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10.15252/msb.20209833
|
Single-cell transcriptomics reveals immune response of intestinal cell types to viral infection
|
2021
|
Figure 1
|
<p><strong>Figure 1. Interferons protect human intestinal organoids from HAstV1 infection.</strong></p><p><strong>A</strong>. Cryo-sections of human organoids were analyzed for the presence of enterocytes (E-cad), Goblet cells (Muc-2) and tight junctions (ZO-1) by indirect immunofluorescence. Nuclei are stained with DAPI. Scale bar 25 μm.</p><p><strong>B</strong>. Human intestinal organoids were incubated with media (mock) or infected with HAstV1. 16hpi organoids were frozen, cryo-sectioned, and HAstV1 infected cells were visualized by indirect immunofluorescence (HAstV1 (red), nuclei (DAPI, blue). Scale bar 25 μm.</p><p><strong>C</strong>. Human intestinal organoids were incubated with media (mock) or infected with HAstV1. Organoids at 16 hpi were fixed and the presence of HAstV1 infected cells (green) were visualized by indirect immunofluorescence. Apical and basolateral membranes were immunostained for actin (magenta) and Laminin (red) respectively. Nuclei are stained with DAPI (blue). Scale bar is 20 μm.</p><p><strong>D.</strong> Quantification of C with the percentage of infected cells determined.</p><p><strong>E</strong>. Human intestinal organoids were infected with HAstV1. At indicated time post-infection the increase in viral copy number was determined by q-RT-PCR.</p><p><strong>F</strong>. Human intestinal organoids were incubated with media (mock) or infected with HAstV1. At 24 hpi the presence of IFNλ in the media was tested by ELISA. Dotted line indicates detection limit of the assay.</p><p><strong>G</strong>. Same as E but for the induced levels of either type I IFN (IFNβ1) or type III IFN (IFNλ).</p><p><strong>H</strong>. Human intestinal organoids were pre-treated for 24h with 2000IU/mL of IFNβ1 or 300ng/mL of IFNλ1-3. Interferons were maintained during the course of infection and the amount of HAstV1 copy numbers was assayed 24hpi by q-RT-PCR.</p><p>Data information: <strong>A-G</strong> Three biological replicates were performed for each experiment. Representative immunofluorescence images are shown. Error bars indicate the standard deviation. Statistics are from unpaired t-test.</p>
|
https://api.sourcedata.io/file.php?figure_id=41858
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||
10.15252/msb.20209833
|
Single-cell transcriptomics reveals immune response of intestinal cell types to viral infection
|
2021
|
Figure 3
|
<p><strong>Figure 3. Single-cell profiling and multiplex <em>in situ</em> RNA hybridization of human ileum-derived organoids.</strong></p><p><strong>A</strong>. UMAP of scRNA-Seq data from human ileum-derived organoids (n=16,682 cells); dots corresponding to cells are colored by the cell type.</p><p><strong>B</strong>. Dot plot of the top-three marker genes for each cell type. The dot size represents the percentage of cells expressing the gene; the color represents average expression across the cell type. Fig.S3B shows an extended list of the marker genes. All cell-type-defining marker genes are provided in Dataset EV2.</p><p><strong>C</strong>. Representative images showing multiplex <em>in situ</em> RNA hybridization of marker genes in an organoid. DAPI in blue.</p><p><strong>D-I</strong>. Visualizations for cell-type markers for the major intestinal cell types, showing single-cell expression intensities of the cell-type markers on the UMAP (left) and multiplex <em>in situ</em> RNA hybridization; red corresponds to viral RNA and a green corresponds to cell type markers (right).</p><p><strong>J-M.</strong> Percentage of stem cells (OLFM4) goblet cell (FGCBP), mature enterocytes (APOA4) and cells of the enterocyte lineage (FGCBP) from the total organoid cells population (black bar) in mock-treated organoids and after HAstV1 infection. The percentage of infected cells (red bars) and bystander cells (blue bars) within each cell type is shown. The data was obtained from multiplex in situ RNA hybridization in 2D organoids. n=10, mean ± SEM. Statistics show comparison of infected cells between mock-treated, 4h pi and 16h pi organoids. An Ordinary one-way ANOVA and Tukey's multiple comparisons test was used. n.s non significant, * p<0.05, ** p<0.01, *** p<0.001.</p>
|
https://api.sourcedata.io/file.php?figure_id=41862
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||
10.15252/msb.20209833
|
Single-cell transcriptomics reveals immune response of intestinal cell types to viral infection
|
2021
|
Figure 5
|
<p><strong>Figure 5. Multiplex <em>in situ</em> RNA FISH visualizes immune signature in HastV1-infected and bystander cells.</strong></p><p><strong>A.</strong> One image per condition was used to show the multiplex in situ RNA FISH. A representative region of the images was chosen and cropped in order to have a zoom-in of a specific area for better visualization. Shown are the enterocyte lineage marker FABP6 (green), HAstV1 infection (white), and CCL2 gene expression (red) of mock-treated and infected organoids. DAPI is in blue. White arrows show co-localization of FABP6 and CCL2 with HAstV1 signal. Scale bar 100µm.</p><p><strong>B-D.</strong> Fluorescence intensity (arbitrary units) of innate immune marker expression in stem cells (OLFM4 positive), goblet cells (FCGBP positive), enterocyte lineage cells (FABP6 positive), and mature enterocytes (APOA4 positive). Bystander cells are in blue and infected cells in red. 10-90 percentile box plots, each dot represents one cell (mock N=2274, 4h N=3682, 16h N=1510. C. mock N=2693, 4h N=3706, 16h N=1921. D. mock N=2274, 4h N=3706, 16h N=1514.) . Blue statistics show a comparison of bystander cells between cell lineages and red statistics show the comparison of infected cells between cell lineages. Ordinary one-way ANOVA and Tukey's multiple comparisons test were used. Grey statistics show the comparison between infected and bystander cells within each cell lineage. Unpaired t-test with Welch's correction was used. n.s non significant, * p<0.05, ** p<0.01, *** p<0.001, **** p<0.0001.</p><h1 id="section-1"><br></h1><h1 id="extended-view-figure-legends">Extended View Figure Legends</h1>
|
https://api.sourcedata.io/file.php?figure_id=41866
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10.15252/embj.2021109783
|
Spt5 histone binding activity preserves chromatin during transcription by RNA polymerase II
|
2022
|
Figure 1
|
<p><strong>Figure 1</strong></p><p>Eukaryotic Spt5N binds histones H3-H4 via an evolutionarily conserved motif. (<strong>A</strong>) Domain structure of Spt5 / NusG proteins. The enlarged inset shows a conserved region of Spt5N from <em>Saccharomyces cerevisiae</em> (S.c.), <em>Schizosaccharomyces pombe</em> (S.p.), <em>Aspergillus nidulans</em> (A.n.), <em>Homo sapiens</em> (H.s.), <em>Xenopus laevis</em> (X.l.) and <em>Arabidopsis thaliana</em> (A.t.). Spt5N contains three invariant residues that were mutated in Spt5-3A (indicated by red asterisks), whilst residues with conservative substitutions are denoted by blue asterisks. (<strong>B</strong>) GST, GST-MCM2N (human) and GST-Spt5N (yeast) were mixed as indicated with yeast histones H3-H4, in the presence of glutathione agarose beads (see STAR method for further details). The input and pulldown samples were analysed by SDS-PAGE before staining with colloidal Coomassie blue. The asterisks denote truncations of GST-Spt5N. (<strong>C</strong>) Similar experiment to (B) but with histones H2A-H2B. (<strong>D</strong>) Similar experiment to (B) to compare histone binding by GST-MCM2N and GST-MCM2N-2A (with Y81A Y90A mutations of conserved residues). (<strong>E</strong>) Analogous experiment to (D), comparing histone binding by GST-Spt5 and GST-Spt5N-3A (with F180A E184A V187A mutations of conserved residues). (<strong>F</strong>) Budding yeast Spt5N and Spt5N-3A were expressed as fusions to Protein A in budding yeast cells. Cell extracts were treated with DNase as indicated, to release nucleosomal histone complexes from chromatin, before immunoprecipitation (IP) of Spt5N / Spt5N-3A on magnetic beads coated with IgG. The bound proteins were eluted and then analysed by mass spectrometry (the panel indicates the detected spectral counts). (<strong>G</strong>) Samples from an analogous experiment to that shown in (F) were analysed by immunoblotting of the indicated factors. The asterisk indicates a non-specific band in the immunoblot for histone H2B. (<strong>H</strong>). Budding yeast cells expressing fusions of Spt5N and Spt5N-3A to Protein A were grown in parallel with cells expressing the equivalent wild type and mutant versions of fission yeast Spt5N (Sp Spt5N and Sp Spt5N-3A - the latter contained the F146A, E150A and V153A mutations). See also Figure EV1.</p>
|
https://api.sourcedata.io/file.php?figure_id=45929
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||
10.15252/embj.2021109783
|
Spt5 histone binding activity preserves chromatin during transcription by RNA polymerase II
|
2022
|
Figure 2
|
<p><strong>Figure 2</strong></p><p>Mutation of the histone-binding motif of Spt5N is lethal, even in the presence of wild type Spt5. (<strong>A</strong>) Linearised versions of the indicated plasmids were transformed into <em>SPT5-9MYC</em> budding yeast cells and integrated at the <em>ura3</em> locus. For each transformation, four colonies were analysed by immunoblotting and DNA sequencing as shown. Colonies transformed with plasmid expressing Spt5-3A either lost the plasmid (1), contained the <em>SPT5-3A</em> DNA but failed to express Spt5-3A protein (2+4) or experienced a gene conversion and thus expressed wild type Spt5 from the integrated plasmid DNA (3). (<strong>B</strong>) Serial dilutions of yeast cells expressing the indicated fragments of wild type Spt5 or Spt5-3A from the <em>GAL1,10</em> promoter were grown on the indicated medium, together with a control of wild type cells. (<strong>C</strong>) Yeast cells were generated that expressed Protein A-tagged versions of wild type Spt5 (full length or the indicated truncations), or full length Spt5-3A, under the control of the <em>GAL1,10</em> promoter. Cells were grown in medium containing galactose and the ProteinA-tagged Spt5 proteins were isolated from cell extracts on magnetic beads coated with IgG. Association of the tagged Spt5 proteins with the elongating form of Pol II was monitored by immunoblotting, using antibodies specific to the indicated phosphorylation sites in the C-Terminal Domain repeats of the Rpb1 subunit of Pol II. (<strong>D</strong>) Control and <em>spt5-AID</em> strains were grown at 30°C in rich medium, before addition of auxin (0.5 mM 3-indoleacetic acid or IAA) for 1 hour. Spt5 protein was monitored in cell extracts by immunoblotting. (<strong>E</strong>) Serial dilutions of control cells or <em>spt5-AID</em> cells, expressing the indicated versions of Spt5 from the <em>GAL1,10</em> promoter, were grown on the indicated medium.</p>
|
https://api.sourcedata.io/file.php?figure_id=45931
|
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"P27692"
]
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"uniprot_ids": [
"A0A6V8S3R7"
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},
{
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]
},
{
"ext_dbs": "NCBI gene",
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"ext_tax_names": "Saccharomyces cerevisiae S288C",
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"mapping_status": "mapped",
"ncbi_gene_id": "854999",
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"role": "intervention",
"text": "Spt5",
"type": "geneprod",
"uniprot_ids": [
"P27692"
]
}
] |
||
10.15252/embj.2021109783
|
Spt5 histone binding activity preserves chromatin during transcription by RNA polymerase II
|
2022
|
Figure 3
|
<p><strong>Figure 3</strong></p><p>The histone-binding activity of Spt5N is dispensable for progression of the Pol II elongation complex through transcription units. (<strong>A</strong>) Experimental procedure, based on the yeast strains YCE281, YCE350 and YCE356. (<strong>B</strong>) Immunoblot analysis at the indicated times for the samples described in (A). (<strong>C</strong>) Cells from the end of the experiment described in (A) were fixed and processed for ChIP-Seq, using antibodies specific for phosphorylated Serine 5 in the C-Terminal Domain of the Pol II catalytic subunit Rpb1 (CTD-Ser5P). For each of the three indicated strains, the histograms represent the normalized read density (DNA sequence read count per million reads, or RPM), across a sample gene body. (<strong>D</strong>) Average of the normalised read density (RPM) for the CTD-Ser5P ChIP-Seq data from two independent experiments, for regions spanning 1kb upstream and downstream of the Transcription Start Site (TSS) of actively transcribed genes across the yeast genome (the analysis focussed on 821 actively transcribed genes, as described in Materials and Methods). (<strong>E</strong>) For each transcribed gene, an RNA Pol II Traveling ratio was calculated as indicated. (<strong>F</strong>) Log2 values of the calculated Pol II traveling ratios for each actively transcribed gene were arranged in order from low to high and then plotted against percentile. (<strong>G</strong>) Principal component analysis of two independent experiments, for the Pol II CTD-Ser5P ChIP-Seq signal across the yeast genome in the three indicated strains.</p>
|
https://api.sourcedata.io/file.php?figure_id=45933
|
[
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"ext_ids": "H9NB31",
"ext_tax_ids": "4932",
"ext_tax_names": "Saccharomyces cerevisiae",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "Rpb1",
"type": "geneprod",
"uniprot_ids": [
"H9NB31"
]
}
] |
||
10.15252/embj.2021109783
|
Spt5 histone binding activity preserves chromatin during transcription by RNA polymerase II
|
2022
|
Figure 4
|
<sd-panel><p><strong>Figure 4</strong></p> <p>Spt5N histone binding activity preserves nucleosome integrity during transcription. (<strong>A</strong>) Samples from the experiment described in Figure 3A were also processed for MNase-Seq. For each of the three indicated strains, the histograms represent the normalized DNA sequence read count per million reads (RPM), across a sample gene body. (<strong>B</strong>) Average of the normalised read density (RPM) for the MNase-Seq data from two independent experiments, for regions spanning 1kb upstream and downstream of the Transcription Start Site (TSS) of actively transcribed genes across the yeast genome (as above, the analysis focussed on 821 active genes, as described in Materials and Methods). (<strong>C</strong>) Samples from the same experiment were further processed for ChIP-Seq using antibodies to histone H3K4me3. For each of the three indicated strains, the normalised read count per million reads is presented across a sample gene body. (<strong>D</strong>) Average of the normalised read density (RPM) for the H3K4me3 ChIP-Seq datasets from two independent experiments, for regions spanning 1kb upstream and downstream of the Transcription Start Site (TSS) of actively transcribed genes. (<strong>E</strong>) Principal component analysis of two independent experiments, for the H3K4me3 ChIP-Seq signals across the yeast genome in the three indicated strains. (<strong>F</strong>) Ratio of the H3K4me3 ChIP-Seq signal (TSS to +500 bp) in cells expressing Spt5-3A and cells expressing wild type Spt5. The boxes extend from the 25<sup>th</sup> to 75<sup>th</sup> percentiles whilst the 'whiskers' illustrate the minimum and maximal values and the lines within each box correspond to the median values. The data are expressed as a function of the gene expression level, based on the read density of the ChIP-Seq data for CTD-Ser5P (from TSS to TTS) in Figure 3, ordered from lowest to highest values in four quartiles (colour coded as indicated). The correlation between H3K4me3 in cells expressing Spt5-3A (<em>spt5-AID GAL-SPT5-3A)</em> and control cells (<em>spt5-AID GAL-SPT5</em>) is progressively worse from Q1 to Q4, for genes expressed at progressively higher levels.</p></sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=45935
|
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"ext_ids": "A0A6A5Q536",
"ext_tax_ids": "4932",
"ext_tax_names": "Saccharomyces cerevisiae",
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"mapping_status": "mapped",
"ncbi_gene_id": null,
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"role": "assayed",
"text": "histone H3",
"type": "geneprod",
"uniprot_ids": [
"A0A6A5Q536"
]
}
] |
||
26666269
|
10.15252/emmm.201505505
|
Endothelial cell-derived Angiopoietin-2 is a therapeutic target in treatment-naive and Bevacizumab-resistant glioblastoma
|
2015
|
Figure 1
|
<p>Figure 1: Endothelial Ang-2 upregulation correlates with WHO grading in human gliomas. ELISA displaying human Ang-2 (A) and Ang-1 (B) level in serum of healthy patients (Ang-2 n=4; Ang-1 n=21) or patients with low grade glioma (WHOII) (n=5), anaplastic astrocytoma (WHOIII) (n=7) or glioblastoma (WHOIV) (n=39) are shown. The TCGA database was accessed to obtain gene expression level for Ang-1, Ang-2, Tie2 and Tie1 in GBM in comparison to normal brain (C). Ang-2 expression and quantitative analysis of Ang-2 in healthy human brain (n=3), low grade diffuse glioma (n=14), anaplastic astrocytoma (n=12) or glioblastoma (n=11) is shown (D). Co-staining of Ang-2 and vWF (endothelial cells), αSMA (mural cells) and IBA1 (microglia) in different glioblastoma specimen. Normal brain tissue was used to assess Ang-2 staining specificity (E). Ang-2 predicts survival of glioblastoma patients (F). If not indicated differently, Kruskall-Wallis (Dunn´s post test) was applied, ** p < 0.05, *** p < 0.005; data are mean ± SEM</p>
|
https://api.sourcedata.io/file.php?figure_id=5251
|
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"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "Ang-2",
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"uniprot_ids": [
"O15123"
]
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{
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"text": "Ang-2",
"type": "geneprod",
"uniprot_ids": [
"O15123"
]
},
{
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"role": "assayed",
"text": "Ang-2",
"type": "geneprod",
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"O15123"
]
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{
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"mapping_status": "mapped",
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"role": "assayed",
"text": "Ang-1",
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"text": "Ang-1",
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"B4DTQ9"
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"mapping_status": "mapped",
"ncbi_gene_id": "11601",
"original_type": "gene",
"role": "assayed",
"text": "Ang-2",
"type": "geneprod",
"uniprot_ids": [
"O35608",
"B9EHQ4"
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},
{
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"mapping_status": "mapped",
"ncbi_gene_id": "7010",
"original_type": "gene",
"role": "assayed",
"text": "Tie2",
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"Q02763",
"Q59HG2"
]
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{
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"role": "assayed",
"text": "Tie1",
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"uniprot_ids": [
"P35590",
"B4DTW8"
]
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{
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"uniprot_ids": [
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"ext_ids": "O15123",
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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": "Ang-2",
"type": "geneprod",
"uniprot_ids": [
"O15123"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P62736",
"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": "αSMA",
"type": "geneprod",
"uniprot_ids": [
"P62736"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P55008",
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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": "IBA1",
"type": "geneprod",
"uniprot_ids": [
"P55008"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "O15123",
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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": "Ang-2",
"type": "geneprod",
"uniprot_ids": [
"O15123"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "O15123",
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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": "Ang-2",
"type": "geneprod",
"uniprot_ids": [
"O15123"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P04275",
"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": "vWF",
"type": "geneprod",
"uniprot_ids": [
"P04275"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "O15123",
"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": "Ang-2",
"type": "geneprod",
"uniprot_ids": [
"O15123"
]
}
] |
|
26666269
|
10.15252/emmm.201505505
|
Endothelial cell-derived Angiopoietin-2 is a therapeutic target in treatment-naive and Bevacizumab-resistant glioblastoma
|
2015
|
Figure 2
|
<p>Figure 2: Endothelial Ang-2 expression reduced pericyte coverage and increased macrophage infiltration in experimental glioblastoma. GL261 cells were intracerebrally transplanted in wild type or Ang-2 gain-of-function mice (Ang-2 DT). Brain tumor sections were stained with antibodies against CD31 and desmin (A), and microvessel densities (MVD) and pericyte coverage were determined (WT n=14; Ang-2 DT n=6) (B). FACS analysis of infiltrating macrophages in Ang-2 DT normal brain (w/o tumor) compared to WT is shown (C, dot plot; D, quantification) (WT n=5; Ang-2 DT n=3). Immunohistochemistry staining for monocytes/macrophages (F4/80) and neutrophils (Ly6G; arrowheads) in brain tumors derived from WT or Ang-2 overexpressing mice (E), Quantitative analysis of C (F) (WT n=14; Ang-2 DT n=10). Kaplan-Meier survival curve of GL261 tumor-bearing WT and Ang-2 DT mice (WT n=17; Ang-2 DT n=14) (E). Statistical analyses were performed using an unpaired Student´s t-test (B, F), one-way Anova (Tukey post test) (D), Log-rank and Wilcoxon (G) * p < 0.05, ** p < 0.01; data are mean ± SEM</p>
