSD1 depends on p53.</title>
<p>(<bold>A</bold>) Left: p53 knockdown reverses the enhanced clearance of SOD1<sup>G85R</sup> proteins conferred by the UBE4B and LSD1 double knockdown. Total amounts of shRNAs were adjusted to be equal with nontargeting CTRL shRNAs. Right: quantification of insoluble aggregated SOD1<sup>G85R</sup> in pellet fractions from HEK293T cells transfected with control, double (UBE4B/LSD1), or triple (UBE4B/LSD1/p53) shRNAs (<italic>n</italic> = 2). (<bold>B</bold>) The degenerative TDP-43<sup>M337V</sup> eye phenotype is exacerbated by the knockdown of the <italic>Drosophila</italic> homolog of p53 (p53 RNAi), or by the overexpression of a dominant-negative p53 mutant (p53.R155H). Expression of p53 RNAi, p53.R155H, and TDP-43<sup>M337V</sup> are driven by GMR-Gal4. (<bold>C</bold>) The p53-activating drug Tenovin-1 (TEN1) protects spinal cord motor neurons from SOD1<sup>G85R</sup>-induced proteotoxicity. Rat spinal cord cultures were grown as described in Materials and Methods and treated with 0.8 μM TEN1 or vehicle (VEH) DMSO, followed by infection of HSV-SOD1<sup>G85R</sup> or the HSV-LacZ control after 24 h. At day 5 post-infection, cells were fixed and stained with a motor neuron-specific anti-neurofilament H (NF-H) antibody. Left: representative images of motor neurons in each condition. Scale bar = 50 μm. Right: quantification of motor neuron survival (one-way ANOVA with multiple comparisons and Tukey correction). Data represent means ± SEM. (<bold>D</bold>) Schematic of the SUNS pathway. A reduction in UBE4B and LSD1 function synergistically activates the p53-mediated transcriptional program, promoting clearance of misfolded and aggregated proteins via increased proteasomal and autophagic clearance. The numerical data used to make this figure can be found in <xref rid="pbio.1002114.s001" ref-type="supplementary-material">S1 Data</xref>.</p>
|
https://api.sourcedata.io/file.php?figure_id=4342
|
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"text": "SOD1",
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"V9HWC9"
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},
{
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"ncbi_gene_id": "6647",
"original_type": "gene",
"role": "intervention",
"text": "SOD1",
"type": "geneprod",
"uniprot_ids": [
"P00441",
"V9HWC9"
]
},
{
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"ext_ids": "P16884",
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"ext_tax_names": "Rattus norvegicus",
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"mapping_status": "mapped",
"ncbi_gene_id": null,
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"text": "neurofilament H",
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"uniprot_ids": [
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}
] |
|
23361001
|
10.1038/ncomms2400
|
Selective escape of proteins from the mitochondria during mitophagy
|
2013
|
f1
|
<p>(<b>a</b>) MEFs stably expressing EGFP-<named-entity id="named-entity-451">Parkin</named-entity> were exposed to <named-entity id="named-entity-452">CCCP</named-entity> (30 μM) for the indicated times and then subjected to immunoblot analysis (IB) with antibodies to the indicated proteins. The asterisk indicates a nonspecific band. (<b>b</b>) SH-SY5Y cells were exposed to <named-entity id="named-entity-453">CCCP</named-entity> (10 μM) for the indicated times and then subjected to immunoblot analysis. (<b>c</b>) MEFs stably expressing EGFP-<named-entity id="named-entity-454">Parkin</named-entity> were treated with <named-entity id="named-entity-455">CCCP</named-entity> (30 μM) for the indicated times, fixed, permeabilized and subjected to immunofluorescence analysis with antibodies to <named-entity id="named-entity-456">FKBP38</named-entity> and to <named-entity id="named-entity-457">cytochrome <i>c</i></named-entity> and with a confocal microscope. The fluorescence of EGFP-<named-entity id="named-entity-458">Parkin</named-entity> was monitored directly. (<b>d</b>) Higher-magnification views of the boxed areas in <b>c</b>. Scale bar (<b>c</b>,<b>d</b>), 10 μm.</p>
|
https://api.sourcedata.io/file.php?figure_id=3295
|
[
{
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"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",
"ext_ids": "P62897",
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"ext_tax_names": "Mus musculus",
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"mapping_status": "mapped",
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"text": "cytochrome c",
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},
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"text": "FKBP38",
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]
},
{
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"ext_ids": "Q9WVS6",
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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": "Parkin",
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},
{
"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,
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"role": "assayed",
"text": "Parkin",
"type": "geneprod",
"uniprot_ids": [
"Q9WVS6"
]
}
] |
|
23361001
|
10.1038/ncomms2400
|
Selective escape of proteins from the mitochondria during mitophagy
|
2013
|
f2
|
<p>(<b>a</b>,<b>c</b>) MEFs (<b>a</b>) or HeLa cells (<b>c</b>) stably expressing <named-entity id="named-entity-460">FLAG</named-entity>-<named-entity id="named-entity-461">Parkin</named-entity> and either EGFP-<named-entity id="named-entity-462">VAP-A</named-entity> or HA-<named-entity id="named-entity-463">VAP-A</named-entity> were treated with <named-entity id="named-entity-464">CCCP</named-entity> (30 and 10 μM, respectively) for the indicated times, fixed, permeabilized and subjected to immunofluorescence analysis with antibodies to <named-entity id="named-entity-465">FKBP38</named-entity>, to HA or to <named-entity id="named-entity-466">FLAG</named-entity> (M2). The fluorescence of EGFP-<named-entity id="named-entity-467">VAP-A</named-entity> was also monitored directly. (<b>b</b>,<b>d</b>) Higher-magnification views of the boxed areas in <b>a</b> and <b>c</b>, respectively. (<b>e</b>) NIH 3T3 cells stably expressing EGFP-<named-entity id="named-entity-468">Parkin</named-entity> were incubated in the absence or presence of <named-entity id="named-entity-469">CCCP</named-entity> (30 μM) for 4 h, after which whole-cell homogenates as well as cytosolic, ER and mitochondrial fractions were prepared and subjected to immunoblot analysis. Scale bar (<b>a</b>–<b>d</b>), 10 μm.</p>
|
https://api.sourcedata.io/file.php?figure_id=3296
|
[
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"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": "FKBP38",
"type": "geneprod",
"uniprot_ids": [
"Q14318"
]
},
{
"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": "Q9P0L0",
"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": "VAP-A",
"type": "geneprod",
"uniprot_ids": [
"Q9P0L0"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q9P0L0",
"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": "VAP-A",
"type": "geneprod",
"uniprot_ids": [
"Q9P0L0"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q9P0L0",
"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": "VAP-A",
"type": "geneprod",
"uniprot_ids": [
"Q9P0L0"
]
},
{
"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"
]
}
] |
|
23361001
|
10.1038/ncomms2400
|
Selective escape of proteins from the mitochondria during mitophagy
|
2013
|
f3
|
<p>(<b>a</b>) MEFs stably expressing EGFP-tagged wild-type (WT) or T240R mutant forms of <named-entity id="named-entity-472">Parkin</named-entity> as well as <named-entity id="named-entity-473">FLAG</named-entity>-tagged <named-entity id="named-entity-474">VAP-A</named-entity> were incubated in the absence or presence of <named-entity id="named-entity-475">CCCP</named-entity> (30 μM) for 24 h, fixed, permeabilized and subjected to immunofluorescence analysis with antibodies to <named-entity id="named-entity-476">FKBP38</named-entity>, to <named-entity id="named-entity-477">FLAG</named-entity> (M2) and to <named-entity id="named-entity-478">cytochrome <i>c</i></named-entity>. The fluorescence of EGFP was also monitored directly. (<b>b</b>) MEFs as in <b>a</b> were treated with <named-entity id="named-entity-479">CCCP</named-entity> (30 μM) for the indicated times and then subjected to immunoblot analysis. (<b>c</b>) MEFs stably expressing EGFP-<named-entity id="named-entity-480">Parkin</named-entity> and <named-entity id="named-entity-481">FLAG</named-entity>-<named-entity id="named-entity-482">VAP-A</named-entity> were incubated in the absence or presence of <named-entity id="named-entity-483">CCCP</named-entity> (30 μM) and <named-entity id="named-entity-484">lactacystin</named-entity> (10 μM) for 24 h, fixed, permeabilized and subjected to immunofluorescence analysis with antibodies to <named-entity id="named-entity-485">FKBP38</named-entity>, to <named-entity id="named-entity-486">FLAG</named-entity> (M2) and to <named-entity id="named-entity-487">cytochrome <b>c</b></named-entity>. The fluorescence of EGFP-<named-entity id="named-entity-488">Parkin</named-entity> was also monitored directly. (<b>d</b>) MEFs stably expressing EGFP-<named-entity id="named-entity-489">Parkin</named-entity> were incubated for 12 h in the absence or presence of <named-entity id="named-entity-490">CCCP</named-entity> (30 μM) and <named-entity id="named-entity-491">lactacystin</named-entity> (10 μM) as indicated and then subjected to immunoblot analysis. Scale bar (<b>a</b>,<b>c</b>), 10 μm.</p>
|
https://api.sourcedata.io/file.php?figure_id=3297
|
[
{
"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": "Uniprot",
"ext_ids": "P62897",
"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": "cytochrome c",
"type": "geneprod",
"uniprot_ids": [
"P62897"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "O35465",
"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": "FKBP38",
"type": "geneprod",
"uniprot_ids": [
"O35465"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q9WV55",
"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": "VAP-A",
"type": "geneprod",
"uniprot_ids": [
"Q9WV55"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P62897",
"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": "cytochrome c",
"type": "geneprod",
"uniprot_ids": [
"P62897"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "O35465",
"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": "FKBP38",
"type": "geneprod",
"uniprot_ids": [
"O35465"
]
},
{
"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",
"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",
"ext_ids": "Q9WV55",
"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": "VAP-A",
"type": "geneprod",
"uniprot_ids": [
"Q9WV55"
]
},
{
"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"
]
}
] |
|
23361001
|
10.1038/ncomms2400
|
Selective escape of proteins from the mitochondria during mitophagy
|
2013
|
f4
|
<p>(<b>a</b>) Domain organization of <named-entity id="named-entity-493">FKBP38</named-entity>, <named-entity id="named-entity-494">Omp25</named-entity> and the chimeric proteins <named-entity id="named-entity-495">Omp25</named-entity>/<named-entity id="named-entity-496">FKBP38</named-entity> and <named-entity id="named-entity-497">FKBP38</named-entity>/<named-entity id="named-entity-498">Omp25</named-entity>, as well as a summary of their localization and ability to undergo translocation during mitophagy as determined in (<b>b</b>). (<b>b</b>) MEFs stably expressing <named-entity id="named-entity-499">FLAG</named-entity>-<named-entity id="named-entity-500">Parkin</named-entity> and EGFP-tagged forms of <named-entity id="named-entity-501">FKBP38</named-entity>, <named-entity id="named-entity-502">Omp25</named-entity>, <named-entity id="named-entity-503">Omp25</named-entity>/<named-entity id="named-entity-504">FKBP38</named-entity> or <named-entity id="named-entity-505">FKBP38</named-entity>/<named-entity id="named-entity-506">Omp25</named-entity> were treated with <named-entity id="named-entity-507">CCCP</named-entity> (30 μM) for 4 h, fixed, permeabilized and subjected to immunofluorescence analysis with antibodies to <named-entity id="named-entity-508">cytochrome <i>c</i></named-entity> and to <named-entity id="named-entity-509">FLAG</named-entity> (rabbit polyclonal). The fluorescence of EGFP was also monitored directly. Scale bar, 10 μm. (<b>c</b>) MEFs stably expressing mCherry-tagged <named-entity id="named-entity-510">Parkin</named-entity> and EGFP-tagged forms of <named-entity id="named-entity-511">FKBP38</named-entity>, <named-entity id="named-entity-512">Omp25</named-entity>, <named-entity id="named-entity-513">Omp25</named-entity>/<named-entity id="named-entity-514">FKBP38</named-entity> or <named-entity id="named-entity-515">FKBP38</named-entity>/<named-entity id="named-entity-516">Omp25</named-entity> were incubated in the absence or presence of <named-entity id="named-entity-517">CCCP</named-entity> (30 μM) for 24 h and then subjected to immunoblot analysis.</p>
|
https://api.sourcedata.io/file.php?figure_id=3298
|
[
{
"ext_dbs": "NCBI gene",
"ext_ids": "14232",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "14232",
"original_type": "gene",
"role": "intervention",
"text": "FKBP38",
"type": "geneprod",
"uniprot_ids": [
"O35465"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "24071",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "24071",
"original_type": "gene",
"role": "intervention",
"text": "Omp25",
"type": "geneprod",
"uniprot_ids": [
"Q9D6K5"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "24071",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "24071",
"original_type": "gene",
"role": "intervention",
"text": "Omp25",
"type": "geneprod",
"uniprot_ids": [
"Q9D6K5"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P62897",
"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": "cytochrome c",
"type": "geneprod",
"uniprot_ids": [
"P62897"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "O35465",
"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": "FKBP38",
"type": "geneprod",
"uniprot_ids": [
"O35465"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "O35465",
"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": "FKBP38",
"type": "geneprod",
"uniprot_ids": [
"O35465"
]
},
{
"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",
"ext_ids": "Q9D6K5",
"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": "Omp25",
"type": "geneprod",
"uniprot_ids": [
"Q9D6K5"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "14232",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "14232",
"original_type": "gene",
"role": "intervention",
"text": "FKBP38",
"type": "geneprod",
"uniprot_ids": [
"O35465"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "24071",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "24071",
"original_type": "gene",
"role": "intervention",
"text": "Omp25",
"type": "geneprod",
"uniprot_ids": [
"Q9D6K5"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "24071",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "24071",
"original_type": "gene",
"role": "intervention",
"text": "Omp25",
"type": "geneprod",
"uniprot_ids": [
"Q9D6K5"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "O35465",
"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": "FKBP38",
"type": "geneprod",
"uniprot_ids": [
"O35465"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "O35465",
"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": "FKBP38",
"type": "geneprod",
"uniprot_ids": [
"O35465"
]
},
{
"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",
"ext_ids": "Q9D6K5",
"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": "Omp25",
"type": "geneprod",
"uniprot_ids": [
"Q9D6K5"
]
}
] |
|
23361001
|
10.1038/ncomms2400
|
Selective escape of proteins from the mitochondria during mitophagy
|
2013
|
f5
|
<p>(<b>a</b>) MEFs stably expressing <named-entity id="named-entity-520">FLAG</named-entity>-<named-entity id="named-entity-521">Parkin</named-entity> and either EGFP-<named-entity id="named-entity-522">Bcl-2</named-entity> or EGFP-<named-entity id="named-entity-523">Bcl-x<sub>L</sub></named-entity> were incubated in the absence or presence of <named-entity id="named-entity-524">CCCP</named-entity> (30 μM) for 24 h and then subjected to immunoblot analysis. (<b>b</b>) Domain organization of <named-entity id="named-entity-525">Bcl-2</named-entity>, <named-entity id="named-entity-526">Bcl-x<sub>L</sub></named-entity>, and the chimeric proteins <named-entity id="named-entity-527">Bcl-2</named-entity>/x<sub>L</sub> and <named-entity id="named-entity-528">Bcl-x<sub>L</sub></named-entity>/2, as well as a summary of their localization and ability to translocate during mitophagy, as determined in <b>c</b>. (<b>c</b>) MEFs stably expressing <named-entity id="named-entity-529">FLAG</named-entity>-<named-entity id="named-entity-530">Parkin</named-entity> and EGFP-tagged forms of <named-entity id="named-entity-531">Bcl-2</named-entity>, Bcl-x<sub>L,</sub> <named-entity id="named-entity-532">Bcl-2</named-entity>/x<sub>L</sub> or <named-entity id="named-entity-533">Bcl-x<sub>L</sub></named-entity>/2 were incubated in the absence or presence of <named-entity id="named-entity-534">CCCP</named-entity> (30 μM) for 4 h, fixed, permeabilized and subjected to immunofluorescence analysis with antibodies to <named-entity id="named-entity-535">cytochrome <i>c</i></named-entity> and to <named-entity id="named-entity-536">FLAG</named-entity> (rabbit polyclonal). The fluorescence of EGFP was also monitored directly. (<b>d</b>) Higher-magnification views of the boxed areas in <b>c</b>. Scale bar (<b>c</b>,<b>d</b>), 10 μm.</p>
|
https://api.sourcedata.io/file.php?figure_id=3299
|
[
{
"ext_dbs": "NCBI gene",
"ext_ids": "12043",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "12043",
"original_type": "gene",
"role": "intervention",
"text": "Bcl-2",
"type": "geneprod",
"uniprot_ids": [
"P10417",
"Q6NTH7",
"Q8BQK4"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "12048",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "12048",
"original_type": "gene",
"role": "intervention",
"text": "Bcl-xL",
"type": "geneprod",
"uniprot_ids": [
"Q64373",
"O35843",
"Q5HZH3"
]
},
{
"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": "NCBI gene",
"ext_ids": "12043",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "12043",
"original_type": "gene",
"role": "intervention",
"text": "Bcl-2",
"type": "geneprod",
"uniprot_ids": [
"P10417",
"Q6NTH7",
"Q8BQK4"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "12048",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "12048",
"original_type": "gene",
"role": "intervention",
"text": "Bcl-xL,",
"type": "geneprod",
"uniprot_ids": [
"Q64373",
"O35843",
"Q5HZH3"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P10417",
"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": "Bcl-2",
"type": "geneprod",
"uniprot_ids": [
"P10417"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q64373",
"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": "Bcl-xL",
"type": "geneprod",
"uniprot_ids": [
"Q64373"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P62897",
"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": "cytochrome c",
"type": "geneprod",
"uniprot_ids": [
"P62897"
]
},
{
"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"
]
}
] |
|
23361001
|
10.1038/ncomms2400
|
Selective escape of proteins from the mitochondria during mitophagy
|
2013
|
f7
|
<p>(<b>a</b>) MEFs stably expressing EGFP-<named-entity id="named-entity-537">FKBP38</named-entity>(N402K) and <named-entity id="named-entity-538">FLAG</named-entity>-<named-entity id="named-entity-539">Parkin</named-entity> were incubated in the absence or presence of <named-entity id="named-entity-540">CCCP</named-entity> (30 μM) for 4 h, fixed, permeabilized and subjected to immunofluorescence analysis with antibodies to <named-entity id="named-entity-541">cytochrome <i>c</i></named-entity> and to <named-entity id="named-entity-542">FLAG</named-entity> (rabbit polyclonal). The fluorescence of EGFP-<named-entity id="named-entity-543">FKBP38</named-entity>(N402K) was also monitored directly. Higher-magnification views of the boxed areas are shown in the right panels of each set. (<b>b</b>) MEFs stably expressing EGFP-<named-entity id="named-entity-544">FKBP38</named-entity>(N402K), mCherry-<named-entity id="named-entity-545">FKBP38</named-entity> and <named-entity id="named-entity-546">FLAG</named-entity>-<named-entity id="named-entity-547">Parkin</named-entity> were incubated in the absence or presence of <named-entity id="named-entity-548">CCCP</named-entity> (30 μM) for 4 h, fixed, permeabilized and subjected to immunofluorescence analysis with antibodies to <named-entity id="named-entity-549">FLAG</named-entity> (M2). The fluorescence of EGFP-<named-entity id="named-entity-550">FKBP38</named-entity>(N402K) and mCherry-<named-entity id="named-entity-551">FKBP38</named-entity> was also monitored directly. (<b>c</b>) MEFs stably expressing <named-entity id="named-entity-552">FLAG</named-entity>-<named-entity id="named-entity-553">Parkin</named-entity> and either EGFP-<named-entity id="named-entity-554">FKBP38</named-entity> or EGFP-<named-entity id="named-entity-555">FKBP38</named-entity>(N402K) were incubated in the absence or presence of <named-entity id="named-entity-556">CCCP</named-entity> (30 μM) for 24 h and then subjected to immunoblot analysis. (<b>d</b>) Densitometric quantitation of EGFP fusion protein abundance in immunoblots similar to those in (<b>c</b>). Data are expressed relative to the corresponding control value (<named-entity id="named-entity-557">CCCP</named-entity> 0 h) and are means±s.d., from three independent experiments. **<i>P</i>0.01 (Student’s <i>t</i> test). (<b>e</b>) MEFs stably expressing EGFP-<named-entity id="named-entity-558">Bcl-2</named-entity>(H235R) and <named-entity id="named-entity-559">FLAG</named-entity>-<named-entity id="named-entity-560">Parkin</named-entity> were incubated in the absence or presence of <named-entity id="named-entity-561">CCCP</named-entity> (30 μM) for 4 h, fixed, permeabilized and subjected to immunofluorescence analysis with antibodies to <named-entity id="named-entity-562">cytochrome <i>c</i></named-entity> and to <named-entity id="named-entity-563">FLAG</named-entity> (rabbit polyclonal). The fluorescence of EGFP-<named-entity id="named-entity-564">Bcl-2</named-entity>(H235R) was also monitored directly. Higher-magnification views of the boxed areas are shown in the right panels of each set. (<b>f</b>) Photoconversion assay with KikGR fusion proteins. Cells are exposed to UV (364 nm) and then treated with <named-entity id="named-entity-565">CCCP</named-entity> to induce mitophagy. Red signals represent preexisting protein, whereas green signals represent newly synthesized protein. (<b>g</b>) HeLa cells stably expressing <named-entity id="named-entity-566">FLAG</named-entity>-<named-entity id="named-entity-567">Parkin</named-entity> were transiently transfected with vectors for KikGR-<named-entity id="named-entity-568">FKBP38</named-entity>ΔN47 or KikGR-<named-entity id="named-entity-569">FKBP38</named-entity>ΔN47(N402K), exposed to UV, incubated in the absence or presence of <named-entity id="named-entity-570">CCCP</named-entity> (10 μM) for 4 h, and then monitored for red and green KikGR fluorescence. Scale bar (<b>a</b>,<b>b</b>,<b>e</b>,<b>g</b>), 10 μm.</p>
|
https://api.sourcedata.io/file.php?figure_id=3301
|
[
{
"ext_dbs": "Uniprot",
"ext_ids": "P62897",
"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": "cytochrome c",
"type": "geneprod",
"uniprot_ids": [
"P62897"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "O35465",
"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": "FKBP38",
"type": "geneprod",
"uniprot_ids": [
"O35465"
]
},
{
"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": "NCBI gene",
"ext_ids": "14232",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "14232",
"original_type": "gene",
"role": "intervention",
"text": "FKBP38",
"type": "geneprod",
"uniprot_ids": [
"O35465"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "O35465",
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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": "FKBP38",
"type": "geneprod",
"uniprot_ids": [
"O35465"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "O35465",
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"ext_tax_names": "Mus musculus",
"mapping_source": "direct",
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"ncbi_gene_id": null,
"original_type": "protein",
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"text": "FKBP38",
"type": "geneprod",
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"O35465"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "O35465",
"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": "FKBP38",
"type": "geneprod",
"uniprot_ids": [
"O35465"
]
},
{
"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": "NCBI gene",
"ext_ids": "14232",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "14232",
"original_type": "gene",
"role": "intervention",
"text": "FKBP38",
"type": "geneprod",
"uniprot_ids": [
"O35465"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "O35465",
"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": "FKBP38",
"type": "geneprod",
"uniprot_ids": [
"O35465"
]
},
{
"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",
"ext_ids": "P10417",
"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": "Bcl-2",
"type": "geneprod",
"uniprot_ids": [
"P10417"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P62897",
"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": "cytochrome c",
"type": "geneprod",
"uniprot_ids": [
"P62897"
]
},
{
"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": "NCBI gene",
"ext_ids": "23770",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "23770",
"original_type": "gene",
"role": "intervention",
"text": "FKBP38",
"type": "geneprod",
"uniprot_ids": [
"Q14318",
"B2R8G6"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q14318",
"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": "FKBP38",
"type": "geneprod",
"uniprot_ids": [
"Q14318"
]
}
] |
|
23361001
|
10.1038/ncomms2400
|
Selective escape of proteins from the mitochondria during mitophagy
|
2013
|
f8
|
<p>(<b>a</b>) Wild-type (<i><named-entity id="named-entity-572">Mfn2</named-entity></i><super>+/+</super>) and <i><named-entity id="named-entity-573">Mfn2</named-entity></i> knockout (<i><named-entity id="named-entity-574">Mfn2</named-entity></i><super>–/–</super>) MEFs stably expressing mCherry-<named-entity id="named-entity-575">Parkin</named-entity> were incubated in the absence or presence of <named-entity id="named-entity-576">CCCP</named-entity> (30 μM) for 4 h, fixed, permeabilized and subjected to immunofluorescence analysis with antibodies to <named-entity id="named-entity-577">FKBP38</named-entity> and to <named-entity id="named-entity-578">cytochrome <i>c</i></named-entity>. The fluorescence of mCherry-<named-entity id="named-entity-579">Parkin</named-entity> was also monitored directly. (<b>b</b>) MEFs as in <b>a</b> but expressing EGFP-<named-entity id="named-entity-580">Parkin</named-entity> were treated with <named-entity id="named-entity-581">CCCP</named-entity> (30 μM) for the indicated times and then subjected to immunoblot analysis. The asterisk indicates a nonspecific band. (<b>c</b>) Wild-type MEFs stably expressing EGFP-<named-entity id="named-entity-582">Parkin</named-entity> and <named-entity id="named-entity-583">FLAG</named-entity>-<named-entity id="named-entity-584">VAP-A</named-entity> were incubated in the absence or presence of <named-entity id="named-entity-585">CCCP</named-entity> (30 μM) or <named-entity id="named-entity-586">nocodazole</named-entity> (10 μM) for 6 h as indicated, fixed, permeabilized and subjected to immunofluorescence analysis with antibodies to <named-entity id="named-entity-587">cytochrome <i>c</i></named-entity>, to <named-entity id="named-entity-588">FLAG</named-entity> and to <named-entity id="named-entity-589">FKBP38</named-entity>. The fluorescence of EGFP-<named-entity id="named-entity-590">Parkin</named-entity> was also monitored directly. (<b>d</b>) Higher-magnification views of the boxed areas in (<b>c</b>,<b>e</b>). Wild-type MEFs stably expressing <named-entity id="named-entity-591">FLAG</named-entity>-<named-entity id="named-entity-592">Parkin</named-entity> and EGFP-<named-entity id="named-entity-593">FKBP38</named-entity> were incubated in the absence or presence of <named-entity id="named-entity-594">CCCP</named-entity> (30 μM) for 10 h and then subjected to immuno-electron microscopic analysis with antibodies to GFP. Black arrowheads indicate the mitochondria. White arrowheads indicate small vesicle. (<b>f</b>) Wild-type (<i><named-entity id="named-entity-595">Fkbp38</named-entity></i><super>+/+</super>) and <i><named-entity id="named-entity-596">Fkbp38</named-entity></i> knockout (<i><named-entity id="named-entity-597">Fkbp38</named-entity></i><super>−/−</super>) MEFs stably expressing <named-entity id="named-entity-598">FLAG</named-entity>-<named-entity id="named-entity-599">Parkin</named-entity> and either EGFP or EGFP-<named-entity id="named-entity-600">FKBP38</named-entity> were incubated in the absence or presence of <named-entity id="named-entity-601">CCCP</named-entity> (30 μM) for 24 h and then stained with allophycocyanin (APC)-labelled <named-entity id="named-entity-602">annexin V</named-entity> and <named-entity id="named-entity-603">propidium iodide</named-entity> (<named-entity id="named-entity-604">PI</named-entity>) for flow cytometric analysis of the percentage of apoptotic cells (<named-entity id="named-entity-605">annexin V</named-entity><super>+</super> and PI<super>+</super> cells). Data are means±s.d., from three independent experiments. (<b>g</b>) Model for <named-entity id="named-entity-606">FKBP38</named-entity> and <named-entity id="named-entity-607">Bcl-2</named-entity> translocation from the mitochondria. Damaged mitochondria accumulate <named-entity id="named-entity-608">PINK1</named-entity> and recruit <named-entity id="named-entity-609">Parkin</named-entity>. <named-entity id="named-entity-610">FKBP38</named-entity> and <named-entity id="named-entity-611">Bcl-2</named-entity> then translocate from the damaged mitochondria to the ER in order to escape degradation during mitophagy. Scale bars (<b>a</b>,<b>c</b>,<b>d</b>), 10 μm; (<b>e</b>), 500 nm.</p>
|
https://api.sourcedata.io/file.php?figure_id=3302
|
[
{
"ext_dbs": "NCBI gene",
"ext_ids": "170731",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "170731",
"original_type": "gene",
"role": "intervention",
"text": "Mfn2",
"type": "geneprod",
"uniprot_ids": [
"Q80U63"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "170731",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "170731",
"original_type": "gene",
"role": "intervention",
"text": "Mfn2",
"type": "geneprod",
"uniprot_ids": [
"Q80U63"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "170731",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "170731",
"original_type": "gene",
"role": "intervention",
"text": "Mfn2",
"type": "geneprod",
"uniprot_ids": [
"Q80U63"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P62897",
"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": "cytochrome c",
"type": "geneprod",
"uniprot_ids": [
"P62897"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "O35465",
"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": "FKBP38",
"type": "geneprod",
"uniprot_ids": [
"O35465"
]
},
{
"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",
"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",
"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",
"ext_ids": "P62897",
"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": "cytochrome c",
"type": "geneprod",
"uniprot_ids": [
"P62897"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "O35465",
"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": "FKBP38",
"type": "geneprod",
"uniprot_ids": [
"O35465"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "O35465",
"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": "FKBP38",
"type": "geneprod",
"uniprot_ids": [
"O35465"
]
},
{
"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",
"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",
"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",
"ext_ids": "Q9WV55",
"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": "VAP-A",
"type": "geneprod",
"uniprot_ids": [
"Q9WV55"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "14232",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "14232",
"original_type": "gene",
"role": "intervention",
"text": "Fkbp38",
"type": "geneprod",
"uniprot_ids": [
"O35465"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "14232",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "14232",
"original_type": "gene",
"role": "intervention",
"text": "Fkbp38",
"type": "geneprod",
"uniprot_ids": [
"O35465"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "14232",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "14232",
"original_type": "gene",
"role": "intervention",
"text": "Fkbp38",
"type": "geneprod",
"uniprot_ids": [
"O35465"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "14232",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "14232",
"original_type": "gene",
"role": "intervention",
"text": "FKBP38",
"type": "geneprod",
"uniprot_ids": [
"O35465"
]
}
] |
|
30446498
|
10.15252/emmm.201808861
|
Rescuing ocular development in an anophthalmic pig by blastocyst complementation
|
2018
|
Figure 1
|
<sd-panel><p><strong>Figure 1. Generation of <sd-pretag id="sdPretag79349800sm" type="geneprod" role="component">E44</sd-pretag> chimeric porcine fetus <em>in vivo</em> by complementation of <em>MITF</em><sup>L247S/L247S</sup> <sd-pretag id="sdPretag2065220650sm" type="organism" role="component">embryos</sd-pretag> with donor <sd-pretag id="sdPretag1853898710sm" type="subcellular" role="component">blastomeres</sd-pretag> derived from LW <sd-pretag id="sdPretag1209747957sm" type="cell" role="component">PEFs</sd-pretag></strong>.</p><p> (A) Four fetuses (named <sd-pretag id="sdPretag1112163449sm" type="geneprod" role="intervention">NW-1</sd-pretag>, <sd-pretag id="sdPretag1202430837sm" type="geneprod" role="intervention">NW-2</sd-pretag>, <sd-pretag id="sdPretag725699367sm" type="geneprod" role="intervention">NW-3</sd-pretag> and <sd-pretag id="sdPretag318020663sm" type="geneprod" role="component">NW-4</sd-pretag>) with different <sd-pretag id="sdPretag232431560sm" type="tissue" role="component">eye</sd-pretag> morphology were retrieved at E44 by caesarean section.</p><p> (B) <sd-pretag id="sdPretag821797955sm" type="geneprod" role="intervention">DraI</sd-pretag> digestion of <sd-pretag id="sdPretag960327611sm" category="assay">PCR</sd-pretag> products from the multiple organs of the four fetuses (Upper). NC, negative control with no genomic <sd-pretag id="sdPretag2038315795sm" type="molecule" role="assayed">DNA</sd-pretag> loaded. Mut, <em>MITF</em><sup>L247S/L247S</sup> genomic <sd-pretag id="sdPretag995244443sm" type="molecule" role="assayed">DNA</sd-pretag> loaded. WT, LW genomic <sd-pretag id="sdPretag324988943sm" type="molecule" role="assayed">DNA</sd-pretag> loaded. Multiple organs of the four fetuses were examined for <sd-pretag id="sdPretag1817286046sm" type="geneprod_organism" role="assayed"><em>KIT</em></sd-pretag> expression by agarose <sd-pretag id="sdPretag1031203320sm" category="assay">gel electrophoresis</sd-pretag> (Bottom). Mut, <em>MITF</em><sup>L247S/L247S</sup> genomic <sd-pretag id="sdPretag923167362sm" type="molecule" role="component">DNA</sd-pretag> loaded. WT, LW genomic DNA loaded.</p></sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=23580
|
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{
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"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "396810",
"original_type": "gene",
"role": "assayed",
"text": "KIT",
"type": "geneprod",
"uniprot_ids": [
"Q2HWD6"
]
},
{
"ext_dbs": "NCBI gene",
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"A0A8D1UQM7",
"A0A8D1UQU3",
"D2JUK1",
"D2JUK2",
"D2JUK3",
"I3LTE0",
"Q4LE87"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "414902",
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"ext_tax_names": "Sus scrofa",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "414902",
"original_type": "gene",
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"text": "MITF",
"type": "geneprod",
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}
] |
|
30446498
|
10.15252/emmm.201808861
|
Rescuing ocular development in an anophthalmic pig by blastocyst complementation
|
2018
|
Figure 2
|
<sd-panel><p><strong>Figure 2. Allogenic contribution and rescue RPEs in the E44 chimeric fetus.</strong></p><p> (A) Representative microscopic appearances of the <sd-pretag id="sdPretag1413052602sm" type="tissue" role="component">retina</sd-pretag> and <sd-pretag id="sdPretag1017085490sm" type="cell_tissue" role="component">RPE</sd-pretag> cells (arrowhead) of a chimeric, a WT and a Mut fetus at the same gestational age by H&E staining. WT, Bama WT fetus. Mut, Bama <em>MITF</em><sup>L247S/L247S</sup> fetus. NW-2, the chimeric fetus. Scale bars, 100 μm.</p><p> (B) Representative <sd-pretag id="sdPretag953057200sm" category="assay">immunofluorescence</sd-pretag> images showed the expression of multiple <sd-pretag id="sdPretag651467873sm" type="tissue" role="component">RPE</sd-pretag> markers <sd-pretag id="sdPretag484048590sm" type="geneprod" role="assayed"><em>Pax6</em></sd-pretag>, <sd-pretag id="sdPretag794142786sm" type="geneprod" role="assayed"><em>MITF</em></sd-pretag> and <sd-pretag id="sdPretag969999277sm" type="geneprod" role="assayed"><em>Bestrophin</em></sd-pretag> in the chimeric fetuses. Blue, Hochst3342. WT, Bama WT fetus as positive control. NW-2, the chimeric fetus. MITF<sup>L247S/L247S</sup> fetus as negative control. Scale bars, 50 μm.</p></sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=23582
|
[
{
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"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "414902",
"original_type": "gene",
"role": "intervention",
"text": "MITF",
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"A0A8D1BHD2",
"A0A8D1RBX1",
"A0A8D1UQM7",
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"D2JUK1",
"D2JUK2",
"D2JUK3",
"I3LTE0",
"Q4LE87"
]
},
{
"ext_dbs": "NCBI gene",
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"A0A287B431",
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"A0A8D1RBX1",
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"A0A8D1UQU3",
"D2JUK1",
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},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q8WMR7",
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"ext_tax_names": "Sus scrofa",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "Bestrophin",
"type": "geneprod",
"uniprot_ids": [
"Q8WMR7"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q4LE87",
"ext_tax_ids": "9823",
"ext_tax_names": "Sus scrofa",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
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"text": "MITF",
"type": "geneprod",
"uniprot_ids": [
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]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "A0A286ZPU0",
"ext_tax_ids": "9823",
"ext_tax_names": "Sus scrofa",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
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"role": "assayed",
"text": "Pax6",
"type": "geneprod",
"uniprot_ids": [
"A0A286ZPU0"
]
}
] |
|
30446498
|
10.15252/emmm.201808861
|
Rescuing ocular development in an anophthalmic pig by blastocyst complementation
|
2018
|
Figure 3
|
<sd-panel><p><strong>Figure 3. Characterized porcine <sd-pretag id="sdPretag1005027746sm" type="cell" role="component">RPE</sd-pretag> cells derived from E60 chimeric fetus by complementation of Bama <em>MITF</em><sup>L247S/L247S</sup> <sd-pretag id="sdPretag1253736785sm" type="organism" role="component">embryos</sd-pretag> with WT <sd-pretag id="sdPretag715347726sm" type="subcellular" role="component">blastomeres</sd-pretag></strong>.</p><p> (A) Representative <sd-pretag id="sdPretag2093106997sm" category="assay">light microscopic</sd-pretag> images show that the <em>in vitro</em> cultured <sd-pretag id="sdPretag761584729sm" type="cell" role="component">RPE</sd-pretag> cells exhibited a hexagonal shape. D3, D5 and D11, cultured for 3 days, 5 days and 11 days, respectively. Scale bars, 100 μm.</p><p> (B, C and D) Representative <sd-pretag id="sdPretag533036900sm" category="assay">immunofluorescence</sd-pretag> images showed the expression of <sd-pretag id="sdPretag158914414sm" type="geneprod_tissue" role="assayed">RPE</sd-pretag>-specific markers, including <sd-pretag id="sdPretag1828952243sm" type="geneprod" role="assayed"><em>RPE65</em></sd-pretag> (B), <sd-pretag id="sdPretag580147178sm" type="geneprod" role="assayed"><em>ZO-1</em></sd-pretag> (C) and <sd-pretag id="sdPretag1436449734sm" type="geneprod" role="assayed"><em>Bestrophin</em></sd-pretag> (D), respectively, in the cultured <sd-pretag id="sdPretag628399865sm" type="cell_tissue" role="component">RPE</sd-pretag> cells. Scale bars, 50 μm.</p><p> (E) Semi-<sd-pretag id="sdPretag77347900sm" category="assay">quantitative RT</sd-pretag>-<sd-pretag id="sdPretag869838032sm" category="assay">PCR</sd-pretag> analysis of <sd-pretag id="sdPretag120569663sm" type="tissue" role="component">RPE</sd-pretag> functional markers in cultured porcine <sd-pretag id="sdPretag2009996037sm" type="cell_tissue" role="component">RPE</sd-pretag> cells. <sd-pretag id="sdPretag1233517087sm" type="geneprod" role="component"><em>GAPDH</em></sd-pretag> was used to confirm the cDNA quality of all the samples.</p><p> (F) <sd-pretag id="sdPretag1180365098sm" category="assay">Western blotting</sd-pretag> identified three RPE markers in porcine <sd-pretag id="sdPretag553124676sm" type="cell" role="component">RPE</sd-pretag> cells. <sd-pretag id="sdPretag1983613368sm" type="geneprod" role="component"><em>GAPDH</em></sd-pretag> served as a housekeeping gene control.</p><p> (G) <sd-pretag id="sdPretag830121697sm" category="assay">ELISA</sd-pretag> identified secreted <sd-pretag id="sdPretag1434103010sm" type="geneprod" role="assayed">VEGF</sd-pretag> and <sd-pretag id="sdPretag2126952215sm" type="geneprod" role="assayed">PEDF</sd-pretag> in chimeric and WT porcine <sd-pretag id="sdPretag1014402736sm" type="cell_tissue" role="component">RPE</sd-pretag> cells. Media were collected at 48 hours after the cells were seeded onto 12-well cell culture plates to be used for analyses. The results are representative of three independent experiments and were evaluated using a two-tailed t-test. No significant differences were identified. Data are presented as the mean ± standard error mean (SEM). WT, <sd-pretag id="sdPretag2108019546sm" type="cell" role="component">RPE</sd-pretag> cells cultured from the NW-8 fetus. <sd-pretag id="sdPretag1883030509sm" type="cell" role="component">CH</sd-pretag>, <sd-pretag id="sdPretag319844882sm" type="cell" role="component">RPE</sd-pretag> cells cultured from chimeric NW-7 fetus.</p></sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=23584
|
[
{
"ext_dbs": "Uniprot",
"ext_ids": "F1S830",
"ext_tax_ids": "9823",
"ext_tax_names": "Sus scrofa",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "RPE65",
"type": "geneprod",
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"F1S830"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q8WMR7",
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"ext_tax_names": "Sus scrofa",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
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"text": "Bestrophin",
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},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q7YS63",
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"ext_tax_names": "Sus scrofa",
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"mapping_status": "mapped",
"ncbi_gene_id": null,
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"text": "ZO-1",
"type": "geneprod",
"uniprot_ids": [
"Q7YS63"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q0PM28",
"ext_tax_ids": "9823",
"ext_tax_names": "Sus scrofa",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "PEDF",
"type": "geneprod",
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},
{
"ext_dbs": "Uniprot///Uniprot",
"ext_ids": "F1RQ05///P49151",
"ext_tax_ids": "9823///9823",
"ext_tax_names": "Sus scrofa///Sus scrofa",
"mapping_source": "unknown",
"mapping_status": "unmapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "VEGF",
"type": "geneprod",
"uniprot_ids": []
}
] |
|
30446498
|
10.15252/emmm.201808861
|
Rescuing ocular development in an anophthalmic pig by blastocyst complementation
|
2018
|
Figure 4
|
<sd-panel><p><strong>Figure 4. Generation of a full-term chimeric piglet from Bama <em>MITF</em><sup>L247S/L247S</sup> cloned and <sd-pretag id="sdPretag2027047403sm" type="geneprod" role="intervention">Bama</sd-pretag><sd-pretag id="sdPretag1597574091sm" type="geneprod" role="reporter"> GFP</sd-pretag>-labeled cloned <sd-pretag id="sdPretag303336625sm" type="organism" role="component">embryos</sd-pretag></strong>.</p><p> (A) The full-term chimera (NW-16) piglet was born and showed normal development, size and morphology of the <sd-pretag id="sdPretag692722177sm" type="tissue" role="component">eyes</sd-pretag>.</p><p> (B) Digestion of the <em>MITF</em> <sd-pretag id="sdPretag287963768sm" category="assay">PCR</sd-pretag> products in multiple organs of the full-term chimeric pig. NC, negative control with no genomic <sd-pretag id="sdPretag930290757sm" type="molecule" role="component">DNA</sd-pretag> loaded. Mut, MITF<sup>L247S/L247S</sup> genomic DNA loaded. WT, Bama <sd-pretag id="sdPretag1567625636sm" type="geneprod" role="reporter">GFP</sd-pretag>-labeled genomic <sd-pretag id="sdPretag905447797sm" type="molecule" role="component">DNA</sd-pretag> loaded. In the chimera piglet, <em><sd-pretag id="sdPretag386417226sm" type="geneprod" role="reporter">GFP</sd-pretag>-</em>specific primers were used to further confirm the chimeric contribution to multiple organs in the piglet. <sd-pretag id="sdPretag737444812sm" type="geneprod" role="component"><em>GAPDH</em></sd-pretag> was used to confirm the DNA quality of all the samples. NC, negative control with no genomic <sd-pretag id="sdPretag190366047sm" type="molecule" role="component">DNA</sd-pretag> loaded. Mut, Bama <em>MITF</em><sup>L247S/L247S</sup> genomic <sd-pretag id="sdPretag1540726214sm" type="molecule" role="component">DNA</sd-pretag> loaded. WT, Bama <sd-pretag id="sdPretag534524440sm" type="geneprod" role="reporter">GFP</sd-pretag>-labeled genomic <sd-pretag id="sdPretag1940421850sm" type="molecule" role="assayed">DNA</sd-pretag> loaded.</p><p> (C) Representative <sd-pretag id="sdPretag1760223094sm" category="assay">microscopic</sd-pretag> appearances of the corneal <sd-pretag id="sdPretag1268644755sm" type="cell" role="component">epithelial cells</sd-pretag> of the chimeric piglet staining by H&E. Scale bars, 100 μm.</p><p> (D) Representative microscopic appearances of the <sd-pretag id="sdPretag863869535sm" type="tissue" role="component">retina</sd-pretag> cells of the chimeric piglet staining by H&E. Scale bars, 100 μm.</p></sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=23586
|
[
{
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"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "414902",
"original_type": "gene",
"role": "assayed",
"text": "MITF",
"type": "geneprod",
"uniprot_ids": [
"A0A287B431",
"A0A8D1BHD2",
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"A0A8D1UQM7",
"A0A8D1UQU3",
"D2JUK1",
"D2JUK2",
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"I3LTE0",
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},
{
"ext_dbs": "NCBI gene",
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"ext_tax_names": "Sus scrofa",
"mapping_source": "ncbi_gene",
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"text": "MITF",
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},
{
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"ncbi_gene_id": "414902",
"original_type": "gene",
"role": "intervention",
"text": "MITF",
"type": "geneprod",
"uniprot_ids": [
"A0A287B431",
"A0A8D1BHD2",
"A0A8D1RBX1",
"A0A8D1UQM7",
"A0A8D1UQU3",
"D2JUK1",
"D2JUK2",
"D2JUK3",
"I3LTE0",
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]
}
] |
|
30446498
|
10.15252/emmm.201808861
|
Rescuing ocular development in an anophthalmic pig by blastocyst complementation
|
2018
|
Figure 5
|
<sd-panel><p><strong>Figure 5. The <sd-pretag id="sdPretag899255035sm" type="cell" role="component">RPEs</sd-pretag> and corneal <sd-pretag id="sdPretag2129102321sm" type="cell" role="component">epithelial cells</sd-pretag> are <sd-pretag id="sdPretag1802481748sm" type="geneprod" role="reporter">GFP</sd-pretag>-labeled donor derived and characterized.</strong></p><p> (A) Representative <sd-pretag id="sdPretag1208546550sm" type="geneprod" role="reporter">GFP</sd-pretag>-labeled <sd-pretag id="sdPretag208451207sm" type="subcellular" role="component">blastomeres</sd-pretag> that contributed to the chimeric porcine <sd-pretag id="sdPretag1679955814sm" type="cell_tissue" role="component">RPE</sd-pretag> cells are shown with <sd-pretag id="sdPretag779330661sm" category="assay">immunofluorescence</sd-pretag> staining. Scale bars, 25 μm.</p><p> (B) Representative <sd-pretag id="sdPretag760907630sm" type="geneprod" role="reporter">GFP</sd-pretag>-labeled <sd-pretag id="sdPretag1334325226sm" type="subcellular" role="component">blastomeres</sd-pretag> that contributed to the chimeric porcine corneal <sd-pretag id="sdPretag1309610323sm" type="cell" role="component">epithelial cells</sd-pretag>. Almost all <sd-pretag id="sdPretag1520529515sm" type="cell" role="component">RPE</sd-pretag> cells and corneal <sd-pretag id="sdPretag1272580189sm" type="cell" role="component">epithelial cells</sd-pretag> of the chimera stained with anti-<sd-pretag id="sdPretag1529999619sm" type="geneprod" role="reporter">GFP</sd-pretag> antibody. Scale bars, 75 μm.</p><p> (C) Representative <sd-pretag id="sdPretag543873531sm" category="assay">immunofluorescence</sd-pretag> images showed the expression of an <sd-pretag id="sdPretag830180823sm" type="tissue" role="component">RPE</sd-pretag> marker (BEST) in <sd-pretag id="sdPretag715081749sm" type="geneprod" role="reporter">GFP</sd-pretag>-labeled cells. Scale bars, 50 μm.</p><p> (D) Representative <sd-pretag id="sdPretag993174659sm" category="assay">immunofluorescence</sd-pretag> images showed the expression of a <sd-pretag id="sdPretag202920372sm" type="cell" role="component">corneal epithelial cell</sd-pretag> marker (K12) in <sd-pretag id="sdPretag397427845sm" type="geneprod" role="reporter">GFP</sd-pretag>-labeled cells. WT, Bama WT piglet. Mut, Bama <em>MITF</em><sup>L247S/L247S</sup> piglet. CH, chimeric piglet. Scale bars, 50 μm.</p><p> <strong>Expanded View Figure Legends</strong></p></sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=23588
|
[
{
"ext_dbs": "Uniprot",
"ext_ids": "Q8WMR7",
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"ext_tax_names": "Sus scrofa",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "BEST",
"type": "geneprod",
"uniprot_ids": [
"Q8WMR7"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "F1RXG3",
"ext_tax_ids": "9823",
"ext_tax_names": "Sus scrofa",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "K12",
"type": "geneprod",
"uniprot_ids": [
"F1RXG3"
]
}
] |
|
10.1101/2020.01.31.929042
|
The novel coronavirus 2019 (2019-nCoV) uses the SARS-coronavirus receptor ACE2 and the cellular protease TMPRSS2 for entry into target cells
|
2020
|
Fig. 1.
|
<sd-panel> <p>2019-nCoV-S and SARS-S facilitates entry into a similar panel of mammalian cell lines.Analysis of 2019-nCoV-S expression (A) and pseudotype incorporation (B) by Western blot. Representative blots from three experiments are shown. ß-Actin (cell lysates) and VSV-M (particles) served as loading controls. (C) Cell lines of human and animal origin were inoculated with pseudotyped VSV harboring VSV-G, SARS-S or 2019-nCoV-S. At 16 h postinoculation, pseudotype entry was analyzed. Shown are the combined data of three experiments. Error bars indicate SEM.</p> </sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=31469
|
[
{
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"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": "2019-nCoV-S",
"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": "2019-nCoV-S",
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"P0DTC2"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "43740568",
"ext_tax_ids": "2697049",
"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": "2019-nCoV-S",
"type": "geneprod",
"uniprot_ids": [
"P0DTC2",
"A0A679G9E9",
"A0A6G7K2L4"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "1489668",
"ext_tax_ids": "694009",
"ext_tax_names": "Severe acute respiratory syndrome-related coronavirus",
"mapping_source": "unmapped",
"mapping_status": "unmapped",
"ncbi_gene_id": "1489668",
"original_type": "gene",
"role": "intervention",
"text": "SARS-S",
"type": "geneprod",
"uniprot_ids": []
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "1489834",
"ext_tax_ids": "11277",
"ext_tax_names": "Vesicular stomatitis Indiana virus",
"mapping_source": "unmapped",
"mapping_status": "unmapped",
"ncbi_gene_id": "1489834",
"original_type": "gene",
"role": "intervention",
"text": "VSV-G",
"type": "geneprod",
"uniprot_ids": []
}
] |
||
10.1101/2020.01.31.929042
|
The novel coronavirus 2019 (2019-nCoV) uses the SARS-coronavirus receptor ACE2 and the cellular protease TMPRSS2 for entry into target cells
|
2020
|
Fig. 2.
|
<sd-panel> <p>2019-nCoV-S utilizes ACE2 as cellular receptor.(A) The S protein of 2019-nCoV clusters phylogenetically with S proteins of known bat-associated betacoronaviruses (see also SI Figure 1 for more details). (B) Alignment of the receptor binding motif of SARS-S with corresponding sequences of bat-associated betacoronavirus S proteins that are able or unable to use ACE2 as cellular receptor reveals that 2019-nCoV possesses amino acid residues crucial for ACE2 binding. (C) 293T cells transiently expressing ACE2 of human (dark blue) or bat (light blue) origin, human APN (purple) or hDPP4 (green) were inoculated with pseudotyped VSV harboring VSV-G, SARS-S, 2019-nCoV-S, MERS-S or 229E-S. At 16 h postinoculation, pseudotype entry was analyzed. The average of three independent experiments is shown. Error bars indicate SEM.</p> </sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=31470
|
[
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"ext_tax_names": "Homo sapiens",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "59272",
"original_type": "gene",
"role": "intervention",
"text": "ACE2",
"type": "geneprod",
"uniprot_ids": [
"Q9BYF1",
"A0A7I2V4H0"
]
},
{
"ext_dbs": "NCBI gene",
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"ext_tax_names": "Homo sapiens",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "290",
"original_type": "gene",
"role": "intervention",
"text": "APN",
"type": "geneprod",
"uniprot_ids": [
"P15144",
"Q59E93"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "1803",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "1803",
"original_type": "gene",
"role": "intervention",
"text": "hDPP4",
"type": "geneprod",
"uniprot_ids": [
"P27487",
"A0A7I2V2X8"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "43740568",
"ext_tax_ids": "2697049",
"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": "2019-nCoV-S",
"type": "geneprod",
"uniprot_ids": [
"P0DTC2",
"A0A679G9E9",
"A0A6G7K2L4"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "918758",
"ext_tax_ids": "11137",
"ext_tax_names": "Human coronavirus 229E",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "918758",
"original_type": "gene",
"role": "intervention",
"text": "229E-S",
"type": "geneprod",
"uniprot_ids": [
"P15423"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "14254594",
"ext_tax_ids": "1335626",
"ext_tax_names": "Middle East respiratory syndrome-related coronavirus",
"mapping_source": "unmapped",
"mapping_status": "unmapped",
"ncbi_gene_id": "14254594",
"original_type": "gene",
"role": "intervention",
"text": "MERS-S",
"type": "geneprod",
"uniprot_ids": []
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "1489668",
"ext_tax_ids": "694009",
"ext_tax_names": "Severe acute respiratory syndrome-related coronavirus",
"mapping_source": "unmapped",
"mapping_status": "unmapped",
"ncbi_gene_id": "1489668",
"original_type": "gene",
"role": "intervention",
"text": "SARS-S",
"type": "geneprod",
"uniprot_ids": []
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "1489834",
"ext_tax_ids": "11277",
"ext_tax_names": "Vesicular stomatitis Indiana virus",
"mapping_source": "unmapped",
"mapping_status": "unmapped",
"ncbi_gene_id": "1489834",
"original_type": "gene",
"role": "intervention",
"text": "VSV-G",
"type": "geneprod",
"uniprot_ids": []
}
] |
||
10.1101/2020.01.31.929042
|
The novel coronavirus 2019 (2019-nCoV) uses the SARS-coronavirus receptor ACE2 and the cellular protease TMPRSS2 for entry into target cells
|
2020
|
Fig. 3.