|
https://api.sourcedata.io/file.php?figure_id=5252
|
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"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "11601",
"original_type": "gene",
"role": "intervention",
"text": "Ang-2",
"type": "geneprod",
"uniprot_ids": [
"O35608",
"B9EHQ4"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "11601",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "11601",
"original_type": "gene",
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"text": "Ang-2",
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"uniprot_ids": [
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"B9EHQ4"
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},
{
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"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
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{
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},
{
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"text": "desmin",
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},
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{
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{
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"text": "F4/80",
"type": "geneprod",
"uniprot_ids": [
"Q61549"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P35461",
"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": "Ly6G",
"type": "geneprod",
"uniprot_ids": [
"P35461"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "11601",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "11601",
"original_type": "gene",
"role": "intervention",
"text": "Ang-2",
"type": "geneprod",
"uniprot_ids": [
"O35608",
"B9EHQ4"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "11601",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "11601",
"original_type": "gene",
"role": "intervention",
"text": "Ang-2",
"type": "geneprod",
"uniprot_ids": [
"O35608",
"B9EHQ4"
]
}
] |
|
26666269
|
10.15252/emmm.201505505
|
Endothelial cell-derived Angiopoietin-2 is a therapeutic target in treatment-naive and Bevacizumab-resistant glioblastoma
|
2015
|
Figure 3
|
<p>Figure 3: Infiltrating leukocyte subsets in human glioma. Paraffin sections of healthy human brain (n=3), low grade glioma (n=12), anaplastic astrocytoma (n=7) and glioblastoma (n=9) were stained for IBA1 (macrophages/microglia), CD15 (granulocytes) and CD3 (T-cells) (A). Quantification of leukocyte subsets in human glioma specimens (B). For statistical analysis Kruskall-Wallis (Dunn´s post test) was applied.* p < 0.05, ** p < 0.01; data are mean ± SEM</p>
|
https://api.sourcedata.io/file.php?figure_id=5253
|
[
{
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"ext_ids": "P55008",
"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": "IBA1",
"type": "geneprod",
"uniprot_ids": [
"P55008"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P07766",
"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": "CD3",
"type": "geneprod",
"uniprot_ids": [
"P07766"
]
}
] |
|
26666269
|
10.15252/emmm.201505505
|
Endothelial cell-derived Angiopoietin-2 is a therapeutic target in treatment-naive and Bevacizumab-resistant glioblastoma
|
2015
|
Figure 4
|
<p>Figure 4: Dual anti-Ang-2 and anti-VEGF therapy acts synergistic on vascular normalization and macrophage infiltration in experimental GBM. Immunofluorescence staining of CD31 and desmin in GL261 glioblastoma after single and dual treatment with anti-Ang-2 (AMG386) and anti-VEGF (aflibercept) (A). Corresponding quantitative analysis of microvessel densities and pericytes numbers (B; control n=24; AMG386 n=10; aflibercept n=12; AMG386 + aflibercept n=13). Staining for mouse IgG (red) as a surrogate parameter for vascular leakage and CD31 (green) is shown in GL261 glioblastoma sections following different anti-angiogenic treatments (C) with quantification in (D; n=3). Quantification of necrotic areas in GL261 glioblastoma sections after anti-angiogenic treatment is shown as percent of whole tumor area (E; control, aflibercept, AMG386 + aflibercept n=4; AMG386 n=3). Analysis of Glut1 immunoreactivity in GL261 glioblastoma sections (F; n=3). Double-immunofluorescence stainings of macrophages (F4/80) and tumor vessels (vWF) in mouse GBM after treatment with AMG386, aflibercept or the combination of both are shown in (G). Quantitatve analysis of tumor infiltrating leukocytes (F4/80+, CD3+, Ly-6G+) following anti-angiogenic treatment is displayed in (H; control n=28; AMG386 n=12; aflibercept n=11; AMG386 + aflibercept n=12). Kaplan-Meier survival analysis of GL261 tumors grown in C57BL/6 mice following anti-angiogenic treatment (I; control n=38; AMG386 n=13; aflibercept n=12; AMG386 + aflibercept n=13). Double-immunofluorescence stainings with anti-F4/80 and anti-CD206 in brain tumor sections of mice treated with anti-Ang-2 (AMG386), anti-VEGF (aflibercept) or the combination of both are shown in (J). Corresponding quantitative analyses of tumor infiltrating F4/80+ cells and CD206+ cells, and the ratio of CD206+ vs. F4/80+ upon anti-angiogenic therapy are displayed in (K; control n=21; AMG386 n=13; aflibercept n=9; AMG386 + aflibercept n=4). Flow cytometry of tumor infiltrating macrophages following enzymatic dissociation of mouse GL261 brain tumors plus/minus anti-angiogenic therapy. Percent of CD206+ (L) and MHC class IIHI cells (M) among CD45+CD11b+GR1-F4/80+ cells are displayed (L,M; control n=4; AMG386 n=4; aflibercept n=5; AMG386 + aflibercept n=5). Statistical analyses were performed using one-way ANOVA and Tukey’s multiple comparison except for Log-rank and Wilcoxon (I) and Kruskall Wallis (B). * p < 0.05, ** p < 0.01, *** p < 0.005, # p < 0.005 of aflibercept + AMG386 vs aflibercept; data are mean ± SEM (A-K)</p>
|
https://api.sourcedata.io/file.php?figure_id=5254
|
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"text": "VEGF",
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]
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{
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"text": "vWF",
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]
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{
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{
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"P22646"
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"ext_dbs": "Uniprot",
"ext_ids": "P35461",
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"ext_tax_names": "Mus musculus",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
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"role": "assayed",
"text": "Ly-6G",
"type": "geneprod",
"uniprot_ids": [
"P35461"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "11601",
"ext_tax_ids": "10090",
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"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "11601",
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"text": "Ang-2",
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"O35608",
"B9EHQ4"
]
},
{
"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": "22339",
"original_type": "gene",
"role": "intervention",
"text": "VEGF",
"type": "geneprod",
"uniprot_ids": [
"Q00731"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q61549",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
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"role": "assayed",
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]
},
{
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"ext_ids": "Q61549",
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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": "F4/80",
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"uniprot_ids": [
"Q61549"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q61549",
"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": "F4/80",
"type": "geneprod",
"uniprot_ids": [
"Q61549"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q61830",
"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": "CD206",
"type": "geneprod",
"uniprot_ids": [
"Q61830"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q61830",
"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": "CD206",
"type": "geneprod",
"uniprot_ids": [
"Q61830"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q61830",
"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": "CD206",
"type": "geneprod",
"uniprot_ids": [
"Q61830"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q61549",
"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": "F4/80",
"type": "geneprod",
"uniprot_ids": [
"Q61549"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P24788",
"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": "CD11b",
"type": "geneprod",
"uniprot_ids": [
"P24788"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P47791",
"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": "GR1",
"type": "geneprod",
"uniprot_ids": [
"P47791"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q61830",
"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": "CD206",
"type": "geneprod",
"uniprot_ids": [
"Q61830"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P06800",
"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": "CD45",
"type": "geneprod",
"uniprot_ids": [
"P06800"
]
}
] |
|
26666269
|
10.15252/emmm.201505505
|
Endothelial cell-derived Angiopoietin-2 is a therapeutic target in treatment-naive and Bevacizumab-resistant glioblastoma
|
2015
|
Figure 5
|
<p>Figure 5: Anti-VEGF therapy led to decreased infiltration of CD68+ macrophages in human GBM. Anti-CD68 (A), anti-CSFR1 (B) and anti-CD206 (C) immunohistochemistry of patient samples derived from treatment-naive GBM (n=24), post-radiochemotherapy (S/RTx/CTx) (n=7) and post-radiochemotherapy + bevacizumab (S/RTx/CTx/Bev) (n=29) therapy is shown. Corresponding quantification of tumor infiltrating cells is displayed (anti-CD68, D), (anti-CSF1R, E) and (anti-CD206, F). Ratio of CD206+ vs. CD68+ cells (G). Amount of CD206+ perivascular cells per blood vessel (H). Double staining of Ang-2 (brown) and CD206 (red) of a S / RTx / CTx / Bev patient, arrowheads indicating perivascular CD206+ cells around Ang-2+ vessels (I). Arrows pointing on parenchymal CD206+ cells (I). CD206+ cells in relation to the percentage of hypoxic (CAIX positive) tumor area (J). Statistical analysis: Kruskall-Wallis (Dunn´s post test). * p < 0.05, ** p < 0.01; data are mean ± SEM</p>
|
https://api.sourcedata.io/file.php?figure_id=5255
|
[
{
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"ext_ids": "7422",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "7422",
"original_type": "gene",
"role": "intervention",
"text": "VEGF",
"type": "geneprod",
"uniprot_ids": [
"P15692",
"A0A0Y0IMM4",
"A2A2V4"
]
},
{
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"ext_ids": "P34810",
"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": "CD68",
"type": "geneprod",
"uniprot_ids": [
"P34810"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P34810",
"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": "CD68",
"type": "geneprod",
"uniprot_ids": [
"P34810"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P07333",
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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": "CSFR1",
"type": "geneprod",
"uniprot_ids": [
"P07333"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P22897",
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"text": "CD206",
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"uniprot_ids": [
"P22897"
]
},
{
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"ext_ids": "P34810",
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"P34810"
]
},
{
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"ext_ids": "P34810",
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"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "CD68",
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"uniprot_ids": [
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]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P07333",
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"role": "assayed",
"text": "CSF1R",
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},
{
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},
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},
{
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"text": "Ang-2",
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{
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"ext_ids": "O15123",
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"original_type": "protein",
"role": "assayed",
"text": "Ang-2",
"type": "geneprod",
"uniprot_ids": [
"O15123"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P22897",
"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": "CD206",
"type": "geneprod",
"uniprot_ids": [
"P22897"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P22897",
"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": "CD206",
"type": "geneprod",
"uniprot_ids": [
"P22897"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P22897",
"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": "CD206",
"type": "geneprod",
"uniprot_ids": [
"P22897"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q16790",
"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": "CAIX",
"type": "geneprod",
"uniprot_ids": [
"Q16790"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P22897",
"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": "CD206",
"type": "geneprod",
"uniprot_ids": [
"P22897"
]
}
] |
|
26666269
|
10.15252/emmm.201505505
|
Endothelial cell-derived Angiopoietin-2 is a therapeutic target in treatment-naive and Bevacizumab-resistant glioblastoma
|
2015
|
Figure 6
|
<p>Figure 6: Bevacizumab therapy leads to reduced vessel density and increased Ang-2 expression. Immunohistochemistry stainings with antibodies directed against CD31 (A) and Ang-2 (B) in treatment-naive GBM, post-radiochemotherapy (S/RTx/CTx) and post-radiochemotherapy + bevacizumab (S/RTx/CTx/Bev) therapy are displayed. Quantitative analyses of microvessel densities and Ang-2+ vessels are shown in (C) and (D). The ratio of Ang-2+ vs. CD31+ vessels was determined in (E). Western Blot and corresponding quantification of CD31 and Ang-2 in control and aflibercept treated mice (F). CAIX staining of treatment-naive GBM and S / RTx / CTx / Bev patients (G). Analyses of hypoxic (CAIX+) area with regard to the whole tumor in human GBM (H). Tumor-infiltrating lymphocytes (CD8/CD3) in human patients (I). Kruskall-Wallis (Dunn´s post test). * p < 0.05, *** p < 0.005; treatment-naive GBM n=26, S/RTx/CTx n=7, S/RTx/CTx/Bev n=29; data are mean ± SEM</p>
|
https://api.sourcedata.io/file.php?figure_id=5256
|
[
{
"ext_dbs": "Uniprot",
"ext_ids": "O15123",
"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": "Ang-2",
"type": "geneprod",
"uniprot_ids": [
"O15123"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "O15123",
"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": "Ang-2",
"type": "geneprod",
"uniprot_ids": [
"O15123"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P16284",
"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": "CD31",
"type": "geneprod",
"uniprot_ids": [
"P16284"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "O15123",
"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": "Ang-2",
"type": "geneprod",
"uniprot_ids": [
"O15123"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "O15123",
"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": "Ang-2",
"type": "geneprod",
"uniprot_ids": [
"O15123"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P16284",
"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": "CD31",
"type": "geneprod",
"uniprot_ids": [
"P16284"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "O35608",
"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": "Ang-2",
"type": "geneprod",
"uniprot_ids": [
"O35608"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q08481",
"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": "CD31",
"type": "geneprod",
"uniprot_ids": [
"Q08481"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q16790",
"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": "CAIX",
"type": "geneprod",
"uniprot_ids": [
"Q16790"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q16790",
"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": "CAIX",
"type": "geneprod",
"uniprot_ids": [
"Q16790"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P07766",
"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": "CD3",
"type": "geneprod",
"uniprot_ids": [
"P07766"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P01732",
"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": "CD8",
"type": "geneprod",
"uniprot_ids": [
"P01732"
]
}
] |
|
30573670
|
10.15252/embj.201899466
|
CRISPR/Cas9 searches for a protospacer adjacent motif by lateral diffusion
|
2018
|
Figure 3
|
<sd-panel> <p><strong>Figure 3. Multiple PAM influence on binding to a target site</strong></p> <ol type="A"> <li> <p>DNA and crRNA sequence used for experiments of a single target and multiple PAMs. DNA sequence is shown for the single-target single-PAM construct and schematic representation is shown for multiple-PAM containing constructs.</p> </li> <li> <p>FRET histogram of all binding events from the construct containing a single PAM next to the partial target. Y axis represents total number of counts.</p> </li> <li> <p>Example FRET traces from single-target multiple-PAM experiments. Top trace shows an example of a single-step binding event and a binding event that starts at a lower FRET state before transitioning to productive binding high-FRET state. Bottom trace shows an example of FRET fluctuations between the high-FRET state and lower FRET states.</p> </li> <li> <p>A histogram showing the percentage of dynamic. The percentage values were obtained from five experiments on five different days. Error bars represent standard error of the mean. The percentage of events showing dynamic binding behavior was calculated by dividing the number of binding events that showed such behavior by the total number of binding events.</p> </li> <li> <p>A scatter plot showing the time Cas9 spends in a lower FRET state before transitioning to a high-FRET state. The dwelltimes increase with the number of PAMs adjacent to the target. Such dwelltime could not be determined for a construct containing a single PAM. The values were obtained from five experiments on five different days. Error bars represent standard error of the mean.</p> </li> </ol> </sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=24324
|
[
{
"ext_dbs": "Uniprot",
"ext_ids": "A0A2W5CL48",
"ext_tax_ids": "",
"ext_tax_names": "",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "Cas9",
"type": "geneprod",
"uniprot_ids": [
"A0A2W5CL48"
]
}
] |
|
30573670
|
10.15252/embj.201899466
|
CRISPR/Cas9 searches for a protospacer adjacent motif by lateral diffusion
|
2018
|
Figure 4
|
<sd-panel> <p><strong>Figure 4. Mechanism of lateral diffusion</strong></p> <ol type="A"> <li> <p>DNA sequences used in tandem target experiments. Complementary sequences to crRNA are marked in pink boxes and PAMs are marked in green boxes. Distances between the protospacers are indicated above the sequences. An illustration of Cas9 binding to each target site resulting in either high FRET (target H) or low FRET (target L) is shown on the right.</p> </li> <li> <p>Example fluorescence traces showing Cas9 transitioning between H and L targets with increasing target distances (right). FRET histograms constructed from events that show fluctuations showing two FRET peaks corresponding to binding to either target. High FRET peak stays the same in each histogram, but lower FRET peak moves to lower FRET values as the distance between targets increases.</p> </li> <li> <p>A scatter plot showing the probability of Cas9 transitioning between targets before dissociation. The values are averages from five measurements and error bars represent standard error of the mean. The transition probability (<em>p = T /</em> (<em>T+D</em>)) was calculated by summing up all the number of FRET transitions (<em>T</em>) and dividing <em>T</em> by the sum of <em>T</em> and the total number of dissociation events (<em>D</em>).</p> </li> <li> <p>A histogram showing all dwelltimes from single-target controls and tandem-target experiments. τ<sub>1</sub> is similar for single-target control and tandem target experiments. τ<sub>2</sub> only appears in tandem target experiments and is over 20-fold higher than τ<sub>1</sub> or τ<sub>st</sub>. The values represent the mean dwelltimes that were obtained by fitting dwelltime distributions by either single or double exponential decay function from five measurements. Error bars represent standard error of the mean.</p> </li> </ol> </sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=24325
|
[
{
"ext_dbs": "Uniprot",
"ext_ids": "A0A2W5CL48",
"ext_tax_ids": "",
"ext_tax_names": "",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "Cas9",
"type": "geneprod",
"uniprot_ids": [
"A0A2W5CL48"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "A0A2W5CL48",
"ext_tax_ids": "",
"ext_tax_names": "",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "Cas9",
"type": "geneprod",
"uniprot_ids": [
"A0A2W5CL48"
]
}
] |
|
10.1101/2020.03.24.005298
|
A unifying structural and functional model of the coronavirus replication organelle: tracking down RNA synthesis
|
2020
|
Fig. 6.