|
<sd-panel> <p>2019-nCoV-S employs TMPRSS2 for S protein priming.Ammonium chloride (A), E64d (CatB/L inhibitor) (B) and/or camostat (TMPRSS2 inhibitor) (B) were added to the indicated target cells before transduction with pseudotypes bearing the indicated glycoproteins. (C) 293T cells transiently expressing ACE2 alone or in combination with TMPRSS2 were incubated with CatB/L inhibitor E64d or PBS as control and inoculated with pseudotypes bearing the indicated viral surface proteins. The average of three independent experiments is shown in panels A-C. Error bars indicate SEM. Statistical significance was tested by two-way ANOVA with Dunnett posttest.</p> </sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=31471
|
[
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"ext_tax_names": "Homo sapiens",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "7113",
"original_type": "gene",
"role": "intervention",
"text": "TMPRSS2",
"type": "geneprod",
"uniprot_ids": [
"O15393",
"A0A7I2V474"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P07858",
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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": "CatB",
"type": "geneprod",
"uniprot_ids": [
"P07858"
]
}
] |
||
10.15252/embj.2019103181
|
RNA m6A methylation regulates sorafenib-resistance in liver cancer through FOXO3-mediated autophagy
|
2020
|
Figure 1
|
<sd-panel> <p><strong>Figure 1. METTL3 was down-regulated in the sorafenib-resistant HCCs.</strong></p> <p>A Gene enrichments analysis on differentially expressed genes between sorafenib-sensitive and sorafenib-resistant human liver tumors.</p> <p>B Venn diagrams show overlapped genes in signaling pathways response to sorafenib.</p> <p>C Heatmap of overlapped expressed genes in response to sorafenib-resistance.</p> <p>D The mRNA expression level of METTL3 in sorafenib-sensitive (n=3) and sorafenib-resistant (n=3) human liver tumors.</p> <p>E Expression of METTL3 was significantly down-regulated in advanced stage of liver cancer from TCGA.</p> <p>F METTL3 RNA levels between naïve HepG-2 cells (n=3) and sorafenib-resistant HepG-2 cells (n=10).</p> <p>G The IC50 of sorafenib-resistant HepG-2 cells treated with sorafenib under hypoxia condition (1%O<sub>2</sub>).</p> <p>H The protein level of METTL3 in sorafenib-resistant HepG-2 cells treated with sorafenib under hypoxia condition (1%O<sub>2</sub>).</p> <p>I The global RNA m<sup>6</sup>A level in naïve HepG-2 and sorafenib-resistant HepG-2 determined by dot-blotting assay under hypoxia condition (1%O<sub>2</sub>).</p> <p>Data information: In all relevant panels, ***p<0.001; ****p<0.0001; Two-tailed t-test. Data are presented as mean ± SD and are representative of 3 independent experiments.</p> </sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=32446
|
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"mapping_status": "mapped",
"ncbi_gene_id": "56339",
"original_type": "gene",
"role": "assayed",
"text": "METTL3",
"type": "geneprod",
"uniprot_ids": [
"Q86U44"
]
},
{
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"ext_tax_names": "Homo sapiens",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "56339",
"original_type": "gene",
"role": "assayed",
"text": "METTL3",
"type": "geneprod",
"uniprot_ids": [
"Q86U44"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "56339",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "56339",
"original_type": "gene",
"role": "assayed",
"text": "METTL3",
"type": "geneprod",
"uniprot_ids": [
"Q86U44"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q86U44",
"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": "METTL3",
"type": "geneprod",
"uniprot_ids": [
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]
}
] |
||
10.15252/embj.2019103181
|
RNA m6A methylation regulates sorafenib-resistance in liver cancer through FOXO3-mediated autophagy
|
2020
|
Figure 2
|
<sd-panel> <p><strong>Figure 2. Knockdown of METTL3 enhanced sorafenib-resistance in HCC.</strong></p> <p>A-B Clonogenic survival of METTL3-knockdown (A) and METTL3-overexpression (B) in normal liver cell line WRL68 cells for 7 days in normoxia condition (21% O<sub>2</sub>) and quantification of clusters in A-1 and B-1, respectively.</p> <p>C-D The IC50 of METTL3-knockdown SMMC-7721 cells (C) and Bel-7402 cells (D) after treated with sorafenib for 24h under hypoxia condition (1%O<sub>2</sub>).</p> <p>E Overexpression of wild type METTL3 or catalytic mutant METTL3 in sorafenib-resistant HepG-2 cells.</p> <p>F The global RNA m<sup>6</sup>A level in sorafenib-resistant HepG-2 cells with wild type METTL3-overexpression or catalytic mutant METTL3-overexpression by dot-blotting assay.</p> <p>G-I Rescue of shRNA-resistant wild type METTL3 but not catalytic mutant METTL3 sensitized METTL3-knockdown SMMC-7721 cells (G), Bel-7402 cells (H) and sorafenib-resistant HepG-2 cells (I) to sorafenib treatment. The IC50 of the cells was measured after treated with sorafenib for 24h under hypoxia condition (1%O<sub>2</sub>).</p> <p>J Cell survival assay of sorafenib-resistant HepG-2 cells with wild type METTL3 overexpression or catalytic mutant METTL3 overexpression after treated with sorafenib for 24h under hypoxia condition (1%O<sub>2</sub>). Scale bar, 1mm.</p> <p>K Capillary-like structures in HUVECs treated with the tumor-conditioned medium (TCM) from control HCCs and METTL3-knockdown HCCs cultured under hypoxic conditions for 48 h. Quantification of the number of tubes with image J in K-1.</p> <p>L-M The relative mRNA expression levels of angiogenesis genes were detected in SMMC-7721 cells (L) and Bel-7402 cells (M) with METTL3-knockdown by RT-PCR assay.</p> <p>N The protein levels of VEGF-A in METTL3-knockdown HCCs.</p> <p>O The protein levels of PDGF-B in METTL3-knockdown HCCs.</p> <p>Data information: In all relevant panels, *p<0.05; **p<0.01; ***p<0.001; ****p<0.0001; Two-tailed t-test. Data are presented as mean ± SD and are representative of 3 independent experiments.</p> </sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=32447
|
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{
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"uniprot_ids": [
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},
{
"ext_dbs": "NCBI gene",
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"text": "METTL3",
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},
{
"ext_dbs": "NCBI gene",
"ext_ids": "56339",
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"ext_tax_names": "Homo sapiens",
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"mapping_status": "mapped",
"ncbi_gene_id": "56339",
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},
{
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"ext_ids": "56339",
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"text": "METTL3",
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},
{
"ext_dbs": "NCBI gene",
"ext_ids": "56339",
"ext_tax_ids": "9606",
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"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
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"original_type": "gene",
"role": "intervention",
"text": "METTL3",
"type": "geneprod",
"uniprot_ids": [
"Q86U44"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P01127",
"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": "PDGF-B",
"type": "geneprod",
"uniprot_ids": [
"P01127"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P15692",
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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": "VEGF-A",
"type": "geneprod",
"uniprot_ids": [
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}
] |
||
10.15252/embj.2019103181
|
RNA m6A methylation regulates sorafenib-resistance in liver cancer through FOXO3-mediated autophagy
|
2020
|
Figure 3
|
<sd-panel> <p><strong>Figure 3. METTL3-dependent sorafenib-resistance in HCC was mediated by promoting autophagy in HCC.</strong></p> <p><strong>A Electron micrographs of METTL3-knockdown SMMC-7721 cells under hypoxia for 48 h.</strong></p> <p><strong>B-D Protein levels of LC3 I/II in</strong> METTL3-knockdown SMMC-7721 (B), Bel-7402 (C) and HepG-2 (D) cells <strong>under hypoxia condition for 48h.</strong></p> <p><strong>E Protein level of LC3 I/II in HepG-2 and sorafenib-resistant HepG-2 cells under hypoxia condition for 48h.</strong></p> <p><strong>F-H Overexpression of shRNA-resistant wild type METTL3 but not catalytic mutant METTL3 rescue autophagy phenotype in METTL3-knockdown SMMC-7721 cells (F), Bel-7402 cells (G) and</strong> sorafenib-resistant HepG2 cells (H) <strong>by representative immunostaining images of LC3 under hypoxia condition for 48h. Scale bar, 200μm.</strong> Quantification of the numbers of <strong>GFP-LC3 puncta/cell</strong> by Imaris in F-1, G-1 and H-1, respectively.</p> <p><strong>I-K Protein levels of LC3 I/II in</strong> METTL3-knockdown SMMC-7721 cells (I), Bel-7402 cells (J) and HepG-2 cells (K) <strong>treated with or without 3-MA under hypoxia condition for 24h.</strong></p> <p>L-N The IC50 of sorafenib in SMMC-7721 cells (L), Bel-7402 cells (M) and HepG-2 cells (N) treated with or without <strong>3-MA</strong> for 24h under hypoxia condition (1%O<sub>2</sub>).</p> <p>Data information: In all relevant panels, *p<0.05; **p<0.01; ***p<0.001; ****p<0.0001; Two-tailed t-test. Data are presented as mean ± SD and are representative of 3 independent experiments.</p> </sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=32448
|
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||
10.15252/embj.2019103181
|
RNA m6A methylation regulates sorafenib-resistance in liver cancer through FOXO3-mediated autophagy
|
2020
|
Figure 4
|
<sd-panel> <p><strong>Figure 4. RNA m<sup>6</sup>A-Seq identified FOXO3 as a downstream target of METTL3-mediated m<sup>6</sup>A modification under hypoxia.</strong></p> <p><strong>A Gene Set Enrichment Analysis (GSEA) output images of cellular response to stress pathways displaying a correlation of differentially regulated genes in METTL3-knockdown HepG2, SMMC-7721 and Bel-7402 cells with the C5. biological process symbol set. (p < 0.001).</strong></p> <p><strong>B The KEGG analysis shows that FOXO3 involved in hypoxia and autophagy.</strong></p> <p><strong>C Protein level of FOXO3 in METTL3-knockdown HCCs under hypoxia for 48h.</strong></p> <p><strong>D Half-life of FOXO3 mRNA in Bel-7402 cells and correspondent METTL3-knockdown Bel-7402 cells treated with actinomycin D.</strong></p> <p><strong>E Half-life of FOXO3 protein in Bel-7402 cells and correspondent METTL3-knockdown Bel-7402 cells treated with cycloheximide. Quantification of the protein optical density by Image J in E-1.</strong></p> <p><strong>F Analysis of FOXO3 mRNA in non-ribosome portion (<40S), 40S, 60S, 80S and polysome for the METTL3-knockdown Bel-7402 cells compare to control cells under hypoxia for 48h.</strong></p> <p><strong>G Knockdown of YTHDF1 and YTHDF2 in Bel-7402 cells by lentiviral shRNAs.</strong></p> <p><strong>H Knockdown of YTHDF1 but not YTHDF2 abolished the increase of FOXO3 protein level in METTL3-overexpressing Bel-7402 cells. Quantification of the protein optical density by Image J in H-1 and H-2.</strong></p> <p><strong>I RNA level of FOXO3 in YTHDF1-knockdown Bel-7402 cells by RT-PCR.</strong></p> <p><strong>J The m<sup>6</sup>A-IP sequencing under hypoxia proved the m<sup>6</sup>A modification participated in regulation of FOXO3. The YTHDF1 binding site locates at the 3'UTR of FOXO3.</strong></p> <p><strong>K 800 bp of FOXO3 3'UTR containing the m<sup>6</sup>A modification site was cloned into luciferase reporter vector. Mutation of m<sup>6</sup>A consensus sequence was generated by replacing adenosine with thymine.</strong></p> <p><strong>L Relative luciferase activity of the wild-type and mutant form of FOXO3 3'UTR reporter vectors in Bel-7402 cells with various levels of METTL3 and YTHDF1.</strong></p> <p><strong>M Knockdown of METTL3 reduced the m<sup>6</sup>A methylation in FOXO3 mRNA by the m<sup>6</sup>A MeRIP analysis.</strong></p> <p><strong>N Knockdown of METTL3 reduced the m<sup>6</sup>A methylation in FOXO3 mRNA by the YTHDF1-RIP analysis.</strong></p> <p>O Correlation analysis of the RNA expression levels of METTL3 and <strong>FOXO3</strong> in liver tumor cohort (Kim-90) by Pearson.</p> <p><strong>P</strong> Correlation analysis of the RNA expression levels of YTHDF1 and <strong>FOXO3</strong> in liver tumor cohort (Kim-90) by Pearson.</p> <p>Data information: In all relevant panels, *p<0.05; **p<0.01; ***p<0.001; ****p<0.0001; Two-tailed t-test. Data are presented as mean ± SD and are representative of 3 independent experiments.</p> </sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=32449
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] |
||
10.15252/embj.2019103181
|
RNA m6A methylation regulates sorafenib-resistance in liver cancer through FOXO3-mediated autophagy
|
2020
|
Figure 5
|
<sd-panel> <p><strong>Figure 5. Overexpression of FOXO3 rescued the m<sup>6</sup>A-dependent sorafenib-sensitivity under hypoxia by inhibiting autophagy.</strong></p> <p>A Validation of biomarker genes related to autophagy in FOXO3-knockdown Bel-7402 cells by RT-PCR.</p> <p>B Protein level of FOXO3 in naïve HepG-2 and sorafenib-resistant HepG-2 cells under hypoxia for 48h.</p> <p>C Protein levels of LC3 I/II in FOXO3-knockdown SMMC-7721 cells.</p> <p>D Overexpression of FOXO3 in sorafenib-resistant HepG-2 cells by Western blot.</p> <p>E Protein levels of LC3 I/II in METTL3-knockdown & FOXO3-overexpression <strong>SMMC-7721 cells under hypoxia for 48 h.</strong></p> <p>F <strong>Electron micrographs of METTL3-knockdown SMMC7721 cells and METTL3-knockdown &</strong> FOXO3-overexpression <strong>SMMC7721 cells under hypoxia for 48 h.</strong></p> <p><strong>G Representative Immunostaining images of LC3 in METTL3-knockdown SMMC7721 cells and METTL3-knockdown &</strong> FOXO3-overexpression <strong>SMMC7721 cells under hypoxia for 48 h. Scale bar, 200μm. The quantification of the numbers of GFP-LC3 puncta/cell by Imaris in G-1.</strong></p> <p><strong>H Representative Immunostaining images of LC3 in naïve HepG-2 cells and sorafenib-resistant HepG-2 cells under hypoxia for 48 h. Scale bar, 200μm. The quantification of the numbers of GFP-LC3 puncta/cell by Imaris in H-1.</strong></p> <p><strong>I The IC50 of METTL3-knockdown SMMC7721 cells with overexpressing FOXO3 after treated with sorafenib for 24h under hypoxia condition.</strong></p> <p><strong>J The IC50 of naïve HepG-2 cells and sorafenib-resistant HepG-2 cells with overexpressing FOXO3 after treated with sorafenib for 24h under hypoxia condition.</strong></p> <p><strong>K Cell survival assay of METTL3-knockdown SMMC7721 cells with overexpressing FOXO3 after treated with sorafenib for 24h under hypoxia condition.</strong></p> <p><strong>L Cell survival assay of naïve HepG-2 cells and sorafenib-resistant HepG-2 cells with overexpressing FOXO3 after treated with sorafenib for 24h under hypoxia condition.</strong></p> <p>Data information: In all relevant panels, *p<0.05; **p<0.01; ***p<0.001; ****p<0.0001; Two-tailed t-test. Data are presented as mean ± SD and are representative of 3 independent experiments.</p> </sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=32450
|
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||
10.15252/embj.2019103181
|
RNA m6A methylation regulates sorafenib-resistance in liver cancer through FOXO3-mediated autophagy
|
2020
|
Figure 6
|
<sd-panel> <p><strong>Figure 6. METTL3-depletion significantly enhanced sorafenib-resistance via the METTL3/FOXO3 axis <em>in vivo</em>.</strong></p> <p><strong>A Depletion of METTL3 in Hepa1-6 cells by CRISPR-Cas9 knockout enhanced sorafenib-resistance in vivo.</strong></p> <p><strong>B-C Growth curve (B) and tumor weight (C) of Hepa1-6 cells derived xenografts in the subcutaneous implantation mice model in six treatment groups for 12 days (n=5).</strong></p> <p><strong>D Knockdown of METTL3 slightly increased liver tumor growth treated with sorafenib in orthotopic xenograft mouse model. Stable METTL3-knockdown Bel-7402 cells and control cells were injected into the liver of each NOD/SCID mouse. 3 weeks after injection, livers were separated for pathological analysis. Red circle indicates tumors in the livers.</strong></p> <p><strong>E Liver tumors in orthotopic xenograft mouse model were confirmed by hematoxylin and eosin staining.</strong></p> <p><strong>F Overexpression of FOXO3 rescued sorafenib-resistance mediated by METTL3-knockdown in xenograft liver tumors. Representative xenograft tumors at endpoint, containing 6 groups.</strong></p> <p><strong>G-H Growth curve (G) and tumor weight (H) of Hepa1-6 cells derived xenografts in the subcutaneous implantation mice model in 6 treatment groups for 10 days (n=5).</strong></p> <p><strong>I H&E and immunohistochemical images of Ki67, LC3-B, VEGF-A in Hepa1-6 cells derived xenografts in 6 treatment groups.</strong></p> <p><strong>J-L Quantification of Ki67 (K), LC3-B (K), and VEGF-A (L) expression in immunohistochemical images by Image Pro Plus (IPP) analysis.</strong></p> <p>Data information: In all relevant panels, *p<0.05; **p<0.01; ***p<0.001; ****p<0.0001; Two-tailed t-test. Data are presented as mean ± SD.</p> </sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=32451
|
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||
10.15252/embj.2019103181
|
RNA m6A methylation regulates sorafenib-resistance in liver cancer through FOXO3-mediated autophagy
|
2020
|
Figure 7
|
<sd-panel> <p><strong>Figure 7. METTL3-depletion significantly enhanced sorafenib-resistance in HCC patient-derived xenografts.</strong></p> <p><strong>A Graphic illustration of two human liver cancer PDXs mouse model based sorafenib (SOR) treatment regimen.</strong></p> <p><strong>B-D <em>In vivo</em> analyses of tumor (B), growth (C), and weight (D) in mice that were subcutaneously implanted with tumor tissues from two human liver cancer patients and divided into four groups.</strong></p> <p><strong>E H&E and immunohistochemical images of Ki67, LC3-B, VEGF-A in randomly selected PDX#1 and PDX#2 tumors.</strong></p> <p><strong>F-H Quantification of Ki67 (F), LC3-B (G), and VEGF-A (H) expression in immunohistochemical images from PDX tumors by Image Pro Plus (IPP) analysis.</strong></p> <p><strong>I Knockdown of METTL3 by siRNA in PDX#1 and PDX#2 tissues were confirmed by Western blot.</strong></p> <p><strong>J</strong> Working model<strong>. The molecular mechanisms of m<sup>6</sup>A-dependent sorafenib-resistance in liver cancer. The expression of METTL3 was down-regulated in sorafenib-resistant liver cancer, and caused decrease of FOXO3 by the m<sup>6</sup>A modification in an YTHDF1-dependent manner. Degradation of FOXO3 thus promoted autophagy-associated sorafenib-resistance in liver cancer.</strong></p> <p>Data information: In all relevant panels, *p<0.05; **p<0.01; ***p<0.001; ****p<0.0001; Two-tailed t-test. Data are presented as mean ± SD.</p> </sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=32452
|
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"ext_ids": "P46013",
"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": "Ki67",
"type": "geneprod",
"uniprot_ids": [
"P46013"
]
},
{
"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": "LC3-B",
"type": "geneprod",
"uniprot_ids": [
"Q9GZQ8"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P15692",
"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": "VEGF-A",
"type": "geneprod",
"uniprot_ids": [
"P15692"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "56339",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "56339",
"original_type": "gene",
"role": "intervention",
"text": "METTL3",
"type": "geneprod",
"uniprot_ids": [
"Q86U44"
]
}
] |
||
23925298
|
10.1038/ncomms3267
|
The TFEB orthologue HLH-30 regulates autophagy and modulates longevity in Caenorhabditis elegans
|
2013
|
f1
|
<p>(<b>a</b>) Nuclear localization of <named-entity id="named-entity-335">HLH-30</named-entity> was visualized by fluorescence microscopy in day 1 adult wild-type (WT) (upper panel) and <i><named-entity id="named-entity-336">glp-1</named-entity>(e2141)</i> (lower panel) animals expressing <named-entity id="named-entity-337">HLH-30</named-entity>::GFP raised at the non-permissive temperature (25 °C). Inserts show enlarged intestinal cells. Graph shows percentage of animals with <named-entity id="named-entity-338">HLH-30</named-entity> in the nuclei of intestinal cells (four biological replicates, ~50 animals each, mean±s.d., **<i>P</i>0.01, Student’s <i>t</i>-test). Magnification × 100; scale bar, 100 μm. (<b>b</b>) Expression of <i><named-entity id="named-entity-339">hlh-30</named-entity></i> and putative autophagy-related and lysosomal target genes was measured by quantitative PCR (qPCR) in day 1 adult WT and <i><named-entity id="named-entity-340">glp-1</named-entity>(e2141)</i> animals raised at 25 °C (mean±s.d. of three biological replicates, *<i>P</i>0.05, **<i>P</i>0.01, Student’s <i>t</i>-test). (<b>c</b>) Expression of <i><named-entity id="named-entity-341">hlh-30</named-entity></i> and putative autophagy-related and lysosomal target genes was measured by qPCR in day 1 adult <i><named-entity id="named-entity-342">glp-1</named-entity>(e2141)</i> and <i><named-entity id="named-entity-343">glp-1</named-entity>(e2141)</i>; <i><named-entity id="named-entity-344">hlh-30</named-entity>(tm1978)</i> animals raised at 25 °C (mean±s.d. of three biological replicates, *<i>P</i>0.05, **<i>P</i>0.01, Student’s <i>t</i>-test). <i><named-entity id="named-entity-345">ctsa</named-entity>*</i> is a <named-entity id="named-entity-346">cathepsin A</named-entity> orthologue (cosmid <named-entity id="named-entity-347">C08H9.1</named-entity> (ref. <bibrinl rid="b30">30</bibrinl>)). See <sir rid="S1" refobjid="ncomms3267-s1">Supplementary Fig. 1</sir> for qPCR analyses of <i><named-entity id="named-entity-348">hlh-30</named-entity>(tm1978)</i> (control for <b>c</b>) and WT and <i><named-entity id="named-entity-349">glp-1</named-entity>(e2141)</i> animals fed bacteria expressing <i><named-entity id="named-entity-350">hlh-30</named-entity></i> dsRNA. (<b>d</b>,<b>e</b>) GFP::<named-entity id="named-entity-351">LGG-1</named-entity> punctae were quantified in (<b>d</b>) hypodermal seam cells or (<b>e</b>) proximal intestinal cells of L3 larvae of WT and <i><named-entity id="named-entity-352">glp-1</named-entity>(e2141)</i> animals. Animals were fed bacteria expressing control or <i><named-entity id="named-entity-353">hlh-30</named-entity></i> dsRNA for two generations at 20 °C. Eggs were then transferred to plates seeded with the appropriate dsRNA-expressing bacteria at 25 °C and analysed at the L3 larval stage (mean±s.e.m. of ~300 seam cells and ~25 intestines, **<i>P</i>0.01, Student’s <i>t-</i>test). (<b>f</b>,<b>g</b>) <i><named-entity id="named-entity-354">glp-1</named-entity>(e2141)</i> animals expressing (<b>f</b>) <named-entity id="named-entity-355">LMP-1</named-entity>::GFP or (<b>g</b>) <named-entity id="named-entity-356">SQST-1</named-entity>::GFP were raised at the non-permissive temperature (25 °C) and fed bacteria expressing control or <i><named-entity id="named-entity-357">hlh-30</named-entity></i> dsRNA from hatching. Micrographs of the posterior intestine were taken on day 1 of adulthood, and <named-entity id="named-entity-358">LMP-1</named-entity>::GFP fluorescence (mean±s.d. of ~10 animals, **<i>P</i>0.01, Student’s <i>t</i>-test) and <named-entity id="named-entity-359">SQST-1</named-entity>::GFP foci (mean±s.d. of ~30 animals, **<i>P</i>0.01, Student’s <i>t</i>-test) were quantified. Experiments were performed at least three times with similar results. See Supplementary Fig. S2a,c for images of whole animals and Supplementary Fig. S2b,d for replicates. Magnification, × 200; scale bar, 100 μm.</p>
|
https://api.sourcedata.io/file.php?figure_id=3328
|
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"text": "hlh-30",
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"H2KZZ2"
]
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"mapping_source": "ncbi_gene",
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"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "5476",
"original_type": "gene",
"role": "assayed",
"text": "ctsa",
"type": "geneprod",
"uniprot_ids": [
"P10619",
"B4E324",
"X6R5C5",
"X6R8A1"
]
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{
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"P13508"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "177157",
"ext_tax_ids": "6239",
"ext_tax_names": "Caenorhabditis elegans",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "177157",
"original_type": "gene",
"role": "intervention",
"text": "hlh-30",
"type": "geneprod",
"uniprot_ids": [
"H2KZZ2"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "177157",
"ext_tax_ids": "6239",
"ext_tax_names": "Caenorhabditis elegans",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "177157",
"original_type": "gene",
"role": "assayed",
"text": "hlh-30",
"type": "geneprod",
"uniprot_ids": [
"H2KZZ2"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "177157",
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"ext_tax_names": "Caenorhabditis elegans",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
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"type": "geneprod",
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]
},
{
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"ext_ids": "177157",
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"ext_tax_names": "Caenorhabditis elegans",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "177157",
"original_type": "gene",
"role": "assayed",
"text": "hlh-30",
"type": "geneprod",
"uniprot_ids": [
"H2KZZ2"
]
},
{
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"ext_ids": "176286",
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"ext_tax_names": "Caenorhabditis elegans",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "176286",
"original_type": "gene",
"role": "intervention",
"text": "glp-1",
"type": "geneprod",
"uniprot_ids": [
"P13508"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "177157",
"ext_tax_ids": "6239",
"ext_tax_names": "Caenorhabditis elegans",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "177157",
"original_type": "gene",
"role": "intervention",
"text": "hlh-30",
"type": "geneprod",
"uniprot_ids": [
"H2KZZ2"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q09490",
"ext_tax_ids": "6239",
"ext_tax_names": "Caenorhabditis elegans",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "LGG-1",
"type": "geneprod",
"uniprot_ids": [
"Q09490"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "176286",
"ext_tax_ids": "6239",
"ext_tax_names": "Caenorhabditis elegans",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "176286",
"original_type": "gene",
"role": "intervention",
"text": "glp-1",
"type": "geneprod",
"uniprot_ids": [
"P13508"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "177157",
"ext_tax_ids": "6239",
"ext_tax_names": "Caenorhabditis elegans",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "177157",
"original_type": "gene",
"role": "intervention",
"text": "hlh-30",
"type": "geneprod",
"uniprot_ids": [
"H2KZZ2"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q11117",
"ext_tax_ids": "6239",
"ext_tax_names": "Caenorhabditis elegans",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "LMP-1",
"type": "geneprod",
"uniprot_ids": [
"Q11117"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q11117",
"ext_tax_ids": "6239",
"ext_tax_names": "Caenorhabditis elegans",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "LMP-1",
"type": "geneprod",
"uniprot_ids": [
"Q11117"
]
},
{
"ext_dbs": "Uniprot///Uniprot",
"ext_ids": "F1LIM5///Q22436",
"ext_tax_ids": "6239///6239",
"ext_tax_names": "Caenorhabditis elegans///Caenorhabditis elegans",
"mapping_source": "unknown",
"mapping_status": "unmapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "SQST-1",
"type": "geneprod",
"uniprot_ids": []
},
{
"ext_dbs": "Uniprot///Uniprot",
"ext_ids": "F1LIM5///Q22436",
"ext_tax_ids": "6239///6239",
"ext_tax_names": "Caenorhabditis elegans///Caenorhabditis elegans",
"mapping_source": "unknown",
"mapping_status": "unmapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "SQST-1",
"type": "geneprod",
"uniprot_ids": []
}
] |
|
23925298
|
10.1038/ncomms3267
|
The TFEB orthologue HLH-30 regulates autophagy and modulates longevity in Caenorhabditis elegans
|
2013
|
f2
|
<p>(<b>a</b>) Nuclear localization of <named-entity id="named-entity-362">HLH-30</named-entity> was quantified in day 1 adult animals expressing <named-entity id="named-entity-363">HLH-30</named-entity>::GFP. Animals were fed bacteria expressing control or <i><named-entity id="named-entity-364">tor</named-entity></i> dsRNA from hatching and raised at 20 °C (three biological replicates, ~50 animals each, mean±s.d., **<i>P</i>0.01, Student’s <i>t</i>-test). (<b>b</b>,<b>c</b>) Expression of putative autophagy-related and lysosomal target genes was measured by quantitative PCR in day 1 (<b>b</b>) WT (N2) and (<b>c</b>) <i><named-entity id="named-entity-365">hlh-30</named-entity>(tm1978)</i> animals fed bacteria expressing control or <i><named-entity id="named-entity-366">tor</named-entity></i> dsRNA from hatching (20 °C). Data are mean±s.d. of biological triplicates. *<i>P</i>0.05, **<i>P</i>0.01; Student’s <i>t</i>-test. <i><named-entity id="named-entity-367">csta</named-entity></i>* is a <named-entity id="named-entity-368">cathepsin A</named-entity> orthologue (cosmid <named-entity id="named-entity-369">C08H9.1</named-entity> (ref. <bibrinl rid="b30">30</bibrinl>)).(<b>d</b>) Lifespan analysis of WT animals and <i><named-entity id="named-entity-370">hlh-30</named-entity>(tm1978)</i> mutants fed bacteria expressing control or <i><named-entity id="named-entity-371">tor</named-entity></i> dsRNA from day 1 of adulthood was carried out at 20 °C. See <sir rid="S1" refobjid="ncomms3267-s1">Supplementary Table S3</sir> for details of lifespan analyses and replicate experiments.</p>
|
https://api.sourcedata.io/file.php?figure_id=3329
|
[
{
"ext_dbs": "NCBI gene",
"ext_ids": "172167",
"ext_tax_ids": "6239",
"ext_tax_names": "Caenorhabditis elegans",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "172167",
"original_type": "gene",
"role": "intervention",
"text": "tor",
"type": "geneprod",
"uniprot_ids": [
"Q95Q95"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "H2KZZ0",
"ext_tax_ids": "6239",
"ext_tax_names": "Caenorhabditis elegans",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "HLH-30",
"type": "geneprod",
"uniprot_ids": [
"H2KZZ0"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "H2KZZ0",
"ext_tax_ids": "6239",
"ext_tax_names": "Caenorhabditis elegans",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "HLH-30",
"type": "geneprod",
"uniprot_ids": [
"H2KZZ0"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "177157",
"ext_tax_ids": "6239",
"ext_tax_names": "Caenorhabditis elegans",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "177157",
"original_type": "gene",
"role": "intervention",
"text": "hlh-30",
"type": "geneprod",
"uniprot_ids": [
"H2KZZ2"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "172167",
"ext_tax_ids": "6239",
"ext_tax_names": "Caenorhabditis elegans",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "172167",
"original_type": "gene",
"role": "intervention",
"text": "tor",
"type": "geneprod",
"uniprot_ids": [
"Q95Q95"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "177157",
"ext_tax_ids": "6239",
"ext_tax_names": "Caenorhabditis elegans",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "177157",
"original_type": "gene",
"role": "intervention",
"text": "hlh-30",
"type": "geneprod",
"uniprot_ids": [
"H2KZZ2"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "172167",
"ext_tax_ids": "6239",
"ext_tax_names": "Caenorhabditis elegans",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "172167",
"original_type": "gene",
"role": "intervention",
"text": "tor",
"type": "geneprod",
"uniprot_ids": [
"Q95Q95"
]
}
] |
|
23925298
|
10.1038/ncomms3267
|
The TFEB orthologue HLH-30 regulates autophagy and modulates longevity in Caenorhabditis elegans
|
2013
|
f3
|
<p>Lifespan analyses of (<b>a</b>) WT (N2) and (<b>b</b>) germline-less <i><named-entity id="named-entity-373">glp-1</named-entity>(e2141)</i> animals raised at the non-permissive temperature (25 °C) and fed bacteria expressing control or <i><named-entity id="named-entity-374">hlh-30</named-entity></i> dsRNA from day 1 of adulthood were carried out at 20 °C. Lifespan analyses of (<b>c</b>) dietary-restricted <i><named-entity id="named-entity-375">eat-2</named-entity>(ad1116)</i> mutants, (<b>d</b>) insulin/IGF-1 receptor <i><named-entity id="named-entity-376">daf-2</named-entity>(e1370)</i> mutants, (<b>e</b>) mitochondrial respiration <i><named-entity id="named-entity-377">clk-1</named-entity>(e2519)</i> mutants and (<b>f</b>) mRNA translation <i><named-entity id="named-entity-378">rsks-1</named-entity>(sv31)</i> mutants, fed bacteria expressing control or <i><named-entity id="named-entity-379">hlh-30</named-entity></i> dsRNA from day 1 of adulthood (<b>c</b>,<b>d</b>,<b>f</b>) or larval L4 stage (<b>e</b>), were carried out at 20 °C. See <sir rid="S1" refobjid="ncomms3267-s1">Supplementary Table S2</sir> for details of lifespan analyses including at least three independent experiments.</p>
|
https://api.sourcedata.io/file.php?figure_id=3330
|
[
{
"ext_dbs": "NCBI gene",
"ext_ids": "176554",
"ext_tax_ids": "6239",
"ext_tax_names": "Caenorhabditis elegans",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "176554",
"original_type": "gene",
"role": "intervention",
"text": "rsks-1",
"type": "geneprod",
"uniprot_ids": [
"Q9NAH6"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "175072",
"ext_tax_ids": "6239",
"ext_tax_names": "Caenorhabditis elegans",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "175072",
"original_type": "gene",
"role": "intervention",
"text": "eat-2",
"type": "geneprod",
"uniprot_ids": [
"Q9U298"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "175410",
"ext_tax_ids": "6239",
"ext_tax_names": "Caenorhabditis elegans",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "175410",
"original_type": "gene",
"role": "intervention",
"text": "daf-2",
"type": "geneprod",
"uniprot_ids": [
"Q968Y9",
"A0A0K3ARE8",
"A0A0K3ARZ1",
"A0A0K3AUA1",