|
<sd-panel> <p>IEM detection of viral markers in MERS-CoV-infected cells.(A-G) Immunogold labeling of thawed cryo-sections of MERS-CoV-infected Huh7 cells (12 hpi) for the detection of the indicated viral proteins. (A-C) Structural proteins were detected on virions (black arrowheads) and, for the M and S proteins, also on Golgi cisterna. While regions containing DMS (white arrowheads) and CM labelled for the N protein (D) and nsp3 (G), the M and S protein were not detected in these areas. (H-I) Immunogold labeling of dsRNA in HPF-FS samples of MERS-CoV-infected Huh7 cells (13 hpi). The label accumulated on DMVs, which could be easily detected in this type of samples (grey arrowheads), while the regions with CM and DMSs, which appeared as dark areas among the DMV clusters, where devoid of dsRNA signal. G, Golgi complex; m, mitochondria. Scale bars, 250 nm.</p> </sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=33434
|
[
{
"ext_dbs": "Uniprot",
"ext_ids": "R9UNX5",
"ext_tax_ids": "1335626",
"ext_tax_names": "Middle East respiratory syndrome-related coronavirus",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "M",
"type": "geneprod",
"uniprot_ids": [
"R9UNX5"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "R9UNX5",
"ext_tax_ids": "1335626",
"ext_tax_names": "Middle East respiratory syndrome-related coronavirus",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "M",
"type": "geneprod",
"uniprot_ids": [
"R9UNX5"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "A0A141LLD8",
"ext_tax_ids": "1335626",
"ext_tax_names": "Middle East respiratory syndrome-related coronavirus",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "N protein",
"type": "geneprod",
"uniprot_ids": [
"A0A141LLD8"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "A0A141LLB8",
"ext_tax_ids": "1335626",
"ext_tax_names": "Middle East respiratory syndrome-related coronavirus",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "nsp3",
"type": "geneprod",
"uniprot_ids": [
"A0A141LLB8"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "W6A028",
"ext_tax_ids": "1335626",
"ext_tax_names": "Middle East respiratory syndrome-related coronavirus",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "S protein",
"type": "geneprod",
"uniprot_ids": [
"W6A028"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "W6A028",
"ext_tax_ids": "1335626",
"ext_tax_names": "Middle East respiratory syndrome-related coronavirus",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "S proteins",
"type": "geneprod",
"uniprot_ids": [
"W6A028"
]
}
] |
||
30530633
|
10.15252/embr.201846221
|
Mouse fetal intestinal organoids: new model to study epithelial maturation from suckling to weaning
|
2018
|
Figure 2
|
<sd-panel><p><strong>Figure 2</strong> - <strong>Small <sd-pretag id="sdPretag283779571sm" type="tissue" role="component">intestinal fetal</sd-pretag> organoids recapitulate suckling-to-weaning transition <em>in vitro</em></strong>.</p><p> <strong>A-G</strong> <sd-pretag id="sdPretag685066530sm" category="assay">Real</sd-pretag>-<sd-pretag id="sdPretag1544831807sm" category="assay">time qPCR</sd-pretag> analysis of fetal organoids cultured for one month showing decrease in relative expression of indicated neonatal markers <strong>A</strong> <sd-pretag id="sdPretag961315792sm" type="geneprod" role="assayed"><em>Ass1</em></sd-pretag>, <strong>B</strong> <sd-pretag id="sdPretag110127558sm" type="geneprod" role="assayed"><em>Blimp-1</em></sd-pretag>, <strong>C</strong> <em>FcRn</em> and <strong>D</strong> <sd-pretag id="sdPretag787166546sm" type="geneprod" role="assayed"><em>Lct</em></sd-pretag> and increase of the adult markers <strong>E</strong> <em>Sis</em>, <strong>F</strong> <em>Treh</em> and <strong>G</strong> <sd-pretag id="sdPretag2037167415sm" type="geneprod" role="intervention"><em>Arg2</em></sd-pretag> (n=3 individual wells from single organoid culture (see material and methods); experiment was repeated in four to eight independent organoid cultures with similar results). <strong>H-L.</strong> Enzyme <sd-pretag id="sdPretag8208300sm" category="assay">activity assay</sd-pretag> of fetal organoids for <strong>H</strong> Lactase, <strong>I</strong> sucrase, <strong>J</strong> maltase, <strong>K</strong> trehalase and <strong>L</strong> arginase. Activity is given in µM <sd-pretag id="sdPretag993971913sm" type="molecule" role="component">glucose</sd-pretag>/µg <sd-pretag id="sdPretag1088299090sm" type="geneprod" role="intervention">protein·min<sup>-1</sup></sd-pretag> (experiment was generated from single organoid culture (see material and methods) and repeated in 3 independent organoid cultures with similar results).</p><p> Data information: Data are presented as mean ± SEM. ND not detected, *p<0.05, **p<0.01, ***p<0.001, NS not significant, relative to expression or activity level at day 3 (one-way ANOVA).</p></sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=23969
|
[
{
"ext_dbs": "NCBI gene",
"ext_ids": "11847",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "11847",
"original_type": "gene",
"role": "assayed",
"text": "Arg2",
"type": "geneprod",
"uniprot_ids": [
"O08691"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "11898",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "11898",
"original_type": "gene",
"role": "assayed",
"text": "Ass1",
"type": "geneprod",
"uniprot_ids": [
"P16460",
"Q3UJ34"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "14132",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "14132",
"original_type": "gene",
"role": "assayed",
"text": "FcRn",
"type": "geneprod",
"uniprot_ids": [
"Q61559",
"Q6PKB0"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "226413",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "226413",
"original_type": "gene",
"role": "assayed",
"text": "Lct",
"type": "geneprod",
"uniprot_ids": [
"F8VPT3"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "12142",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "12142",
"original_type": "gene",
"role": "assayed",
"text": "Blimp-1",
"type": "geneprod",
"uniprot_ids": [
"Q60636"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "69983",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "69983",
"original_type": "gene",
"role": "assayed",
"text": "Sis",
"type": "geneprod",
"uniprot_ids": [
"F8VQM5"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "58866",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "58866",
"original_type": "gene",
"role": "assayed",
"text": "Treh",
"type": "geneprod",
"uniprot_ids": [
"Q9JLT2",
"E9PYP7"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "O08691",
"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": "arginase",
"type": "geneprod",
"uniprot_ids": [
"O08691"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P70699",
"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": "maltase",
"type": "geneprod",
"uniprot_ids": [
"P70699"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "F8VPT3",
"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": "Lactase",
"type": "geneprod",
"uniprot_ids": [
"F8VPT3"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "F8VQM5",
"ext_tax_ids": "10090",
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"ext_ids": "Q9JLT2",
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"ext_tax_names": "Mus musculus",
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] |
|
30530633
|
10.15252/embr.201846221
|
Mouse fetal intestinal organoids: new model to study epithelial maturation from suckling to weaning
|
2018
|
Figure 3
|
<sd-panel><p><strong>Figure 3</strong> - <strong>Fetal organoids resemble adult organoids after one month in culture</strong>.</p><p> <strong>A-G</strong> Relative expression detected by <sd-pretag id="sdPretag1421187240sm" category="assay">Real</sd-pretag>-<sd-pretag id="sdPretag897429407sm" category="assay">time qPCR</sd-pretag> in fetal organoids ( ) and adult organoids ( ). Neonatal markers <strong>A</strong> <sd-pretag id="sdPretag1095698709sm" type="geneprod" role="assayed"><em>Ass1</em></sd-pretag>, <strong>B</strong> <sd-pretag id="sdPretag1042392998sm" type="geneprod" role="assayed"><em>Blimp-1</em></sd-pretag>, <strong>C</strong> <em>FcRn</em> and <strong>D</strong> <sd-pretag id="sdPretag1469947426sm" type="geneprod" role="assayed"><em>Lct</em></sd-pretag> in fetal organoids cultured for one month compare to levels adult organoids. Mature markers <strong>E</strong> <em>Sis</em>, <strong>F</strong> <em>Treh</em> and <strong>G</strong> <sd-pretag id="sdPretag574938972sm" type="geneprod" role="assayed"><em>Arg2</em></sd-pretag> increase in fetal organoids to adult levels (n=3 individual wells from single organoid culture (see material and methods); experiment was repeated in four independent organoid cultures with similar results). <strong>H-L</strong> <sd-pretag id="sdPretag757665261sm" category="assay">Enzyme activity assay</sd-pretag> of fetal ( ) and adult ( ) organoids. <strong>H</strong> Lactase activity is higher in fetal organoids decreasing to adult levels at day 28, while <strong>I</strong> sucrase, <strong>J</strong> maltase, <strong>K</strong> trehalase and <strong>L</strong> <sd-pretag id="sdPretag1071632025sm" type="geneprod" role="assayed">arginase</sd-pretag> increase to adult levels. Activity is given in µM <sd-pretag id="sdPretag101919257sm" type="molecule" role="component">glucose</sd-pretag>/µg <sd-pretag id="sdPretag1940678281sm" type="geneprod" role="intervention">protein·min<sup>-1</sup></sd-pretag> (n=3 independent organoid cultures).</p><p> Data information: Data are presented as mean ± SEM. ND not detected, *p<0.05, **p<0.01, ***p<0.001, NS not significant, in A-G between fetal and adult organoids and in H-L relative to adult levels (t-test).</p></sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=23971
|
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"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "69983",
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{
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"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
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"Q9JLT2",
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"ext_tax_names": "Mus musculus",
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}
] |
|
30530633
|
10.15252/embr.201846221
|
Mouse fetal intestinal organoids: new model to study epithelial maturation from suckling to weaning
|
2018
|
Figure 4
|
<sd-panel><p><strong>Figure 4</strong> - <strong>Dexamethasone accelerates maturation of fetal organoids.</strong></p><p> <strong>A, B, E, F</strong> Maturation is accelerated in <sd-pretag id="sdPretag749573958sm" type="molecule" role="component">dexamethasone</sd-pretag> treated fetal organoids ( ) compared to control ( ), as revealed by <sd-pretag id="sdPretag614581570sm" category="assay">real</sd-pretag>-<sd-pretag id="sdPretag41993176sm" category="assay">time qPCR</sd-pretag>. Decrease in relative expression of neonatal marker <strong>A</strong> <sd-pretag id="sdPretag378794242sm" type="geneprod" role="assayed"><em>Blimp-1</em></sd-pretag> and increase in expression of adult marker <strong>B</strong> <em>Sis</em> occur earlier in <sd-pretag id="sdPretag1574965629sm" type="molecule" role="intervention">dexamethasone</sd-pretag> treated organoids, but expression of adult marker <strong>E</strong> <em>Treh</em> and <strong>F</strong> <em>Arg2</em> remains unchanged (n=3 individual wells from single organoid culture (see material and methods); experiment was repeated in four independent organoid cultures with similar results).</p><p> <strong>C,D,G,H</strong> <sd-pretag id="sdPretag520759737sm" type="molecule" role="component">Dexamethasone</sd-pretag> treatment accelerates increase in activity of <strong>E</strong> sucrase, <strong>F</strong> maltase, <strong>G</strong> trehalase and <strong>H</strong> arginase reaching adult organoid level ( ) at day 13 of the culture. Activity is given in µM <sd-pretag id="sdPretag284727737sm" type="molecule" role="component">glucose</sd-pretag>/µg <sd-pretag id="sdPretag398315401sm" type="geneprod" role="intervention">protein·min<sup>-1</sup></sd-pretag> (n = 3 independent organoid cultures).</p><p> Data information: Data are presented as mean ± SEM. ND not detected, *p<0.05, ***p<0.001, NS not significant, between control and <sd-pretag id="sdPretag473019715sm" type="molecule" role="intervention">dexamethasone</sd-pretag> treated organoids (two-way ANOVA). Expression values of control fetal organoids and control adult organoids in B, E and F are the same as Figure 3E-G and enzyme activity levels of fetal organoids in C, D, G and H are the same as 3I-L.</p></sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=23973
|
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]
},
{
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"mapping_status": "mapped",
"ncbi_gene_id": "69983",
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"text": "Sis",
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"uniprot_ids": [
"F8VQM5"
]
},
{
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"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "maltase",
"type": "geneprod",
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]
},
{
"ext_dbs": "Uniprot",
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]
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"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
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"role": "assayed",
"text": "Treh",
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"E9PYP7"
]
},
{
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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": "arginase",
"type": "geneprod",
"uniprot_ids": [
"O08691"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q9JLT2",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
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"text": "trehalase",
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"uniprot_ids": [
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]
}
] |
|
30530633
|
10.15252/embr.201846221
|
Mouse fetal intestinal organoids: new model to study epithelial maturation from suckling to weaning
|
2018
|
Figure 5
|
<sd-panel><p><strong>Figure 5</strong> - <strong><sd-pretag id="sdPretag1949810976sm" type="cell" role="component">Spheroids</sd-pretag> and <sd-pretag id="sdPretag779744354sm" type="tissue" role="component">organoids</sd-pretag> show the same protein expression pattern, independently of culture stage/passage.</strong></p><p> <strong>A</strong> <sd-pretag id="sdPretag85525050sm" category="assay">Microscopic</sd-pretag> images of fetal organoids at day 3, 13, 20 and 30 of culture. Scale bars: 500 µm.</p><p> <strong>B</strong> Percentage of fetal <sd-pretag id="sdPretag30024445sm" type="cell" role="component">spheroids</sd-pretag> decreases during culture (n=3 individual wells from single organoid culture (see material and methods); experiment was repeated in ten independent organoid cultures with similar results).</p><p> <strong>C-E</strong> <sd-pretag id="sdPretag1379799018sm" category="assay">Immmunohistochemistry</sd-pretag> of fetal organoids for <strong>C</strong> <sd-pretag id="sdPretag1573020100sm" type="geneprod" role="component">Ass1</sd-pretag> <strong>D</strong> Sis and <strong>E</strong> <sd-pretag id="sdPretag1903932062sm" type="geneprod" role="assayed">Arg2</sd-pretag>. Quantification of 3 slides per staining, 7 to 10 organoids / <sd-pretag id="sdPretag1553298788sm" type="cell" role="component">spheroids</sd-pretag> per slide. Scale bars: 50µm.</p><p> Data information: In B, data are presented as mean ± SEM. ***p<0.001, relative to number of <sd-pretag id="sdPretag1520371783sm" type="cell" role="component">spheroids</sd-pretag> at day 3 (one-way ANOVA).</p><p> <strong>Expanded View Figure Legends</strong></p></sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=23975
|
[
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"ncbi_gene_id": null,
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"text": "Arg2",
"type": "geneprod",
"uniprot_ids": [
"O08691"
]
},
{
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"ext_tax_names": "Mus musculus",
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{
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"text": "Sis",
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"uniprot_ids": [
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]
}
] |
|
10.15252/embr.202050145
|
Carbonic anhydrase 7 bundles filamentous actin and regulates dendritic spine morphology and density
|
2021
|
Figure 1
|
<sd-panel> <p><strong>Figure 1. Subcellular localization of CA7 and CA2 in fibroblasts.</strong></p> <p>(A) NIH3T3 fibroblasts co-expressing DsRed-CA7 and EGFP-CA2 (<em>n</em> = 4 independent replicates).</p> <p>(B-E) Co-localization of EGFP and the two CA isoforms with filamentous actin studied in fibroblasts expressing (B) EGFP, (C) EGFP-CA2, or (D, E) EGFP-CA7 and stained with phalloidin-594 to visualize F-actin (<em>n</em> = 4, 10 and 8 independent replicates, respectively). A magnification of the area marked with the yellow rectangle in (C) and (D) shows the localization of EGFP-CA2 and EGFP-CA7 compared to phalloidin-594. (E) EGFP-CA7 caused a prominent overexpression phenotype with thick and curvy cytosolic actin bundles (arrow) and plasmalemmal protrusions (arrowhead).</p> <p>(F-H) The normalized fluorescence emission intensity profiles for F-actin (red line) and (F) EGFP, (G) EGFP-CA2, or (H) EGFP-CA7 (black line).</p> <p>Data information: For the plots, pixel intensities were measured through the cross-section of the cell indicated by the yellow line in panels B-D. Scale bar in (A-E) 20 µm.</p> </sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=39022
|
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"text": "CA2",
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"text": "CA2",
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{
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"ext_tax_names": "Mus musculus",
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"mapping_status": "mapped",
"ncbi_gene_id": null,
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"text": "CA2",
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]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q9ERQ8",
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"ext_tax_names": "Mus musculus",
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"mapping_status": "mapped",
"ncbi_gene_id": null,
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"role": "assayed",
"text": "CA7",
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"uniprot_ids": [
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]
}
] |
||
10.15252/embr.202050145
|
Carbonic anhydrase 7 bundles filamentous actin and regulates dendritic spine morphology and density
|
2021
|
Figure 2
|
<sd-panel> <p><strong>Figure 2. CA7 binds to filamentous actin and increases actin bundling.</strong></p> <p>(A) Actin co-sedimentation assay shows that CA7 binds to F-actin. The binding is enhanced at more acidic pH (6.5 vs. 7.4) <em>n</em> = 3 independent replicates at each actin concentration, two-way ANOVA, P < 0.001.</p> <p>(B) Fluorescence time‐lapse images of F-actin bundling in an <em>in vitro</em> bundling assay. A mixture of unlabeled and Rhodamine labelled non-muscle actin was polymerized in the absence (PBS control, upper panel) or presence of mCA7 (lower panel). Numbers in images indicate the time after the onset of the experiment (0, 5 and 23 min). Intensity based Fire-coloring (Fiji) was used to visualize intensity changes. Scale bar 10 µm.</p> <p>(C) Quantification of the mean increase in filament length (<em>n</em> = 10 filaments at each time point) and the mean relative fluorescence intensity values of cross-sections for individual filaments /bundles (<em>n</em> = 30 - 31) in the absence and presence of mCA7 (1.12 µM). The data were analyzed using a general mixed model with time as a within-unit factor and the presence of CA7 as a between-unit factor. <em>n</em> = 3 independent repetitions, experiment repeats were included as a covariate and were non-significant.</p> <p>(D) Kymographs showing different time points in the line of interest (line width 1 µm) from the experiments analyzed in (C). Kymographs were generated with Fiji Multi Kymograph function. Total time is 159 frames = 26.5 minutes. Scale bar 5 μm (full height is 20 μm). F-actin bundles can be detected as clear lines in kymographs.</p> <p>(E) Fluorescence time‐lapse images of F-actin bundling in an <em>in vitro</em> bundling assay. A mixture of unlabeled and Rhodamine labelled non-muscle actin was polymerized in the presence of mCA7 (0.11 µM). Numbers above images indicate the time after the onset of the experiment (22 min -23 min 20 sec). Intensity based Fire-coloring (Fiji) was used to visualize intensity changes. White arrows highlight the bundling filaments. Scale bar 5 μm. This is a representative video from 8 similar experiments.</p> <p>Data information: Data are presented as mean ± SEM in (A) and mean ± SD in (C).</p> </sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=39024
|
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}
] |
||
10.15252/embr.202050145
|
Carbonic anhydrase 7 bundles filamentous actin and regulates dendritic spine morphology and density
|
2021
|
Figure 3
|
<sd-panel> <p><strong>Figure 3. CA7 overexpressing NIH3T3 are resistant to latrunculin B treatment.</strong></p> <p>(A,B) NIH3T3 cells transfected with DsRed (A) or DsRed-CA7 (B) were incubated in growth medium with 5 µM Latrunculin B for 0, 2, 5, 10, or 30 minutes, or in an equal amount of DMSO for 60 minutes. Analyses of experiments show that in cells transfected with DsRed-CA7 F-actin structures collapse more slowly (0 min: 83% "normal"; 2 min: 80%, p = 0.44; 5 min: 74%, p = 0.39; 10 min: 27%, p = 0.08; 30 min: 16%, p = 0.02; DMSO: 82%, p = 0.99; tested against 0 min with two-way ANOVA, Dunnett's multiple comparison test) than in the DsRed-transfected ones (0 min: 89% "normal"; 2 min: 48%, p = 0.14; 5 min: 31%, p = 0.04; 10 min: 2%, p = 0.001; 30 min: 0.7%, p = 0.001; DMSO: 88%, p = 0.8; tested against 0 min with two-way ANOVA, Dunnett's multiple comparison test) . For the analysis, cells were categorized to three groups as "normal", "some shape/F-actin left" and "round". The upper panel shows example images of the cells in all three categories for (A) DsRed- or (B) DsRed-CA7 transfected cells (actin visualized with Phalloidin-488).</p> <p>Data information: A hundred cells per each time point from each experiment (n = 3) were counted and categorized. Scale bar 50 µm. Data are presented as mean ± SEM.</p> </sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=39026