"A0A0K3AXA0"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "175729",
"ext_tax_ids": "6239",
"ext_tax_names": "Caenorhabditis elegans",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "175729",
"original_type": "gene",
"role": "intervention",
"text": "clk-1",
"type": "geneprod",
"uniprot_ids": [
"P48376"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "176286",
"ext_tax_ids": "6239",
"ext_tax_names": "Caenorhabditis elegans",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "176286",
"original_type": "gene",
"role": "intervention",
"text": "glp-1",
"type": "geneprod",
"uniprot_ids": [
"P13508"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "177157",
"ext_tax_ids": "6239",
"ext_tax_names": "Caenorhabditis elegans",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "177157",
"original_type": "gene",
"role": "intervention",
"text": "hlh-30",
"type": "geneprod",
"uniprot_ids": [
"H2KZZ2"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "177157",
"ext_tax_ids": "6239",
"ext_tax_names": "Caenorhabditis elegans",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "177157",
"original_type": "gene",
"role": "intervention",
"text": "hlh-30",
"type": "geneprod",
"uniprot_ids": [
"H2KZZ2"
]
}
] |
|
23925298
|
10.1038/ncomms3267
|
The TFEB orthologue HLH-30 regulates autophagy and modulates longevity in Caenorhabditis elegans
|
2013
|
f4
|
<p>(<b>a</b>) Expression of <i><named-entity id="named-entity-382">hlh-30</named-entity></i> was measured by quantitative PCR (qPCR) in day 1 adult WT (N2), <i><named-entity id="named-entity-383">eat-2</named-entity>(ad1116)</i> (dietary restriction, DR), <i><named-entity id="named-entity-384">daf-2</named-entity>(e1370)</i> (insulin/IGF-1 signaling), <i><named-entity id="named-entity-385">clk-1</named-entity>(e2519)</i> (mitochondrial respiration) and <i><named-entity id="named-entity-386">rsks-1</named-entity>(sv31)</i> (mRNA translation) animals (mean±s.d. of three biological replicates, *<i>P</i>0.05, Student’s <i>t</i>-test). (<b>b</b>) Nuclear localization of <named-entity id="named-entity-387">HLH-30</named-entity> was quantified in day 1 adult WT, <i><named-entity id="named-entity-388">eat-2</named-entity></i>, <i><named-entity id="named-entity-389">daf-2</named-entity></i>, <i><named-entity id="named-entity-390">clk-1</named-entity></i> and <i><named-entity id="named-entity-391">rsks-1</named-entity></i> mutants (mean±s.d. of four biological replicates, ~50 animals each, **<i>P</i>0.01, analysis of variance). (<b>c</b>) Lifespan analysis of WT and transgenic animals overexpressing <named-entity id="named-entity-392">HLH-30</named-entity>::GFP, and raised and maintained on OP50 was carried out at 20 °C. See <sir rid="S1" refobjid="ncomms3267-s1">Supplementary Table S7</sir> for details of lifespan analyses and replicate experiments. (<b>d</b>) GFP::<named-entity id="named-entity-393">LGG-1</named-entity> punctae were quantified in hypodermal seam cells of WT animals or animals overexpressing <named-entity id="named-entity-394">HLH-30</named-entity> (<i>n</i>>300, ±s.e.m., **<i>P</i>0.01, Student’s <i>t</i>-test). The increase in GFP::<named-entity id="named-entity-395">LGG-1</named-entity> punctae observed in animals overexpressing <named-entity id="named-entity-396">HLH-30</named-entity> could be reversed by <i><named-entity id="named-entity-397">atg-18</named-entity></i> RNAi treatment (data not shown). (<b>e</b>) <i><named-entity id="named-entity-398">TFEB</named-entity></i> expression was measured by qPCR in the livers of 4.5-month-old female (F) and male (M) mice fed AL or subjected to DR for 5.5 weeks starting at 3 months of age (mean±s.e.m. of ~20 mice per group, *<i>P</i>0.05, Student’s <i>t</i>-test). (<b>f</b>) <named-entity id="named-entity-399">TFEB</named-entity> protein was detected by western blotting of nuclear fractions from the livers of five female and five male mice fed AL or subjected to DR. Actin was included as a loading control, see <sir rid="S1" refobjid="ncomms3267-s1">Supplementary Fig. S8</sir> for additional controls. (<b>g</b>) <named-entity id="named-entity-400">TFEB</named-entity> protein levels in <figr rid="f4">Fig. 4f</figr> were quantified by densitometry and normalized to actin (mean±s.d., *<i>P</i>0.05, Student’s <i>t</i>-test).</p>
|
https://api.sourcedata.io/file.php?figure_id=3331
|
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"ext_tax_names": "Caenorhabditis elegans",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "175729",
"original_type": "gene",
"role": "intervention",
"text": "clk-1",
"type": "geneprod",
"uniprot_ids": [
"P48376"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "175410",
"ext_tax_ids": "6239",
"ext_tax_names": "Caenorhabditis elegans",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "175410",
"original_type": "gene",
"role": "intervention",
"text": "daf-2",
"type": "geneprod",
"uniprot_ids": [
"Q968Y9",
"A0A0K3ARE8",
"A0A0K3ARZ1",
"A0A0K3AUA1",
"A0A0K3AXA0"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "175072",
"ext_tax_ids": "6239",
"ext_tax_names": "Caenorhabditis elegans",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "175072",
"original_type": "gene",
"role": "intervention",
"text": "eat-2",
"type": "geneprod",
"uniprot_ids": [
"Q9U298"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "176554",
"ext_tax_ids": "6239",
"ext_tax_names": "Caenorhabditis elegans",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "176554",
"original_type": "gene",
"role": "intervention",
"text": "rsks-1",
"type": "geneprod",
"uniprot_ids": [
"Q9NAH6"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "H2KZZ0",
"ext_tax_ids": "6239",
"ext_tax_names": "Caenorhabditis elegans",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "HLH-30",
"type": "geneprod",
"uniprot_ids": [
"H2KZZ0"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "175729",
"ext_tax_ids": "6239",
"ext_tax_names": "Caenorhabditis elegans",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "175729",
"original_type": "gene",
"role": "intervention",
"text": "clk-1",
"type": "geneprod",
"uniprot_ids": [
"P48376"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "175410",
"ext_tax_ids": "6239",
"ext_tax_names": "Caenorhabditis elegans",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "175410",
"original_type": "gene",
"role": "intervention",
"text": "daf-2",
"type": "geneprod",
"uniprot_ids": [
"Q968Y9",
"A0A0K3ARE8",
"A0A0K3ARZ1",
"A0A0K3AUA1",
"A0A0K3AXA0"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "175072",
"ext_tax_ids": "6239",
"ext_tax_names": "Caenorhabditis elegans",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "175072",
"original_type": "gene",
"role": "intervention",
"text": "eat-2",
"type": "geneprod",
"uniprot_ids": [
"Q9U298"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "177157",
"ext_tax_ids": "6239",
"ext_tax_names": "Caenorhabditis elegans",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "177157",
"original_type": "gene",
"role": "assayed",
"text": "hlh-30",
"type": "geneprod",
"uniprot_ids": [
"H2KZZ2"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "176554",
"ext_tax_ids": "6239",
"ext_tax_names": "Caenorhabditis elegans",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "176554",
"original_type": "gene",
"role": "intervention",
"text": "rsks-1",
"type": "geneprod",
"uniprot_ids": [
"Q9NAH6"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "177157",
"ext_tax_ids": "6239",
"ext_tax_names": "Caenorhabditis elegans",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "177157",
"original_type": "gene",
"role": "intervention",
"text": "HLH-30",
"type": "geneprod",
"uniprot_ids": [
"H2KZZ2"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "177157",
"ext_tax_ids": "6239",
"ext_tax_names": "Caenorhabditis elegans",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "177157",
"original_type": "gene",
"role": "intervention",
"text": "HLH-30",
"type": "geneprod",
"uniprot_ids": [
"H2KZZ2"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "177157",
"ext_tax_ids": "6239",
"ext_tax_names": "Caenorhabditis elegans",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "177157",
"original_type": "gene",
"role": "intervention",
"text": "HLH-30",
"type": "geneprod",
"uniprot_ids": [
"H2KZZ2"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q09490",
"ext_tax_ids": "6239",
"ext_tax_names": "Caenorhabditis elegans",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "LGG-1",
"type": "geneprod",
"uniprot_ids": [
"Q09490"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q09490",
"ext_tax_ids": "6239",
"ext_tax_names": "Caenorhabditis elegans",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "LGG-1",
"type": "geneprod",
"uniprot_ids": [
"Q09490"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "21425",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "21425",
"original_type": "gene",
"role": "assayed",
"text": "TFEB",
"type": "geneprod",
"uniprot_ids": [
"Q9R210",
"Q3UKG7",
"Q6P203",
"Q8C5F1"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q9R210",
"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": "TFEB",
"type": "geneprod",
"uniprot_ids": [
"Q9R210"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q9R210",
"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": "TFEB",
"type": "geneprod",
"uniprot_ids": [
"Q9R210"
]
}
] |
|
10.15252/embj.2019103629
|
Polarized sorting of Patched enables cytoneme-mediated Hedgehog reception in the Drosophila wing disc
|
2020
|
Figure 1
|
<sd-panel> <p><strong>Figure 1. The SNARE proteins Synaptobrevin (Syb) and Synaptotagmin (Syt1) are located at receiving cytonemes.</strong></p> <p><strong>A)</strong> GFP tagged Syb protein expressed in Hh-receiving cells co-localizes with endogenous immuno-labelled Ptc along the apico-basal axis (3D reconstruction). Vesicles containing Syb and Ptc are visualized at lateral and basal planes (arrows), and can be detected along cytonemes marked with Syb-GFP (arrowhead).</p> <p><strong>B)</strong> Expression of the GFP tagged Syt1 also co-localizes with inmmuno-labelled endogenous Ptc at vesicles (lateral plane, arrows point at vesicles with co-localization) and decorates the cytoneme membranes (basal plane, arrowheads indicate cytonemes).</p> <p><strong>C)</strong> GRASP experiment shows exocytic events in Hh-receiving cells at basal membrane contacts. Hh-receiving cells express the GFP barrel 1-10 tagged to Syb and Hh-producing cells express the complementary GFP barrel 11 tagged to the membrane protein CD4. Note the fluorescent discrete punctae (arrows) along Hh producing cells cytonemes (stabilized with Ihog-RFP) crossing the reception area.</p> <p><strong>D)</strong> Expression in receiving cells of the Syb functional partner Syx1A tagged to GFP. Note a strong localization in clusters close to the basal membrane in the 3D reconstruction (left panel) and in confocal lateral and basal planes, including cytonemes (right panels, arrows and arrowhead indicate vesicle-like structures along cytoenemes).</p> <p>Data information: Scale bars 10 μm.</p> </sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=31953
|
[
{
"ext_dbs": "Uniprot",
"ext_ids": "P18502",
"ext_tax_ids": "7227",
"ext_tax_names": "Drosophila melanogaster",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "Ptc",
"type": "geneprod",
"uniprot_ids": [
"P18502"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P18502",
"ext_tax_ids": "7227",
"ext_tax_names": "Drosophila melanogaster",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "Ptc",
"type": "geneprod",
"uniprot_ids": [
"P18502"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P18489",
"ext_tax_ids": "7227",
"ext_tax_names": "Drosophila melanogaster",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "Syb",
"type": "geneprod",
"uniprot_ids": [
"P18489"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P18489",
"ext_tax_ids": "7227",
"ext_tax_names": "Drosophila melanogaster",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "Syb",
"type": "geneprod",
"uniprot_ids": [
"P18489"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P18489",
"ext_tax_ids": "7227",
"ext_tax_names": "Drosophila melanogaster",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "Syb",
"type": "geneprod",
"uniprot_ids": [
"P18489"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P18502",
"ext_tax_ids": "7227",
"ext_tax_names": "Drosophila melanogaster",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "Ptc",
"type": "geneprod",
"uniprot_ids": [
"P18502"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P21521",
"ext_tax_ids": "7227",
"ext_tax_names": "Drosophila melanogaster",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "Syt1",
"type": "geneprod",
"uniprot_ids": [
"P21521"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q03043",
"ext_tax_ids": "7227",
"ext_tax_names": "Drosophila melanogaster",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "CD4",
"type": "geneprod",
"uniprot_ids": [
"Q03043"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q9VM64",
"ext_tax_ids": "7227",
"ext_tax_names": "Drosophila melanogaster",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "Ihog",
"type": "geneprod",
"uniprot_ids": [
"Q9VM64"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P18489",
"ext_tax_ids": "7227",
"ext_tax_names": "Drosophila melanogaster",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "Syb",
"type": "geneprod",
"uniprot_ids": [
"P18489"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q24547",
"ext_tax_ids": "7227",
"ext_tax_names": "Drosophila melanogaster",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "Syx1A",
"type": "geneprod",
"uniprot_ids": [
"Q24547"
]
}
] |
||
10.15252/embj.2019103629
|
Polarized sorting of Patched enables cytoneme-mediated Hedgehog reception in the Drosophila wing disc
|
2020
|
Figure 2
|
<sd-panel> <p><strong>Figure 2. Polarized Ptc vesicle fusion to basolateral membranes is SNARE complex dependent:</strong></p> <p><strong>A)</strong> Ptc protein distribution in a wing disc (3D reconstitution) under down-regulation of the SNARE proteins Syb and Syt1 in the dorsal compartment (D), keeping the ventral compartment (V) as a WT internal control. Note the basal accumulation of endogenous Ptc (arrowheads) when knocking down Syb or Syt1.</p> <p><strong>B)</strong> Confocal images of immuno-labelled endogenous Ptc and cytonemes stabilized with Ihog-RFP protruding from Hh producing cells in wild type receiving cells (left panel), or B') when either blocking exocytosis by down-regulating Syb (middle panel) or B'') blocking endocytosis by expressing a dominant negative form of the <em>Drosophila</em> Dynamin, Shibire (right panel) in the Hh-receiving cells. Endogenous Ptc in wild type conditions cannot be visualized due to its rapid internalization and processing after Hh reception; while blocking exocytosis causes an accumulation of basal Ptc in intracellular punctae (arrowheads), and endocytosis inhibition leads to Ptc accumulation at the plasma membrane (arrows).</p> <p><strong>C)</strong> Confocal apical (left) and basal (right) images of a <em>shi<sup>ts</sup></em> mutant wing disc expressing Syb RNAi dorsally (D) to also block exocytosis, keeping the ventral compartment (V) as an internal control where just endocytosis is inhibited. After dorsal Syb RNAi induction, endocytosis was inhibited in the whole <em>shi<sup>ts</sup></em> disc by incubation at restrictive temperature. Note the dorsal reduction of Ptc at plasma membrane after blocking exocytosis.</p> <p><strong>D)</strong> Quantification of Ptc-GFP levels (Yac construct) along the wing disc apico-basal axis, integrating both fluorescence intensity and signal area (Integrated Density). The graph on the left shows values for wild type situations in purple (average in blue), while Syb RNAi treatment values are shown in green (average in orange). Note a clear shift of higher values towards the basal side of the discs after inhibition of Syb function. The graph to the right shows correlation coefficients between the maximum Ptc value and distance from the basal side (-1=basal, +1=apical) of discs after RNAi expression for different SNARE proteins and the wild type. Central horizontal lines show median values of N=7-16, box shows lower and upper quartiles and the whiskers show the maximum and minimum excluding outliers. A basal association is particularly noticeable for Syb, Syx1A and α-Snap down-regulation. Right panel is a scheme illustrating the wild type and RNAi-treated patterns of quantified Ptc-GFP levels distribution along the wing disc apico-basal axis.</p> <p>Data information: Scale bars 10 μm.</p> </sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=31954
|
[
{
"ext_dbs": "NCBI gene",
"ext_ids": "36080",
"ext_tax_ids": "7227",
"ext_tax_names": "Drosophila melanogaster",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "36080",
"original_type": "gene",
"role": "intervention",
"text": "Syb",
"type": "geneprod",
"uniprot_ids": [
"P18489",
"H1UUB1"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "36080",
"ext_tax_ids": "7227",
"ext_tax_names": "Drosophila melanogaster",
"mapping_source": "ncbi_gene",
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] |
||
10.15252/embj.2019103629
|
Polarized sorting of Patched enables cytoneme-mediated Hedgehog reception in the Drosophila wing disc
|
2020
|
Figure 3
|
<sd-panel> <p><strong>Figure 3. Patched traffics from the apical to the basal side of the wing disc through Multi Vesicular Bodies</strong>:</p> <p>A) Electron Microscopy imaging of wing discs expressing the UAS-Ptc-GFP construct for 24 hours in receiving cells using Ptc-Gal4; TubGal80<sup>ts</sup>. Left panel shows areas with anti-GFP immuno-labelling (marked in blue) throughout the apico/basal axis of the wing disc epithelium a) anti-GFP gold-labelling corresponding to Ptc is located on the apical membrane and early endosomes towards MVB formation. b) Ptc immuno-gold labelling is present in multivesicular bodies (MVBs) subapically (top right panels). b1) Note that subapical MVBs appear as less dense with greater Ptc labelling on the MVB outer membranes. c) Ptc label is also present in MVBs close to the basal membrane (lower right panels), c1) Note that basolateral Ptc MVBs are significantly denser and richer in Ptc positive intraluminal vesicles (ILV).</p> <p>B) Endogenous Ptc subcellular localization after endocytosis inhibition by the dorsal expression of a dominant negative form of Rab5. The top panel is a schematic representation of the localized expression. The left panel is a digital 3D reconstruction and the right panel shows an apical and basal confocal sections. Note that accumulation of Ptc occurs at both the apical and basal sides of the dorsal part of the disc, compared to the wild type control on the ventral side.</p> <p>C) Digital 3D reconstruction (left) and apical and basal confocal sections (right) of endogenous Ptc localization after endocytosis inhibition by the dorsal expression of a dominant negative form of <em>shibire</em>. Note the same apical and basal accumulation as after expression of Rab5<sup>DN</sup>, and comparing to the ventral wild type half.</p> <p>Data information: Scale bars (B, C), 10 μm.</p> </sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=31956
|
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"X2JE15"
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||
10.15252/embj.2019103629
|
Polarized sorting of Patched enables cytoneme-mediated Hedgehog reception in the Drosophila wing disc
|
2020
|
Figure 4
|
<sd-panel> <p><strong>Figure 4. Basal polarization of the Ptc receptor through MVB requires the ESCRT complex:</strong></p> <p><strong>A)</strong> 3D reconstructions of immuno-labelled endogenous Ptc of wing discs in wild type condition and after RNAi expression for different ESCRT complex components. All RNAis' expression result in Ptc accumulation in large structures, located apically under Hrs (ESCRT-0 component) inhibition, and basally under inhibition of the ESCRT components I (Tsg101), II (Vps22) and III (Shrub). Graphs depicting signal values from apical to basal show a shift of higher intensity curves either towards acute apical or basal accumulation.</p> <p><strong>B)</strong> Detailed confocal imaging of immuno-labelled endogenous Ptc localization after clonal Tsg101 down-regulation. The image shows abnormal accumulation of Ptc clusters in basal cytonemes emanating from receiving cells (arrows), since in wild type conditions Ptc visualization at basal membranes is not possible due to its rapid internalization and processing after Hh reception (see Fig 2B).</p> <p><strong>C)</strong> Ptc accumulation in these punctated structures (arrows) is also visualized on receiving cytonemes stabilized with the co-receptor Ihog-RFP and after Tsg101 inhibition.</p> <p><strong>D)</strong> 3D reconstruction of Hh producing cytoneme network stabilized by Ihog-RFP shows that Ptc accumulation after Tsg101 treatment localizes above the signal sending cytoneme extensions (arrow).</p> <p>Data Information: Scale bars 10 μm.</p> </sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=31958
|
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] |
||
10.15252/embj.2019103629
|
Polarized sorting of Patched enables cytoneme-mediated Hedgehog reception in the Drosophila wing disc
|
2020
|
Figure 5
|
<sd-panel> <p><strong>Figure 5. Ptc basal vesicles are enriched with extracellular vesicle markers:</strong></p> <p><strong>A)</strong> Confocal image of wing disc expressing the human tetraspanin CD63-GFP expressed in the Hh receiving cells colocalizing with Ptc (Bac.Ptc-cherry) in vesicle-like structures (yellow arrows) along basal cytonemes.</p> <p><strong>B)</strong> <em>In vivo</em> confocal frames of abdominal histoblasts showing colocalization of CD63-Cherry and Ptc (Yac.Ptc-GFP) at punctae moving in anterograde direction along cytonemes (white arrowheads show trajectory in time-lapse frames).</p> <p><strong>C)</strong> Lateral confocal plane of wing disc showing endogenous Ptc colocalizing with the <em>Drosophila</em> tetraspanin Tsp96F-RFP (orthologous to the mammalian tetraspanin CD9/CD81) (yellow arrows indicate co-localization in punctate structures).</p> <p><strong>D)</strong> Basolateral <em>in vivo</em> imaging of abdominal histoblasts expressing Tsp96F-RFP in the Hh receiving cells shows colocalization with Ptc-GFP at mobile punctae (yellow arrows).</p> <p><strong>E)</strong> Tsp96F-RFP expressed in wing disc Hh-receiving cells also shows localization in basal cytonemes stabilized by Ihog-CFP expression (yellow arrows indicate Tsp96F-RFP-positive punctate structures).</p> <p><strong>F)</strong> Frames showing <em>in vivo</em> localization of Tsp96-RFP punctae to cytonemes stabilized with Ihog-CFP expressed in the abdominal histoblasts Hh-receiving cells, moving in an anterograde fashion towards the P compartment (white arrowheads show trajectory in time-lapse frames).</p> <p><strong>G)</strong> Confocal imaging of receiving cells expressing the HA tagged Tsp96F construct also shows co-localization with endogenous Ptc at cytonemes (yellow arrows indicate Tsp96F-HA and Ptc co-localizing punctate structures).</p> <p><strong>H)</strong> Western blot against HA-tag of Immuno-Precipitated sample (IP), Depleted Sample (Dep), High Speed Sample (HSS) Whole Sample and Control sample from a co-immunoprecipitation experiment isolating GFP of Tsp96F-HA and Ptc-GFP expressing larvae or GFP and Tsp96F-HA expressing larvae as negative control. Arrowhead indicates the positive band corresponding to Tsp96F-HA expected molecular weight (30-40 kDa), present in all samples including the immuno-precipitated one and not present in the negative control sample.</p> <p>Data Information: Scale bars 10 μm.</p> </sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=31960
|
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{
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"ncbi_gene_id": null,
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] |
||
10.15252/embj.2019103629
|
Polarized sorting of Patched enables cytoneme-mediated Hedgehog reception in the Drosophila wing disc
|
2020
|
Figure 6
|
<sd-panel> <p><strong>Figure 6. Excess of HA tagged Tsp96F blocks Ptc MVBs polarized exocytosis: A)</strong> 3D reconstruction of wing disc immuno-labelled for endogenous Ptc and dorsally over-expressing the Tsp96F-HA construct, keeping the ventral side of the disc in wild type condition as internal control. Note the dorsal accumulation of Ptc in very large punctae across the apico-basal axis, but mainly at the basal side of the epithelium. On the right, graphs represent fluorescence values from apical to basal, comparing dorsal and ventral sides and showing a shift of the highest values towards the basal side after Tsp96-HA expression.</p> <p><strong>B)</strong> Confocal image of a wing disc with a clone expressing Tsp96F-HA and immuno-labelled with anti-Ptc and anti-HA antibodies, which co-localize in the large basolateral punctae (yellow arrows).</p> <p><strong>C)</strong> Electron microscopy image from immunolabelled (anti-GFP) Hh-receiving cells of a wing disc expressing Ptc-GFP and Tsp96F-HA. The detailed image shows large sac structures that accumulate several dense MVBs positive labelled for Ptc.</p> <p>Data Information: Scale bars (B), 10 μm.</p> </sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=31962
|
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]
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"text": "Ptc",
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"uniprot_ids": [
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]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P18502",
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"ext_tax_names": "Drosophila melanogaster",
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{
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"ext_ids": "Q9V3X2",
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"uniprot_ids": [
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] |
||
10.15252/embj.2019103629
|
Polarized sorting of Patched enables cytoneme-mediated Hedgehog reception in the Drosophila wing disc
|
2020
|
Figure 7
|
<sd-panel> <p><strong>Figure 7. Ptc is secreted in extracellular vesicles from wing disc cultured cells: A)</strong> Ptc is mainly secreted in small EVs (P100K) from Cl8 cells.</p> <p><strong>B)</strong> Large EVs (lEVs), small EVs (sEVs) and very small EVs (vsEVs) were analysed in triplicate by Western blotting. Note that sEVs are enriched in Ptc and in the EV-associated proteins Syntaxin1 (Synt1A), Late bloomer (Lbm) and Hsp70.</p> <p><strong>C)</strong> Fractionation of sEVs by Sucrose Density Gradient: Ptc partially co-fractioned with Synt1A, Lbm and Hsp70. Note that while unprocessed form of co-receptor Ihog does not co-fraction with Ptc, the processed form does in the same subpopulation.</p> <p><strong>D)</strong> Fractionation of sEVs by Size Exclusion Chromatography: Ptc perfectly co-fractioned with Synt1A, Lbm and Hsp70. In agreement with the density gradient analysis, unprocessed form of co-receptor Ihog does not co-fraction with Ptc in the same subpopulation of sEVs.</p> <p><strong>E)</strong> Effect on EV-associated Ptc secretion after gene silencing on Cl8 cells by dsRNAs against the SNARE proteins Syb and α-Snap, the tetraspanin Tsp96F and the ESCRT components Hrs, Tsg101, Shrub and Vps4. Hsp70 in cells and EVs is detected by different exposition time.</p> </sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=31963
|
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||
10.15252/embj.2019103629
|
Polarized sorting of Patched enables cytoneme-mediated Hedgehog reception in the Drosophila wing disc
|
2020
|
Figure 8
|
<sd-panel> <p><strong>Figure 8. ESCRT machinery and SNARE-mediated exocytosis are required for Ptc exposure at basal membrane:</strong></p> <p><strong>A)</strong> Projection images of three confocal sections (1 μm) at the basal side of wing discs expressing the Bac constructs for Hh-GFP and Ptc-cherry, used to analyse co-localization between the ligand and the receptor in wild type conditions and after inhibition of vesicle fusion (Syb RNAi), vesicle trafficking (Hrs RNAi) or Ptc protein degradation (Dor RNAi). Boxplot shows co-localization rates using the Manders coefficient for proportion of red covered by green in projected images for wing discs temporally expressing RNAi against ESCRT proteins Hrs and Vps4, SNAREs Syb and α-Snap, and Dor as control for effects after Ptc degradation-blocking, as well as temporally over-expressing the Tsp96F-HA. Central horizontal lines show median values of N=8-12 (see Apendix Table S2), box shows lower and upper quartiles and the whiskers show the maximum and minimum excluding. Note the significant reduction in co-localization rates (1= total coverage of red by green) after RNAi expression for both ESCRT and SNARE proteins as well as after Tsp96F-HA over-expression, while RNAi expression for Dor presents greater co-localization. Significance levels for pairwise test (Wilcoxon) ***P<0.001, **P<0.01, *P<0.05.</p> <p><strong>B)</strong> Projection images of three confocal sections (1 μm) from the apical side of the wing discs. Quantification of co-localization rates as in (A) but using apical projection images; central horizontal lines show median values of N=8-12 (see Apendix TableS2), box shows lower and upper quartiles and the whiskers show the maximum and minimum excluding outliers. Note that at the apical side no clear significant reduction in co-localization rates (1= total coverage of red by green) is observed after RNAi expression or in Tsp96F-HA over-expression. Significance levels for pairwise test (Wilcoxon) ***P<0.001, **P<0.01, *P<0.05, +P<0.1.</p> <p><strong>C)</strong> Correlation coefficients between the maximum value of quantified integrated density (integrating both fluorescence intensity and signal area) for Ptc-GFP values (Yac construct) and distance from the basal side (-1=basal, +1=apical). Box plot shows quantification data of discs after RNAi expression for the vacuole sorting protein Dor (necessary for Ptc degradation), the ESCRT Hrs, the SNARE Syb as well as after over-expression of the Tsp96F-HA construct and wild type condition. Central horizontal lines show median values of N=8-12, box shows lower and upper quartiles and the whiskers show the maximum and minimum excluding outliers. Note the apical localization of Ptc-GFP highest values after degradation impairment (Dor RNAi) in contrast to the basal shift resulting from exocytosis deficiency (Syb RNAi).</p> <p>Data Information: Scale bars 10 μm.</p> </sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=31964
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||
10.15252/embj.2019103629
|
Polarized sorting of Patched enables cytoneme-mediated Hedgehog reception in the Drosophila wing disc
|
2020
|
Figure 9
|
<sd-panel> <p><strong>Figure 9. Hindering traffic and basal exocytosis of Ptc results in flattening of the Hh signalling gradient:</strong></p> <p><strong>A)</strong> Confocal images at the lateral plane showing the immunostaining of the medium threshold Hh target Collier (Col) of wild type wing discs and discs after inhibition of vesicle fusion (α-Snap RNAi), vesicle trafficking (Hrs RNAi) or in over-expression of the Tsp96F-HA. Quantification of gradient lengths (μm) using Collier signal and normalized to the wing pouch size, showing the proportion of wing pouch covered by signal (1=total coverage). Quantification was performed for wild type condition as well as in temporally regulated RNAi expression for the ESCRT complex proteins Hrs, Tsg101, Shrub and Vps4 and for the SNARE proteins Syb, Snap24, α-Snap, as well as in transient over-expression of the Tsp96F-HA. Central horizontal lines show median values of N=7-22 (see Apendix TableS2), box shows lower and upper quartiles and the whiskers show the maximum and minimum excluding outliers. Note a slight but significant increase in the length of Col signal for all treatment compared to the wild type condition. Significance levels for pairwise test (Wilcoxon) ***P<0.001, **P<0.01, *P<0.05.</p> <p><strong>B)</strong> Lateral confocal images and quantification of the extension of immuno-labeled Engrailed as the high threshold Hh target. Quantification shows number of cell diameters covered by signal from the posterior/anterior border marked by Hh-GFP (Bac construct); central horizontal lines show median values of N=6-10 (see Apendix TableS2), box shows lower and upper quartiles and the whiskers show the maximum and minimum excluding outliers. Note a significant reduction after RNAi expression, suggesting Hh reception impairment and flattening of the signal gradient. Significance levels for pairwise test (Wilcoxon) ***P<0.001, **P<0.01, *P<0.05.</p> <p><strong>C)</strong> Lateral confocal images and quantification of Ptc transcription as a Hh target through immunolabeling of the reporter β−galactosidase (Ptc-LacZ). Middle graph shows the extension covered by signal normalized to wing pouch size, in wild type condition (N=6) or after ectopic expression of the Tsp96F-HA construct (N=9). Green shaded areas show data variability and dotted line gives the average values. Note the greater distance covered after Tsp96F-HA transient expression. Boxplot (right) shows distance quantifications with central horizontal lines showing median values of N=6-9 (see Appendix Table S2), box showing lower and upper quartiles and whiskers showing the maximum and minimum excluding outliers. Note a significant extension under Tsp96F-HA expression, suggesting again flattening of the signal gradient. Significance levels for pairwise test (Wilcoxon) ***P<0.001.</p> <p>Data Information: Scale bars 10 μm.</p> </sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=31965
|
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] |
||
25515659
|
10.15252/embj.201489279
|
Spontaneous development of hepatocellular carcinoma with cancer stem cell properties in PR-SET7-deficient livers.
|
2015
|
Figure 1
|
<p>PR-SET7 is required for proper liver organogenesis during embryonic development
<list list-type="simple"><list-item><p>A
Representative pictures of embryos at 18.5 days postcoitum (E18.5) and hematoxylin and eosin staining of whole-mount embryo sections from <italic>PR-SET7</italic><sup><italic>loxp</italic></sup>/<italic>Alfp-Cre (PR-SET7</italic><sup><italic>ΔHepE</italic></sup><italic>)</italic> mice and control littermates (<italic>WT</italic>).