|
[
{
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"ncbi_gene_id": "12354",
"original_type": "gene",
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"text": "CA7",
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"Q9ERQ8",
"G3XA26",
"Q3UND9"
]
},
{
"ext_dbs": "NCBI gene",
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"ext_tax_names": "Mus musculus",
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"ncbi_gene_id": "12354",
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"Q9ERQ8",
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]
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{
"ext_dbs": "NCBI gene",
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"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
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"mapping_status": "mapped",
"ncbi_gene_id": "12354",
"original_type": "gene",
"role": "intervention",
"text": "CA7",
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"uniprot_ids": [
"Q9ERQ8",
"G3XA26",
"Q3UND9"
]
}
] |
||
10.15252/embr.202050145
|
Carbonic anhydrase 7 bundles filamentous actin and regulates dendritic spine morphology and density
|
2021
|
Figure 5
|
<sd-panel> <p><strong>Figure 5. Subcellular localization of the chimeric CA7 constructs in fibroblasts.</strong></p> <p>(A-C) NIH3T3 fibroblasts expressing EGFP-CA7-mutant1 (A), EGFP-CA7-mutant2 (B), and EGFP-CA7-mutant3 (C). F-actin is visualized with Phalloidin-594. In the right-most panel of (A-C) are the normalized fluorescence intensity profiles of the mutated CA7 EGFP signal (black) and actin (red) and the yellow line in left-most panels indicates the cross-section from which the pixel intensities were measured. Scale bars 20 µm.</p> <p>(D) Analysis of the mutated CA7 and F-actin co-localization in cultured fibroblasts. Scatterplots of fluorescent intensities per pixel (EGFP vs. Phalloidin-594) along a cross section through a representative cell. Pearson's correlation coefficient (r) for the analyzed cell is given in each panel.</p> <p>(E) Pearson's correlation coefficient values calculated for the depicted constructs and compared to CA7. F-actin had a strong positive correlation coefficient with EGFP-CA7 (r = 0.91 ± 0.02, <em>n</em> = 26 cells). Neither EGFP alone (r = 0.01 ± 0.03, <em>n</em> = 56) nor EGFP-CA2 (r = 0.09 ± 0.03, <em>n</em> = 53) co-localized with F-actin (<em>P</em> < 0.0001 for both constructs, when compared to CA7). From the five mutated CA7 constructs, EGFP-CA7-mutant1 (r= 0.51 ± 0.04, <em>P</em> < 0.0001, <em>n</em> = 25) and EGFP-CA7-mutant3 (r = 0.72 ± 0.03, <em>P</em> = 0.05, <em>n</em> = 21) co-localized less with F-actin actin when compared to CA7. The co-localization of the other four mutated CA7 constructs, EGFP-CA7-mutant2 (r = 0.92 ± 0.02, <em>P</em> = 0.99, <em>n</em> = 18), EGFP-CA7-R223E (r = 0.86 ± 0.02, <em>P</em> = 0.99, <em>n</em> = 24) and EGFP-CA7-H96/98C (r = 0.79 ± 0.04, <em>P</em> = 0.14, <em>n</em> = 18) did not differ significantly from that of CA7. Data are shown as mean ± SEM. Data did not pass Shapiro-Wilk test for normality, statistical comparison against CA7 was done with Kruskall-Wallis test corrected for multiple comparisons.</p> </sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=39030
|
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"text": "CA7",
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"uniprot_ids": [
"Q9ERQ8",
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},
{
"ext_dbs": "NCBI gene",
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"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
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"text": "CA7",
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] |
||
10.15252/embr.202050145
|
Carbonic anhydrase 7 bundles filamentous actin and regulates dendritic spine morphology and density
|
2021
|
Figure 6
|
<sd-panel> <p><strong>Figure 6. Localization of the overexpressed CA2 and CA7 in neurons.</strong></p> <p>(A) Isoform-specific subcellular localization shown in cultured hippocampal neurons (DIV14) co-expressing DsRed-CA7 (<em>left</em>) and EGFP-CA2 (<em>middle</em>).</p> <p>(B,C) Representative confocal images of precocious <em>in vivo</em> expression of (B) EGFP-CA2 and (C) EGFP-CA7 in P40 mouse cortical layer 2/3 pyramidal neurons. Neurons were transfected at E14.5 with EGFP-CA2 or EGFP-CA7 using <em>in utero</em> electroporation and images were taken from fixed slices. Right panels in (B) and (C) show higher magnification of the primary apical dendrite marked with a box.</p> <p>(D) The expression of EGFP-CA7 disrupted the normal spine morphology and induced the formation of thick, filopodia-like protrusions.</p> <p>Data information: <em>n</em> = 5 independent repeats for cultured neurons and two animals/construct <em>in vivo</em>. Scale bar in (A) 5 µm; (B and C): 5 µm, insets in (B, C) and panel D: 25 µm.</p> </sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=39032
|
[
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"ext_tax_names": "Rattus norvegicus",
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"text": "CA2",
"type": "geneprod",
"uniprot_ids": [
"P27139"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "B2RZ61",
"ext_tax_ids": "10116",
"ext_tax_names": "Rattus norvegicus",
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{
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{
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},
{
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"ncbi_gene_id": null,
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"text": "CA7",
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"uniprot_ids": [
"Q9ERQ8"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q9ERQ8",
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"ext_tax_names": "Mus musculus",
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"ncbi_gene_id": null,
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"role": "assayed",
"text": "CA7",
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"uniprot_ids": [
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}
] |
||
10.15252/embr.202050145
|
Carbonic anhydrase 7 bundles filamentous actin and regulates dendritic spine morphology and density
|
2021
|
Figure 7
|
<sd-panel> <p><strong>Figure 7. Layer 2/3 cortical pyramidal neurons in CA7 KO mice have high dendritic spine density and smaller spines but mEPSC frequency and amplitude are not affected</strong></p> <p>(A) Comparison of mEPSCs in cortical layer 2/3 pyramidal neurons from P30 - P40 WT and CA7 KO mice. Sample traces of mEPSC recordings from WT and CA7 KO neurons, low-pas filtered at 1 kHz (left). The data are summarized in the bar diagrams (right). mEPSC frequency (<em>P</em> = 0.63) and amplitude (<em>P</em> = 0.90) were not significantly different between WT and CA7 KO and neurons (<em>n</em> = 7 and 5 neurons, respectively, Student's independent samples <em>t</em>-test).</p> <p>(B) Representative confocal images of apical dendrites from Lucifer Yellow injected cortical layer 2/3 pyramidal neurons from WT and CA7 KO mice. The dendritic spine density and spine head size were examined in fixed slice preparations from P34 - P37 mice. Scale bar 2 µm.</p> <p>(C) Summary of the spine density analysis done from the Lucifer Yellow injected neurons. Spine density was a higher in CA7 KO neurons both in apical and basal dendrites (n = 28 neurons for both) compared to WT (n= 29 neurons for apical and n=30 for basal dendrite analysis) (<em>P</em> = 0.000002 for apical dendrites, analyzed with Mann-Whitney test, and <em>P</em> = 6,8 x 10<sup>-8</sup> for basal dendrites, Student's <em>t</em>-test with Welch-correction.) A total of 8279 spines were analyzed from four CA7 KO mice and 8730 spines from two WT control mice.</p> <p>(D) The spine head width distribution7differed significantly between the genotypes (n= 467 spines from WT and n = 421 spines from CA7 KO animals, 15 neurons analyzed from both genotypes, Wilcoxon rank sum test with continuity correction, W = 134540, <em>P</em> < 0.001).</p> <p>Data information: Data in (A) and (C) are given as mean + SEM.</p> <p>Expanded View Figure Legends</p> </sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=39033
|
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"mapping_status": "mapped",
"ncbi_gene_id": "12354",
"original_type": "gene",
"role": "intervention",
"text": "CA7",
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"Q3UND9"
]
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"ext_tax_names": "Mus musculus",
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"text": "CA7",
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"ext_dbs": "NCBI gene",
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"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
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"ncbi_gene_id": "12354",
"original_type": "gene",
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"Q9ERQ8",
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}
] |
||
27110680
|
10.1038/nchembio.1230
|
Chemical modulation of chaperone-mediated autophagy by retinoic acid derivatives
|
2013
|
figf1
|
<p>(<b>a</b>) Knockdown of <named-entity id="named-entity-253">RARα</named-entity> in NIH3T3 mouse fibroblasts was conducted using two different shRNAs, sh1 and sh2, compared to control (Ctr). Left, representative immunoblot. Actin is shown as loading control and full-length blots are shown in <sir rid="S1" refobjid="nchembio.1230-S1">Supplementary Figure 21</sir>. Right, amounts of <named-entity id="named-entity-254">RARα</named-entity> in control and knockdown cells determined by densitometric quantification of immunoblots represented by the one shown on the left. Values are normalized for actin and expressed as multiples of control (None) values; <i>n</i> = 3. (<b>b</b>) Rates of degradation of long-lived proteins in control and <named-entity id="named-entity-255">RARα</named-entity>(−) cells maintained in the presence or absence of serum for 12 h. Values are expressed as percentage of proteolysis; <i>n</i> = 3. (<b>c</b>,<b>d</b>) Percentage of degradation due to lysosomes (<b>c</b>) and macroautophagy (<b>d</b>) in cells assayed as in <b>b</b> but treated with inhibitors of lysosomal proteolysis (<b>c</b>) or with <named-entity id="named-entity-256">3-methyladenine</named-entity> (<named-entity id="named-entity-257">3MA</named-entity>) to block macroautophagy (<b>d</b>). Values are expressed as percentage of total protein degradation sensitive to the lysosomal inhibitors; <i>n</i> = 3. In all panels, all values are mean ± s.e.m., and differences with control are significant for *<i>P</i> 0.05.</p>
|
https://api.sourcedata.io/file.php?figure_id=3208
|
[
{
"ext_dbs": "NCBI gene",
"ext_ids": "19401",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "19401",
"original_type": "gene",
"role": "intervention",
"text": "RARα",
"type": "geneprod",
"uniprot_ids": [
"P11416",
"Q3U3R3",
"Q3U5E7"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P11416",
"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": "RARα",
"type": "geneprod",
"uniprot_ids": [
"P11416"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "19401",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "19401",
"original_type": "gene",
"role": "intervention",
"text": "RARα",
"type": "geneprod",
"uniprot_ids": [
"P11416",
"Q3U3R3",
"Q3U5E7"
]
}
] |
|
27110680
|
10.1038/nchembio.1230
|
Chemical modulation of chaperone-mediated autophagy by retinoic acid derivatives
|
2013
|
figf2
|
<p>(<b>a</b>) Immunoblot for <named-entity id="named-entity-259">LC3-II</named-entity> in control mouse fibroblasts (Ctr) or those knocked down for <named-entity id="named-entity-260">RARα</named-entity> (<named-entity id="named-entity-261">RARα</named-entity>(−)) maintained in the presence or absence of serum for the indicated times. Where indicated, protease inhibitors (PI) against lysosomal proteolysis were added. Actin is shown as a loading control. 'I' and 'II' designate different forms of LC3, as described in the text. (<b>b</b>) Amounts of <named-entity id="named-entity-262">LC3-II</named-entity> determined by densitometric quantification of immunoblots. Values are expressed as fold change in value relative to serum-supplemented control cells; <i>n</i> = 4. (<b>c</b>) Ratio of the amounts of <named-entity id="named-entity-263">LC3-II</named-entity> in cells treated with protease inhibitors compared to untreated cells (None). Values are expressed as fold change in value relative to untreated cells; <i>n</i> = 4. (<b>d</b>,<b>e</b>) Autophagic flux in the same cells as in <b>c</b> expressing mCherry-GFP–<named-entity id="named-entity-264">LC3-II</named-entity> and maintained in the presence or absence of serum. Shown in <b>d</b> are representative merged channel images; scale bars, 2 μm. Arrows indicate autolysosomes (red). Shown in <b>e</b> are the quantification of the number of autophagosomes (mCherry and GFP positive) per cell (left) and percentage of autolysosomes (mCherry positive and GFP negative; right) in >50 cells in at least four different fields. AV, autophagic vacuoles. (<b>f</b>) Control and <named-entity id="named-entity-265">RARα</named-entity>(−) cells were transfected with the KFERQ-mCherry1 photoactivatable reporter, and after photoactivation they were maintained in medium with or without serum. Left, representative images. Graph shows quantification of the number of puncta per cell in >50 cells using the CMA reporter in at least four different fields. Nuclei are labeled with <named-entity id="named-entity-266">DAPI</named-entity>. Scale bars, 10 μm. In <b>b</b>, <b>c</b>, <b>e</b> and <b>f</b>, all values are mean ± s.e.m. Differences with control (marked with asterisk) or with serum-supplemented cells (marked with §) are significant for <i>P</i> 0.05. Full-field fluorescence images and full-length blots are shown in <sir rid="S1" refobjid="nchembio.1230-S1">Supplementary Figures 2</sir> and <sir rid="S1" refobjid="nchembio.1230-S1">21</sir>, respectively.</p>
|
https://api.sourcedata.io/file.php?figure_id=3209
|
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"ncbi_gene_id": "19401",
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"text": "RARα",
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{
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"mapping_status": "mapped",
"ncbi_gene_id": "19401",
"original_type": "gene",
"role": "intervention",
"text": "RARα",
"type": "geneprod",
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},
{
"ext_dbs": "Uniprot///Uniprot",
"ext_ids": "Q9CQV6///Q91VR7",
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"ext_tax_names": "Mus musculus///Mus musculus",
"mapping_source": "unknown",
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"ncbi_gene_id": null,
"original_type": "protein",
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"text": "LC3",
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{
"ext_dbs": "Uniprot///Uniprot",
"ext_ids": "Q9CQV6///Q91VR7",
"ext_tax_ids": "10090///10090",
"ext_tax_names": "Mus musculus///Mus musculus",
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{
"ext_dbs": "Uniprot///Uniprot",
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},
{
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"ext_dbs": "Uniprot///Uniprot",
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"ext_tax_names": "Mus musculus///Mus musculus",
"mapping_source": "unknown",
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"ncbi_gene_id": null,
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},
{
"ext_dbs": "Uniprot///Uniprot",
"ext_ids": "Q9CQV6///Q91VR7",
"ext_tax_ids": "10090///10090",
"ext_tax_names": "Mus musculus///Mus musculus",
"mapping_source": "unknown",
"mapping_status": "unmapped",
"ncbi_gene_id": null,
"original_type": "protein",
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"text": "LC3",
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{
"ext_dbs": "NCBI gene",
"ext_ids": "19401",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "19401",
"original_type": "gene",
"role": "intervention",
"text": "RARα",
"type": "geneprod",
"uniprot_ids": [
"P11416",
"Q3U3R3",
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] |
|
27110680
|
10.1038/nchembio.1230
|
Chemical modulation of chaperone-mediated autophagy by retinoic acid derivatives
|
2013
|
figf3
|
<p>(<b>a</b>) Rates of degradation of long-lived proteins in mouse fibroblasts untreated (None) or treated with 40 μM <named-entity id="named-entity-268">ATRA</named-entity> and maintained in the presence or absence of serum. Values are expressed as a percentage of proteolysis; <i>n</i> = 3. (<b>b</b>) Percentage of lysosomal degradation calculated after treatment with inhibitors of lysosomal proteolysis for 12 h; <i>n</i> = 3. (<b>c</b>) Immunoblot for <named-entity id="named-entity-269">LC3-II</named-entity> of the same cells as in <b>a</b> and <b>b</b> maintained in the presence or absence of serum and protease inhibitors (PI). Top, representative immunoblot. Actin is shown as loading control. Bottom, ratio of amount of <named-entity id="named-entity-270">LC3-II</named-entity> in cells treated with PI to that in untreated cells. Values are expressed as fold change in value relative to untreated cells; <i>n</i> = 4. 'I' and 'II' designate different forms of LC3, as described in the text. (<b>d</b>,<b>e</b>) Autophagic flux in untreated and <named-entity id="named-entity-271">ATRA</named-entity>-treated cells expressing mCherry-GFP–<named-entity id="named-entity-272">LC3-II</named-entity> and maintained in the presence or absence of serum. Shown in <b>d</b> are representative merged-channel images. Arrows indicate autolysosomes (red). Scale bar, 2 μm. Shown in <b>e</b> are the number of autophagosomes (left) and percentage of autolysosomes (right) after quantification of >50 cells. AV, autophagic vacuoles. (<b>f</b>) Mouse fibroblasts expressing the KFERQ-mCherry1 photoactivatable reporter with or without <named-entity id="named-entity-273">ATRA</named-entity> and after photoactivation maintained in the presence or absence of serum. Left, representative images. Nuclei are labeled with <named-entity id="named-entity-274">DAPI</named-entity>. Scale bars, 10 μm. Graph shows quantification of the number of puncta per cell in >50 cells. All values in <b>a</b>–<b>c</b>, <b>e</b> and <b>f</b> are mean ± s.e.m., and differences with untreated (marked with asterisk) or with serum-supplemented cells (marked with §) are significant for <i>P</i> 0.01. Full-field fluorescence images and full-length blots are shown in <sir rid="S1" refobjid="nchembio.1230-S1">Supplementary Figures 3</sir> and <sir rid="S1" refobjid="nchembio.1230-S1">21</sir>, respectively.</p>
|
https://api.sourcedata.io/file.php?figure_id=3210
|
[
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"ext_tax_names": "Mus musculus///Mus musculus",
"mapping_source": "unknown",
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"ncbi_gene_id": null,
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"text": "LC3",
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"uniprot_ids": []
},
{
"ext_dbs": "Uniprot///Uniprot",
"ext_ids": "Q9CQV6///Q91VR7",
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"ext_tax_names": "Mus musculus///Mus musculus",
"mapping_source": "unknown",
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"text": "LC3",
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},
{
"ext_dbs": "Uniprot///Uniprot",
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"ext_tax_names": "Mus musculus///Mus musculus",
"mapping_source": "unknown",
"mapping_status": "unmapped",
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"original_type": "protein",
"role": "assayed",
"text": "LC3",
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"uniprot_ids": []
},
{
"ext_dbs": "Uniprot///Uniprot",
"ext_ids": "Q91VR7///Q9CQV6",
"ext_tax_ids": "10090///10090",
"ext_tax_names": "Mus musculus///Mus musculus",
"mapping_source": "unknown",
"mapping_status": "unmapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "LC3",
"type": "geneprod",
"uniprot_ids": []
},
{
"ext_dbs": "Uniprot///Uniprot",
"ext_ids": "Q91VR7///Q9CQV6",
"ext_tax_ids": "10090///10090",
"ext_tax_names": "Mus musculus///Mus musculus",
"mapping_source": "unknown",
"mapping_status": "unmapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "LC3",
"type": "geneprod",
"uniprot_ids": []
}
] |
|
27110680
|
10.1038/nchembio.1230
|
Chemical modulation of chaperone-mediated autophagy by retinoic acid derivatives
|
2013
|
figf5
|
<p>(<b>a</b>) Mouse fibroblasts expressing the KFERQ-mCherry1 photoactivatable reporter without (None) or with 20 μM of the indicated compounds imaged 16 h after photoactivation. Insets show higher-magnification images. Nuclei are labeled with <named-entity id="named-entity-284">DAPI</named-entity>. Scale bars, 10 μm. (<b>b</b>) Quantification of the effect of increasing concentrations of GR1 on the same cells. Untreated cells and cells treated with 40 μM <named-entity id="named-entity-285">ATRA</named-entity> are also shown. Representative images are shown in <sir rid="S1" refobjid="nchembio.1230-S1">Supplementary Figure 7</sir>. Graph shows the average number of fluorescent puncta per cell, quantified in >50 cells. All values are mean ± s.e.m. (<b>c</b>) Mouse fibroblasts were cotransfected with the human <named-entity id="named-entity-286">RARα</named-entity> (<named-entity id="named-entity-287">hRARα</named-entity>) receptor, a relevant reporter luciferase plasmid and the non–retinoid-regulated <i>Renilla</i> reporter to control for transfection. Values show relative luciferase units (RLU) detected in cells subjected to the indicated concentrations of <named-entity id="named-entity-288">ATRA</named-entity> or the three retinoid derivatives for 12 h. (<b>d</b>) Cells transfected as in <b>c</b> were treated with 100 nM of <named-entity id="named-entity-289">ATRA</named-entity> alone or in the presence of the indicated concentrations of the three retinoid derivatives or the antagonist <named-entity id="named-entity-290">BMS614</named-entity> for 12 h. Values are shown as RLU. (<b>e</b>) Mouse fibroblasts were cotransfected with the human <named-entity id="named-entity-291">RXR receptor</named-entity>, a relevant reporter luciferase plasmid and the non–retinoid-regulated <i>Renilla</i> reporter to control for transfection. Values show relative luciferase units detected in cells subjected to the indicated concentrations of <named-entity id="named-entity-292">ATRA</named-entity> or the three retinoid derivatives for 12 h. (<b>f</b>) Cells transfected as in <b>e</b> were treated with 10 μM of <named-entity id="named-entity-293">ATRA</named-entity> alone or in the presence of the indicated concentrations of the three retinoid derivatives or the antagonist <named-entity id="named-entity-294">BMS614</named-entity> for 12 h. Values are shown as RLU. Values in <b>c</b>–<b>f</b> are mean ± s.e.m.; <i>n</i> = 4–6. (<b>g</b>) Left, immunoblot for <named-entity id="named-entity-295">LC3-II</named-entity> in cells treated with 20 μM of the retinoid derivatives and protease inhibitors (PIs), as labeled. Actin is shown as loading control, and full-length blots are shown in <sir rid="S1" refobjid="nchembio.1230-S1">Supplementary Figure 21</sir>. The amount of <named-entity id="named-entity-296">LC3-II</named-entity> in untreated cells, expressed as fold change relative to control (middle), and the increase in <named-entity id="named-entity-297">LC3-II</named-entity> after PI treatment (<named-entity id="named-entity-298">LC3-II</named-entity> flux, right), expressed as fold change, were calculated from the densitometric quantification of immunoblots. Values are mean ± s.e.m.; <i>n</i> = 3.</p>
|
https://api.sourcedata.io/file.php?figure_id=3212
|
[
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"text": "RARα",
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{
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},
{
"ext_dbs": "Uniprot///Uniprot///Uniprot",
"ext_ids": "P19793///P48443///P28702",
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"ncbi_gene_id": null,
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"text": "RXR",
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},
{
"ext_dbs": "Uniprot///Uniprot///Uniprot",
"ext_ids": "P19793///P28702///P48443",
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}
] |
|
27110680
|
10.1038/nchembio.1230
|
Chemical modulation of chaperone-mediated autophagy by retinoic acid derivatives
|
2013
|
figf6
|
<p>(<b>a</b>) Rates of degradation of long-lived proteins in control mouse fibroblasts or <named-entity id="named-entity-299">RARα</named-entity>(−) or <named-entity id="named-entity-300">LAMP-2A</named-entity>(−) (<named-entity id="named-entity-301">L-2A</named-entity>(−)) cells left untreated (None) or treated with 20 μM of the indicated compounds. Values are expressed as the fold change in proteolytic rate relative to the rate in untreated cells for each group; <i>n</i> = 3. (<b>b</b>–<b>d</b>) Control mouse fibroblasts or <named-entity id="named-entity-302">RARα</named-entity>(−), <named-entity id="named-entity-303">LAMP-2A</named-entity>(−) or <named-entity id="named-entity-304">LAMP-2B</named-entity>(−) (<named-entity id="named-entity-305">L-2B</named-entity>(−)) cells were transfected with the KFERQ-mCherry1 photoactivatable reporter with or without the indicated compounds (20 μM). In <b>b</b> are shown the representative fields and high-magnification images (insets) for GR1. Nuclei are labeled with <named-entity id="named-entity-306">DAPI</named-entity>. Representative fields for GR2 and AR7 are shown in <sir rid="S1" refobjid="nchembio.1230-S1">Supplementary Figure 13</sir>. Scale bars, 10 μm. (<b>c</b>,<b>d</b>) Average number of fluorescent puncta per cell quantified in >50 cells in at least four different fields in control cells and <named-entity id="named-entity-307">RAR</named-entity>(−) (<b>c</b>) or <named-entity id="named-entity-308">LAMP-2B</named-entity>(−) (<b>d</b>) cells. No puncta were detected in <named-entity id="named-entity-309">LAMP-2A</named-entity>(−) cells. (<b>e</b>) Mouse fibroblasts transfected with the KFERQ-mCherry1 photoactivatable reporter with the indicated concentrations of AR7 or GR1 or with both compounds to reach the same final concentration, as indicated. Top, representative fields and high-magnification images (insets). Nuclei are labeled with <named-entity id="named-entity-310">DAPI</named-entity>. Bottom, quantification of the number of fluorescent puncta per field in each condition. Scale bars, 10 μm. In <b>a</b>, <b>c</b>, <b>d</b> and <b>e</b>, values are mean ± s.e.m.; <i>n</i> > 50 cells. Differences with untreated samples (marked with asterisk) or between single and combined treatments (§) are significant for <i>P</i> 0.01.</p>
|
https://api.sourcedata.io/file.php?figure_id=3213
|
[
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"text": "LAMP-2A",
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"P17047",
"Q8C5K0"
]
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"ext_tax_names": "Mus musculus",
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"Q3U3R3",
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]
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{
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]
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"P17047",
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]
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"ext_tax_names": "Mus musculus",
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"ncbi_gene_id": "16784",
"original_type": "gene",
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},
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"P17047",
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{
"ext_dbs": "NCBI gene",
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"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "19401",
"original_type": "gene",
"role": "intervention",
"text": "RARα",
"type": "geneprod",
"uniprot_ids": [
"P11416",
"Q3U3R3",
"Q3U5E7"
]
}
] |
|
27110680
|
10.1038/nchembio.1230
|
Chemical modulation of chaperone-mediated autophagy by retinoic acid derivatives
|
2013
|
figf7
|
<p>(<b>a</b>) Immunoblot for the indicated proteins in homogenates (Hom) and lysosomes (Lys) isolated from cells untreated (None) or treated for 12 h with 20 μM of the indicated compounds. (<b>b</b>) mRNA levels of <named-entity id="named-entity-311">LAMP-2A</named-entity> in control mouse fibroblasts (left) or <named-entity id="named-entity-312">RARα</named-entity>(−) cells (right) treated with AR7 or <named-entity id="named-entity-313">paraquat</named-entity> (<named-entity id="named-entity-314">PQ</named-entity>) as in <b>a</b>; <i>n</i> = 4–5. Values are presented as fold change in mRNA relative to untreated cells. (<b>c</b>) Cellular viability of control (left) or <named-entity id="named-entity-315">LAMP-2A</named-entity>(−) (right) fibroblasts exposed to 2 mM or 0.5 mM <named-entity id="named-entity-316">paraquat</named-entity>, respectively, and treated with the indicated compounds for 12 h before or after the <named-entity id="named-entity-317">paraquat</named-entity> treatment; <i>n</i> = 3. (<b>d</b>) Viability of mouse fibroblasts transfected with the indicated concentrations of a plasmid encoding <named-entity id="named-entity-318">α-synuclein</named-entity> and left untreated (None) or treated with 1 mM <named-entity id="named-entity-319">paraquat</named-entity> alone or in the presence of 20 μM AR7; <i>n</i> = 3. In <b>b</b>–<b>d</b>, all values are mean ± s.e.m. Differences with cells that are untreated (marked with asterisk) or those treated only with <named-entity id="named-entity-320">paraquat</named-entity> (§) were significant for <i>P</i> 0.001. Full-length blots are shown in <sir rid="S1" refobjid="nchembio.1230-S1">Supplementary Figure 21</sir>. (<b>e</b>) Immunoblot for <named-entity id="named-entity-321">α-synuclein</named-entity> (<named-entity id="named-entity-322">α-syn</named-entity>) in the same cells as in <b>d</b>. Top, higher-exposure blot to highlight oligomeric (oligo) species. Asterisk denotes nonspecific band. M, monomer; MW, molecular weight.</p>
|
https://api.sourcedata.io/file.php?figure_id=3214
|
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"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "16784",
"original_type": "gene",
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"text": "LAMP-2A",
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"P17047",
"Q8C5K0"
]
},
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"P11416",
"Q3U3R3",
"Q3U5E7"
]
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{
"ext_dbs": "NCBI gene",
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"ext_tax_names": "Mus musculus",
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"mapping_status": "mapped",
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"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "20617",
"original_type": "gene",
"role": "intervention",
"text": "α-synuclein",
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"ext_tax_names": "Mus musculus",
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"mapping_status": "mapped",
"ncbi_gene_id": "20617",
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"role": "intervention",
"text": "α-synuclein",
"type": "geneprod",
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"O55042"
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}
] |
|
10.15252/embj.2019101996
|
The N-end rule ubiquitin ligase UBR2 mediates NLRP1B inflammasome activation by anthrax lethal toxin
|
2019
|
Figure 1
|
<sd-panel> <p><strong>Figure 1. The N-end rule pathway controls LT-induced NLRP1B inflammasome activation.</strong></p> <p>A, B Effects of basic and bulky hydrophobic amino acids on LT-induced pyroptosis and caspase-1 activation in RAW<sup>RA</sup> cells. Cells were pre-treated with 10 mM indicated amino acids prior to LT stimulation. Cell viability was measured by using the ATP assay and data shown are mean values ± SD from three replicates (A). Mock, DMEM medium. Cell supernatants were subjected to anti-caspase-1 immunoblotting and the lysates were blotted with the anti-tubulin antibody (B). p10, mature caspase-1; p45, caspase-1 precursor.</p> <p>C, D Effects of basic and bulky hydrophobic amino acids on LT-induced RFP-ASC specks formation in RAW<sup>RA</sup> cells. Fluorescence images were taken on a confocal microscopy (C). The percentages of cells showing RFP-ASC specks (mean values ± SD from three replicates) are in (D).</p> <p>E Effects of basic and bulky hydrophobic amino acids on LT-induced caspase-1 activation in <em>Tlr4<sup>-/-</sup></em> iBMDMs. Cells were treated as that in (A). Cell supernatants were subjected to anti-caspase-1 immunoblotting and the lysates were blotted with the anti-tubulin or anti-MEK3 antibody.</p> </sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=30609
|
[
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"ext_ids": "P15917",
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"ext_tax_names": "Bacillus anthracis",
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"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "intervention",
"text": "LT",
"type": "geneprod",
"uniprot_ids": [
"P15917"
]
},
{
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"ext_tax_names": "Bacillus anthracis",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "intervention",
"text": "LT",
"type": "geneprod",
"uniprot_ids": [
"P15917"
]
},
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"ext_dbs": "Uniprot",
"ext_ids": "P29452",
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"ext_tax_names": "Mus musculus",
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"mapping_status": "mapped",
"ncbi_gene_id": null,
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"text": "caspase-1",
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"P29452"
]
},
{
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"text": "caspase-1",
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"P29452"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P29452",
"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": "caspase-1",
"type": "geneprod",
"uniprot_ids": [
"P29452"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P15917",
"ext_tax_ids": "1392",
"ext_tax_names": "Bacillus anthracis",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "intervention",
"text": "LT",
"type": "geneprod",
"uniprot_ids": [
"P15917"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q9EPB4",
"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": "ASC",
"type": "geneprod",
"uniprot_ids": [
"Q9EPB4"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P29452",
"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": "caspase-1",
"type": "geneprod",
"uniprot_ids": [
"P29452"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P29452",
"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": "caspase-1",
"type": "geneprod",
"uniprot_ids": [
"P29452"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P15917",
"ext_tax_ids": "1392",
"ext_tax_names": "Bacillus anthracis",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "intervention",
"text": "LT",
"type": "geneprod",
"uniprot_ids": [
"P15917"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "O09110",
"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": "MEK3",
"type": "geneprod",
"uniprot_ids": [
"O09110"
]
}
] |
||
10.15252/embj.2019101996
|
The N-end rule ubiquitin ligase UBR2 mediates NLRP1B inflammasome activation by anthrax lethal toxin
|
2019
|
Figure 2
|
<sd-panel> <p><strong>Figure 2. The ubiquitin ligase UBR2 is required for LT-induced NLRP1B activation.</strong></p> <p>A RFP-ASC specks formation assay of the effect of <em>Ubr2</em> knockdown on LT-induced inflammasome activation. RAW<sup>RA</sup> cells were transfected with a control siRNA or <em>Ubr2</em>-targeting siRNA mixtures for 60 h followed by LT treatment. The numbers in the merged panel are the percentages of the cells showing RFP-ASC specks.</p> <p>B Effect of <em>Ubr2</em> stable knockdown on caspase-1 activation in RAW<sup>RA</sup> cells. Cells stably expressing a control or <em>Ubr2</em>-targeting shRNA were incubated with WT LT (+) or its E687C mutant (-) for 3 h.</p> <p>C Effects of <em>Ubr2</em> knockdown (siRNA #05) on LT-induced NLRP1B inflammasome activation reconstituted in 293T cells. Cells were treated with WT LT (+) or its E687C mutant (-).</p> <p>D, E Effect of <em>Ubr2</em> knockout on NLRP1B or NAIP2-NLRC4 inflammasome activation. WT and <em>Ubr2</em><sup>-/-</sup> iBMDMs were treated with LT or BsaK for 3 h. Cell viability was measured by using the ATP assay and data shown are mean values ± SD from three replicates (D).</p> </sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=30610
|
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"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "224826",
"original_type": "gene",
"role": "intervention",
"text": "Ubr2",
"type": "geneprod",
"uniprot_ids": [
"Q6WKZ8",
"Q3UPU3"
]
},
{
"ext_dbs": "NCBI gene",
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"mapping_status": "mapped",
"ncbi_gene_id": "224826",
"original_type": "gene",
"role": "intervention",
"text": "Ubr2",
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"uniprot_ids": [
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"Q3UPU3"
]
},
{
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"ext_tax_names": "Bacillus anthracis",
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{
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},
{
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"P15917"
]
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"ext_tax_names": "Homo sapiens",
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"mapping_status": "mapped",
"ncbi_gene_id": "23304",
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"text": "Ubr2",
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"Q8IWV8",
"B3KXG6"
]
},
{
"ext_dbs": "Uniprot",
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"ext_tax_names": "Bacillus anthracis",
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"ext_dbs": "NCBI gene",
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"text": "Ubr2",
"type": "geneprod",
"uniprot_ids": [
"Q6WKZ8",
"Q3UPU3"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "A0A069BGK0",
"ext_tax_ids": "28450",
"ext_tax_names": "Burkholderia pseudomallei",
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"text": "BsaK",
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"uniprot_ids": [
"A0A069BGK0"
]
},
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] |
||
10.15252/embj.2019101996
|
The N-end rule ubiquitin ligase UBR2 mediates NLRP1B inflammasome activation by anthrax lethal toxin
|
2019
|
Figure 3
|
<sd-panel> <p><strong>Figure 3. UBE2O functions together with UBR2 to mediate NLRP1B inflammasome activation.</strong></p> <p>A Immunoblotting of caspase-1 activation in Ubrs-knockdown BMDMs derived from the 129/Sv mice. Cells were transfected with the indicated siRNA for 60 h, and then treated with WT LT (+) or its E687C mutant (-) for 3 h.</p> <p>B-D Immunoblotting of caspase-1 activation in E2s-knockdown BMDMs derived from the 129/Sv mice. Additional <em>Ube2o</em> siRNAs were used to confirm the inhibitory effect of <em>Ube2o</em> knockdown on LT-induced caspase-1 activation (C). <em>Ube2o</em> knockdown efficiency was measured by qPCR and are shown as mean values ± SD from three replicates.</p> <p>E RFP-ASC specks formation assay of the effect of <em>Ube2o</em> knockdown (siRNA <em>Ube2o</em>-01) on LT-induced inflammasome activation in RAW<sup>RA</sup> cells. The percentages of cells showing RFP-ASC specks (mean values ± SD from three replicates) are in (D).</p> <p>F Co-immunoprecipitation interaction of UBE2O and UBR2. Myc-UBE2O and Flag-UBR2 were co-expressed in 293T cells and cell lysates were subjected to anti-Flag immunoprecipitation followed by immunoblotting analyses as shown.</p> </sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=30611
|
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"ncbi_gene_id": null,
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"text": "caspase-1",
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]
},
{
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"P15917"
]
},
{
"ext_dbs": "NCBI gene",
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]
},
{
"ext_dbs": "NCBI gene",
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]
},
{
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]
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"ext_ids": "Q9EPB4",
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"ext_tax_names": "Mus musculus",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
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"text": "ASC",
"type": "geneprod",
"uniprot_ids": [
"Q9EPB4"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "224826",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "224826",
"original_type": "gene",
"role": "intervention",
"text": "UBR2",
"type": "geneprod",
"uniprot_ids": [
"Q6WKZ8",
"Q3UPU3"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q6WKZ8",
"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": "UBR2",
"type": "geneprod",
"uniprot_ids": [
"Q6WKZ8"
]
}
] |
||
10.15252/embj.2019101996
|
The N-end rule ubiquitin ligase UBR2 mediates NLRP1B inflammasome activation by anthrax lethal toxin
|
2019
|
Figure 4
|
<sd-panel> <p><strong>Figure 4. LT cleavage of NLRP1B triggers N-end rule-mediated degradation of NLRP1B for inflammasome activation.</strong></p> <p>A Domain structure of NLRP1B. The LT cleavage site and the FIIND auto-cleavage site are marked.</p> <p>B Effect of LT treatment on NLRP1B protein level. 293T cells were transfected with Flag-NLRP1B expression plasmid for 24 h, and cells were then treated with WT LT (+) or its E687C mutant (-) for 4 h. Shown is the anti-Flag immunoblot of the total cell lysates.</p> <p>C RFP-ASC specks formation in 293T cells expressing an indicated NLRP1B variant. Cells were treated with LT for 3 h. Scale bar, 20 μm. 1-983 and 984-C (residues 984 to the C terminus) are the FIIND-mediated autocleaved fragments of NLRP1B.</p> <p>D, E Effect of MG132 and Leu on LT-induced NLRP1B degradation. 293T cells expressing NLRP1B (1-983)-HA were treated with LT and MG132 for 8 h. 10 mM Leu was added to cells 30 min prior to LT treatment. Shown are the anti-HA and anti-tubulin immunoblots of the total cell lysates.</p> <p>F LT-induced ubiquitination of NLRP1B. 293T cells expressing NLRP1B (1-983)-HA were treated with LT and/or MG132 for 6 h. Cells were then harvested for anti-HA immunoprecipitation and subjected to immunoblotting analyses using indicated antibodies.</p> <p>Expanded View Figure Legends</p> </sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=30612
|
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"text": "LT",
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]
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]
},
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"ext_ids": "Q2LKW6",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
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"uniprot_ids": [
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]
}
] |
||
27520969
|
10.15252/emmm.201606413
|
IFNλ is a Potent Anti-Influenza Therapeutic without the Inflammatory Side Effects of IFNα Treatment
|
2016
|
Figure 1
|
<p><strong>Fig</strong><strong>ure</strong><strong> 1. Therapeutic administration of IFN</strong><strong>α and IFNλ</strong><strong> differentially influences the outcome of IAV induced disease. </strong></p>
<p><strong>A</strong>. Relative antiviral activity of IFNα (circles) or IFNλ (triangles). AEC cultures were stimulated for 4hrs with stated IFN at specified concentrations (ng/ml) and induction of indicated ISGs was assessed by qPCR (data shown is representative of four independent experiments, n=3-4).</p>
<p><strong>B, C</strong><strong>.</strong> Mice were pretreated with equivalent doses of IFNα (1.45μg/50μl) or IFNλ (2.6μg/50μl) or Veh Ctrl (squares, 50μl PBS) 24hrs prior to infection with PR8; weight loss and survival was assessed throughout infection (B), and viral load (C) assessed at 4dpi (data shown is representative of two independent experiments, n=8-10 (B), n=3 (C)).</p>
<p><strong>D, E</strong><strong>.</strong> Mice were infected with PR8 and treated with equivalent doses of IFNα or IFNλ or Veh Ctrl at days 2, 4 and 5 post infection; survival and weight loss was monitored (D, data pooled from 4 independent experiments, n=12-29) and viral load assessed at 4dpi (E) (data representative of two independent experiments, n=3-5).</p>
<p>Data information: Significance assessed by Log-rank (Mantel-Cox) test (survival), 2-way ANOVA (weight loss) and Unpaired t tests (viral load). * indicates IFNα:Veh Ctrl, <sup>+</sup> indicates IFNλ:Veh Ctrl, and ° indicates IFNα:IFNλ. * P=0.0236, <sup>+</sup> P=0.0236 *** P<0.0001, <sup>+++</sup> P<0.001 (B); * P= 0.012, <sup>+</sup> P=0.012 (C); * P=0.0443, <sup>+</sup> P=0.035, °° P=0.0015 (D); ** P=0.0081, <sup>++</sup> P=0.0066 (E). Symbols on the right of graphs indicate significance of whole curve. Graphs show mean ± SEM.</p>