</p></list-item><list-item><p>B
Hematoxylin and eosin staining of liver sections.
</p></list-item><list-item><p>C
Immunohistochemical staining of liver sections with albumin antibody.
</p></list-item><list-item><p>D
qPCR analysis of <italic>Albumin</italic>,<italic>Afp</italic> and <italic>HNF4</italic> mRNA levels. Bars represent mean values of mRNA levels normalized to glyceraldehyde-3-phosphate dehydrogenase (<italic>GAPDH</italic>) mRNA and SEM from samples of four individual mice. *<italic>P</italic>-value < 0.01.
</p></list-item><list-item><p>E
Immunohistochemical staining of liver sections with cyclin B1 antibody.
</p></list-item><list-item><p>F
Immunohistochemical staining of liver sections with γH2AX antibody.
</p></list-item></list></p>
|
https://api.sourcedata.io/file.php?figure_id=7604
|
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] |
|
25515659
|
10.15252/embj.201489279
|
Spontaneous development of hepatocellular carcinoma with cancer stem cell properties in PR-SET7-deficient livers.
|
2015
|
Figure 2
|
<p>Postnatal inactivation of PR-SET7 in hepatocytes leads to cell death
<list list-type="simple"><list-item><p>A
Macroscopic appearance of livers in 120-day-old (P120) wild-type (WT) and <italic>PR-SET7</italic><sup><italic>loxp</italic></sup>/<italic>Alb-Cre</italic> (KO) mice. Note, small adenomatous foci in KO livers.
</p></list-item><list-item><p>B
Representative hematoxylin and eosin staining of liver sections from P120 wild-type (WT) and <italic>PR-SET7</italic><sup><italic>loxp</italic></sup>/<italic>Alb-Cre (PR-SET7</italic><sup><italic>ΔHepA</italic></sup><italic>)</italic> mice. Arrows show three areas containing morphologically different hepatocytes. Right panels: zoom-in to Area-A—'normal zone', to Area-B—'necrotic zone' and to Area-C—'regenerative zone'.
</p></list-item><list-item><p>C
Immunohistological staining of liver sections from P120 <italic>PR-SET7</italic><sup><italic>ΔHepA</italic></sup> mice and control littermates (WT) with HNF4 antibody.
</p></list-item><list-item><p>D
TUNEL staining of liver sections from P120 <italic>PR-SET7</italic><sup><italic>ΔHepA</italic></sup> mice and control littermates (WT). Note that cells containing enlarged nuclei (white arrows) are TUNEL negative.
</p></list-item><list-item><p>E
Immunohistological staining with γH2AX and albumin (Alb) antibodies.
</p></list-item></list></p>
|
https://api.sourcedata.io/file.php?figure_id=7605
|
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] |
|
25515659
|
10.15252/embj.201489279
|
Spontaneous development of hepatocellular carcinoma with cancer stem cell properties in PR-SET7-deficient livers.
|
2015
|
Figure 3
|
<p>PR-SET7-deficient hepatocytes die via necrosis in a cell division-dependent manner
<list list-type="simple"><list-item><p>A
Electronmicroscopic images of cells containing enlarged nuclei in P120 <italic>PR-SET7</italic><sup><italic>ΔHepA</italic></sup> livers and normal hepatocytes in control littermates (WT). White arrows indicate: (Nuc) nuclei; (ER) endoplasmic reticulum; (Mit) mitochondrium; (PM) plasma membrane; (a) swollen mitochondria; (b) swollen endoplasmic reticulum; (c) disorganized endoplasmic reticulum; (d) disrupted plasma membrane; and (e) disorganized pieces of endoplasmic reticulum encircling mitochondria to form autophagosomes.
</p></list-item><list-item><p>B
Immunohistological staining of liver sections from P120 <italic>PR-SET7</italic><sup><italic>ΔHepA</italic></sup> mice and control littermates (WT) with H4K20Me<sub>1</sub> and H4K20Me<sub>3</sub> antibodies. Normal (Area-A), Necrotic (Area-B) and Regenerative (Area-C) hepatocyte-containing areas are indicated. Arrows show the loss of H4K20Me<sub>1</sub> signal from the large necrotic nuclei.
</p></list-item><list-item><p>C–F
Partial (2/3<sup>rd</sup>) hepatectomy was performed in 45-day-old <italic>PR-SET7</italic><sup><italic>ΔHepA</italic></sup> mice and control littermates (WT). Two weeks later, at postnatal day 60 (P60) liver sections were stained with hematoxylin and eosin (C) or γH2AX (D) or H4K20Me<sub>1</sub> (E) or HNF4 and F4/80 (F) antibodies.
</p></list-item></list></p>
|
https://api.sourcedata.io/file.php?figure_id=7606
|
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"type": "geneprod",
"uniprot_ids": [
"P62806"
]
},
{
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"ext_ids": "P62806",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
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"mapping_status": "mapped",
"ncbi_gene_id": null,
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"role": "assayed",
"text": "H4",
"type": "geneprod",
"uniprot_ids": [
"P62806"
]
},
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"Q2YDW7",
"A0A0G2JFK5",
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"text": "γH2AX",
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},
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}
] |
|
25515659
|
10.15252/embj.201489279
|
Spontaneous development of hepatocellular carcinoma with cancer stem cell properties in PR-SET7-deficient livers.
|
2015
|
Figure 4
|
<p>Compensatory proliferation of neighboring hepatocytes and ductal progenitor cells in FGF7 signal-containing microenvironment
<list list-type="simple"><list-item><p>A, B
Immunohistological staining of liver sections from P120 <italic>PR-SET7</italic><sup><italic>ΔHepA</italic></sup> mice and control littermates (WT) with Ki67, albumin (Alb) and A6 or HNF4 antibodies as indicated. Arrows depict the different areas in the sections as indicated above (Fig.<xref ref-type="fig" rid="fig01">1B</xref>). Asterisks (*) indicate Ki67<sup>+</sup> hepatocytes. Small arrows (>) indicate Ki67<sup>+</sup> non-hepatic cells. Note the lack of co-staining of cells with HNF4 and A6 antibodies.
</p></list-item><list-item><p>C
Immunohistological staining of liver sections from P120 <italic>PR-SET7</italic><sup><italic>ΔHepA</italic></sup> mice and control littermates (WT) with FGF7 and A6 antibodies.
</p></list-item><list-item><p>D
Relative mRNA levels of <italic>FGF7</italic>. Bars represent mean <italic>FGF7</italic> mRNA levels normalized to <italic>GAPDH</italic> mRNA and SEM from samples of 5 individual 45 days or 120-day-old mice. The data are presented as fold over values obtained with wild-type P45 samples. *<italic>P</italic>-value < 0.01.
</p></list-item></list></p>
|
https://api.sourcedata.io/file.php?figure_id=7607
|
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"uniprot_ids": [
"P36363",
"Q544I6"
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}
] |
|
25515659
|
10.15252/embj.201489279
|
Spontaneous development of hepatocellular carcinoma with cancer stem cell properties in PR-SET7-deficient livers.
|
2015
|
Figure 5
|
<p>ROS accumulation, STAT3 activation and late-onset spontaneous development of hepatocellular carcinoma in <italic>PR-SET7</italic><sup><italic>ΔHepA</italic></sup> mice
<list list-type="simple"><list-item><p>A
Analysis of reactive oxygen species (ROS) accumulation in frozen liver sections from 120-day-old (P120) and 240-day-old (P240) <italic>PR-SET7</italic><sup><italic>ΔHepA</italic></sup> mice and control littermates (WT).
</p></list-item><list-item><p>B
Immunohistological staining of liver sections from P240 animals with phospho-STAT3 antibody.
</p></list-item><list-item><p>C
Western blot analysis of liver extracts from P45, P120 and P240 mice with STAT3 and phospho-STAT3 antibodies.
</p></list-item><list-item><p>D
Macroscopic appearance of livers in P240 <italic>PR-SET7</italic><sup><italic>ΔHepA</italic></sup> mice and control littermates (WT).
</p></list-item><list-item><p>E
Serum alanine aminotransferase (ALT) levels in P45, P120 and P240 mice. Bars represent mean values of ALT levels and SEM from liver extracts of five individual mice. *<italic>P</italic>-value < 0.01.
</p></list-item><list-item><p>F
Representative hematoxylin and eosin staining of liver sections from P240 <italic>PR-SET7</italic><sup><italic>ΔHepA</italic></sup> mice and control littermates (WT). Two different magnifications are shown.
</p></list-item><list-item><p>G
Relative mRNA levels of selected oncofetal genes. Bars represent mean <italic>Afp, H19, GPC-3</italic> and <italic>CTGF</italic> mRNA levels normalized to <italic>GAPDH</italic> mRNA and SEM from samples of 5 individual 240-day-old mice. The data are presented as fold over values obtained with wild-type samples. *<italic>P</italic>-value < 0.01.
</p></list-item></list></p>
<p>Source data are available online for this figure.</p>
|
https://api.sourcedata.io/file.php?figure_id=7608
|
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] |
|
25515659
|
10.15252/embj.201489279
|
Spontaneous development of hepatocellular carcinoma with cancer stem cell properties in PR-SET7-deficient livers.
|
2015
|
Figure 6
|
<p>Hepatocellular carcinoma in P240 PR-SET7-deficient mice is composed of cells expressing hepatic progenitor cell markers
<list list-type="simple"><list-item><p>A, B
Immunohistological staining of liver sections from P240 <italic>PR-SET7</italic><sup><italic>ΔHepA</italic></sup> mice and control littermates (WT) with Afp and HNF4 (A) or Ki-67 and albumin (Alb) (B) antibodies.
</p></list-item><list-item><p>C–E
Double staining of liver sections with A6 and HNF4 (C) or Sox9 and Alb (D) or CD133 and HNF4 (E) antibodies. Right panels show larger magnifications of stainings performed in <italic>PR-SET7</italic><sup><italic>ΔHepA</italic></sup> liver sections.
</p></list-item></list></p>
|
https://api.sourcedata.io/file.php?figure_id=7609
|
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"text": "Sox9",
"type": "geneprod",
"uniprot_ids": [
"Q04887"
]
}
] |
|
25515659
|
10.15252/embj.201489279
|
Spontaneous development of hepatocellular carcinoma with cancer stem cell properties in PR-SET7-deficient livers.
|
2015
|
Figure 7
|
<p>Quantitative assessment and xenograft tumor formation potential of progenitor-derived carcinoma cells
<list list-type="simple"><list-item><p>A
P240 <italic>PR-SET7</italic><sup><italic>ΔHepA</italic></sup> liver sections were double-stained with A6 and Sox9 (upper panel) or CD133 and Sox9 (lower panel). Pie charts at the right represent average percentages of cells stained positively with the indicated markers after counting DAPI-stained cells in 5 high-power fields (HPF) in liver sections of 3 different mice.
</p></list-item><list-item><p>B
Cell duplication rate of primary hepatocytes from P240 <italic>PR-SET7</italic><sup><italic>ΔHepA</italic></sup> livers in culture.
</p></list-item><list-item><p>C
Pictures of representative subcutaneous xenograft tumors dissected from immunodeficient mice 20 days after injection with primary hepatocytes from P240 <italic>PR-SET7</italic><sup><italic>ΔHepA</italic></sup> livers or Hepa 1–6 cells. Right panel shows average tumor volumes (<italic>n</italic> = 3) dissected at the indicated time points following injection.
</p></list-item><list-item><p>D, E
Hematoxylin and eosin and immunohistological staining with A6, HNF4, Sox9 and CD133 antibodies of tumor sections from xenografts dissected 20 or 30 days after injection with primary hepatocytes from P240 <italic>PR-SET7</italic><sup><italic>ΔHepA</italic></sup> livers.
</p></list-item></list></p>
|
https://api.sourcedata.io/file.php?figure_id=7610
|
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] |
|
10.15252/embj.2020106188
|
TPL-2 kinase induces phagosome acidification to promote macrophage killing of bacteria
|
2021
|
Figure 1
|
<p><strong>Figure 1 - <em>Tpl2</em>[D270A] mutation impairs phagosome maturation</strong></p><p><strong>A.</strong> Phagocytic uptake of fluorescently-labelled latex beads by WT and <em>Tpl2</em>[D270A] (<em>Tpl2</em><sup>D270/D270A</sup>) BMDMs. Intracellular fluorescence was monitored following uptake of AF488 latex beads by BMDMs, (n = 4 wells).</p><p><strong>B.</strong> Intra-phagosomal proteolysis in WT and <em>Tpl2</em>[D270A] BMDMs was assayed following uptake of DQ Green BSA / AF594 latex beads. As positive assay control, BMDMs were separately pre-treated with 100 μg/ml leupeptin for 1 h to inhibit serine-cysteine proteases (n = 4 wells).</p><p><strong>C.</strong> Cathepsin activity assay in WT and <em>Tpl2</em>[D270A] BMDMs 0.5 h after uptake of latex beads. BMDMs were stained with the Magic Red cathepsin L substrate (red). Average fluorescence intensity of the cathepsin probe per cell was quantified (n = 40-51 cells).</p><p><strong>D.</strong> Intra-phagosomal acidification in WT and <em>Tpl2</em>[D270A] BMDMs was monitored following uptake of BCECF-coupled latex beads. BMDMs were pre-treated with 1 μM bafilomycin A1 for 15 min to inhibit V-ATPases (n = 4 wells).</p><p><strong>E.</strong> pH assay in WT and <em>Tpl2</em>[D270A] BMDMs upon 0.5 h after incubation with latex beads. BMDMs were stained with the LysoTracker Red DND-99 dye (red). Average fluorescence intensity of the Lysotracker Red probe per cell was quantified (n = 95-126 cells).</p><p><strong>F.</strong> Intra-phagosomal oxidative burst in WT and <em>Tpl2</em>[D270A] BMDMs was assayed following uptake of OxyBURST Green BSA / AF594 latex beads. BMDMs were pre-treated with 1 μM bafilomycin A1 for 15 min to inhibit ROS production (n = 4 wells)</p><p><strong>G.</strong> Reactive oxygen species assay in WT and <em>Tpl2</em>[D270A] BMDMs upon 0.5 h after incubation with latex beads. BMDMs were stained with the ROS Deep Red dye. Average fluorescence intensity of the ROS Deep Red probe per cell was quantified (n = 80-110 cells)</p><p>Data information: One representative experiment out of three shown. Error bars and shaded areas represent SEM. **** P < 0.0001. Panels (<strong>B, D, F</strong>) Paired Mann-Whitney t-test; All differences relative to WT are ****. Panels (<strong>C, E, G</strong>) Student's unpaired t-test.</p>
|
https://api.sourcedata.io/file.php?figure_id=39646
|
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"ncbi_gene_id": "26410",
"original_type": "gene",
"role": "intervention",
"text": "Tpl2",
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{
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{
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{
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] |
||
10.15252/embj.2020106188
|
TPL-2 kinase induces phagosome acidification to promote macrophage killing of bacteria
|
2021
|
Figure 2
|
<p><strong>Figure 2 - <em>Tpl2</em>[D270A] mutation promotes phagosome maturation independently of MAP kinase activation</strong></p><p><strong>A-F.</strong> Experiments were performed using murine BMDMs. <strong>(A)</strong> Intra-phagosomal proteolysis in WT, <em>Nfkb1</em>[SSAA] (<em>Nfkb1</em><sup>SSAA/SSAA</sup>) and <em>Nfkb1</em>[SSAA]/<em>Tpl2</em>[D270A] BMDMs was monitored as Fig 1B (n = 4 wells). <strong>(B)</strong> Intra-phagosomal acidification in WT, <em>Nfkb1</em>[SSAA] and <em>Nfkb1</em>[SSAA]/<em>Tpl2</em>[D270A] BMDMs was monitored as in Fig 1C (n = 4 wells). <strong>(C)</strong> Cell extracts from LPS-stimulated <em>Nfkb1</em>[SSAA] and <em>Nfkb1</em>[SSAA]/<em>Tpl2</em>[D270A] BMDMs were immunoblotted for the indicated antigens. <strong>(D)</strong> Intra-phagosomal proteolysis in WT and inhibitor-treated BMDMs (n = 4 wells) was monitored as in Fig 1B. BMDMs were pre-treated with 0.1 μM PD0325901 (10 min) to inhibit MEK1, pre-treated with 1 μM VX-745 (1 h) to inhibit p38α and pre-treated with 10 μM C34 (1 h) to inhibit TPL-2. <strong>(E).</strong> Intra-phagosomal acidification in WT and inhibitor-treated BMDMs (see (D) for conditions) was assayed as in Fig 1C (n = 4 wells). <strong>(F)</strong> Cell extracts from LPS-stimulated, inhibitor-treated WT and <em>Tpl2</em>[D270A] BMDMs were immunoblotted for the indicated antigens. 1 μM bafilomycin A1 was added to inhibit V-ATPases.</p><p><strong>G-K.</strong> Experiments were performed using human primary monocyte-derived macrophages. (<strong>G)</strong> Intra-phagosomal proteolysis in human macrophages was monitored following uptake of DQ Green BSA / AF594 latex beads. TPL-2 catalytic kinase activity was blocked by pre-treatment with 10 μM C34 for 1 h (n = 4 wells). <strong>(H)</strong> Intra-phagosomal acidification in human macrophages was monitored following uptake of BCECF-coupled latex beads (n = 4 wells). <strong>(I)</strong> Intra-phagosomal proteolysis in human macrophages was assayed as in Fig 2G. MAP kinase activity was inhibited by combinatorial pre-treatment with 0.1 μM PD0325901 (MEK1 inhibition) for 10 min and 1 μM VX-745 (p38 inhibition) for 1 h (n = 4 wells). <strong>(J)</strong> Intra-phagosomal acidification in human macrophages was monitored as in Fig 2H (n = 4 wells). <strong>(K)</strong> Cell extracts from LPS-stimulated, inhibitor-treated primary human macrophages were immunoblotted for p-ERK1/2, ERK1/2, p-p38, p38 and HSP90.</p><p>Data information: One representative experiment out of three shown. Error bars and shaded areas represent SEM. **** P < 0.0001. Panels (<strong>A, B, D, E, G, H, I, J</strong>) Paired Mann-Whitney t-test; all differences relative to WT are ****.</p>
|
https://api.sourcedata.io/file.php?figure_id=39647
|
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"ncbi_gene_id": "26410",
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"text": "Tpl2",
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"Q07174",
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]
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{
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"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "18033",
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{
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] |
||
10.15252/embj.2020106188
|
TPL-2 kinase induces phagosome acidification to promote macrophage killing of bacteria
|
2021
|
Figure 3
|
<p><strong>Figure 3 - <em>Tpl2</em>[D270A] mutation alters the protein composition of phagosomes</strong></p><p>WT and <em>Tpl2</em>[D270A] BMDMs were incubated with latex beads for 0.5h. Latex bead phagosomes were purified from <em>Tpl2</em>[D270A] and WT BMDMs and analysed by mass spectrometry. Biological triplicates were analysed for each genotype.</p><p><strong>A.</strong> Heatmap of selected proteins that were significantly downregulated in BMDMs from <em>Tpl2</em>[D270A] mice relative to WT (P < 0.05). Selected hits were grouped into clusters according to their molecular functions.</p><p><strong>B.</strong> Gene Set Enrichment Analysis (GSEA) of significantly downregulated biological processes in phagosomal fractions. Changes of <em>Tpl2</em>[D270A] phagosomes relative to WT. Dot colour; enrichment score. Dot size; statistical significance.</p><p><strong>C.</strong> Protein intensities of V-ATPase subunits from phagosomes purified from WT and <em>Tpl2</em>[D270A] BMDMs, (n = 3 biological replicates).</p><p><strong>D.</strong> Protein intensities of RAB5 and LAMP-1 from phagosome proteome analysis of WT and <em>Tpl2</em>[D270A] BMDMs (n = 3 biological replicates) (left). Immunoblot of isolated phagosomes from WT and <em>Tpl2</em>[D270A] BMDMs probed for RAB5, LAMP-1 and vimentin. Phagosomal fractions of two biological replicates were pooled. One representative experiment out of two shown (right) (n = 2).</p><p>Data information: Data were analysed by Student's t-test. Error bars represent SEM. * P < 0.05, ** P < 0.01, *** P < 0.001, **** P < 0.0001.</p>
|
https://api.sourcedata.io/file.php?figure_id=39649
|
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"ext_dbs": "Uniprot///Uniprot///Uniprot",
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||
10.15252/embj.2020106188
|
TPL-2 kinase induces phagosome acidification to promote macrophage killing of bacteria
|
2021
|
Figure 4
|
<p><strong>Figure 4 - TPL-2 induces phosphorylation of DMXL1, a V-ATPase regulatory protein</strong></p><p><strong>A.</strong> TPL-2-dependent phosphoproteome following phagocytosis of latex beads (0.5 h) was determined by TMT mass spectrometry. Volcano plot representing the significance (-log<sub>10</sub> P-values after Welch's t-test) vs. phosphorylation fold change (Welch difference ratios) between WT and <em>Tpl2</em>[D270A] BMDMs. Five biological replicates were analysed per genotype (n = 5). Three of the most highly and significantly downregulated phospho-sites in <em>Tpl2</em>[D270A] BMDMs relative to WT, as well as unaltered DMXL1 phospho-sites, are shown.</p><p><strong>B.</strong> Total cell lysates from WT and <em>Tpl2</em>[D270A] BMDMs 0.5h after incubation with latex beads were immunoblotted for phospho-DMXL1 (S1903) and HSP90 (loading control).</p><p><strong>C-F.</strong> <em>Dmxl1</em> was knocked down in WT iBMDMs or <em>Tpl2</em>[D270A] iBMDMs by RNA interference using a SMARTpool ON-TARGETplus siRNA for 48 h. ON-TARGETplus non-targeting pool functioned as siRNA control. <strong>(C)</strong> qRT-PCR analysis of RNA extracted from iBMDMs was used to check the efficiency of <em>Dmxl1</em> knockdown (D, E). <em>Dmxl1</em> mRNA levels were normalised to <em>Hprt</em> mRNA levels and fold changes calculated (ΔC<sub>t</sub> values) (n = 4). <strong>(D)</strong> Intra-phagosomal acidification was assayed following uptake of BCECF-coupled latex beads by WT iBMDMs. As a control, BMDMs were pre-treated with 1 μM bafilomycin A1 for 15 min to directly block V-ATPase function (n = 4 wells). <strong>(E)</strong> Intra-phagosomal acidification was assayed following uptake of BCECF-coupled latex beads by <em>Tpl2</em>[D270A] iBMDMs (n = 4 wells). <strong>(F)</strong> Simultaneous with <em>Dmxl1</em> siRNA knockdown, WT iBMDMs were co-transfected with plasmids expressing either 3xFLAG-DMXL1 (1773-2047) or 3xFLAG-DMXL1 S1903A/S1904A (1773-2047). Intra-phagosomal acidification was monitored as in Fig 4E (n = 4 wells). Immunoblot analysis of total cell lysates for FLAG demonstrated similar expression levels of the two DMXL1 polypeptides in iBMDMs. qRT-PCR analysis of RNA extracted from iBMDMs confirmed that <em>Dmxl1</em> mRNA was efficiently knocked down (n = 4) (right) in cells expressing either 3xFLAG-DMXL1 (1773-2047) or 3xFLAG-DMXL1 S1903A/S1904A (1773-2047).</p><p><strong>G</strong>. Simultaneous with <em>Dmxl1</em> siRNA knockdown<em>, Tpl2</em>[D270A] iBMDMs were co-transfected with a plasmid expressing 3xFLAG-DMXL1 (1773-2047). Intra-phagosomal acidification was monitored (n = 4 wells) (left). Immunoblot analysis of total cell lysates for FLAG demonstrated strong of 3xFLAG-DMXL1 (1773-2047) in iBMDMs (right).</p><p><strong>H.</strong> WT and <em>Tpl2</em>[D270A] BMDMs were treated with latex beads (1:50) for 30 min and ATP6V1C1 was immunoprecipitated from cell extracts. Immunoblot analysis of eluates for ATP6V1C1 and co-immunoprecipitated ATP6V0D1 (left). ATP6V1C1 binding to ATP6V0D1 was quantified from three independent experiments (centre, n =3). Immunoblot analysis of total cell lysates for both V-ATPase subunits and HSP90 (right).</p><p><strong>Data Information: (B-H)</strong> One representative experiment out of three shown. Error bars and shaded areas represent SEM. **** P < 0.0001. Panels <strong>(D-G)</strong> Paired Mann-Whitney t-test. All differences relative to WT are ****. US, unstimulated; UT, untransfected; NT, non-targeting siRNA pool. Panel (<strong>H</strong>) Student's unpaired t-test. ** P < 0.01.</p>
|
https://api.sourcedata.io/file.php?figure_id=39651
|
[
{
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"ext_ids": "26410",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "26410",
"original_type": "gene",
"role": "intervention",
"text": "Tpl2",
"type": "geneprod",
"uniprot_ids": [
"Q07174",
"Q3UEB8"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "26410",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "26410",
"original_type": "gene",
"role": "intervention",
"text": "Tpl2",
"type": "geneprod",
"uniprot_ids": [
"Q07174",
"Q3UEB8"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q6PNC0",
"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": "DMXL1",
"type": "geneprod",
"uniprot_ids": [
"Q6PNC0"
]
}
] |
||
10.15252/embj.2020106188
|
TPL-2 kinase induces phagosome acidification to promote macrophage killing of bacteria
|
2021
|
Figure 5
|
<p><strong>Figure 5 - <em>Tpl2</em>[D270A] mutation impairs maturation of <em>Staphylococcus aureus</em> phagosomes</strong></p><p><strong>A-K.</strong> BMDMs of the indicated genotypes were infected with YFP-<em>S. aureus</em> (MOI 10) for 1 h. <strong>(A)</strong> Phagocytic uptake (CFU) of YFP-labelled <em>S. aureus</em> into BMDMs of indicated genotypes 1h post-infection (n = 12; 2 biological and 6 technical replicates per condition per experiment). <strong>(B)</strong> Representative images of YFP<sup>+</sup> BMDMs labelled with Magic Red cathepsin L substrate (red) and DAPI (nuclear stain) 1h post-infection. <strong>(C)</strong> Quantification of Magic Red cathepsin L staining from panel (A). Average fluorescence intensity of Magic Red cathepsin L substrate per cell relative to fluorescence intensity of YFP-<em>S.aureus</em> (n = 26-29 cells). <strong>(D)</strong> Quantification of Magic Red cathepsin L staining co-localised with YFP-<em>S. aureus</em> from panel (A) (n = 26-29 cells). <strong>(E)</strong> Representative images of YFP<sup>+</sup> BMDMs labelled with LysoTracker Red DND-99 dye (red) and DAPI, 1h post-infection with YFP-<em>S. aureus</em> (green).<strong>(F)</strong> Quantification of LysoTracker Red signal from panel (D). Average fluorescence intensity of LysoTracker Red per cell relative to fluorescence intensity of YFP-<em>S. aureus</em> (n = 66-98 cells). <strong>(G)</strong> Quantification of LysoTracker Red co-localisation with YFP-<em>S. aureus</em> from panel (D) (n = 66-98 cells). <strong>(H)</strong> Representative images of BMDMs stained with an anti-EEA1 antibody (red) and DAPI, 1h post-infection with YFP-<em>S. aureus</em> (green). <strong>(I)</strong> Quantification of EEA1<sup>+</sup> <em>S. aureus</em>-containing phagosomes from panel (G) (n = 27 cells). <strong>(J)</strong> Representative images of BMDMs stained with an anti-LAMP-1 antibody (red) and DAPI, 1h post-infection with YFP-<em>S. aureus</em> (green). <strong>(K)</strong> Quantification of LAMP-1<sup>+</sup> <em>S. aureus</em> phagosomes from panel (I) (n = 25 cells).</p><p>Data information: One representative experiment out of three shown. Error bars represent SEM. P < 0.01, **** P < 0.0001. Student's unpaired t-test.</p>
|
https://api.sourcedata.io/file.php?figure_id=39652
|
[
{
"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": "cathepsin L",
"type": "geneprod",
"uniprot_ids": [
"Q6LAF5"
]
},
{
"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": "cathepsin L",
"type": "geneprod",
"uniprot_ids": [
"Q6LAF5"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q6LAF5",
"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": "cathepsin L",
"type": "geneprod",
"uniprot_ids": [
"Q6LAF5"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q6LAF5",
"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": "cathepsin L",
"type": "geneprod",
"uniprot_ids": [
"Q6LAF5"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q8BL66",
"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": "EEA1",
"type": "geneprod",
"uniprot_ids": [
"Q8BL66"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q8BL66",
"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": "EEA1",
"type": "geneprod",
"uniprot_ids": [
"Q8BL66"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P11438",
"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": "LAMP-1",
"type": "geneprod",
"uniprot_ids": [
"P11438"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P11438",
"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": "LAMP-1",
"type": "geneprod",
"uniprot_ids": [
"P11438"
]
}
] |
||
26582768
|
10.15252/embr.201540476
|
Abo1, a conserved bromodomain AAA-ATPase, maintains global nucleosome occupancy and organization
|
2015
|
Figure 1
|
<p><strong>Figure 1. Impact of Abo1 on transcriptome signatures. </strong></p>
<p><strong>A</strong> Domain architecture of <em>S. pombe </em>bromodomain AAA-ATPases. The D1 and D2 ATPase domains (AAA) are shaded blue and orange, respectively, and the bromodomain (BD) is grey. The percentage similarity to each other and the indicated proteins was determined by FASTA sequence comparison [74] using the scoring matrix BLOSUM50.</p>
<p><strong>B</strong> Venn diagrams showing overlap between genes up-regulated (1.5 fold) in <em>abo1</em>Δ mutants with genes up-regulated under the indicated condition, along with the significance of the overlaps (based on hypergeometric distribution).</p>