|
https://api.sourcedata.io/file.php?figure_id=9576
|
[
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"ext_tax_names": "Mus musculus///Mus musculus",
"mapping_source": "unknown",
"mapping_status": "unmapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "intervention",
"text": "IFNλ",
"type": "geneprod",
"uniprot_ids": []
},
{
"ext_dbs": "Uniprot///Uniprot",
"ext_ids": "Q8CGK6///Q4VK74",
"ext_tax_ids": "10090///10090",
"ext_tax_names": "Mus musculus///Mus musculus",
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},
{
"ext_dbs": "Uniprot///Uniprot",
"ext_ids": "Q8CGK6///Q4VK74",
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"ext_tax_names": "Mus musculus///Mus musculus",
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"role": "intervention",
"text": "IFNλ",
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},
{
"ext_dbs": "Uniprot///Uniprot",
"ext_ids": "Q8CGK6///Q4VK74",
"ext_tax_ids": "10090///10090",
"ext_tax_names": "Mus musculus///Mus musculus",
"mapping_source": "unknown",
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"role": "intervention",
"text": "IFNλ",
"type": "geneprod",
"uniprot_ids": []
}
] |
|
27520969
|
10.15252/emmm.201606413
|
IFNλ is a Potent Anti-Influenza Therapeutic without the Inflammatory Side Effects of IFNα Treatment
|
2016
|
Figure 2
|
<p><strong>Fig</strong><strong>ure</strong><strong> 2. IFNα treatment correlates with increased inflammation during IAV infection. </strong></p>
<p><strong>A, B</strong><strong>.</strong> Mice were infected with PR8 and treated with IFNα (circles, 1.45μg/50μl), IFNλ (triangles, 2.6μg/50μl) or Veh Ctrl (squares) as previously stated. Concentrations of stated proinflammatory cytokines in BAL fluid was measured by multiplex cytokine assay (A) and flow cytometric quantification of pDCs and Inflammatory Monocytes in the lung was performed (B) (data shown is representative of two independent experiments, n=2-6).</p>
<p><strong>C, D</strong><strong>.</strong> Lung sections from control and infected mice treated as indicated, were stained by TUNEL for apoptotic cells at 6dpi. Quantification of TUNEL+ cells in whole lung slides by Icy Spot Detector (ICY-R3M2Y2) (C) (data shown is pooled from three independent experiments, n=3-8). Red arrowheads indicate TUNEL signal (D). Scale bar, 200 μM (data shown is representative of two independent experiments, n=3-4).</p>
<p>Data information: Significance assessed by 2-way ANOVA with Bonferroni post tests (where * denotes IFNα:Veh Ctrl, <sup>+</sup> indicates IFNλ:Veh Ctrl , and ° indicates IFNα:IFNλ). Symbols on the right of graphs indicate statistical significance of the whole curve. IL-6 whole curve: ** 0.0041, ° P=0.0144. IL-6 5 d.p.i.: ** P=0.001884, °° P=0.001645. IP-10 5 d.p.i.: ** P=0.004897, °° P=0.005354. MCP-1 5.d.p.i.: ** P=0.007473, °° P= 0.002003. Eotaxin whole curve: * 0.0235, ° P=0.0386. Eotaxin 5 d.p.i. *** P=0.000149, °° P=0.001975. Mip-1α 5 d.p.i.: °° P= 0.002921 (A). Plasmacytoid Dendritic Cells: * P=0.0211, °° P= 0.006965. Inflammatory monocytes ** P=0.007842, °° P=0.000895 (B). ** P=0.0011, <sup>++</sup> P=0.0051, °°° P=0.0005 (C). Graphs show mean ± SEM.</p>
|
https://api.sourcedata.io/file.php?figure_id=9577
|
[
{
"ext_dbs": "Uniprot///Uniprot",
"ext_ids": "Q8CGK6///Q4VK74",
"ext_tax_ids": "10090///10090",
"ext_tax_names": "Mus musculus///Mus musculus",
"mapping_source": "unknown",
"mapping_status": "unmapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "intervention",
"text": "IFNλ",
"type": "geneprod",
"uniprot_ids": []
},
{
"ext_dbs": "Uniprot///Uniprot",
"ext_ids": "Q8CGK6///Q4VK74",
"ext_tax_ids": "10090///10090",
"ext_tax_names": "Mus musculus///Mus musculus",
"mapping_source": "unknown",
"mapping_status": "unmapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "intervention",
"text": "IFNλ",
"type": "geneprod",
"uniprot_ids": []
}
] |
|
27520969
|
10.15252/emmm.201606413
|
IFNλ is a Potent Anti-Influenza Therapeutic without the Inflammatory Side Effects of IFNα Treatment
|
2016
|
Figure 3
|
<p><strong>Fig</strong><strong>ure</strong><strong> 3. IFNα, but not IFNλ treatment induces </strong><strong>pulmonary </strong><strong>cytokine secretion through activation of immune cells. </strong></p>
<p><strong>A, B</strong><strong>.</strong> IL-6, IP-10 and MCP-1 concentrations were measured by multiplex cytokine assay in AEC culture supernatants (A) and Macrophage, pDC and cDC culture supernatants (B) at 24hrs post stimulation with IFNα4 (0.725ng/ml) or IFNλ2 (1.3ng/ml) or LPS (AEC only) (data shown is representative of two independent experiments, n=3-6).</p>
<p><strong>C</strong>. BAL samples taken from mice treated with IFNα, IFNλ or Veh Ctrl at specified time points (data shown is representative of two independent experiments, n=5-6).</p>
<p>Data information: Significance assessed by Unpaired t tests where * denotes IFNα:Veh Ctrl and ° indicates IFNα:IFNλ. IFNλ:Veh Ctrl was not significant. IL6 pDC: *** P=0.0004, °°° P= 0.0005, IL6 cDC: * P=0.0102, ° P=0.0151. IP-10 macrophage: ** P=0.0033, °° P=0.0033, pDC: **** P<0.0001, °°°° P<0.0001, cDC: ** P= 0.0013, °° P=0.0013, MCP-1 macrophage: **** P<0.0001, °°° P=0.003 (B). IL-6 10hrs: * P=0.0112, ° P=0.0262, 18hrs: * P=0.0314, ° P=0.373. IP-10 10hrs: * P= 0.0261, ° P=0.0472. MCP-1 10hrs: ** P=0.0081, ° P=0.0206, 18hrs: ** P=0.0089, ° P=0.01 (C).</p>
|
https://api.sourcedata.io/file.php?figure_id=9578
|
[
{
"ext_dbs": "Uniprot",
"ext_ids": "P10148",
"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": "MCP-1",
"type": "geneprod",
"uniprot_ids": [
"P10148"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P17515",
"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": "IP-10",
"type": "geneprod",
"uniprot_ids": [
"P17515"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P07351",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "intervention",
"text": "IFNα4",
"type": "geneprod",
"uniprot_ids": [
"P07351"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q4VK74",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "intervention",
"text": "IFNλ2",
"type": "geneprod",
"uniprot_ids": [
"Q4VK74"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P08505",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "IL-6",
"type": "geneprod",
"uniprot_ids": [
"P08505"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P10148",
"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": "MCP-1",
"type": "geneprod",
"uniprot_ids": [
"P10148"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P17515",
"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": "IP-10",
"type": "geneprod",
"uniprot_ids": [
"P17515"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P07351",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "intervention",
"text": "IFNα4",
"type": "geneprod",
"uniprot_ids": [
"P07351"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q4VK74",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "intervention",
"text": "IFNλ2",
"type": "geneprod",
"uniprot_ids": [
"Q4VK74"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P08505",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "IL-6",
"type": "geneprod",
"uniprot_ids": [
"P08505"
]
},
{
"ext_dbs": "Uniprot///Uniprot",
"ext_ids": "Q8CGK6///Q4VK74",
"ext_tax_ids": "10090///10090",
"ext_tax_names": "Mus musculus///Mus musculus",
"mapping_source": "unknown",
"mapping_status": "unmapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "intervention",
"text": "IFNλ",
"type": "geneprod",
"uniprot_ids": []
}
] |
|
27520969
|
10.15252/emmm.201606413
|
IFNλ is a Potent Anti-Influenza Therapeutic without the Inflammatory Side Effects of IFNα Treatment
|
2016
|
Figure 4
|
<p><strong>Fig</strong><strong>ure</strong><strong> 4. Pathogenicity-related gene clusters are specifically induced by IFNα, not by IFNλ treatment. </strong></p>
<p>Mice were treated with IFNα (1.45μg/50μl), IFNλ (2.6μg/50μl) or Veh Ctrl (50μl PBS), and whole lungs were taken at 18hrs post treatment for global analysis by Illumina.SingleColor.Mouse WG-6_V2_0_R0_1127 microarrays. Samples (n=5) were normalized to the median of the vehicle control group and filtered for a fold change of 1.5, yielding 553 genes differently regulated between treatments (One way ANOVA, P<0.01, Benjamini-Hochberg multiple test correction), of which 429 genes are upregulated. K means clustering revealed six gene clusters, one of which encompassed genes primarily induced by IFNα4 (A), while the remaining clusters contained genes upregulated by both IFNα4 and IFNλ2 (B). The two clusters of genes were analysed by Ingenuity Pathway Analysis (IPA) (C,D).</p>
|
https://api.sourcedata.io/file.php?figure_id=9579
|
[
{
"ext_dbs": "Uniprot",
"ext_ids": "P07351",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "intervention",
"text": "IFNα4",
"type": "geneprod",
"uniprot_ids": [
"P07351"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P07351",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "intervention",
"text": "IFNα4",
"type": "geneprod",
"uniprot_ids": [
"P07351"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q4VK74",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "intervention",
"text": "IFNλ2",
"type": "geneprod",
"uniprot_ids": [
"Q4VK74"
]
}
] |
|
27520969
|
10.15252/emmm.201606413
|
IFNλ is a Potent Anti-Influenza Therapeutic without the Inflammatory Side Effects of IFNα Treatment
|
2016
|
Figure 5
|
<p><strong>Fig</strong><strong>ure</strong><strong> 5. IFNα, but not IFNλ treatment induces cytokine secretion from human immune cells. </strong></p>
<p><strong>A</strong>. Human AEC cultures were stimulated for 4hrs with IFNα (circles) or IFNλ (triangles) at specified concentrations then assessed for stated ISG induction by qPCR (data is representative of 2 independent experiments, n=3).</p>
<p><strong>B</strong><strong>, C</strong><strong>.</strong> ISG induction in human PBMCs was assessed at 4 and 24hrs post IFNα (21 U/ml) or IFNλ (1.2 ng/ml) stimulation (B). PBMC proinflammatory cytokine secretion was measured by multiplex cytokine assay at 4 and 24hrs post stimulation with IFNα or IFNλ (C) (data shown is pooled from 6 independent donors).</p>
<p>Data information: Significance tested by 2-way ANOVA where * denotes IFNα:Veh Ctrl and ° indicates IFNα:IFNλ. IFNλ:Veh Ctrl was not significant. IRF7: ** P=0.0037, Rsad2 4hrs: ** P=0.0038, °° P=0.037, 24hrs: * P=0.0234. OAS1 4hrs: * P=0.0328, ° P=0.0358, 24hrs: **** P<0.0001 (B). IL-6: * P=0.0124, ** P=0.0021. MCP-1 4hrs: **** P<0.0001, °°° P=0.001, 24hrs: ** P=0.0046, °° P= 0.005. IP-10 4hrs: ** P=0.0033, °° P= 0.0024, 24hrs: ** P=0.0011, °°° P=0.001 (C).</p>
|
https://api.sourcedata.io/file.php?figure_id=9580
|
[
{
"ext_dbs": "Uniprot///Uniprot///Uniprot///Uniprot",
"ext_ids": "Q8IZI9///K9M1U5///Q8IZJ0///Q8IU54",
"ext_tax_ids": "9606///9606///9606///9606",
"ext_tax_names": "Homo sapiens///Homo sapiens///Homo sapiens///Homo sapiens",
"mapping_source": "unknown",
"mapping_status": "unmapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "intervention",
"text": "IFNλ",
"type": "geneprod",
"uniprot_ids": []
},
{
"ext_dbs": "Uniprot///Uniprot///Uniprot///Uniprot",
"ext_ids": "Q8IZI9///K9M1U5///Q8IZJ0///Q8IU54",
"ext_tax_ids": "9606///9606///9606///9606",
"ext_tax_names": "Homo sapiens///Homo sapiens///Homo sapiens///Homo sapiens",
"mapping_source": "unknown",
"mapping_status": "unmapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "intervention",
"text": "IFNλ",
"type": "geneprod",
"uniprot_ids": []
},
{
"ext_dbs": "Uniprot///Uniprot///Uniprot///Uniprot",
"ext_ids": "Q8IZI9///K9M1U5///Q8IZJ0///Q8IU54",
"ext_tax_ids": "9606///9606///9606///9606",
"ext_tax_names": "Homo sapiens///Homo sapiens///Homo sapiens///Homo sapiens",
"mapping_source": "unknown",
"mapping_status": "unmapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "intervention",
"text": "IFNλ",
"type": "geneprod",
"uniprot_ids": []
}
] |
|
27596438
|
10.15252/emmm.201505971
|
ZEB1-mediated melanoma cell plasticity enhances resistance to MAPK inhibitors
|
2016
|
Figure 1
|
<p><strong>Figure 1</strong><strong>.</strong> <strong>High </strong><strong>levels of </strong><strong>ZEB1 expression </strong><strong>are </strong><strong>correlate</strong><strong>d</strong><strong> with low </strong><strong>MITF</strong><strong> level</strong><strong>s</strong><strong> and</strong> <strong>are</strong><strong> associated with inherent resistance to </strong><strong>MAPKi</strong><strong> in </strong><strong><em>BRAF</em></strong><strong><em><sup>V600</sup></em></strong><strong>-mutated </strong><strong>melanoma cell lines</strong></p>
<p>(A) Pearson correlation between <em>ZEB1</em> and <em>MITF</em> mRNA expression in 61 melanoma cell lines available through the CCLE. (B) ZEB1, ZEB2, TWIST1 and MITF expression in a panel of <em>BRAF</em><em><sup>V600</sup></em>-mutated melanoma cells assessed by Western blot. GLO and C-09.10 cells are patient-derived short-term cultures. Actin was used as a loading control. (C) Quantitative PCR analyses of <em>ZEB1</em>, <em>ZEB2</em>, <em>TWIST1 </em>and <em>MITF</em> in the same panel of cell lines. mRNA expression levels are represented relatively to C-09.10 cells, in which the levels were arbitrarily fixed at 1 (n=3, mean ± SD). The dotted line separates ZEB1<sup>high</sup> (left) and ZEB1<sup>low</sup> (right) cell lines. (D) Tukey box plot of <em>ZEB1</em>, <em>ZEB2</em>, <em>TWIST1</em>, and <em>MITF</em> mRNA expression according to the IC50 of the drug (µM) administered (BRAFi/MEKi), in melanoma cell lines from the CCLE (n=28) (Student’s t-Test). High <em>ZEB1</em>, low <em>ZEB2</em>, and low <em>MITF</em> expression levels were correlated with BRAFi (PLX4720) and MEKi (AZD6244) resistance. PLX4720 is an analog of PLX4032. (E) IC50 values of PLX4032 (µM) in the panel of <em>BRAF</em><em><sup>V600</sup></em> melanoma cells as determined by ATP assay (n=3, mean ± SD). For SKMEL24 and WM793, IC50 was >8µM.</p>
|
https://api.sourcedata.io/file.php?figure_id=9817
|
[
{
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"ext_tax_names": "Homo sapiens",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "4286",
"original_type": "gene",
"role": "assayed",
"text": "MITF",
"type": "geneprod",
"uniprot_ids": [
"O75030",
"A0A087WXU1",
"A0A8I5KSZ4",
"B4DNC7"
]
},
{
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"mapping_status": "mapped",
"ncbi_gene_id": "6935",
"original_type": "gene",
"role": "assayed",
"text": "ZEB1",
"type": "geneprod",
"uniprot_ids": [
"P37275",
"B2RBI8",
"B4DGU2"
]
},
{
"ext_dbs": "Uniprot",
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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": "MITF",
"type": "geneprod",
"uniprot_ids": [
"O75030"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q15672",
"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": "TWIST1",
"type": "geneprod",
"uniprot_ids": [
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]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P37275",
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"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
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"text": "ZEB1",
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]
},
{
"ext_dbs": "Uniprot",
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"text": "ZEB2",
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"uniprot_ids": [
"O60315"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "4286",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "4286",
"original_type": "gene",
"role": "assayed",
"text": "MITF",
"type": "geneprod",
"uniprot_ids": [
"O75030",
"A0A087WXU1",
"A0A8I5KSZ4",
"B4DNC7"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "6935",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "6935",
"original_type": "gene",
"role": "assayed",
"text": "ZEB1",
"type": "geneprod",
"uniprot_ids": [
"P37275",
"B2RBI8",
"B4DGU2"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "6935",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "6935",
"original_type": "gene",
"role": "assayed",
"text": "ZEB1",
"type": "geneprod",
"uniprot_ids": [
"P37275",
"B2RBI8",
"B4DGU2"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "6935",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "6935",
"original_type": "gene",
"role": "assayed",
"text": "ZEB1",
"type": "geneprod",
"uniprot_ids": [
"P37275",
"B2RBI8",
"B4DGU2"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "4286",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "4286",
"original_type": "gene",
"role": "assayed",
"text": "MITF",
"type": "geneprod",
"uniprot_ids": [
"O75030",
"A0A087WXU1",
"A0A8I5KSZ4",
"B4DNC7"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "4286",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "4286",
"original_type": "gene",
"role": "assayed",
"text": "MITF",
"type": "geneprod",
"uniprot_ids": [
"O75030",
"A0A087WXU1",
"A0A8I5KSZ4",
"B4DNC7"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "7291",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "7291",
"original_type": "gene",
"role": "assayed",
"text": "TWIST1",
"type": "geneprod",
"uniprot_ids": [
"Q15672"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "6935",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "6935",
"original_type": "gene",
"role": "assayed",
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] |
|
27596438
|
10.15252/emmm.201505971
|
ZEB1-mediated melanoma cell plasticity enhances resistance to MAPK inhibitors
|
2016
|
Figure 2
|
<p><strong>Figure </strong><strong>2</strong><strong>.</strong> <strong>High ZEB1 </strong><strong>and </strong><strong>low </strong><strong>MITF</strong><strong> level</strong><strong>s</strong> <strong>are</strong><strong> associated with inherent resistance to </strong><strong>MAPKi</strong><strong> in </strong><strong><em>BRAF</em></strong><strong><em><sup>V600</sup></em></strong><strong>-</strong><strong>mutated </strong><strong>melanoma </strong><strong>tumors</strong></p>
<p>(A) Pearson correlation between <em>ZEB1</em> and <em>MITF</em> mRNA expression levels in 467 melanoma tumors from TCGA data set. (B) Representative pictures of ZEB1 and MITF immunostaining in primary melanomas. Scale bar = 40 µm. The aberrant activation of ZEB1 in melanomas is correlated with a MITF<sup>low</sup> phenotype. (C) Representative pictures of ZEB1 immunostaining in <em>BRAF</em><em><sup>V600</sup></em> tumors from patients, classified in ZEB1 high, int and low subgroups, based on the intensity of ZEB1 staining and on the percentage of cells positive for ZEB1. Scale bar = 80 µm. (D) Pie charts representing the distribution of ZEB1 alone (upper part), or ZEB1 and TWIST1 (lower part) immunohistochemical staining in tumors according to their initial response to vemurafenib +/- cobimetinib treatment. ZEB1 +/- TWIST1 levels are higher in MAPKi primary resistant melanomas (initial non-responders) compared to tumors that initially respond to treatment (n=70, Fisher’s exact test). (E) Representative pictures of ZEB1 and MITF immunostainings, before and after vemurafenib treatment, in the tumor from patient 1, exhibiting primary resistance to BRAFi. Scale bar = 80 µm. Right: Magnification of MITF<sup>high</sup> and MITF<sup>low</sup> clones in the resistant tumor under treatment. Arrows indicate endothelial and stromal cells that also show positive staining for ZEB1, besides tumor cells.</p>
|
https://api.sourcedata.io/file.php?figure_id=9818
|
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] |
|
27596438
|
10.15252/emmm.201505971
|
ZEB1-mediated melanoma cell plasticity enhances resistance to MAPK inhibitors
|
2016
|
Figure 3
|
<p><strong>Figure </strong><strong>3</strong><strong>.</strong> <strong>ZEB1 expression is activated in </strong><strong><em>BRAF</em></strong><strong><em><sup>V600</sup></em></strong><strong>-</strong><strong>mutated </strong><strong>melanoma cell lines with acquired resistance to </strong><strong>BRAFi</strong><strong> and </strong><strong>in </strong><strong>biopsies from patients relapsing while under treatment</strong></p>
<p>(A) PLX4032 IC50 (µM) of sensitive A375 and SKMEL5 and resistant (A375-R, SKMEL5-R) cell lines, as well as of GOKA and ESP cells, two BRAFi-resistant patient-derived short-term cultures, as determined by ATP assay (n=3, mean ± SD). For ESP, IC50 was >8µM. (B) Western blot analyses of ZEB1, TWIST1 and FRA1 in A375-R and SKMEL5-R <em>versus</em> the parental naive cells, and in GOKA and ESP cells. GAPDH was used as a loading control. (C) Quantitative PCR analyses of <em>ZEB1 </em>and <em>MITF</em> in A375-R and SKMEL5-R <em>versus</em> the parental naive cells, and in GOKA and ESP cells. mRNA expression levels are represented as arbitrary units (a.u). Statistical difference relative to sensitive A375 cells is shown (n=3, mean ± SD, Student’s t-test). (D) Representative pictures of ZEB1 and MITF immunostainings in tumors from patients 2, 3 and 4, before and after vemurafenib treatment. Scale bar = 40 µm. For ZEB1 staining in patient 4, the inset shows a magnification. Arrows point at stromal cells (s). All other cells positive for ZEB1 are tumor cells.</p>
|
https://api.sourcedata.io/file.php?figure_id=9819
|
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|
27596438
|
10.15252/emmm.201505971
|
ZEB1-mediated melanoma cell plasticity enhances resistance to MAPK inhibitors
|
2016
|
Figure 4
|
<p><strong>Figure 4</strong><strong>.</strong> <strong><em>ZEB1</em></strong><strong> overexpression in </strong><strong>A375 </strong><strong>melanoma cell</strong><strong>s </strong><strong>potentiates </strong><strong>the conversion </strong><strong>into</strong><strong> a </strong><strong>MITF</strong><strong><sup>low</sup></strong><strong>/p75</strong><strong><sup>high</sup></strong><strong> stem-like tumor initiating phenotype</strong><strong>,</strong> <strong>and </strong><strong>promotes</strong> <strong>resistance to </strong><strong>MAPKi</strong> (A) A375 cells were infected with retroviruses expressing <em>ZEB1</em>. Western blot analyses of ZEB1 and p75. GAPDH was used as a loading control. (B) Quantitative PCR analyses of <em>MITF</em>, <em>p75</em>, <em>ABCB5</em> and <em>JARID1B</em> upon <em>ZEB1 </em>expression. mRNA expression levels are represented relatively to control cells, in which the levels were fixed at 1 (mean ± SD, n=3, Student’s t-test). (C) Soft agar colony formation assay upon <em>ZEB1</em> expression. Scale bar = 200 µm. Histograms represent quantitative analyses (mean ± SD, n=3, Student’s t-test). (D) 2 x 10<sup>6</sup> Control or <em>ZEB1</em>-overexpressing A375 cells were injected subcutaneously into <em>nude</em> mice. The mean tumor volume for 5 mice is represented ± SEM (Student’s t-test). (E) Western blot analyses of ZEB1, MITF, P-ERK, and TWIST1 levels in control or <em>ZEB1</em>-expressing cells +/- 150 nM PLX4032 treatment for 24 h. GAPDH was used as a loading control. (F) FACS analyses of p75 cell surface expression upon <em>ZEB1</em> overexpression, after 10 days treatment with or without 150 nM PLX4032. Bar chart representing the mean percentage of p75-high, int and low cells from 2 independent experiments (Fisher’s Exact Test). (G) Control or ZEB1-overexpressing A375 cells were transfected with control or p75-siRNA. <em>p75 </em>and <em>MITF</em> expression levels were was analyzed by quantitative PCR after 48 h. mRNA expression levels are represented relatively to control cells transfected with siRNA Control, in which the levels were fixed at 1 (mean ± SD, n=2). (H) Clonogenic assay +/- PLX4032 (150 nM), +/- GDC-0973 (5 nM) treatment for 10 days. The graphs represent the mean number of colonies (± SD) in 3 independent experiments (Student’s t-test). (I) Number of weeks of chronic exposure to PLX4032 before emergence of resistance in control or ZEB1-expressing cells (n=3, Student’s t-test).</p>