|
https://api.sourcedata.io/file.php?figure_id=5150
|
[
{
"ext_dbs": "NCBI gene",
"ext_ids": "2543084",
"ext_tax_ids": "284812",
"ext_tax_names": "Schizosaccharomyces pombe 972h-",
"mapping_source": "unmapped",
"mapping_status": "unmapped",
"ncbi_gene_id": "2543084",
"original_type": "gene",
"role": "intervention",
"text": "abo1",
"type": "geneprod",
"uniprot_ids": []
}
] |
|
26582768
|
10.15252/embr.201540476
|
Abo1, a conserved bromodomain AAA-ATPase, maintains global nucleosome occupancy and organization
|
2015
|
Figure 2
|
<p><strong>Figure 2. Deletion of </strong><strong><em>abo1</em></strong><strong><em><sup>+</sup></em></strong><strong> results in the perturbation of nucleosomal organization at coding sequences. </strong></p>
<p><strong>A</strong> Normalised cumulative nucleosome (150 ± 30 bp size class) position frequency profiles for 4013 <em>S. pombe</em> genes aligned at the transcription start site (TSS) plotted from low MNase (biorep1) and high MNase (biorep 2) datasets. <em>P-</em>values (calculated using a two-tailed unpaired <em>t</em>-test) for the difference in means between random <em>n</em> = 100 subsets of the frequency values at the points indicated by the dotted lines (“-4” nucleosome and “+4” nucleosome) are shown.</p>
<p><strong>B</strong> Nucleosome position frequency values for the coding regions of 4013 <em>S. pombe</em> genes were <em>k</em>-means clustered (<em>k</em> = 9) using the <em>abo1</em>∆ data from biorep 1 (low MNase) and displayed with positive values coloured yellow and other values coloured blue (left-hand panel). The cluster order was then used to display the equivalent wild type frequency values in the right-hand panel.</p>
<p><strong>C</strong> Level of histone gene mRNAs was determined by qRT-PCR. Data are the mean of four independent biological repeats and error bars are ±SEM. Two-tailed unpaired <em>t</em>-tests showed no significant differences (<em>P</em> > 0.05) between wild type and <em>abo1</em>Δ cells.</p>
<p><strong>D</strong> Whole cell extracts were subjected to western blotting with histone H3 (Abcam), histone H2A (Abcam) and tubulin antibodies. Examples of the primary data are shown (left) along with a quantification of histone H2A and H3 levels normalized to tubulin (right). Data are the mean of at least three independent repeats and error bars represent ±SEM. <em>P-</em>values were calculated using a two-tailed unpaired <em>t</em>-test.</p>
|
https://api.sourcedata.io/file.php?figure_id=5151
|
[
{
"ext_dbs": "NCBI gene",
"ext_ids": "2543084",
"ext_tax_ids": "284812",
"ext_tax_names": "Schizosaccharomyces pombe 972h-",
"mapping_source": "unmapped",
"mapping_status": "unmapped",
"ncbi_gene_id": "2543084",
"original_type": "gene",
"role": "intervention",
"text": "abo1",
"type": "geneprod",
"uniprot_ids": []
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "2543084",
"ext_tax_ids": "284812",
"ext_tax_names": "Schizosaccharomyces pombe 972h-",
"mapping_source": "unmapped",
"mapping_status": "unmapped",
"ncbi_gene_id": "2543084",
"original_type": "gene",
"role": "intervention",
"text": "abo1",
"type": "geneprod",
"uniprot_ids": []
},
{
"ext_dbs": "Uniprot///Uniprot",
"ext_ids": "P09988///P10651",
"ext_tax_ids": "284812///284812",
"ext_tax_names": "Schizosaccharomyces pombe 972h-///Schizosaccharomyces pombe 972h-",
"mapping_source": "unknown",
"mapping_status": "unmapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "H3",
"type": "geneprod",
"uniprot_ids": []
},
{
"ext_dbs": "Uniprot///Uniprot",
"ext_ids": "P10651///P09988",
"ext_tax_ids": "284812///284812",
"ext_tax_names": "Schizosaccharomyces pombe 972h-///Schizosaccharomyces pombe 972h-",
"mapping_source": "unknown",
"mapping_status": "unmapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "H3",
"type": "geneprod",
"uniprot_ids": []
},
{
"ext_dbs": "Uniprot///Uniprot",
"ext_ids": "P04910///P04909",
"ext_tax_ids": "284812///284812",
"ext_tax_names": "Schizosaccharomyces pombe 972h-///Schizosaccharomyces pombe 972h-",
"mapping_source": "unknown",
"mapping_status": "unmapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "H2A",
"type": "geneprod",
"uniprot_ids": []
},
{
"ext_dbs": "Uniprot///Uniprot",
"ext_ids": "P04910///P04909",
"ext_tax_ids": "284812///284812",
"ext_tax_names": "Schizosaccharomyces pombe 972h-///Schizosaccharomyces pombe 972h-",
"mapping_source": "unknown",
"mapping_status": "unmapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "H2A",
"type": "geneprod",
"uniprot_ids": []
}
] |
|
26582768
|
10.15252/embr.201540476
|
Abo1, a conserved bromodomain AAA-ATPase, maintains global nucleosome occupancy and organization
|
2015
|
Figure 3
|
<p><strong>Figure 3. Abo1</strong> <strong>associates</strong><strong> with FACT and</strong> <strong>suppresses</strong><strong> cryptic transcription. </strong></p>
<p><strong>A</strong> Whole cell extracts (WCE) were prepared from the indicated strains, immunoprecipitated (IP) with anti-GFP antibody and subjected to western blotting with anti-V5-Pk (Serotec) and anti-GFP (Life Technologies) antibodies. Data are representative of three independent biological repeats.</p>
<p><strong>B</strong> As for A.</p>
<p><strong>C</strong> RNA purified from wild type, <em>abo1</em>∆ and <em>spt16-18</em> cells was analysed by northern blotting using a probe to the 3′ end of <em>spbc19c7.11</em> (top panel). RNA (5 µg) used for northern blotting was analysed on an ethidium bromide stained 1% TAE agarose gel (bottom panel). Data are representative of two independent biological repeats.</p>
<p><strong>D</strong> RNA purified from wild type, and <em>abo1</em>∆ cells was analysed by strand specific RT-PCR. RNA from<em> hip1</em>∆ cells was analysed as a control. One primer, complementary to either the forward or reverse transcripts, was included during the reverse transcription step the second primer was then added during PCR amplification. Control reactions omitting the reverse transcription step (-RT) were included to demonstrate the absence of contaminating genomic DNA. Data are representative of two independent biological repeats.</p>
<p><strong>E</strong> The indicated strains were subjected to ChIP analysis with anti-GFP antibodies and the resulting DNA was analysed by qPCR for the indicated locus. Data are the mean of three independent biological repeats and error bars represent ±SEM. <em>P-</em>values were calculated using a two-tailed unpaired <em>t</em>-test. Significant (<em>P</em> < 0.05) values are indicated.</p>
<p><strong>F</strong> ChIP analysis of histone H3 levels at <em>act1</em><em><sup>+</sup></em> was determined by qPCR. Data are the mean of three independent biological repeats and error bars represent ±SEM. <em>P-</em>value was calculated using a two-tailed unpaired <em>t</em>-test.</p>
<p><strong>G</strong> The indicated strains were subjected to ChIP analysis as described for E.</p>
<p><strong>H</strong> Log phase cells were subjected to five-fold serial dilution and spotted onto rich (YE5S) agar or agar supplemented with MMS (0.006%). Plates were incubated for 3-5 days at 30°C or 7 days at 20°C. Images are representative of three independent biological repeats.</p>
|
https://api.sourcedata.io/file.php?figure_id=5152
|
[
{
"ext_dbs": "NCBI gene",
"ext_ids": "2543084",
"ext_tax_ids": "284812",
"ext_tax_names": "Schizosaccharomyces pombe 972h-",
"mapping_source": "unmapped",
"mapping_status": "unmapped",
"ncbi_gene_id": "2543084",
"original_type": "gene",
"role": "intervention",
"text": "abo1",
"type": "geneprod",
"uniprot_ids": []
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "2540750",
"ext_tax_ids": "284812",
"ext_tax_names": "Schizosaccharomyces pombe 972h-",
"mapping_source": "unmapped",
"mapping_status": "unmapped",
"ncbi_gene_id": "2540750",
"original_type": "gene",
"role": "assayed",
"text": "spbc19c7.11",
"type": "geneprod",
"uniprot_ids": []
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "2541355",
"ext_tax_ids": "284812",
"ext_tax_names": "Schizosaccharomyces pombe 972h-",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "2541355",
"original_type": "gene",
"role": "intervention",
"text": "spt16",
"type": "geneprod",
"uniprot_ids": [
"O94267"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "2540219",
"ext_tax_ids": "284812",
"ext_tax_names": "Schizosaccharomyces pombe 972h-",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "2540219",
"original_type": "gene",
"role": "intervention",
"text": "hip1",
"type": "geneprod",
"uniprot_ids": [
"P87314"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "2543084",
"ext_tax_ids": "284812",
"ext_tax_names": "Schizosaccharomyces pombe 972h-",
"mapping_source": "unmapped",
"mapping_status": "unmapped",
"ncbi_gene_id": "2543084",
"original_type": "gene",
"role": "intervention",
"text": "abo1",
"type": "geneprod",
"uniprot_ids": []
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "2540051",
"ext_tax_ids": "284812",
"ext_tax_names": "Schizosaccharomyces pombe 972h-",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "2540051",
"original_type": "gene",
"role": "assayed",
"text": "act1",
"type": "geneprod",
"uniprot_ids": [
"P10989"
]
},
{
"ext_dbs": "Uniprot///Uniprot",
"ext_ids": "P10651///P09988",
"ext_tax_ids": "284812///284812",
"ext_tax_names": "Schizosaccharomyces pombe 972h-///Schizosaccharomyces pombe 972h-",
"mapping_source": "unknown",
"mapping_status": "unmapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "H3",
"type": "geneprod",
"uniprot_ids": []
}
] |
|
26582768
|
10.15252/embr.201540476
|
Abo1, a conserved bromodomain AAA-ATPase, maintains global nucleosome occupancy and organization
|
2015
|
Figure 4
|
<p><strong>Figure 4. Abo1 is required for heterochromatic silencing. </strong></p>
<p><strong>A</strong> The position of <em>ura4</em><em><sup>+</sup></em> reporter alleles in centromere 1 is shown in the top panel. Strains containing the <em>imr::ura4</em><em><sup>+</sup></em> allele were grown to log phase in YE5S medium, subjected to 5-fold serial dilutions and spotted onto YE5S agar or YE5S agar supplemented with 5-FOA (1 mg/ml). Data are representative of three independent biological repeats.</p>
<p><strong>B</strong> Strains carrying the <em>otr::ura4</em><em><sup>+</sup></em> were analysed as described for A.</p>
<p><strong>C</strong> RNA was purified from the indicated strains and the level of centromeric transcripts determined by qRT-PCR. Data is the mean of three independent repeats and error bars indicate ± SEM. <em>P-</em>value was calculated using a two-tailed unpaired <em>t</em>-test.</p>
<p><strong>D</strong> RNA was purified from the indicated strains and subjected to qRT-PCR for the subtelomeric gene, <em>tlh1</em><em><sup>+</sup></em>. Data is the mean of three biological repeats and error bars indicate ± SEM. <em>P-</em>value was calculated using a two-tailed unpaired Student’s <em>t</em>-test.</p>
<p><strong>E</strong> The position of insertion of <em>ade6</em><sup>+</sup> reporter allele in the silent <em>mat</em> locus is shown in the top panel. Log phase cells containing the <em>mat3-M::ade6</em><em><sup>+</sup></em> allele were subjected to five-fold serial dilution and spotted onto YE5S agar plates lacking adenine (Low Ade) were incubated for 4 days at 30°C. Data are representative of at least three independent biological repeats. Note, microarray analysis indicates that deletion of <em>abo1</em><em><sup>+</sup></em> does not influence the expression of <em>ade6</em><em><sup>+</sup></em> (or <em>ura4</em><em><sup>+</sup></em>) when these genes are present at their normal genomic loci.</p>
|
https://api.sourcedata.io/file.php?figure_id=5153
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[
{
"ext_dbs": "NCBI gene",
"ext_ids": "2541932",
"ext_tax_ids": "284812",
"ext_tax_names": "Schizosaccharomyces pombe 972h-",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "2541932",
"original_type": "gene",
"role": "assayed",
"text": "tlh1",
"type": "geneprod",
"uniprot_ids": [
"P0CT33"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "2543084",
"ext_tax_ids": "284812",
"ext_tax_names": "Schizosaccharomyces pombe 972h-",
"mapping_source": "unmapped",
"mapping_status": "unmapped",
"ncbi_gene_id": "2543084",
"original_type": "gene",
"role": "intervention",
"text": "abo1",
"type": "geneprod",
"uniprot_ids": []
}
] |
|
26582768
|
10.15252/embr.201540476
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Abo1, a conserved bromodomain AAA-ATPase, maintains global nucleosome occupancy and organization
|
2015
|
Figure 5
|
<p><strong>Figure 5. Deletion of </strong><strong><em>abo1</em></strong><strong><em><sup>+</sup></em></strong><strong> perturbs centromeric heterochromatin. </strong></p>
<p><strong>A</strong> ChIP analysis was performed on wild type (untagged) and <em>abo1-GFP</em> cells and the resulting DNA analysed by qPCR for centromeric (<em>dh, dg and imr</em>) repeat sequences. Data are the mean of four independent biological repeats and error bars represent ±SEM. <em>P-</em>values calculated using a two-tailed unpaired <em>t</em>-test indicates that all loci are significantly enriched (<em>P </em>< 0.05) relative the untagged control.</p>
<p><strong>B</strong> The indicated strains expressing GFP-Swi6 were subjected to ChIP analysis. The level of centromeric (<em>dg</em>) repeat sequences relative to the euchromatic control locus, <em>adh1</em><em><sup>+</sup></em> was determined by qPCR and scaled to a <em>clr4</em>Δ (- H3 K9me control) mutant. Data are the mean of two independent ChIP experiments and error bars represent the range of the data.</p>
<p><strong>C</strong> ChIP analysis of histone H3 levels at centromeric (<em>dg</em>) repeat sequences was determined by qPCR. Data are the mean of three independent ChIP experiments and error bars are ±SEM.<em> P-</em>values were calculated using a two-tailed unpaired <em>t</em>-test.</p>
<p><strong>D</strong><strong>.</strong> ChIP analysis of Abo1-GFP at centromeric (<em>dh</em> and <em>imr</em>) repeat sequences regions in wild type and <em>pob3</em>Δ cells. Data are the mean of three independent experiments and error bars represent ±SEM. <em>P-</em>values, calculated using a two-tailed unpaired <em>t</em>-test, indicated no significant difference (<em>P</em> > 0.05) for wild type and <em>pob3</em>Δ cells.</p>
<p><strong>E</strong> ChIP analysis of Abo1-GFP at centromeric (<em>dh</em> and <em>imr</em>) repeat sequences in wild type and <em>pob3</em>Δ cells. Data are the mean of duplicate experiments and error bars represent the range of the data.</p>
<p><strong>F</strong> ChIP analysis of Abo1-GFP over the <em>dh</em> and <em>imr</em> regions in wild type and <em>swi6</em>Δ cells. Data are the mean of three independent experiments and error bars represent ±SEM. <em>P-</em>values, calculated using a two-tailed unpaired <em>t</em>-test, indicated no significant differences (<em>P </em>> 0.05) for wild type and <em>swi6</em>Δ cells.</p>
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https://api.sourcedata.io/file.php?figure_id=5154
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[
{
"ext_dbs": "NCBI gene",
"ext_ids": "2543084",
"ext_tax_ids": "284812",
"ext_tax_names": "Schizosaccharomyces pombe 972h-",
"mapping_source": "unmapped",
"mapping_status": "unmapped",
"ncbi_gene_id": "2543084",
"original_type": "gene",
"role": "intervention",
"text": "abo1",
"type": "geneprod",
"uniprot_ids": []
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "2538902",
"ext_tax_ids": "284812",
"ext_tax_names": "Schizosaccharomyces pombe 972h-",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "2538902",
"original_type": "gene",
"role": "assayed",
"text": "adh1",
"type": "geneprod",
"uniprot_ids": [
"P00332"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "2540825",
"ext_tax_ids": "284812",
"ext_tax_names": "Schizosaccharomyces pombe 972h-",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "2540825",
"original_type": "gene",
"role": "intervention",
"text": "clr4",
"type": "geneprod",
"uniprot_ids": [
"O60016"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P40381",
"ext_tax_ids": "284812",
"ext_tax_names": "Schizosaccharomyces pombe 972h-",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "Swi6",
"type": "geneprod",
"uniprot_ids": [
"P40381"
]
},
{
"ext_dbs": "Uniprot///Uniprot",
"ext_ids": "P10651///P09988",
"ext_tax_ids": "284812///284812",
"ext_tax_names": "Schizosaccharomyces pombe 972h-///Schizosaccharomyces pombe 972h-",
"mapping_source": "unknown",
"mapping_status": "unmapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "H3",
"type": "geneprod",
"uniprot_ids": []
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "2541088",
"ext_tax_ids": "284812",
"ext_tax_names": "Schizosaccharomyces pombe 972h-",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "2541088",
"original_type": "gene",
"role": "intervention",
"text": "pob3",
"type": "geneprod",
"uniprot_ids": [
"O94529"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "2541088",
"ext_tax_ids": "284812",
"ext_tax_names": "Schizosaccharomyces pombe 972h-",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "2541088",
"original_type": "gene",
"role": "intervention",
"text": "pob3",
"type": "geneprod",
"uniprot_ids": [
"O94529"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "O14114",
"ext_tax_ids": "284812",
"ext_tax_names": "Schizosaccharomyces pombe 972h-",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "Abo1",
"type": "geneprod",
"uniprot_ids": [
"O14114"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "O14114",
"ext_tax_ids": "284812",
"ext_tax_names": "Schizosaccharomyces pombe 972h-",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "Abo1",
"type": "geneprod",
"uniprot_ids": [
"O14114"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "2541633",
"ext_tax_ids": "284812",
"ext_tax_names": "Schizosaccharomyces pombe 972h-",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "2541633",
"original_type": "gene",
"role": "intervention",
"text": "swi6",
"type": "geneprod",
"uniprot_ids": [
"P40381"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "2541633",
"ext_tax_ids": "284812",
"ext_tax_names": "Schizosaccharomyces pombe 972h-",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "2541633",
"original_type": "gene",
"role": "intervention",
"text": "swi6",
"type": "geneprod",
"uniprot_ids": [
"P40381"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "O14114",
"ext_tax_ids": "284812",
"ext_tax_names": "Schizosaccharomyces pombe 972h-",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "Abo1",
"type": "geneprod",
"uniprot_ids": [
"O14114"
]
}
] |
|
26582768
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10.15252/embr.201540476
|
Abo1, a conserved bromodomain AAA-ATPase, maintains global nucleosome occupancy and organization
|
2015
|
Figure 6
|
<p><strong>Figure 6. Abo1 represses LTR retrotransposons. </strong></p>
<p><strong>A</strong> RNA was extracted from mid log phase cells and <em>Tf2 </em>mRNA levels were determined by qRT-PCR, normalised to <em>act1</em><sup>+</sup> mRNA and scaled relative to the wild type level. Data are the mean of three independent biological repeats and error bars represent ±SEM.</p>
<p><strong>B</strong> Mid log phase cells with the indicated integrated <em>lacZ</em> reporter were subjected to quantitative β-galactosidase assays. Data are the mean of three independent biological repeats and error bars represent ±SEM.</p>
<p><strong>C</strong> As for B</p>
<p><strong>D</strong> ChIP DNA samples from wild type (untagged) and <em>abo1-GFP</em> cells were analysed by qPCR for <em>Tf2</em> LTR. Data are the mean of four independent biological repeats and error bars represent ±SEM.</p>
<p><strong>E</strong> Normalised cumulative nucleosome (150 ± 30 bp) position frequency profiles for <em>Tf2 </em>LTR retrotransposons aligned at the ATG plotted from low MNase (biorep1) and high MNase (biorep 2) datasets.</p>
<p><em>P-</em>values were calculated using a two-tailed unpaired <em>t</em>-test.</p>
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|
[
{
"ext_dbs": "NCBI gene",
"ext_ids": "2543084",
"ext_tax_ids": "284812",
"ext_tax_names": "Schizosaccharomyces pombe 972h-",
"mapping_source": "unmapped",
"mapping_status": "unmapped",
"ncbi_gene_id": "2543084",
"original_type": "gene",
"role": "intervention",
"text": "abo1",
"type": "geneprod",
"uniprot_ids": []
}
] |
|
10.15252/embj.2022111084
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Enzyme-substrate interface targeting by imidazole-based γ-secretase modulators activates γ-secretase and stabilizes its interaction with APP
|
2022
|
Figure 2
|
<sd-panel><p><strong>Figure 2. Ala/Phe mutagenic scanning demonstrates the involvement of the investigated pocket in the regulation of <sd-pretag id="sdPretag1624744959sm" type="geneprod" role="assayed">GSEC</sd-pretag> processivity</strong></p> <p><strong>(A) The graphs depict the <sd-pretag id="sdPretag1890188897sm" type="geneprod" role="assayed">Aβ</sd-pretag> profiles generated by</strong> WT or mutant <sd-pretag id="sdPretag341949429sm" type="geneprod" role="intervention">PSEN1</sd-pretag> <sd-pretag id="sdPretag96828753sm" type="cell" role="intervention">MEF</sd-pretag> cell lines transduced with <sd-pretag id="sdPretag1043111009sm" type="organism" role="component">adenovirus</sd-pretag> encoding <sd-pretag id="sdPretag1892552202sm" type="geneprod" role="intervention">APP<sub>C99</sub></sd-pretag>. <sd-pretag id="sdPretag1758829321sm" category="assay">ELISA</sd-pretag> quantified secreted <sd-pretag id="sdPretag2048614960sm" type="geneprod" role="assayed">Aβ37</sd-pretag>, <sd-pretag id="sdPretag660051857sm" type="geneprod" role="assayed">Aβ38</sd-pretag>, <sd-pretag id="sdPretag520962473sm" type="geneprod" role="assayed">Aβ40</sd-pretag> and <sd-pretag id="sdPretag1826013106sm" type="geneprod" role="assayed">Aβ42</sd-pretag> peptide levels are shown as % of total <sd-pretag id="sdPretag395200044sm" type="geneprod" role="assayed">Aβ</sd-pretag> (sum of the four peptides). The blue, orange, green and purple dotted lines indicate the levels of <sd-pretag id="sdPretag698136938sm" type="geneprod" role="assayed">Aβ37</sd-pretag>, <sd-pretag id="sdPretag1184004822sm" type="geneprod" role="assayed">Aβ38</sd-pretag>, <sd-pretag id="sdPretag105770297sm" type="geneprod" role="assayed">Aβ40</sd-pretag> and <sd-pretag id="sdPretag1816999052sm" type="geneprod" role="assayed">Aβ42</sd-pretag> peptides in the WT Aβ profile, respectively. Data are presented as mean ± SD, N ≥ 3 independent experiments. Mutagenic primers used in the generation of mutant cell lines are listed in Appendix <strong>Table S1</strong>.</p> <p><strong>(B)</strong> <sd-pretag id="sdPretag1094052312sm" category="assay">GSEC</sd-pretag> processivity levels for the cleavage of <sd-pretag id="sdPretag836761027sm" type="geneprod" role="assayed">APP<sub>C99</sub></sd-pretag> determined in WT and mutant <sd-pretag id="sdPretag92016950sm" type="geneprod" role="intervention">PSEN1/GSEC</sd-pretag> cell lines. The mutant Aβ(37+38)/(40+42) ratios are shown as % of the WT cell line. Data presented as mean ± SD, N ≥ 3 independent experiments. As reference, a dotted line was drawn to indicate 10% (WT levels). One-way ANOVA followed by Dunnett's post-hoc test with comparison to WT was used to determine statistical significance (P < 0.05); **P < 0.01, ***P < 0.001, ****P < 0.0001.</p></sd-panel>
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https://api.sourcedata.io/file.php?figure_id=49473
|
[
{
"ext_dbs": "NCBI gene",
"ext_ids": "5663",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "5663",
"original_type": "gene",
"role": "intervention",
"text": "PSEN1",
"type": "geneprod",
"uniprot_ids": [
"P49768",
"A0A024R6A3",
"A0A0S2Z4D2"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "5663",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "5663",
"original_type": "gene",
"role": "intervention",
"text": "PSEN1",
"type": "geneprod",
"uniprot_ids": [
"P49768",
"A0A024R6A3",
"A0A0S2Z4D2"
]
}
] |
||
10.15252/embj.2022111084
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Enzyme-substrate interface targeting by imidazole-based γ-secretase modulators activates γ-secretase and stabilizes its interaction with APP
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2022
|
Figure 3
|
<sd-panel><p><strong>Figure 3. The investigated pocket plays a key role in GSM III-driven modulation</strong></p> <p><strong>(A)</strong> Aβ profiles generated by WT or mutant PSEN1 MEFs lines treated with 1 µM GSM III. The chemical structure of the bicyclic heterocycle GSM III is depicted. Data are presented as mean ± SD, N ≥ 3 independent experiments. The blue, orange, green and purple dotted lines indicate the levels of Aβ37, Aβ38, Aβ40 and Aβ42 peptides in the WT Aβ profile, respectively.</p> <p><strong>(B)</strong> Fold change in GSEC processivity of APP<sub>C99</sub> estimated by the Aβ(37+38)/(40+42) ratio and presented as % of the WT response. The data are presented as mean ± SD, N ≥ 3. The symbol # marks mutations that fully abolished the GSEC response towards GSM III, as indicated by data presented in Appendix <strong>Figure S3</strong>. As reference, a dotted line was drawn to indicate 10% (WT levels). One-way ANOVA followed by Dunnett's post-hoc test with comparison to WT was used to determine statistical significance (P < 0.05). **P < 0.0001, ****P < 0.0001 (F(DFn, DFd): F (32, 101) = 112.5.</p></sd-panel>
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https://api.sourcedata.io/file.php?figure_id=49474
|
[
{
"ext_dbs": "NCBI gene",
"ext_ids": "5663",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "5663",
"original_type": "gene",
"role": "intervention",
"text": "PSEN1",
"type": "geneprod",
"uniprot_ids": [
"P49768",
"A0A024R6A3",
"A0A0S2Z4D2"
]
}
] |
||
10.15252/embj.2022111084
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Enzyme-substrate interface targeting by imidazole-based γ-secretase modulators activates γ-secretase and stabilizes its interaction with APP
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2022
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Figure 4
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<sd-panel><p><strong>Figure 4. <em>In silico</em> and experimental data propose a binding mode for <sd-pretag id="sdPretag1330560298sm" type="small" role="assayed">imidazole</sd-pretag>-based GSM III</strong></p> <p><strong>(A)</strong> <sd-pretag id="sdPretag1059993503sm" type="geneprod" role="assayed">GSEC</sd-pretag>-<sd-pretag id="sdPretag1986017203sm" type="geneprod" role="assayed">APP<sub>C99</sub></sd-pretag> model with GSM <sd-pretag id="sdPretag1016699180sm" type="small" role="intervention">III</sd-pretag> docked in the identified pocket, which is highlighted with a blue square. Colour scheme: <sd-pretag id="sdPretag514575127sm" type="geneprod" role="assayed">PSEN1</sd-pretag> in tan, <sd-pretag id="sdPretag1726914198sm" type="geneprod" role="assayed">PEN-2</sd-pretag> in sienna brown, <sd-pretag id="sdPretag439056062sm" type="geneprod" role="assayed">APH1A</sd-pretag> in <sd-pretag id="sdPretag1107361662sm" type="small" role="assayed">gold</sd-pretag>, <sd-pretag id="sdPretag1312896144sm" type="geneprod" role="assayed">NCSTN</sd-pretag> in green and <sd-pretag id="sdPretag204417362sm" type="geneprod" role="assayed">APP<sub>C83</sub></sd-pretag> substrate fragment in orange. Further information on the construction of this model is given in (Appendix <strong>Figures S4 B-D</strong>).</p> <p><strong>(B)</strong> Binding mode of GSM III at the GSEC-<sd-pretag id="sdPretag842134993sm" type="geneprod" role="assayed">APP<sub>C99</sub></sd-pretag> interface. Colour scheme: <sd-pretag id="sdPretag1509009236sm" type="geneprod" role="assayed">PSEN1</sd-pretag> in tan, and <sd-pretag id="sdPretag948294939sm" type="geneprod" role="assayed">APP<sub>C83</sub></sd-pretag> substrate fragment in orange. Residues involved in drug-target interactions are coloured according to their mode of interaction with the drug (H-bonding: salmon pink, π-stacking: green, general hydrophobic: violet)</p> <p><strong>(C)</strong> Schematic interaction diagram of the GSM III within the GSEC-<sd-pretag id="sdPretag261857821sm" type="geneprod" role="assayed">APP<sub>C99</sub></sd-pretag> complex: <sd-pretag id="sdPretag1699929216sm" type="geneprod" role="assayed">PSEN1</sd-pretag>, <sd-pretag id="sdPretag892743478sm" type="geneprod" role="assayed">NCSTN</sd-pretag> and APP residues are shown in black, green and orange. The <sd-pretag id="sdPretag1467497229sm" type="small" role="assayed">hydrogen</sd-pretag> bond between <sd-pretag id="sdPretag1926217573sm" type="geneprod" role="assayed">PSEN1</sd-pretag> Y106 and GSM III is depicted in green and van der Waals contacts in red. The plot has been generated with LigPlot+ (Wallace et al., 1995).</p> <p>(<strong>D)</strong> Aβ <strong>profiles generated by WT or mutant <sd-pretag id="sdPretag1104627158sm" type="geneprod" role="intervention">PSEN1</sd-pretag> cell lines overexpressing <sd-pretag id="sdPretag770017372sm" type="geneprod" role="intervention">APP<sub>C99</sub></sd-pretag> and treated with increasing concentrations of GSM III</strong>. Data are presented as mean ± SD, N = 2 independent experiments.</p> <p><strong>(E)</strong> <sd-pretag id="sdPretag1791002050sm" category="assay">GSEC</sd-pretag> processivity estimated by the Aβ(37+38)/(40+42) ratio was determined for the dose-response analysis (presented in panel <strong>D</strong>) and shown as % of <sd-pretag id="sdPretag1465799126sm" type="small" role="intervention">DMSO</sd-pretag>. Data are presented as mean ± SD.</p></sd-panel>
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https://api.sourcedata.io/file.php?figure_id=49475
|
[
{
"ext_dbs": "NCBI gene",
"ext_ids": "5663",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "5663",
"original_type": "gene",
"role": "intervention",
"text": "PSEN1",
"type": "geneprod",
"uniprot_ids": [
"P49768",
"A0A024R6A3",
"A0A0S2Z4D2"
]
}
] |
||
10.15252/embj.2022111084
|
Enzyme-substrate interface targeting by imidazole-based γ-secretase modulators activates γ-secretase and stabilizes its interaction with APP
|
2022
|
Figure 5
|
<sd-panel><p><strong>Figure 5. Experimental and <em>in silico</em> analyses implicate GSEC and APP in drug-target interactions</strong></p> <p><strong>(A-C) (A)</strong> Aβ profiles generated by WT and indicated mutant MEF lines in the presence of vehicle (0.1% DMSO), 1 µM GSM III or (<strong>C</strong>) 1 µM GSM II. Data are presented as mean ± SD, N ≥ 3 independent experiments. (<strong>B</strong>) WT and mutant GSEC processivity estimated by the Aβ (37+38)/(40+42) ratio and presented as % of WT. Data presented as mean ± SD, N ≥ 3 independent experiments. One-way ANOVA followed by Dunnett's post-hoc test with comparison to WT was used to determine statistical significance (P < 0.05). *P < 0.01, **P < 0.0001, ***P < 0.001, ****P < 0.0001 (F(DFn, DFd): F (3, 45) = 56.9.</p> <p><strong>(D-E) Analysis of mutant APP substrates with regards to their effects on the response of GSEC to the imidazole-based GSM III.</strong> Aβ profiles secreted by HEK293T cells transiently expressing WT or mutant APP<sub>C99</sub> substrates in presence of vehicle (DMSO) or 1 µM GSM III were analysed by ELISA or mass spectrometry (MS). Mutagenic primers used in the generation of mutant APP<sub>C99</sub> substrates are listed in Appendix <strong>Table S1</strong>. (<strong>D</strong>) ELISA-based Aβ profiles are presented as % of total Aβ (Aβ<sub>37</sub>+ Aβ<sub>38</sub>+ Aβ<sub>40</sub>+ Aβ<sub>42</sub>) (mean ± SD, N ≥ 3); (<strong>E</strong>) APP mutation-driven effects on GSEC processivity according to the Aβ(37+38)/(40+42) ratio are presented as % of the WT condition (mean ± SD). One-way ANOVA followed by Dunnett's post-hoc test with comparison to WT was used to determine statistical significance; ****P < 0.0001. F(DFn, DFd): F (4, 17) = 71.68. <strong>(F)</strong> MS-based profiles show the proportion of individual Aβ peptides on the total immunoprecipitated pool. Data shown as mean of 3 independent experiments. See also (Appendix <strong>Figure S6B</strong>).</p></sd-panel>
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https://api.sourcedata.io/file.php?figure_id=49476
|
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"ext_tax_names": "Homo sapiens",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "351",
"original_type": "gene",
"role": "intervention",
"text": "APP",
"type": "geneprod",
"uniprot_ids": [
"P05067",
"A0A0A0MRG2",
"A0A140VJC8",
"B4DGD0",
"B4DJT9",
"E9PG40"
]
},
{
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"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "351",
"original_type": "gene",
"role": "intervention",
"text": "APP",
"type": "geneprod",
"uniprot_ids": [
"P05067",
"A0A0A0MRG2",
"A0A140VJC8",
"B4DGD0",
"B4DJT9",
"E9PG40"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "351",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "351",
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"role": "intervention",
"text": "APP",
"type": "geneprod",
"uniprot_ids": [
"P05067",
"A0A0A0MRG2",
"A0A140VJC8",
"B4DGD0",
"B4DJT9",
"E9PG40"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "351",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "351",
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"role": "intervention",
"text": "APP",
"type": "geneprod",
"uniprot_ids": [
"P05067",
"A0A0A0MRG2",
"A0A140VJC8",
"B4DGD0",
"B4DJT9",
"E9PG40"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "351",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
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"mapping_status": "mapped",
"ncbi_gene_id": "351",
"original_type": "gene",
"role": "intervention",
"text": "APP",
"type": "geneprod",
"uniprot_ids": [
"P05067",
"A0A0A0MRG2",
"A0A140VJC8",
"B4DGD0",
"B4DJT9",
"E9PG40"
]
}
] |
||
10.15252/embj.2022111084
|
Enzyme-substrate interface targeting by imidazole-based γ-secretase modulators activates γ-secretase and stabilizes its interaction with APP
|
2022
|
Figure 6
|
<sd-panel><p><strong>Figure 6. The pocket filling PSEN 1-V236W mutation mimics key GSM-<sd-pretag id="sdPretag211674711sm" category="assay">GSEC</sd-pretag> interactions and allosterically activates GSEC</strong></p> <p><strong>(A)</strong> <em>In silico</em> data shows that the Trp236 side chain mimics the interactions of the GSM <sd-pretag id="sdPretag640924097sm" type="small" role="assayed">methylimidazole</sd-pretag> ring with the protease. The position of GSM III in absence of substrate (identical with the position of GSM <sd-pretag id="sdPretag1608968434sm" type="small" role="intervention">E2012</sd-pretag> in the <sd-pretag id="sdPretag535930292sm" category="assay">cryo-EM</sd-pretag> structure PDB: 7D8X, Data ref: Yang et al, 2021) is shown in purple, while the binding mode of GSM III suggested by our work is illustrated in grey. The side chain of W236 (indicated in orange) occupies the same space as the <sd-pretag id="sdPretag1248510908sm" type="small" role="assayed">imidazole</sd-pretag> moieties in both GSM binding modes.</p> <p><strong>(B)</strong> Aβ profiles generated by WT or mutant <sd-pretag id="sdPretag1362622619sm" type="geneprod" role="intervention">PSEN1</sd-pretag> cell lines transduced with <sd-pretag id="sdPretag785536365sm" type="geneprod" role="intervention">APP<sub>C99</sub></sd-pretag>. Dotted lines indicate the levels of <sd-pretag id="sdPretag1611894477sm" type="geneprod" role="assayed">Aβ</sd-pretag> peptides (%) in WT profiles. Data presented as mean ± SD, N ≥ 3 independent experiments.</p> <p>(<strong>C</strong>) Pocket filling <sd-pretag id="sdPretag501297213sm" type="geneprod" role="intervention">PSEN1</sd-pretag> V236W and Y106W-V236W substitutions lead to increased Aβ(37+38)/(40+42) ratio, indicating the activation of the sequential <strong>GSEC-mediated cleavage of <sd-pretag id="sdPretag56015952sm" type="geneprod" role="intervention">APP<sub>C99</sub></sd-pretag></strong>. Data presented as mean ± SD, N ≥ 3 independent experiments.</p> <p>(<strong>D</strong>) Aβ profile analysis in <strong>dose-response experiments for GSM III</strong> revealed no modulation of the <sd-pretag id="sdPretag1510914801sm" type="geneprod" role="intervention">PSEN1</sd-pretag> V236W mutant cell line. Data are presented as mean ± SD, N = 2 independent experiments. For comparison purposes, WT and V236W mutant <sd-pretag id="sdPretag286291316sm" type="geneprod" role="intervention">Aβ</sd-pretag> profiles are presented in panel 6B. We note that dose response analyses for <sd-pretag id="sdPretag905787861sm" type="subcellular" role="component">GSM</sd-pretag> II showed similar results <strong>(</strong>Appendix <strong>Figure S8B</strong>)</p> <p><strong>(E</strong>) <sd-pretag id="sdPretag1620569898sm" category="assay">GSEC</sd-pretag> activity <sd-pretag id="sdPretag1138687186sm" category="assay">assay</sd-pretag> using purified <sd-pretag id="sdPretag1384585615sm" type="geneprod" role="assayed">GSEC</sd-pretag> and an APP-based fluorogenic peptide as substrate (Farmery et al., 2003). <strong>Upper panel</strong>: In the non-cleaved state the Dpn (2,<sd-pretag id="sdPretag2097540332sm" type="small" role="assayed">4-dinitrophenyl</sd-pretag>) quencher group suppresses fluorescent emission from the Nma (N-<sd-pretag id="sdPretag145425880sm" type="small" role="assayed">methyl-o-aminobenzoic acid</sd-pretag>) fluorophore through Förster resonance energy transfer (<sd-pretag id="sdPretag1028423228sm" category="assay">FRET</sd-pretag>). Upon GSEC cleavage, the Nma group emits at λ = 430 nm a fluorescent signal upon excitation at λ = 355 nm. <strong>Lower panel:</strong> Specific activities for the purified WT or mutant <sd-pretag id="sdPretag1251172216sm" type="cell" role="component">GSECs</sd-pretag> (bearing the indicated substitutions in <sd-pretag id="sdPretag878799183sm" type="geneprod" role="intervention">PSEN1</sd-pretag>) treated with <sd-pretag id="sdPretag180920694sm" type="small" role="intervention">DMSO</sd-pretag> (vehicle), 10 µM GSMIII or GSM II. Data are normalized to the WT <sd-pretag id="sdPretag1211196551sm" type="geneprod" role="assayed">GSEC</sd-pretag> activity in <sd-pretag id="sdPretag175246174sm" type="small" role="intervention">DMSO</sd-pretag> (vehicle). Data are shown as mean ± SD, N ≥ 3 independent experiments. Significance is shown for meaningful comparisons; two-way ANOVA with comparison to WT was used to determine statistical significance; **P < 0.01, ***P < 0.001, ****P < 0.0001, ns: not significant<strong>.</strong></p> <p><strong>(F</strong>) Transition state analogue inhibitor <sd-pretag id="sdPretag1765938310sm" type="small" role="intervention">L-685,458</sd-pretag> (Inhibitor X) treatment of WT, V236W or Y240W mutant <sd-pretag id="sdPretag2112676281sm" type="geneprod" role="intervention">PSEN1</sd-pretag> cell lines. Inhibitory profiles and derived IC50 values (table) indicate that the <sd-pretag id="sdPretag451396487sm" type="geneprod" role="assayed">PSEN1</sd-pretag>-V236W significantly increases the affinity for the inhibitor. Dotted line indicates 50% inhibition. Data presented as mean ± SD, N = 3 independent experiments.</p></sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=49477
|
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"P49768",
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"ext_tax_names": "Homo sapiens",
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}
] |
||
27638855
|
10.15252/embj.201593454
|
Evi1 regulates Notch activation to induce zebrafish hematopoietic stem cell emergence
|
2016
|
Figure 1
|
<p><strong>Figure 1</strong><strong>.</strong> <strong><em>evi1 </em></strong><strong>is </strong><strong>expressed in emerging HSPCs and critically regulates definitive hematopoiesis.</strong></p>
<p><strong>A.</strong> Whole mount <em>in situ </em>hybridization (WISH) of <em>evi1 </em>at 20 (left) and 32 (middle) hpf. <em>evi1 </em>expression is visible in various structures of the brain, neuronal structures, the posterior pronephric duct (ppnd) and the branchial arches (ba), as well as in the VDA (ventral dorsal aorta) region. Additionally, <em>evi1 </em>co-localizes with the endothelial marker <em>flk1</em> (right).</p>
<p><strong>B, C</strong><strong>. </strong>WISH of <em>runx1/c-myb</em> in HSPCs (B), <em>mpo</em> in neutrophils (left) and <em>l-plastin</em> (right) in monocytes/macrophages (C) at 36 hpf in control (upper) and <em>evi1 </em>MO (lower) injected embryos.</p>
<p><strong>D-G</strong><strong>. </strong>WISH of <em>globin </em>in erythrocytes of 6 dpf old embryos (D), of <em>rag-1 </em>in the thymus of 5 dpf embryos (E; red asterisk), of <em>cd41 </em>at 52 hpf (F), and <em>gata2b </em>at 32 hpf (G) for both control (upper) and <em>evi1 </em>morpholino (lower) injected embryos.</p>
<p><strong>H</strong><strong>. </strong>Quantitation of results is shown for each gene, displaying the percentages of embryos with normal vs. changed expression in each condition. A Fisher´s exact test was applied to calculate statistical significance. P < 0.001 (***).</p>
<p><strong>I</strong><strong>. </strong>WISH of <em>runx1/c-myb </em>in HSPCs of uninjected control and <em>UAS:mEvi1</em> plasmid DNA injected Tg(<em>-1.5hsp70l:Gal4</em>) embryos with heat-shock induction performed at 14 hpf.</p>
<p><strong>J</strong><strong>.</strong> WISH of <em>runx1/c-myb </em>in HSPCs of uninjected control and <em>UAS:mEvi1</em> mRNA in <em>Tg(fli.1:Gal4FF;UAS:RFP)</em> embryos, leading to endothelial-specific <em>evi1 </em>overexpression.</p>
<p><strong>K</strong><strong>.</strong> Graph displays quantitation of results from K and M using the same method as above.</p>
<p>Lateral views are shown, with anterior to the left, dorsal is up. Numbers indicate the amount of embryos with the respective phenotype/total number of embryos analyzed in each experiment. Arrows indicate up- or down-regulation for each gene. A minimum of two biological replicates was performed for each marker with at least n=5 embryos per experiment.</p>
|
https://api.sourcedata.io/file.php?figure_id=9923
|
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"role": "assayed",
"text": "runx1",
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"uniprot_ids": [
"Q9DGB8"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "58126",
"ext_tax_ids": "7955",
"ext_tax_names": "Danio rerio",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "58126",
"original_type": "gene",
"role": "assayed",
"text": "runx1",
"type": "geneprod",
"uniprot_ids": [
"Q9DGB8"
]
}
] |
|
27638855
|
10.15252/embj.201593454
|
Evi1 regulates Notch activation to induce zebrafish hematopoietic stem cell emergence
|
2016
|
Figure 2
|
<p><strong>Figure</strong><strong> 2</strong><strong>.</strong> <strong>Endothelial Notch signaling is dependent on </strong><strong><em>evi1 </em></strong><strong>expression levels</strong></p>
<p><strong>A</strong><strong>. </strong>WISH of <em>notch1b </em>(upper) and <em>dll4 </em>(lower) in both control (left) and <em>evi1 </em>MO injected embryos (right).</p>
<p><strong>B.</strong> WISH of <em>notch1b</em> in uninjected (left) and <em>UAS:mEvi1</em> plasmid DNA injected (right) <em>Tg(fli.1:Gal4FF;UAS:RFP)</em> embryos resulting in endothelial-specific <em>evi1</em> induction.</p>
<p>Lateral views are shown, with anterior to the left, dorsal is up. Squares represent enlargements of the region of interest. Numbers indicate the amount of embryos with the respective phenotype/total number of embryos analyzed in each experiment. Arrows indicate up- or down-regulation for each gene. A minimum of two biological replicates was performed for each marker with at least n=5 embryos per experiment. For each analyzed gene, quantitation of results is shown, displaying the percentages of embryos with normal vs. changed gene expression for each condition. A Fisher´s exact test was applied to calculate statistical significance. n.s., not significant; p<0.01 (**), p < 0.001 (***).</p>
|
https://api.sourcedata.io/file.php?figure_id=9924
|
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"mapping_status": "mapped",
"ncbi_gene_id": "563920",
"original_type": "gene",
"role": "assayed",
"text": "dll4",
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},
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"role": "intervention",
"text": "Evi1",
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"uniprot_ids": [
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},
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"uniprot_ids": [
"A0A8M2BFY6",
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}
] |
|
27638855
|
10.15252/embj.201593454
|
Evi1 regulates Notch activation to induce zebrafish hematopoietic stem cell emergence
|
2016
|
Figure 3
|
<p><strong>Figure </strong><strong>3</strong><strong>.</strong> <strong><em>evi1 </em></strong><strong>regulates HSC emergence from the </strong><strong>V</strong><strong>DA. </strong></p>
<p><strong>A.</strong> Confocal time-lapse live imaging was performed in Tg(<em>c</em><em>-</em><em>myb:GFP;kdrl:mKate-CAAX) </em>embryos from 28 to 42 hpf (Movie EV 1). Shown are three representative time-points in which the transformation from hemogenic endothelial cells to the hematopoietic fate is visible, indicated by the white arrowheads. For each time-point merged images are shown. White arrowheads denote double-positive cells.</p>
<p><strong>B. </strong>Cell counts of total numbers of <em>kdrl+</em><em>cmyb1+</em> cells “in view”, dividing and respectively emerging HSPCs. n=10 movies from n=3 biological replicates were analyzed. A non-parametric Mann-Whitney test was used to test for statistical significance and error bars are shown as ± s.d.</p>
<p><strong>C</strong><strong>. </strong>Gene expression analysis of endothelial (<em>kdrl, flt1, dab2, cdh5</em>) and blood specific genes (<em>c-myb, CD45, CD41, runx1</em>) in sorted <em>kdrl+c</em><em>-</em><em>myb+</em> cells from 34 hpf Tg(<em>c</em><em>-</em><em>myb:GFP;kdrl:mKate-CAAX) </em>embryos. Cells were isolated from 15-25 pooled embryos per sample. Three biological experiments were performed with one representative shown. Error bars indicate s.d.
of three technical replicates for each representative experiment.</p>
|
https://api.sourcedata.io/file.php?figure_id=9925
|
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] |
|
27638855
|
10.15252/embj.201593454
|
Evi1 regulates Notch activation to induce zebrafish hematopoietic stem cell emergence
|
2016
|
Figure 4
|
<p><strong>Figure </strong><strong>4</strong><strong>.</strong><strong> Global and tissue-specific activation of Notch</strong> <strong>or</strong> <strong>upstream </strong><strong>Vegf</strong><strong> signaling is sufficient to rescue HSPCs in </strong><strong><em>evi1</em></strong><strong> morphants.</strong></p>
<p><strong>A.</strong> WISH for <em>runx1/c-myb </em>in 36 hpf <em>evi1 </em>morphant (left) and <em>evi1 </em>morphant transgenic Tg(<em>5xUAS-E1b:6xMYC-notch1a;-1.5hsp70l:Gal4</em>) embryos (right) with global heat-shock (HS) induction at 20 hpf.</p>
<p><strong>B. </strong>WISH for <em>runx1/c-myb</em> in 36 hpf <em>evi1</em> morphant (left) and <em>evi1 </em>morphant transgenic Tg(<em>5xUAS-E1b:6xMYC-notch1a;</em><em>cdh5:gal4ff</em>) embryos with endothelial-specific NICD induction (right).</p>
<p><strong>C. </strong>WISH for <em>runx1/c-myb</em> in 36 hpf <em>evi1 </em>morphant (left) and <em>evi1</em> morphant transgenic Tg(<em>Hsp70l:vegfaa;myl7:eGFP)</em> embryos (right) with global heat-shock induction at 20 hpf.</p>
<p><strong>D</strong><strong>. </strong>WISH for <em>runx1/c-myb </em>in 32 hpf <em>evi1 </em>MO injected embryos (left) and embryos injected with both <em>evi1 </em>MO and capped <em>gata2</em> mRNA (right).</p>
<p><strong>E. </strong>Quantitation of all rescue experiments. Shown are the percentages of embryos displaying normal or changed <em>runx1/c-myb</em> expression. A Fisher´s exact test was applied to calculate statistical significance. (n.s., not significant; p < 0.001 (***); p<0.01 (**)).</p>
<p>Data from three biological replicates are summarized for each experiment, with exception of (D) where data from two experiments are shown. Lateral views are shown, anterior to the left, dorsal is up. Numbers indicate the amount of embryos with the respective phenotype/total number of embryos analyzed in each experiment. Arrows indicate up- or down-regulation of <em>runx1/c-myb </em>in each condition. Arrowheads denote the VDA region.</p>
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https://api.sourcedata.io/file.php?figure_id=9926
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}
] |
|
27638855
|
10.15252/embj.201593454
|
Evi1 regulates Notch activation to induce zebrafish hematopoietic stem cell emergence
|
2016
|
Figure 5
|
<p><strong>Figure 5.</strong> <strong>Endothelial </strong><strong>NICD</strong> <strong>induction </strong><strong>rescues HSC </strong><strong>emergence</strong><strong> from the VDA</strong></p>
<p><strong>A.</strong> Confocal time-lapse live imaging was performed in Tg(<em>c-myb:GFP;</em><em>fli.1:UAS;Gal4:RFP</em><em>) </em><em>evi1</em> morphant embryos (top, Movie EV 2) or in Tg(<em>c-myb:GFP;</em><em>fli.1:UAS;Gal4:RFP</em><em>) </em>crossed to Tg(<em>5xUAS-E1b:6xMYC-notch1a</em>) embryos prior to MO injection (bottom, Movie EV 3) from 28 to 42 hpf. Shown are three representative time-points, in which the transformation from hemogenic endothelial cells to the hematopoietic fate is visible. For each time-point merged images are shown. NICD induction controlled by endothelial <em>fli.1</em> (lower panel) can rescue the <em>evi1 </em>morphant phenotype and increases the number of HSPCs cells emerging from the VDA (arrows).</p>
<p><strong>B. </strong>Cell counts of emerging HSPCs in control and <em>evi1 </em>morphant fish with or without endothelial NICD induction. At least n=5 movies from n=3 biological replicates were analyzed. A non-parametric Mann-Whitney test was used to test for statistical significance and error bars are shown as ± s.d. (n.s., not significant, p<0.05 (*)).</p>
|
https://api.sourcedata.io/file.php?figure_id=9927
|
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] |
|
27638855
|
10.15252/embj.201593454
|
Evi1 regulates Notch activation to induce zebrafish hematopoietic stem cell emergence
|
2016
|
Figure 6
|
<p><strong>Figure 6.</strong> <strong><em>evi1 </em></strong><strong>regulates Notch independent</strong><strong>ly</strong><strong> of the Vegf pathway</strong><strong> and can compensate for Vegf inhibition</strong></p>
<p><strong>A</strong><strong>.</strong> WISH of <em>dll4 </em>(upper) and <em>notch1b </em>(lower) in control injected embryos (left), <em>evi1 </em>morphants (middle) and <em>evi1 </em>morphant transgenic Tg(<em>Hsp70l:vegfaa;myl7:eGFP) </em>embryos at 32 hpf after heat-shock induction at 20 hpf (right).</p>
<p><strong>B</strong><strong>, C</strong><strong>. </strong>WISH of <em>runx1/c-myb </em>(B) or <em>notch1b </em>(C) after treatment with DMSO (left), the VEGF receptor inhibitor SU5461 (middle) and respectively SU5461 after injection of <em>UAS:mEvi1</em> (inducing endothelial evi1 expression) in Tg(<em>fli.1:Gal4FF;UAS:RFP</em>) embryos (right).</p>
<p>Two or more biological replicates are shown for each experiment. Lateral views are shown, anterior to the left, dorsal is up. Numbers indicate the amount of embryos with the respective phenotype/total number of embryos analyzed in each experiment. Arrows indicate up- or down-regulation of the respective gene in each condition. For each analyzed gene, quantitation of results is shown, displaying the percentages of embryos with normal vs. decreased gene expression for each condition. A Fisher´s exact test was applied to calculate statistical significance (p<0.05 (*), p<0.01 (**), p<0.001 (***)).</p>
|
https://api.sourcedata.io/file.php?figure_id=9928
|
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] |
|
27638855
|
10.15252/embj.201593454
|
Evi1 regulates Notch activation to induce zebrafish hematopoietic stem cell emergence
|
2016
|
Figure 7
|
<p><strong>Figure </strong><strong>7</strong><strong>.</strong> <strong><em>evi1 </em></strong><strong>regulates Notch </strong><strong>signaling </strong><strong>via pAKT</strong><strong>.</strong></p>
<p><strong>A.</strong> Expression of <em>runx1/c-myb</em> in the VDA after treatment with DMSO vehicle control (left), the PI3K/AKT inhibitor Wortmannin (WM, middle) and after joined treatment with WM and enforced NICD expression via HS at 14 hpf in Tg(<em>5xUAS-E1b:6xMYC-notch1a;-1.5hsp70l:Gal4</em>) embryos (right). Graph displays quantitation of results. Shown are the percentages of embryos with normal or decreased <em>runx1/c-myb </em>expression for each condition.</p>
<p><strong>B. </strong>Expression of <em>notch1b </em>after treatment with DMSO vehicle control (left) or Wortmannin (WM, middle). Graph displays quantitation of results. Shown are the percentages of embryos with normal or decreased <em>notch1</em><em>b </em>expression for each condition.</p>
<p><strong>C</strong><strong>. </strong>WISH for <em>runx1/c-myb </em>in control injected embryos (upper left), <em>evi1 </em>morphants (upper right) or respectively <em>evi1 </em>MO with myr-AKT injected embryos with HS at 14 hpf (lower right) and <em>evi1 </em>MO with UAS-myr-AKT injected transgenic <em>Tg(fli.1:Gal4FF</em><em><sup>ubs3</sup></em><em>; UAS:RFP)</em><em><sup>rk</sup></em> embryos.</p>
<p><strong>D</strong><strong>. </strong>Quantitation of results from (C). Shown are the percentages of embryos with normal or decreased <em>runx1/c-myb </em>expression for each condition.</p>
<p><strong>E. </strong>WISH for <em>notch1b </em>in <em>evi1 </em>Morpholino injected (left) and <em>evi1 </em>plus UAS:myr-AKT injected transgenic <em>Tg(fli.1:Gal4FF</em><em><sup>ubs3</sup></em><em>; UAS:RFP)</em><em><sup>rk</sup></em> embryos (right). Graph displays quantitation of results. Shown are the percentages of embryos with normal or decreased <em>notch1b </em>expression for each condition.</p>
<p><strong>F</strong><strong>. </strong>Schematic illustration of the role of Evi1 during HSPC emergence and the dual regulation of Notch by the <em>shh-vegf</em> and the <em>evi1</em>-pAKT axis.</p>
<p>Two or more biological replicates are summarized for each experiment. Lateral views are shown, anterior to the left, dorsal is up. Numbers indicate the amount of embryos with the respective phenotype/total number of embryos analyzed in each experiment. Arrows indicate up- or down-regulation of each analyzed gene. A Fisher´s exact test was applied to calculate statistical significance (n.s., not significant, p<0.05 (*), p<0.01 (**), p<0.001 (***)).</p>
|
https://api.sourcedata.io/file.php?figure_id=9929
|
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|
10.15252/embj.2021107826
|
SARS-CoV-2 sensing by RIG-I and MDA5 links epithelial infection to macrophage inflammation
|
2021
|
Figure 1
|
<p><strong>Figure 1.SARS-CoV-2 activates delayed innate immune responses in lung epithelial cells (A-H) Measurements of replication and innate immune induction in Calu-3 lung epithelial cells infected with SARS-CoV-2 at MOIs 0.08, 0.4 and 2 TCID50<sub>VERO</sub>/cell. (A) Replication of SARS-CoV-2 genomic and subgenomic E RNAs (qRT-PCR). (B) Quantification of N staining from cells in (A) by flow cytometry. Mean percentage of N-positive of all live-gated cells is shown +/- SEM, n=2. (C) Representative example of immunofluorescence staining of N protein (green) after SARS-CoV-2 infection of Calu-3 at MOI 0.4 TCID50<sub>VERO</sub>/cell, at time points shown. Nuclei (DAPI, blue), cell mask (red). Scale bar represents 50µM. (D) Quantification of N staining in cells in (C) by immunofluorescence . (E) Infectious virus released from cells in (A) determined by TCID50 on Vero.E6 cells. (F-H) Fold induction of (F) interferons (IFNβ, IFNλ1 and IFNλ3) (G) IFN stimulated genes (CXCL10 and IFIT2) or (H) pro-inflammatory mediators (IL-6 and CCL5) each overlaid with SARS-CoV-2 E (qRT-PCR). All data from cells in (A) at MOI 0.4 TCID50<sub>VERO</sub>/cell. (A -H) Means from replicate wells shown +/- SEM n=2, full growth curve is representative of three independent experiments. (I-K) SARS-CoV-2 infection (MOIs 0.04 (closed symbols) and 0.0004 (open symbols) TCID50<sub>VERO</sub>/cell) in Calu-3 cells with addition of 10ng/ml IFNβ before or after infection at time points shown, measured by (I) E RNA copies (J) N positive cells, (K) released virus (TCID50<sub>VERO</sub>/cell) all measured at 24 hpi. Dotted line indicates untreated. Mean +/- SEM, n=3, One-way ANOVA Light and dark blue * indicates significance for high and low MOIs respectively.</strong></p>
|
https://api.sourcedata.io/file.php?figure_id=41245
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"ext_tax_names": "Homo sapiens",