|
https://api.sourcedata.io/file.php?figure_id=9820
|
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] |
|
27596438
|
10.15252/emmm.201505971
|
ZEB1-mediated melanoma cell plasticity enhances resistance to MAPK inhibitors
|
2016
|
Figure 5
|
<p><strong>Figure </strong><strong>5</strong><strong>.</strong> <strong><em>ZEB1</em></strong><strong> overexpression in </strong><strong>patient-derived </strong><strong>ZEB1</strong><strong><sup>low</sup></strong><strong>/</strong><strong>MITF</strong><strong><sup>high</sup></strong><strong> short-term culture cells</strong> <strong>promotes the conversion </strong><strong>into</strong><strong> a </strong><strong>MITF</strong><strong><sup>low</sup></strong><strong>/p75</strong><strong><sup>high</sup></strong><strong> stem-like phenotype</strong><strong>, </strong><strong>resistan</strong><strong>t</strong><strong> to </strong><strong>MAPKi</strong></p>
<p>(A) C-09.10 short-term culture cells were infected with retroviruses expressing <em>ZEB1</em>. Western blot analyses of ZEB1 and p75. GAPDH was used as a loading control. (B) Quantitative PCR analyses of <em>MITF</em> and <em>p75</em> upon ZEB1 expression. mRNA expression levels are represented relatively to control cells (mean ± SD, n=3, Student’s t-test). (C) Soft agar colony formation assay following <em>ZEB1</em> expression. Scale bar = 200 µm. Histograms represent quantitative analyses (mean ± SD, n=3, Student’s t-test). (D) FACS analyses of p75 cell surface expression upon <em>ZEB1 </em>overexpression. Bar chart representing the mean percentage of p75-high, int, low and negative cells from 2 independent experiments (Fisher’s exact test). (E) Clonogenic assay +/- PLX4032 (100 nM) treatment for 10 days. The graph represents the mean number of colonies in 3 independent experiments (Student’s t-test).</p>
|
https://api.sourcedata.io/file.php?figure_id=9821
|
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] |
|
27596438
|
10.15252/emmm.201505971
|
ZEB1-mediated melanoma cell plasticity enhances resistance to MAPK inhibitors
|
2016
|
Figure 6
|
<p><strong>Figure </strong><strong>6</strong><strong>.</strong> <strong><em>ZEB1</em></strong><strong> knock-down in </strong><strong>ZEB1</strong><strong><sup>high</sup></strong><strong>/</strong><strong>MITF</strong><strong><sup>low</sup></strong> <strong>melanoma cells promotes the </strong><strong>reversible </strong><strong>conversion </strong><strong>into</strong><strong> a </strong><strong>MITF</strong><strong><sup>high</sup></strong><strong>/p75</strong><strong><sup>low</sup></strong><strong> differentiated </strong><strong>phenotype </strong><strong>and </strong><strong>inhibits </strong><strong>tumor growth</strong> <strong><em>in vivo</em></strong></p>
<p>(A) A375 cells were infected with retroviruses expressing a control or <em>ZEB1</em>-shRNA. Western blot analyses of ZEB1 and p75 upon <em>ZEB1</em> knock-down. GAPDH was used as a loading control. High and low exposures (exp) for p75 are shown. (B) Quantitative PCR analyses of <em>MITF</em>, <em>p75</em>, <em>ABCB5</em> and <em>JARID1B</em> upon <em>ZEB1</em> knock-down. mRNA expression levels are represented relatively to shRNA control cells (mean ± SD, n=3, Student’s t-test). (C) FACS analyses of p75 expression upon <em>ZEB1</em> knock-down. Bar chart representing the mean percentage of p75-high, int and low cells from 2 independent experiments (Fisher’s exact test). (D) Soft agar colony formation assay upon <em>ZEB1 </em>knock-down. Scale bar = 200 µm. Histograms represent quantitative analyses (mean ± SD, n=3, Student’s t-test). (E) 2 x 10<sup>6</sup> Control or <em>ZEB1</em>-shRNA A375 cells were injected subcutaneously into <em>nude</em> mice. The mean tumor volume for 5 mice is represented (± SEM). (Student’s t-test). (F) A375 cells were infected with an IPTG-inducible <em>ZEB1</em>-shRNA. Left panel: Western blot analyses of ZEB1 expression ± IPTG (100µM) treatment for 6 days. Actin was used as a loading control. Right panel: 2 x 10<sup>6</sup> IPTG-inducible shRNA-Control or shRNA-ZEB1 A375 cells were injected subcutaneously into <em>nude</em> mice. When the tumor reached 5 mm in diameter, ZEB1 expression was silenced by adding IPTG (10 mM) into the drinking water for 20 days. The mean tumor volume for 5 mice is represented (± SEM). (Student’s t-test). (G) SKMEL5 cells expressing an IPTG-inducible <em>ZEB1</em>-shRNA were treated with IPTG (100µM) for 10 days (+IPTG), then IPTG was removed (-IPTG) and ZEB1, MITF and p75 expression levels were analyzed by Western blot and/or quantitative PCR analyses. GAPDH was used as a protein loading control, mRNA expression levels are represented relatively to untreated cells, in which the levels were fixed at 1 (mean ± SD, n=2).</p>
|
https://api.sourcedata.io/file.php?figure_id=9822
|
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] |
|
27596438
|
10.15252/emmm.201505971
|
ZEB1-mediated melanoma cell plasticity enhances resistance to MAPK inhibitors
|
2016
|
Figure 7
|
<p><strong>Figure </strong><strong>7</strong><strong>.</strong> <strong><em>ZEB1</em></strong><strong> knock-down </strong><strong>sensitizes </strong><strong>naive melanoma</strong> <strong>cells to </strong><strong>BRAFi</strong> <strong>and</strong> <strong>induces cell death in </strong><strong>BRAFi</strong><strong>-resistant melanoma cells</strong></p>
<p>(A) Western blot analyses of ZEB1 and P-ERK in shRNA-control or shRNA-ZEB1-expressing A375 cells +/- 150 nM PLX4032 treatment for 24 h. GAPDH was used as a loading control. (B) Soft agar colony formation assay in A375 cells in the presence or absence of PLX4032 (150 nM). Scale bar = 100 µm. Histograms represent quantitative analyses (mean ± SD, n=3, Student’s t-test). (C) Number of weeks of chronic exposure to PLX4032 before emergence of resistance in control or shRNA-ZEB1-expressing cells (n=3, Student’s t-test). (D) RPMI7951, A375-R and SKMEL5-R were infected with a retrovirus encoding a constitutive shRNA-ZEB1. Short-term cultures of GOKA and ESP cells, derived from vemurafenib-resistant patients, were infected with a lentivirus encoding an IPTG-inducible shRNA-ZEB1. Western blot analyses showing efficient <em>ZEB1</em> knock-down in the different models, ±IPTG (200µM), ±PLX4032 (3µM) as indicated. Induction of cell death was assessed by PARP cleavage. GAPDH or actin were used as loading control. (E) Clonogenic assays in the presence of 3 µM PLX4032, and with or without IPTG (200 µM) as indicated. The graphs represent the mean number of colonies in 3 independent experiments (Student’s t-test). (F) Western blot analyses of ZEB1, p75 and quantitative PCR analyses of <em>MITF</em> in shRNA-Control or shRNA-ZEB1 ESP vemurafenib-resistant patient-derived short-term culture cells. Actin was used as a loading control. mRNA expression levels are represented relatively to control cells (mean ± SD, n=3, Student’s t-test). (G) 2,5 x 10<sup>6</sup> shRNA-Control or shRNA-ZEB1 ESP vemurafenib-resistant cells were injected subcutaneously in nude mice. When the tumor reached 5 mm in diameter, ZEB1 expression was silenced by providing mice with IPTG (10 mM) in their drinking water and orally administering vemurafenib (50 mg/kg) daily for 4 weeks. The mean tumor volume for 5 mice is represented (± SEM). (Student’s t-test). (H) Upper part: Western blot analyses of ZEB1 in shRNA-Control (1 to 4) or shRNA-ZEB1 (5 to 8) ESP xenograft tumors, showing efficient <em>ZEB1</em> knock-down directly in the tumors, after IPTG ±PLX4032 treatment <em>in vivo</em>. Lower part: Representative pictures of ZEB1 immunostaining in shRNA-Control or shRNA-ZEB1 tumors, after IPTG treatment <em>in vivo</em>. Scale bar = 40µm.</p>
|
https://api.sourcedata.io/file.php?figure_id=9823
|
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] |
|
10.15252/embr.202154127
|
Cell Communication Network factor 4 promotes tumor-induced immunosuppression in melanoma
|
2022
|
Figure 1
|
<p><strong>Figure 1 - CCN4 is associated with reduced overall survival of patients diagnosed with primary melanoma and a shift in immune contexture.</strong></p><p>(A) Kaplan-Meier estimate of overall survival of patients diagnosed with primary melanoma stratified by CCN4 transcript abundance, with patients at risk tabulated below graph, as similarly shown in Deng et al. (2019). Original data obtained from SKCM arm of TCGA and stratified based on CCN4 mRNA expression (CCN4 high/positive > 1 FPKM: blue, CCN4 low/negative < 1 FPKM: red). P-value calculated using the Peto & Peto modified Gehan-Wilcoxon test.</p><p>(B) The proportion of CCN4 positive melanoma cells obtained from patients with melanoma obtained prior to treatment (o, n = 15) and from patients that did not respond to immune checkpoint blockade (x, n = 10). Values shown as the proportion of CCN4 positive melanoma cells of the sample ± SE of the sample proportion, given a binomial distribution. A binomial test assessed significance between the proportion of CCN4 positive cells in the sample relative to a null proportion of 1% or less CCN4 positive melanoma cells. Samples with significantly enriched CCN4 positive cells are indicated in red.</p><p>(C) Immune contexture in corresponding primary SKCM tissue samples estimated from bulk RNAseq data using CIBERSORTx deconvolution. Columns ordered from low (left) to high (right) CCN4 expression. Rows hierarchically clustered based on a Euclidian distance metric in R (Ward.D). A non-parametric Mann-Whitney U test assessed significance of difference in immune subset signature between CCN4 high/positive and low/negative groups. The log10 p-values were color coded.</p>
|
https://api.sourcedata.io/file.php?figure_id=45764
|
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] |
||
10.15252/embr.202154127
|
Cell Communication Network factor 4 promotes tumor-induced immunosuppression in melanoma
|
2022
|
Figure 2
|
<p><strong>Figure 2 - CCN4 knockout suppressed melanoma tumor growth in immunocompetent mice.</strong></p><p>(A) CCN4 secretion after CRISPR/Cas9 knockout in B16F0 and YUMM1.7 cell lines. Cell culture media conditioned for 48 hours by the indicated cell line were tested by ELISA (n.d. = not detected). Three biological replicates represented as mean ± SEM.</p><p>(B-E) B16F0 knockout created with Homology-Directed Repair approach with controls for puromycin selection (B16F0-Ctr) created with pBabe-puro retrovirus. YUMM1.7 knockout created with double nickase approach with KO1 and KO2 indicating two different clones. Wildtype (WT: red) B16F0 (B,C) and YUMM1.7 (D,E) cells and CCN4 knockout variants (KO1: blue, KO2: black) were subcutaneously injected into (B,D) C57BL/6 immunocompetent and (C,E) NSG immunocompromised mice. Tumor volumes measured by caliper as a function of time after tumor challenge, with n expressed as the number of mice with tumors over the number of mice injected. The tumor growth profiles for every mouse in the different cohorts is provided in Dataset EV1.</p><p>(F-H) The tumor growth model used to interpret the log-linear tumor growth curves (F). Posterior distributions in the growth rate constant of tumors in NSG mice (G) and in the log-ratio of the net growth rate constants of tumors in NSG relative to C57BL/6 mice (H). Statistical differences in these distributions were assessed using a Chi-squared test summarized in text.</p><p>(I) In a time-matched experiment, average tumor weights of both B16F0 and YUMM1.7 were significantly decreased following CCN4 knockout (KO1). Results summarized as mean ± SEM.</p><p>(J) Significant increases in the number of CD45+ cells were observed in both B16F0 and YUMM1.7 cell lines following CCN4 knockout (KO1). Results summarized as mean ± SEM.</p><p>Data information: In I and J, statistical significance was assessed using a Student's t-test with *: 0.01<p<0.05, **: 0.001<p<0.01, ***: p<0.001 and results representative of at least six biological replicates.</p>
|
https://api.sourcedata.io/file.php?figure_id=45766
|
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||
10.15252/embr.202154127
|
Cell Communication Network factor 4 promotes tumor-induced immunosuppression in melanoma
|
2022
|
Figure 3
|
<p><strong>Figure 3 - CCN4 knockout increased CTL and NK effector cells and decreased MDSC in the tumor microenvironment.</strong></p><p>(A) Representative flow cytometry data of the frequency of tumor-infiltrating CD4+ and CD8+ T cells, NK effector cells, tumor-associated neutrophils (TAN) and MDSC from the live CD45+ compartment in WT and CCN4 knockout (KO1) YUMM1.7 tumors. Gating strategies are illustrated in Appendix Figures S4 and S5. In the right panel, the contour lines enclose 90% of TANs (red line) and MDSC (blue) that were determined based on gating shown in Appendix Figure S5 but here backgated along the GR1/CD11b axes.</p><p>(B-I) Graphs summarizing the change in frequency of immune cells in the YUMM1.7 tumor microenvironment following CCN4 knockout (n=6 /group). (B) CD3+, (C) CD4+, (D) CD8+, (E) NK cells, (F) CD11c+ TAMs, (G) TANs, (H) DCs, and (I) MDSC. Statistical significance was assessed using a Student's t-test using six biological replicates with results annotated with *: 0.01<p<0.05, **: 0.001<p<0.01, and ***: p<0.001.. Results summarized as mean ± SEM.</p><p>(J) CCN4 secretion from CCN4-inducible cells and associated control cell lines in conditioned media with or without 0.5 μg/ml doxycycline, as measured by ELISA (n.d. = not detected). Results from three biological replicates summarized as mean ± SEM.</p><p>(K) Kaplan-Meier summary of the fraction tumor free in a 2x2 factor experimental design (n = 5 / group), where Tet-on vector control (red) versus inducible mCCN4 vector (black) and in the presence (dotted lines) or absence (solid lines) of doxycycline were the two factors.</p><p>(L) Summary of a Cox multivariate proportional hazards analysis where x-axis of the dot-and-whisker plot corresponds to the mean hazard ratio and 95% confidence interval for the indicated variable.</p><p>(M) Representative flow cytometry data of the frequency of tumor-infiltrating MDSC (GR1+ CD11c−/lo : dotted box) from the live CD45+ CD11b+ compartment isolated from CCN4-induced rescue (ID mCCN4 + Dox) and CCN4 knockout (YM1.7-KO1) YUMM1.7 tumors.</p><p>(N) Frequency of MDSC for similarly sized tumors generated from CCN4-induced rescue (gray triangle), CCN4 knockout (blue square), and WT YUMM1.7 cells (red circles). Pairwise differences were assessed using a two-sided homoscedastic (pooled variance) Student's t-test.</p>
|
https://api.sourcedata.io/file.php?figure_id=45768
|
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] |
||
10.15252/embr.202154127
|
Cell Communication Network factor 4 promotes tumor-induced immunosuppression in melanoma
|
2022
|
Figure 4
|
<p><strong>Figure 4 - CCN4 expanded MDSC in the spleens of tumor bearing mice.</strong></p><p>(A-C) Tumor volume of YUMM1.7-WT and CCN4 KO (KO1) compared when size-matched and time-matched on day 28 after tumor challenge. MDSC in the spleens of tumor bearing mice expressed as percentage (B) or weight-basis (C) observed in size-matched versus time-matched experimental designs (n = 5 for size-matched, 4 for time-matched experiments). Statistical significance was assessed using a Student's t-test with results annotated with *: 0.01<p<0.05, **: 0.001<p<0.01, and ***: p<0.001. Results summarized as mean ± SEM.</p><p>(D) Representative flow cytometry data of CD11b+/−/GR-1+/− cells found in WT, KO1, and tumor free (TF) groups.</p><p>(E-H) Graphs summarizing G-MDSCs (E,G) and M-MDSCs (F,H) in the spleens of time-matched YUMM1.7-WT and CCN4 KO (KO1) tumor bearing mice (n = 4/group) expressed as percentage of CD45+ (E,F) and total number per gram spleen (G,H). Statistical significance was assessed using a Student's t-test with results annotated with *: 0.01<p<0.05, **: 0.001<p<0.01, and ***: p<0.001. Results summarized as mean ± SEM.</p><p>(I) Representative flow cytometry data of CD11b+/Ly6Chi/low/Ly6G+/− cells found in WT, KO1, and TF groups.</p><p>(J,K) Suppression of naïve CD8+ T cell proliferation by (J) freshly isolated G-MDSCs and (K) total splenocytes from WT, KO1, and TF groups (n = 3 biological replicates/group) on a per cell basis. ANOVA with post-hoc Tukey tests were used to assess statistical significance, where different letter (a, b, or c) denotes statistically different groups.</p><p>(L) Cell trace profiles of live CD8+ T cells contained within CD45+ cells extracted from WT (red) and KO1 (blue) tumors in a time-matched experiment (TME) and stimulated for three days in vitro with αCD3/αCD28-loaded beads (representative of n = 3 biological replicates/group), with unstimulated cells as a staining control (gray).</p><p>Data information: In panels A-C and E-H, dotted line represents average value found in tumor free mice.</p>
|
https://api.sourcedata.io/file.php?figure_id=45770
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}
] |
||
10.15252/embr.202154127
|
Cell Communication Network factor 4 promotes tumor-induced immunosuppression in melanoma
|
2022
|
Figure 5
|
<p><strong>Figure 5 - Knockout of CCN4 down-regulated CCL2 and CXCL1 expression and decreased glycolysis and glycolytic capacity in YUMM1.7 melanoma cells.</strong></p><p>(A) Cytokine, chemokine, and growth factor expression by YUMM1.7-WT and CCN4-KO cells in vitro assayed using R&D Systems' Mouse XL Cytokine Array. Orange dots represent results for specific cytokine probes while blue dots represent positive and negative controls. Dotted lines enclose a null distribution estimated from positive and negative controls.</p><p>(B-G) ELISA results for CCL2 and CXCL1 secretion after 36 h ex vivo culture (n = 3 biological replicates/group). CCL2 assayed in (B) tumor-conditioned medium (TCM), (D) CD45− medium, and (F) serum. CXCL1 assayed in (C) TCM, (E) CD45− medium, and (G) serum.</p><p>(H-I) Live-dead staining of CD45+ cells isolated from WT and CCN4-KO tumors. Statistical significance was assessed using a Student's t-test with results annotated with ***: p<0.001. Results of biological replicates summarized as mean ± SEM.</p><p>(J-K) Analysis of the extracellular acidification rate (ECAR) associated with (J) glycolysis and (K) glycolytic capacity assayed by Seahorse Analyzer in WT and CCN4-KO tumors (n ≥ 12 biological replicates/group) after 36 hours ex vivo. Statistical significance was assessed using a Student's t-test with results annotated with ***: p<0.001. Results of biological replicates summarized as mean ± SEM.</p><p>(L) Lactate production by isolated CD45− cells after 36 h ex vivo culture (n = 4 biological replicates/group). Statistical significance was assessed using a Student's t-test with results annotated with ***: p<0.001. Results of biological replicates summarized as mean ± SEM.</p>
|
https://api.sourcedata.io/file.php?figure_id=45772
|
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] |
||
10.15252/embr.202154127
|
Cell Communication Network factor 4 promotes tumor-induced immunosuppression in melanoma
|
2022
|
Figure 6
|
<p><strong>Figure 6 - CCN4 directly inhibited CD8</strong>+ <strong>T cell function.</strong></p><p>(A) ELISpot for IFNγ release by CD8+ T cells using parental YUMM1.7 and CCN4-KO YUMM1.7 (KO1) cells as targets and different amount of in vivo activated CD8+ T cells. Statistical significance was assessed using a Student's t-test with results annotated with ***: p<0.001. Results of three biological replicates summarized as mean ± SEM.</p><p>(B) ELISpot for IFNγ release by in vivo activated CD8+ T cells with CCN4-inducible cells as targets in the presence or absence of 0.5 mg/ml doxycycline. Statistical significance was assessed using a Student's t-test with results annotated with ***: p<0.001. Results of biological replicates summarized as mean ± SEM.</p><p>(C) CD8+ T cells isolated from the spleens of C57BL/6 mice that rejected YUMM1.7 tumors were assayed by in vitro ELISpot using variants of the YUMM1.7 cell line as targets (WT YUMM1.7 (Ym1.7) - yellow, CCN4-KO YUMM1.7 (Ym1.7-KO1)- light green, CCN4-KO YUMM1.7 with a blank inducible expression vector (Ym1.7-KO1-IDvector) - dark green and blue, CCN4-KO YUMM1.7 with a CCN4 inducible expression vector (Ym1.7-KO1-IDmCCN4) - purple and red). Representative images shown under indicated condition with scale bar indicating 1 mm. Variants containing the inducible expression vector were also cultured in the absence (dark green and purple) or presence of 0.5 μg/ml doxycycline (blue and red). CD8+ T cells expressing IFNγ and TNFα were quantified following 24 hour co-culture (bar graph). Results shown as mean ± S.D. for three biological replicates. Statistical significance was assessed using a Student's t-test with results annotated with ***: p<0.001 and n.s.: p>0.05.</p>
|
https://api.sourcedata.io/file.php?figure_id=45774
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||
10.15252/embr.202154127
|
Cell Communication Network factor 4 promotes tumor-induced immunosuppression in melanoma
|
2022
|
Figure 7
|