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"text": "CXCL10",
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{
"ext_dbs": "NCBI gene",
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] |
||
10.15252/embj.2021107826
|
SARS-CoV-2 sensing by RIG-I and MDA5 links epithelial infection to macrophage inflammation
|
2021
|
Figure 2
|
<p><strong>Figure 2. Peak SARS-CoV-2 replication precedes innate immune activation. (A-I) (A,C) Representative images of</strong> NF-κB <strong>p65 (A) (red) and IRF3 (C) (red) nuclear localisation in mock or SARS-CoV-2 infected (MOI 0.4 TCID50<sub>VERO</sub>/cell) Calu-3 cells at 24 hpi. SARS-CoV-2 N protein (green. (E and G) Representative images of IL-6 mRNA (E) detected by FISH (red) and N protein (green) , or IFIT1 mRNA (G) (green) with N protein (red), both with nuclei (DAPI, blue) in mock or SARS-CoV-2 infected (MOI 0.4 TCID50<sub>VERO</sub>/cell) Calu-3 cells at 24 hpi. (B, D, F, H, I) Single cell analysis time course quantifying the Integrated Nuclear Intensity of NF-κB p65 (B), IRF3 (D) , or overall integrated intensity for IL-6 (F) or IFIT1 (H) mRNA over time in N protein positive cells and N protein negative cells (I). n=2. Kruskal-Wallis test with Dunn's multiple comparison. * (p<0.05), **** (p<0.0001). Scale bar represents 50µM. (J,K) Secretion of CXCL10 (J) and IL-6 (K) by infected Calu-3 cells (MOIs 0.08, 0.4 and 2 TCID50<sub>VERO</sub>/cell), (ELISA). (L) Lactate dehydrogenase (LDH) release into culture supernatants by mock and SARS-CoV-2 infected Calu-3 cells (MOIs 0.08, 0.4 and 2 TCID<sub>VERO</sub>50/cell) quantified absorbance (492nm). (M) Quantification of live/dead staining of non-adherent cells recovered from supernatants of mock or SARS-CoV-2 infected Calu-3 cultures at 48 and 72hpi. Data information: (J-M) Means from replicate wells shown +/- SEM, n=2, representative of three independent experiments.</strong></p>
|
https://api.sourcedata.io/file.php?figure_id=41247
|
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"Q14653"
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"text": "p65",
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"Q04206"
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"ext_ids": "Q04206",
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"ncbi_gene_id": null,
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]
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] |
||
10.15252/embj.2021107826
|
SARS-CoV-2 sensing by RIG-I and MDA5 links epithelial infection to macrophage inflammation
|
2021
|
Figure 3
|
<p><strong>Figure 3. SARS-CoV-2 is sensed by MDA5 and RIG-I. (A-D) Measurement of (A) viral genomic and subgenomic E RNA at 24 hpi, (B) fold induction of CXCL10 from (A), (C) IFIT2 and (D) IL-6 mRNA (qRT-PCR) from (A) after Remdesivir treatment (0.125-5 μM) of SARS-CoV-2 infected Calu-3 cells (MOI 0.04 TCID50/cell) with Remdesivir added 2h prior to infection. Mean +/- SEM, n=3. (E-H) Measurement of (E) viral genomic and subgenomic E RNA (F) fold induction of CXCL10, (G) IFIT2 and (H) and IL-6 at 24 hpi, of Calu-3 cells with SARS-CoV-2 (MOI 0.04 TCID50<sub>VERO</sub>/cell) with Remdesivir treatment (5μM) prior to, at the time of, or 8 h post-infection. Mean +/- SEM, n=3, One way ANOVA with Dunnett's multiple comparisons test to compare to untreated infected condition ('mock'), ** (p<0.01), *** (p<0.001), **** (p<0.0001). (I) Representative example of immunofluorescence staining of dsRNA (red) and N protein (green) after SARS-CoV-2 infection of Calu-3 at MOI 0.4 TCID50<sub>VERO</sub>/cell, at time points shown. Nuclei (DAPI, blue). Scale bar represents 50µM. (J) RNAi mediated depletion of MAVS, RIG-I or MDA-5, reduced their expression levels as compared to siControl (siCtrl) Mean +/- SEM, n=3. Two-Way ANOVA with Sidak's multiple comparisons test, **** (p<0.0001). (K-O) Fold induction of (K) IFNβ, (L) CXCL10, (M) IFIT2 (N) TNF and (O) IL-6 or in SARS-CoV-2 infected Calu-3 cells (MOI 0.04 TCID50/cell) 24 hpi. Mean +/- SEM, n=3, and compared to siCtrl for each gene by One Way ANOVA with Dunnett's multiple comparisons test, ** (p<0.01), *** (p<0.001), **** (p<0.0001), n.s. : non significant. (P) Live/dead stain counts for non-adherent cells, recovered at 48 hpi from supernatants of SARS-CoV-2 infected Calu-3 cells, depleted for MAVS or RNA sensors, compared to siCtrl. Non-adherent cell counts were determined by acquisition by flowcytometry for a defined period of time. Mean +/-SEM, n=3. Total numbers are compared to siCtrl by unpaired t-test, *** (p<0.001). (Q-R) (Q) Viral E RNA and (R) released infectious virus (TCID50<sub>VERO</sub>/cell) at 24 hpi of infected Calu-3 cells depleted for MAVs, RIG-I or MDA5. Mean +/- SEM, n=3. Each group compared to siCtrl by One Way ANOVA with Dunnett's multiple comparisons test, *, p>0.05, ** (p<0.01), n.s : non significant.</strong></p>
|
https://api.sourcedata.io/file.php?figure_id=41249
|
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"ext_tax_names": "Severe acute respiratory syndrome coronavirus 2",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "43740570",
"original_type": "gene",
"role": "assayed",
"text": "E RNA",
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"uniprot_ids": [
"P0DTC4",
"A0A6B9WFC7",
"A0A6C0QFP9",
"A0A6V7AL81",
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"P09913",
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]
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"ncbi_gene_id": "3570",
"original_type": "gene",
"role": "assayed",
"text": "IL-6",
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"P08887",
"A0A087WTB5",
"A0N0L5"
]
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{
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"ext_tax_names": "Severe acute respiratory syndrome coronavirus 2",
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"ext_tax_names": "Severe acute respiratory syndrome coronavirus 2",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
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"A0A6C0QFP9",
"A0A6V7AL81",
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"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "64135",
"original_type": "gene",
"role": "intervention",
"text": "MDA5",
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"Q9BYX4"
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{
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"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "57506",
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"role": "intervention",
"text": "MAVs",
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"uniprot_ids": [
"Q7Z434"
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] |
||
10.15252/embj.2021107826
|
SARS-CoV-2 sensing by RIG-I and MDA5 links epithelial infection to macrophage inflammation
|
2021
|
Figure 4
|
<p><strong>Figure 4. NF-κB and JAK/STAT signalling drive innate immune responses. (A-C) Fold induction at 24 hpi of (A) CXCL10, (B) IFIT1 or (C) IL-6 mRNA (qRT-PCR) after Calu-3 infection with SARS-CoV-2 over a range of MOIs (0.004, 0.04, 0.4 TCID50<sub>VERO</sub>/cell) in the presence of 10 μM TPCA-1 or DMSO as shown. (D-F) Fold induction at 24 hpi of (D) CXCL10, (E) IFIT2 or (F) IL-6 mRNA (RT-qPCR) after Calu-3 infection with SARS-CoV-2 over a range of MOIs (0.0004, 0.004, 0.04, 0.4 TCID50<sub>VERO</sub>/cell) in the presence of 2 μM Ruxolitinib (Rux) or DMSO as shown. (G-H) Viral genomic and subgenomic E RNA at 24 hpi (RT-qPCR) with DMSO or TPCA (G) or Rux (H) treatment. Data information: (A-H) Mean +/- SEM, n=3, statistical comparisons are made by unpaired t test comparing inhibitor-treated to mock-treated SARS-CoV-2 infected conditions at each MOI and each timepoint. * (p<0.05), ** (p<0.01), *** (p<0.001), **** (p<0.0001). (I) Live/dead stain count from non-adherent cells recovered from supernatants of SARS-CoV-2 infected Calu-3 cultures (MOI 0.04 TCID50<sub>VERO</sub>/cell) 48hpi (flow cytometry). Mean +/- SEM, (n=3). One Way ANOVA comparison of inhibitor-treated infected cells to mock-treated infected cells. *** (p<0.001).</strong></p>
|
https://api.sourcedata.io/file.php?figure_id=41251
|
[
{
"ext_dbs": "NCBI gene",
"ext_ids": "43740570",
"ext_tax_ids": "2697049",
"ext_tax_names": "Severe acute respiratory syndrome coronavirus 2",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "43740570",
"original_type": "gene",
"role": "assayed",
"text": "E RNA",
"type": "geneprod",
"uniprot_ids": [
"P0DTC4",
"A0A6B9WFC7",
"A0A6C0QFP9",
"A0A6V7AL81",
"A0A6V7ALI4"
]
}
] |
||
10.15252/embj.2021107826
|
SARS-CoV-2 sensing by RIG-I and MDA5 links epithelial infection to macrophage inflammation
|
2021
|
Figure 5
|
<p><strong>Figure 5. Epithelial responses to SARS-CoV-2 drive macrophage activation (A) Schematic of experimental design. (B-J) Calu-3 cells were transfected with siRNA targeting MAVS or non-targeting control (siCtrl) (B-D) or treated with DMSO vehicle or inhibitors 10 μM TPCA-1 (E-G) or 2 μM Ruxolitinib (Rux) (H-J) as shown, and were mock-infected or infected with SARS-CoV-2 at MOI 0.04 TCID50<sub>VERO</sub>/cell. Virus containing conditioned media (CoM) was harvested at 48 hpi. MDM were treated with Calu-3 virus containing CoM for 6 hpi, before washing and measuring MDM gene expression (B, E, H), and MDM activation markers by flowcytometry 48 h later (C,D,F,G,I,J) , plotting relative median fluorescent intensity (MFI) compared to mock-infected siCtrl (C, D) or mock-infected DMSO control (F, G, I, J). Legends in (B), (E) and (H) apply to (C,D), (F,G) and (I,J) respectively.</strong> The inhibitors in (E) and (H) were tested side-by-side with the same mock condition. <strong>Mean +/- SEM shown, data from 4-6 independent MDM donors is shown. Statistical comparison by two-tailed paired t-test comparing MDM exposed to control infected CoM to siMAVS/inhibitor treated infected CoM. * (p<0.05), ** (p<0.01), *** (p<0.001). (K-O) MDM were treated with either anti-IFNAR antibody (2.5ug/ml), an isotype control IgG antibody (IgG, 2.5ug/ml), Rux (2 μM), or mock treated during 6 h of exposure to CoM from infected, unmodified Calu-3 cells, before washing and measuring MDM gene expression (K, L, M), and MDM activation markers (N, O) by flowcytometry 48 h later. Both gene expression and relative MFI are compared to mock-treated MDM exposed to CoM from uninfected Calu-3s cells. Mean +/- SEM shown, data from 7-8 independent MDM donors is shown. Statistical testing by one-way paired ANOVA, comparing treated MDMs to untreated control by Dunnett's multiple comparison test, * (p<0.05), ** (p<0.01), *** (p<0.001).</strong></p>
|
https://api.sourcedata.io/file.php?figure_id=41253
|
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"ext_tax_names": "Homo sapiens",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "57506",
"original_type": "gene",
"role": "intervention",
"text": "MAVS",
"type": "geneprod",
"uniprot_ids": [
"Q7Z434"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "57506",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "57506",
"original_type": "gene",
"role": "intervention",
"text": "MAVS",
"type": "geneprod",
"uniprot_ids": [
"Q7Z434"
]
}
] |
||
10.15252/embj.2021107826
|
SARS-CoV-2 sensing by RIG-I and MDA5 links epithelial infection to macrophage inflammation
|
2021
|
Figure 6
|
<p><strong>Figure 6. Pre-existing immune activation exacerbates SARS-CoV-2-dependent inflammation. (A) Schematic of experimental design. (B-H) MDM were primed with 100ng/ml LPS for 2h before exposure to SARS-CoV-2 (MOI 0.02 TCID50<sub>VERO</sub>/cell). (B) Expression of genomic and subgenomic viral E RNA at 48 h post exposure in indicated conditions. (C-G) Host gene expression of (C) CCL5, (D) ISG56, (E) IFIT2, (F) IL-6 or (G) IL-1b was measured 48hpi. (H) IL-1b secretion was detected in culture supernatants at 48 hpi by ELISA. (I) Schematic of experimental design. MDM were exposed to SARS-CoV-2 (MOI 0.02 TCID50<sub>VERO</sub>/cell) for 48 h and subsequently stimulated with 100ng/ml LPS for 24 h. (J-P) (J) Expression of genomic and subgenomic viral E RNA 72 h post-exposure in indicated conditions. (K-O) Host gene expression of (K) CCL5, (L) ISG56, (M) IFIT2, (N) IL-6 and (O) IL-1b. (P) IL-1b secretion was detected in culture supernatants at 48 hpi by ELISA. Data Information: (A-P) Gene expression is shown as fold induction over untreated controls. Data from 8-13 independent donors is shown. Groups were compared as indicated by Wilcoxon matched-pairs signed rank test, *, p<0.05, ** (p<0.01), *** (p<0.001). (Q-V) Calu-3 cells were infected with SARS-CoV-2 (MOI 0.04 TCID50<sub>VERO</sub>/cell) in the presence or absence of 10ng/ml IL-1b. (Q-T) Gene expression of (Q) IFNβ (R), CXCL10, (S) IL-6 and (T) IFIT1 was measured after 24h. Fold induction over untreated mock infection is shown, n=3. (U) Non-adherent cells were collected at 48h post infection and live/dead stained. Cells were acquired by flowcytometry and cell counts determined by time-gating. For statistical comparison, total cell numbers were compared. (V) Viral release into culture supernatants at 24 h was measured by TCID50 on VeroE6 cells. (Q-V) Mock and SARS-CoV-2 infected conditions were compared with or without IL1b-treatment, respectively, by unpaired T test (n=3). *, p<0.05; n.s., non-significant. Mean +/- SEM shown.</strong></p>
|
https://api.sourcedata.io/file.php?figure_id=41255
|
[
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"ext_ids": "P01584",
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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": "IL-1b",
"type": "geneprod",
"uniprot_ids": [
"P01584"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P01584",
"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": "IL1b",
"type": "geneprod",
"uniprot_ids": [
"P01584"
]
}
] |
||
27113762
|
10.15252/embr.201541643
|
SIRT5 promotes IDH2 desuccinylation and G6PD deglutarylation to enhance cellular antioxidant defense
|
2016
|
Figure 1
|
<p><strong>Figure 1. Sirt5 protects cells from oxidative stress. </strong></p><p><strong>(A</strong>) <em>Sirt5</em> deficiency leads to higher ROS levels in MEFs. ROS levels were determined in the indicated MEFs as described in ‘Materials and Methods’. The results are average ± SD of 3 independent experiments **p<0.01 (two-tailed unpaired t-test).</p><p><strong>(B) </strong><em>Sirt5</em> deficiency suppresses GSH production in MEFs. The ratio of [GSH/GSSG] was determined in cell extracts as described in ‘Materials and Methods’. The results are average ± SD of 3 independent experiments *p<0.05 (two-tailed unpaired t-test).</p><p><strong>(C) </strong><em>Sirt5</em> deficiency inhibits NADPH production in MEFs. The ratio of [NADPH/NADP<sup>+</sup>] was determined in cell extracts as described in ‘Materials and Methods’. The results are average ± SD of 3 independent experiments ***p<0.001 (two-tailed unpaired t-test).</p><p><strong>(D)</strong> <em>Sirt5</em> deficiency decreases cell growth. MEF cells were seeded in 6-well plates at a density of 50,000 cells/well, and cell growth rate was carefully monitored every 1-2 days by cell counting for 8 days. The results are average ± SD of 3 independent experiments *p<0.05, ***p<0.001 (two-tailed unpaired t-test).</p><p><strong>(E)</strong> <em>Sirt5</em> deficiency leads to higher sensitivity of MEFs to Paraquat. The levels of cleaved PARP and Caspase-3 were determined by western blot analysis.</p><p><strong>(F) </strong><em>Sirt5</em> protects MEFs from ROS-induced cell death. Wild-type and <em>Sirt5</em> KO MEFs were treated with Paraquat (500 μM) for 24 hrs, and then cell viability was determined by counting the remaining adherent cells. The results are average ± SD of 3 independent experiments **p<0.01 (two-tailed unpaired t-test).</p><p><strong>(G-I)</strong> <em>Sirt5</em> deficiency inhibits the production of NADPH and GSH and increases lipid peroxide in mouse brains after Paraquat injection. Female <em>Sirt5</em> KO and WT littermates (n=3~5 per group) were intraperitoneally injected with saline or paraquat (10 mg/kg) once a week for 3 consecutive weeks. The ratios of [NADPH/NADP<sup>+</sup>] and [GSH/GSSG] and the level of lipid peroxide were determined in tissue extracts. The results are average ± SD. *p<0.05, n.s.: not significant (two-tailed unpaired t-test).</p><p><strong>(J-K) </strong><em>Sirt5</em> KO mice are more sensitive to Paraquat-induced nigrostriatal dopaminergic degeneration. Female <em>Sirt5</em> KO and WT littermates were treated with paraquat as in (G-I). The brain sections were stained to detect tyrosine hydroxylase (TH) positive dopaminergic neurons in the SNc region, as described in ‘Materials and Methods’. Representative immunohistochemistry images (original magnification, 100×; scale bar, 100 μm) and the corresponding quantifications are shown in (J) and (K), respectively. The results are average ± SD. *p<0.05, n.s.: not significant (two-tailed unpaired t-test).</p>
|
https://api.sourcedata.io/file.php?figure_id=7260
|
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"text": "Sirt5",
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"Q8K2C6",
"A0A1Y7VM56"
]
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"ext_dbs": "NCBI gene",
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"Q8K2C6",
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},
{
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]
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"text": "Sirt5",
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"uniprot_ids": [
"Q8K2C6",
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},
{
"ext_dbs": "NCBI gene",
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"text": "Sirt5",
"type": "geneprod",
"uniprot_ids": [
"Q8K2C6",
"A0A1Y7VM56"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "68346",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "68346",
"original_type": "gene",
"role": "intervention",
"text": "Sirt5",
"type": "geneprod",
"uniprot_ids": [
"Q8K2C6",
"A0A1Y7VM56"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "68346",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "68346",
"original_type": "gene",
"role": "intervention",
"text": "Sirt5",
"type": "geneprod",
"uniprot_ids": [
"Q8K2C6",
"A0A1Y7VM56"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "68346",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "68346",
"original_type": "gene",
"role": "intervention",
"text": "Sirt5",
"type": "geneprod",
"uniprot_ids": [
"Q8K2C6",
"A0A1Y7VM56"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "68346",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "68346",
"original_type": "gene",
"role": "assayed",
"text": "Sirt5",
"type": "geneprod",
"uniprot_ids": [
"Q8K2C6",
"A0A1Y7VM56"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P24529",
"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": "TH",
"type": "geneprod",
"uniprot_ids": [
"P24529"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P24529",
"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": "tyrosine hydroxylase",
"type": "geneprod",
"uniprot_ids": [
"P24529"
]
}
] |
|
27113762
|
10.15252/embr.201541643
|
SIRT5 promotes IDH2 desuccinylation and G6PD deglutarylation to enhance cellular antioxidant defense
|
2016
|
Figure 2
|
<p><strong>Figure 2. SIRT5 preserves cellular antioxidant capacity partially through activating NADPH-producing G6PD and IDH2</strong></p>
<p><strong>(A)</strong>Knockdown of <em>SIRT5</em> inhibits NADPH production in HEK293T cells. The ratio of [NADPH/NADP<sup>+</sup>] was determined in cell extracts as described in ‘Materials and Methods’. The results are average ± SD of 3 independent experiments **p<0.01, ***p<0.001 (two-tailed unpaired t-test).</p>
<p><strong>(B) </strong>Knockdown of <em>SIRT5</em> suppresses GSH production in HEK293T cells. The ratio of [GSH/GSSG] was determined in cell extracts as described in ‘Materials and Methods’. The results are average ± SD of 3 independent experiments **p<0.01 (two-tailed unpaired t-test).</p>
<p><strong>(C) </strong>Knockdown of <em>SIRT5</em> leads to higher ROS levels in HEK293T cells. ROS levels were determined in the indicated stable cells as described in ‘Materials and Methods’. The results are average ± SD of 3 independent experiments ***p<0.001 (two-tailed unpaired t-test).</p>
<p><strong>(D)</strong> Knockdown of <em>SIRT5 </em>leads to higher sensitivity to Paraquat. The expression levels of PARP and Caspase-3 were determined by western blot analysis.</p>
<p><strong>(E)</strong> SIRT5 protects HEK293T cells from ROS-induced cell death. The indicated stable HEK293T cells were treated as mentioned above in (D), and then cell viability was determined by counting the remaining adherent cells. The results are average ± SD of 3 independent experiments **p<0.01 (two-tailed unpaired t-test).</p>
<p><strong>(F) </strong>Cartoon representation of major NADPH-producing enzymes in the cell. As shown, G6PD, 6PGD, ME1, IDH1 and MTHFD1 are located in cytosol, while IDH2 and MTHFD2 are located in mitochondria.</p>
<p><strong>(G) </strong>The activities of G6PD/6PGD and IDH1/2 are reduced in stable HEK293T cells with <em>SIRT5</em> knockdown. Activities of the indicated endogenous proteins were determined in cell extracts as described in ‘Materials and Methods’. The results are average ± SD of 3 independent experiments *p<0.05, **p<0.01, ***p<0.001, n.s.: not significant (two-tailed unpaired t-test).</p>
<p><strong>(H) </strong>G6PD and IDH2 are activated by SIRT5 <em>in vitro</em>. Upon pre-incubation with SIRT5 <em>in vitro</em>, the activities of the indicated ectopically expressed proteins were determined as described in ‘Materials and Methods’. The results are average ± SD of 3 independent experiments **p<0.01, n.s.: not significant (two-tailed unpaired t-test).</p>
|
https://api.sourcedata.io/file.php?figure_id=7261
|
[
{
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"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "23408",
"original_type": "gene",
"role": "intervention",
"text": "SIRT5",
"type": "geneprod",
"uniprot_ids": [
"Q9NXA8",
"A0A7P0T9N1",
"A0A7P0Z4N6"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "23408",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "23408",
"original_type": "gene",
"role": "intervention",
"text": "SIRT5",
"type": "geneprod",
"uniprot_ids": [
"Q9NXA8",
"A0A7P0T9N1",
"A0A7P0Z4N6"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "23408",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "23408",
"original_type": "gene",
"role": "intervention",
"text": "SIRT5",
"type": "geneprod",
"uniprot_ids": [
"Q9NXA8",
"A0A7P0T9N1",
"A0A7P0Z4N6"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "23408",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "23408",
"original_type": "gene",
"role": "intervention",
"text": "SIRT5",
"type": "geneprod",
"uniprot_ids": [
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"A0A7P0T9N1",
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]
},
{
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"mapping_status": "mapped",
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"text": "Caspase-3",
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"P42574"
]
},
{
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"ext_ids": "23408",
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"ext_tax_names": "Homo sapiens",
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"A0A7P0Z4N6"
]
},
{
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"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
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"mapping_status": "mapped",
"ncbi_gene_id": "23408",
"original_type": "gene",
"role": "intervention",
"text": "SIRT5",
"type": "geneprod",
"uniprot_ids": [
"Q9NXA8",
"A0A7P0T9N1",
"A0A7P0Z4N6"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P11413",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
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"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "G6PD",
"type": "geneprod",
"uniprot_ids": [
"P11413"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "O75874",
"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": "IDH1",
"type": "geneprod",
"uniprot_ids": [
"O75874"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P52209",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
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"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "6PGD",
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"uniprot_ids": [
"P52209"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "23408",
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"ext_tax_names": "Homo sapiens",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
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"role": "intervention",
"text": "SIRT5",
"type": "geneprod",
"uniprot_ids": [
"Q9NXA8",
"A0A7P0T9N1",
"A0A7P0Z4N6"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P11413",
"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": "G6PD",
"type": "geneprod",
"uniprot_ids": [
"P11413"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P48735",
"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": "IDH2",
"type": "geneprod",
"uniprot_ids": [
"P48735"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q9NXA8",
"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": "SIRT5",
"type": "geneprod",
"uniprot_ids": [
"Q9NXA8"
]
}
] |
|
27113762
|
10.15252/embr.201541643
|
SIRT5 promotes IDH2 desuccinylation and G6PD deglutarylation to enhance cellular antioxidant defense
|
2016
|
Figure 3
|
<p><strong>Figure </strong><strong>3. SIRT5 promotes IDH2 </strong><strong>desuccinylation</strong><strong> and G6PD </strong><strong>deglutarylation</strong><strong> to activate these two enzymes and maintain NADPH homeostasis </strong></p>
<p><strong>(A) </strong>G6PD activity is not regulated by lysine succinylation. Purified Flag-tagged G6PD was incubated with or without succinyl-CoA (1 mM) at 30°C for 15 mins, followed by measurement of G6PD enzyme activity as described in ‘Materials and Methods’. The results are average ± SD of 3 independent experiments. n.s.: not significant (two-tailed unpaired t-test).</p>
<p><strong>(B) </strong>IDH2 activity is suppressed by lysine succinylation. Purified Flag-tagged IDH2 was incubated with or without succinyl-CoA (1 mM) at 30°C for 15 mins, followed by measurement of IDH2 enzyme activity as described in ‘Materials and Methods’. The results are average ± SD of 3 independent experiments *p<0.05 (two-tailed unpaired t-test).</p>
<p><strong>(C)</strong> <em>SIRT5</em> knockdown increases G6PD glutarylation and IDH2 succinylation, respectively, and decreases both enzyme activity. Flag-G6PD or Flag-IDH2 was ectopically expressed in the indicated stable HEK293T cells. G6PD/IDH2 proteins were purified by immunoprecipitated with Flag beads and eluted with Flag peptide, followed by determination of their lysine modifications and enzyme activity. The results are average ± SD of 3 independent experiments **p<0.01, ***p<0.001 (two-tailed unpaired t-test).</p>
<p><strong>(D)</strong> SIRT5 decreases G6PD glutarylation and IDH2 succinylation, and increases both enzyme activity. Flag-G6PD or Flag-IDH2 was co-overexpressed with HA-SIRT5 in HEK293T cells. G6PD and IDH2 proteins were purified by immunoprecipitation with Flag beads and eluted with Flag peptide, followed by determination of their lysine modifications and enzyme activity. The results are average ± SD of 3 independent experiments *p<0.05, **p<0.01 (two-tailed unpaired t-test).</p>
<p><strong>(E)</strong> Cartoon representation of porcine mitochondrial IDH2 structure shows isocitrate binding pocket (PDB ID: 1LWD) [33], made by Pymol (<a href="http://www.pymol.org">www.pymol.org</a>). The protein is colored in light green and isocitrate in rainbow, with Lys 360 and Lys 413 residues in IDH2 being colored in red.</p>
<p><strong>(F-G)</strong> K413 in IDH2 may be a key succinylation site that is directly targeted by SIRT5. The indicated Flag-tagged IDH2 proteins were overexpressed in HEK293T cells with stable<em> SIRT5</em> knockdown or SIRT5 co-overexpression. Wild-type and mutant IDH2 proteins were purified by Flag beads and eluted with Flag peptide, followed by measurement of IDH2 enzyme activity. The results are average ± SD of 3 independent experiments *p<0.05, n.s.: not significant (two-tailed unpaired t-test).</p>
|
https://api.sourcedata.io/file.php?figure_id=7262
|
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