<p><strong>Figure 7 - CCN4 knockout further promoted the anti-tumor effect of immune checkpoint blockade therapy.</strong></p><p>(A) Average tumor volumes of mice bearing YUMM1.7-WT (squares and triangles) or CCN4-KO (KO1, circles and inverted triangles) tumors (n = 4 mice/group). Groups were treated with either αPD1 (triangles and inverted triangles) or isotype control (squares and circles) antibodies when the tumors reached 100 mm3 (dotted line). Statistical significance at each time point was assessed using a Student's t-test with results annotated with *: 0.01<p<0.05, **: 0.001<p<0.01, and ***: p<0.001. Results summarized as mean ± SEM.</p><p>(B) Expression of H-2Kb (top panel) and PD-L1 (bottom panel) were assayed by flow cytometry in WT (red curves) and CCN4-KO (KO1 - blue curves) YUMM1.7 cells with (dotted curves) and without (solid curves) preconditioning with IFNγ. Unstained cells were used as a negative control (shaded curve).</p><p>(C-F) CD45− fraction isolated from WT and CCN4-KO YUMM1.7 tumors in a time-matched experiment were assayed for H-2Kb and PD-L1 expression by flow cytometry. Contour curves enclose 90% (dotted curve) and 50% (solid curves) of CD45− events obtained from WT (red) and CCN4-KO (blue) YUMM1.7 tumors. CD8+ T cells expressing PD1 within the tumor (D) and spleen (E) were assayed by flow cytometry in mice bearing WT and CCN4-KO YUMM1.7 tumors (F). Results representative of three biological replicates and summarized as mean ± SD. Statistical significance was assessed using a Student's t-test.</p><p><strong>Expanded View Figure Legends</strong></p>
|
https://api.sourcedata.io/file.php?figure_id=45775
|
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"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
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"role": "intervention",
"text": "PD1",
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"uniprot_ids": [
"Q02242"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "22402",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "22402",
"original_type": "gene",
"role": "intervention",
"text": "CCN4",
"type": "geneprod",
"uniprot_ids": [
"O54775",
"Q3UFJ5"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q02242",
"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": "PD1",
"type": "geneprod",
"uniprot_ids": [
"Q02242"
]
}
] |
||
10.15252/emmm.202216581
|
LONP1 Targets HMGCS2 to Protect Mitochondrial Function and Attenuate Chronic Kidney Disease
|
2022
|
Figure 1
|
<p><strong>Figure 1. LONP1 is down-regulated in the kidneys of CKD patients and mice and proximal tubular-specific overexpression of <em>Lonp1</em> alleviates renal injury and mitochondrial dysfunction in UUO model.</strong></p><p><strong>A</strong> Immunohistochemical analysis of LONP1 expression in CKD children with mild (n=11), moderate (n=10), or severe fibrosis (n=9). N=4 in Normal group. Scale bar: 50μm.</p><p><strong>B</strong> Immunohistochemical semi-quantitative IOD analysis of LONP1.</p><p><strong>C</strong> Pearson correlation analysis of LONP1 and atrophy and fibrosis score (AFS) in renal biopsy specimens.</p><p><strong>D</strong> Western blot analysis for the expression of LONP1 in UUO models at different time points.</p><p>E Densitometric analysis for the expression of LONP1 (n=3, biological replicates).</p><p>F Deposition of total fibrosis in kidney tissues was determined by Masson's trichrome staining. Scale bar: 50μm.</p><p><strong>G Sirius red staining in</strong> WT and cKI mice after UUO<strong>.</strong> Scale bar: 50μm.</p><p><strong>H</strong> Fibrotic area statistics of <strong>Sirius red staining in</strong> WT and cKI mice after UUO (n=6 in WT+Sham group, n=8 in cKI+Sham or WT+UUO group, n=7 in cKI+UUO group, biological replicates).</p><p>I qRT-PCR analysis of FN1, Collagen I and Collagen III in WT and cKI mice after UUO (n=7 in WT+Sham group, n=8 in the other three groups, biological replicates).</p><p>J, K Western blot and densitometric analysis for the expression of FN1, Collagen I, Collagen III and TGF-β1 (monomer) in WT and cKI mice after UUO (n=3 or 4, biological replicates).</p><p>L qRT-PCR analysis of mtDNA expression in WT and cKI mice after UUO (n=6 or 7, biological replicates).</p><p>M Succinate dehydrogenase (SDH) staining in WT and cKI mice after UUO. Scale bar: 50μm.</p><p>N Transmission electron microscopy images of the mitochondria in tubular cells in WT and cKI mice after UUO. Scale bar: 500nm.</p><p>Data information: In (B, E), data are presented as mean ± SEM. Student's t-test. In (H-L), data are presented as mean ± SEM. One-way ANOVA.</p>
|
https://api.sourcedata.io/file.php?figure_id=51727
|
[
{
"ext_dbs": "Uniprot",
"ext_ids": "P36776",
"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": "LONP1",
"type": "geneprod",
"uniprot_ids": [
"P36776"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q8CGK3",
"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": "LONP1",
"type": "geneprod",
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"Q8CGK3"
]
},
{
"ext_dbs": "Uniprot",
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"ncbi_gene_id": null,
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"text": "Collagen I",
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"P11087"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P08121",
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"ext_tax_names": "Mus musculus",
"mapping_source": "direct",
"mapping_status": "mapped",
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"role": "assayed",
"text": "Collagen III",
"type": "geneprod",
"uniprot_ids": [
"P08121"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P11276",
"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": "FN1",
"type": "geneprod",
"uniprot_ids": [
"P11276"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P04202",
"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": "TGF-β1",
"type": "geneprod",
"uniprot_ids": [
"P04202"
]
}
] |
||
10.15252/emmm.202216581
|
LONP1 Targets HMGCS2 to Protect Mitochondrial Function and Attenuate Chronic Kidney Disease
|
2022
|
Figure 2
|
<p><strong>Figure 2. Proximal tubular-specific deletion of <em>Lonp1</em> aggravates renal injury and mitochondrial dysfunction in UUO model.</strong></p><p><strong>A</strong> Deposition of total fibrosis in kidney tissues was determined by Masson's trichrome staining. Scale bar: 50μm.</p><p><strong>B Sirius red staining in WT and cKO mice after UUO.</strong> Scale bar: 50μm.</p><p><strong>C</strong> Fibrotic area statistics of Sirius red staining in WT and cKO mice after UUO. N=5 in Sham groups. N=7 in UUO groups, biological replicates.</p><p>D, E Western blot and densitometric analysis for the expression of FN1, Collagen I, Collagen III and α-SMA in WT and cKO mice after UUO (n=3, biological replicates).</p><p>F qRT-PCR analysis of FN1, Collagen I, Collagen III and α-SMA in WT and cKO mice after UUO (n=7 or 5 in Sham groups, n=9 in UUO groups, biological replicates).</p><p><strong>G</strong> qRT-PCR analysis of mtDNA expression in WT and cKO mice after UUO (n=7 or 5 in Sham groups, n=7 in UUO groups, biological replicates).</p><p>H Mitochondrial respiratory chain complex I enzymatic activity in WT and cKO mice after UUO (n=4, biological replicates).</p><p>I Transmission electron microscopy images of the mitochondria in tubular cells in WT and cKO mice after UUO. Scale bar: 500nm.</p><p>Data information: Data are presented as mean ± SEM. One-way ANOVA.</p>
|
https://api.sourcedata.io/file.php?figure_id=51728
|
[
{
"ext_dbs": "Uniprot",
"ext_ids": "P62737",
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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": "α-SMA",
"type": "geneprod",
"uniprot_ids": [
"P62737"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P11087",
"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": "Collagen I",
"type": "geneprod",
"uniprot_ids": [
"P11087"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P08121",
"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": "Collagen III",
"type": "geneprod",
"uniprot_ids": [
"P08121"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P11276",
"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": "FN1",
"type": "geneprod",
"uniprot_ids": [
"P11276"
]
}
] |
||
10.15252/emmm.202216581
|
LONP1 Targets HMGCS2 to Protect Mitochondrial Function and Attenuate Chronic Kidney Disease
|
2022
|
Figure 3
|
<p><strong>Figure 3. Proximal tubular-specific overexpression or deletion of <em>Lonp1</em> mitigated or aggravated renal injury and mitochondrial dysfunction in 5/6Nx model.</strong></p><p><strong>A Analysis of blood urea nitrogen (BUN) after 5/6Nx model in WT and cKI mice (n=6 in cKI+Sham group, n=5 in the other three groups,</strong> biological replicates<strong>).</strong></p><p>B <strong>Systolic blood pressure was measured by the computerized tail-cuff system (n=6 in cKI+Sham group, n=5 in the other three groups,</strong> biological replicates<strong>).</strong></p><p><strong>C</strong> Masson's trichrome staining of WT and cKI mice after 5/6Nx. Scale bar: 100μm.</p><p>D qRT-PCR analysis of FN1, Collagen I and Collagen III in WT and cKI mice after 5/6Nx <strong>(n=6 in cKI+Sham group, n=5 in the other three groups,</strong> biological replicates<strong>)</strong></p><p>E <strong>Analysis of blood urea nitrogen (BUN) after 5/6Nx model in WT and cKO mice (n=5 in WT+Sham group, n=6 in the other three groups,</strong> biological replicates<strong>).</strong></p><p><strong>F Systolic blood pressure in WT and cKO mice (n=5 in WT+Sham or cKO+5/6Nx group, n=8 in cKO+Sham or WT+5/6Nx group,</strong> biological replicates<strong>).</strong></p><p>G Masson's trichrome staining of WT and cKO mice after 5/6Nx. Scale bar: 100μm.</p><p>H qRT-PCR analysis of FN1, Collagen I, Collagen III and α-SMA in WT and cKO mice after 5/6Nx (n=5 in WT+Sham group, n=7 in cKO+Sham group, n=6 in 5/6Nx groups, biological replicates).</p><p>I, J Western blot and densitometric analysis for the expression of Collagen I and α-SMA in WT and cKO mice after 5/6Nx (n=4, biological replicates).</p><p>K Mitochondrial respiratory chain complex I enzymatic activity in WT and cKO mice after 5/6Nx (n=4-8, biological replicates).</p><p>L Transmission electron microscopy images of the mitochondria in tubular cells of WT and cKO mice after 5/6Nx. Scale bar: 500nm.</p><p>Data information: Data are presented as mean ± SEM. One-way ANOVA.</p>
|
https://api.sourcedata.io/file.php?figure_id=51730
|
[
{
"ext_dbs": "NCBI gene",
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"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "12842",
"original_type": "gene",
"role": "assayed",
"text": "Collagen I",
"type": "geneprod",
"uniprot_ids": [
"P11087"
]
},
{
"ext_dbs": "NCBI gene",
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"mapping_status": "mapped",
"ncbi_gene_id": "12825",
"original_type": "gene",
"role": "assayed",
"text": "Collagen III",
"type": "geneprod",
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"P08121",
"Q3TVI5"
]
},
{
"ext_dbs": "NCBI gene",
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"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "14268",
"original_type": "gene",
"role": "assayed",
"text": "FN1",
"type": "geneprod",
"uniprot_ids": [
"P11276",
"A0A087WR50",
"A0A087WS56",
"A0A087WSN6",
"B7ZNJ1",
"B9EHT6",
"Q3TBB4",
"Q3UGY5",
"Q3UH17",
"Q3UHL6",
"Q3UHR1",
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]
},
{
"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": "11475",
"original_type": "gene",
"role": "assayed",
"text": "α-SMA",
"type": "geneprod",
"uniprot_ids": [
"P62737"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "12842",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "12842",
"original_type": "gene",
"role": "assayed",
"text": "Collagen I",
"type": "geneprod",
"uniprot_ids": [
"P11087"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "12825",
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"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
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"original_type": "gene",
"role": "assayed",
"text": "Collagen III",
"type": "geneprod",
"uniprot_ids": [
"P08121",
"Q3TVI5"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "14268",
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"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "14268",
"original_type": "gene",
"role": "assayed",
"text": "FN1",
"type": "geneprod",
"uniprot_ids": [
"P11276",
"A0A087WR50",
"A0A087WS56",
"A0A087WSN6",
"B7ZNJ1",
"B9EHT6",
"Q3TBB4",
"Q3UGY5",
"Q3UH17",
"Q3UHL6",
"Q3UHR1",
"Q3UZF9"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P62737",
"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": "α-SMA",
"type": "geneprod",
"uniprot_ids": [
"P62737"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P11087",
"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": "Collagen I",
"type": "geneprod",
"uniprot_ids": [
"P11087"
]
}
] |
||
10.15252/emmm.202216581
|
LONP1 Targets HMGCS2 to Protect Mitochondrial Function and Attenuate Chronic Kidney Disease
|
2022
|
Figure 4
|
<p><strong>Figure 4. LONP1 attenuated TGF-β1-induced mitochondrial dysfunction and fibrotic response in HK2 cells.</strong></p><p><strong>A</strong> Quantification of mitochondrial ROS production (n=4, biological replicates).</p><p>B, C Measurement of oxygen consumption rate (OCR) using an XF96 Extracellular Flux Analyzer. OSR, spare respiratory capacity (n=8-10 in each group, biological replicates).</p><p>D qRT-PCR analysis of FN1, Collagen I, Collagen III, Collagen IV, α-SMA and Vimentin (n=3, biological replicates).</p><p>E, F Western blot and densitometric analysis for the expression of Collagen I, α-SMA, and Vimentin (n=3, two independent experiments were carried out).</p><p>G Quantification of mitochondrial ROS production (n=4, biological replicates).</p><p>H, I Measurement of OCR and OSR using an XF96 Extracellular Flux Analyzer (n=8 or 10 in each group, biological replicates).</p><p>J qRT-PCR analysis of FN1, Collagen I, Collagen III, Collagen IV, α-SMA and Vimentin (n=3, biological replicates).</p><p>K, L Western blot and densitometric analysis for the expression of Collagen I, α-SMA, and Vimentin (n=3, two independent experiments were carried out).</p><p>Data information: In figure A-F, HK2 cells were transfected with vector or <em>Lonp1</em> plasmid, and then treated with TGF-β1 (10ng/mL) for 24h. In figure G-L, HK2 cells were transfected with vector or <em>Lonp1</em> shRNA, and then treated with TGF-β1 (10ng/mL) for 24h. Data are presented as mean ± SEM. One-way ANOVA.</p>
|
https://api.sourcedata.io/file.php?figure_id=51732
|
[
{
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"ext_tax_names": "Homo sapiens",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "59",
"original_type": "gene",
"role": "assayed",
"text": "α-SMA",
"type": "geneprod",
"uniprot_ids": [
"P62736",
"A0AAQ5BGG7",
"A0AAQ5BGI6",
"D2JYH4"
]
},
{
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"ext_ids": "1277",
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"ext_tax_names": "Homo sapiens",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "1277",
"original_type": "gene",
"role": "assayed",
"text": "Collagen I",
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"P02452"
]
},
{
"ext_dbs": "NCBI gene",
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"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
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"role": "assayed",
"text": "Collagen III",
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"P02461",
"A0AAG2UVC5"
]
},
{
"ext_dbs": "NCBI gene",
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"ext_tax_names": "Homo sapiens",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
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"original_type": "gene",
"role": "assayed",
"text": "Collagen IV",
"type": "geneprod",
"uniprot_ids": [
"P02462",
"A5PKV2"
]
},
{
"ext_dbs": "NCBI gene",
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},
{
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"text": "Vimentin",
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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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"role": "assayed",
"text": "α-SMA",
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"uniprot_ids": [
"P62736"
]
},
{
"ext_dbs": "Uniprot",
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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": "Collagen I",
"type": "geneprod",
"uniprot_ids": [
"P02452"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P08670",
"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": "Vimentin",
"type": "geneprod",
"uniprot_ids": [
"P08670"
]
}
] |
||
10.15252/emmm.202216581
|
LONP1 Targets HMGCS2 to Protect Mitochondrial Function and Attenuate Chronic Kidney Disease
|
2022
|
Figure 5
|
<p><strong>Figure 5. HMGCS2 may be the degradation substrate of LONP1.</strong></p><p>A <strong>The proximal renal tubules of <em>Lonp1</em> cKO mice were extracted and detected by mass spectrometry (n=3,</strong> biological replicates<strong>).</strong></p><p>B <strong>Subcellular localization of up-regulated proteins.</strong></p><p>C Western blot validation of the up-regulated proteins in mitochondria <strong>(n=2,</strong> biological replicates<strong>)</strong>.</p><p>D CoIP analysis of interaction between LONP1 and HMGCS2.</p><p>E GST pull down analysis of interaction between LONP1 and HMGCS2.</p><p>F Enzymatic hydrolysis of LONP1 to HMGCS2.</p><p>G Immunofluorescence co-localization analysis of LONP1, HMGCS2 and mitochondria in mPTC (up, scale bar: 20μm) and human kidney tissue (down, scale bar: 200μm).</p>
|
https://api.sourcedata.io/file.php?figure_id=51734
|
[
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"text": "HMGCS2",
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]
},
{
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"role": "assayed",
"text": "LONP1",
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]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P54868",
"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": "HMGCS2",
"type": "geneprod",
"uniprot_ids": [
"P54868"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P36776",
"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": "LONP1",
"type": "geneprod",
"uniprot_ids": [
"P36776"
]
}
] |
||
10.15252/emmm.202216581
|
LONP1 Targets HMGCS2 to Protect Mitochondrial Function and Attenuate Chronic Kidney Disease
|
2022
|
Figure 6
|
<p><strong>Figure 6. Effect of HMGCS2 on mitochondrial function and renal fibrosis.</strong></p><p>A Immunohistochemical analysis of HMGCS2 expression in CKD children. Scale bar: 50μm.</p><p>B Immunohistochemical semi-quantitative IOD analysis of HMGCS2 (n=8 in Control group, n=15 in CKD group).</p><p>C Pearson correlation analysis of HMGCS2 and atrophy and fibrosis score (AFS) in renal biopsy specimens.</p><p>D Western blot analysis for the expression of HMGCS2 in UUO model.</p><p>E Densitometric analysis for the expression of HMGCS2 in UUO model (n=3, biological replicates).</p><p>F, G Western blot and densitometric analysis of HMGCS2 in WT and cKI mice of UUO model (n=3 or 4, biological replicates).</p><p>H, I qRT-PCR and western blotting analysis of Hmgcs2 expression in WT and Hmgcs2<sup>+/-</sup> mice (n=3, biological replicates).</p><p>J Fibrotic area statistics of <strong>Sirius red staining</strong> in WT and Hmgcs2<sup>+/-</sup> mice of UUO model <strong>(n=12 in WT groups, n=8 in</strong> Hmgcs2<sup>+/-</sup> groups, biological replicates).</p><p>K Deposition of total fibrosis in kidney tissues in WT and Hmgcs2<sup>+/-</sup> mice after UUO was determined by Masson's trichrome staining. Scale bar: 50μm.</p><p><strong>L Sirius red staining of</strong> WT and Hmgcs2<sup>+/-</sup> mice of UUO model<strong>.</strong> Scale bar: 50μm.</p><p>M, N Western blot and densitometric analysis for the expression of FN1, α-SMA and Collagen III in WT and Hmgcs2<sup>+/-</sup> mice after UUO (n=6 in control groups, n=8 in UUO groups, biological replicates).</p><p>O qRT-PCR analysis of FN1, α-SMA and Collagen III <strong>in WT and Hmgcs2+/- mice after UUO (n= 10 or 12 in WT groups, n=8 in</strong> Hmgcs2<sup>+/-</sup> groups, biological replicates).</p><p>P Succinate dehydrogenase (SDH) staining <strong>in WT and Hmgcs2+/- mice after UUO</strong>. Scale bar: 100μm.</p><p>Data information: In (B, E, H, I), data are presented as mean ± SEM. Student's t-test. In (G, J, N, O), data are presented as mean ± SEM. One-way ANOVA.</p>
|
https://api.sourcedata.io/file.php?figure_id=51736
|
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"ext_tax_names": "Homo sapiens",
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"role": "assayed",
"text": "HMGCS2",
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"uniprot_ids": [
"P54868"
]
},
{
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"P54868"
]
},
{
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"text": "HMGCS2",
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"P54869"
]
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{
"ext_dbs": "NCBI gene",
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"ext_tax_names": "Mus musculus",
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"mapping_status": "mapped",
"ncbi_gene_id": "15360",
"original_type": "gene",
"role": "intervention",
"text": "Hmgcs2",
"type": "geneprod",
"uniprot_ids": [
"P54869"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P54869",
"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": "Hmgcs2",
"type": "geneprod",
"uniprot_ids": [
"P54869"
]
}
] |
||
10.15252/emmm.202216581
|
LONP1 Targets HMGCS2 to Protect Mitochondrial Function and Attenuate Chronic Kidney Disease
|
2022
|
Figure 7
|
<p><strong>Figure 7. The anti-fibrotic response effect of a novel LONP1 activator in mPTC cells.</strong></p><p>A 10 high docking score molecules showed LONP1 activating effect in cell free LONP1 protease activity assay system, of which 84-B10 showed stronger activity. Bortezomib (Bor), a reported LONP1 inhibitor, is involved as a contrast.</p><p>B 84-B10 dose dependently induced the peptidase activity of LONP1 as estimated by detecting the fluorogenic di-peptide substrate <em><strong>(Z-AA)<sub>2</sub>-Rh110</strong></em> (n=6 or 3, biological replicates).</p><p>C Chemical structure of 84-B10.</p><p>D Proposed binding model of 84-B10 binding to the human <strong>LONP1 catalytic domain.</strong> Three and two-dimensional illustrations of the interaction between 84-B10 and human <strong>LONP1 catalytic domain.</strong></p><p>E Physical interaction between 84-B10 and LONP1 performed by Surface Plasmon Resonance (SPR).</p><p>F Protein levels of HMGCS2 and LONP1 were estimated in mPTCs treated with different concentration of 84-B10 or vehicle (0.1% DMSO) for 24 h.</p><p>G, H Representative immunoblot and densitometric analysis of HMGCS2, FN1, Collagen III, α-SMA and Vimentin in mPTCs treated as indicated. Three independent experiments were carried out and quantification of the abundance of these proteins is shown in panel (n=3 in each group).</p><p>I qRT-PCR analysis of <em>Lonp1</em>, Collagen I, Collagen III, α-SMA, Vimentin and Periostin transcript levels in mPTCs treated as indicated (n=4 in each group, biological replicates).</p><p>J-N Representative Western blot and densitometric analysis of LONP1, FN1, α-SMA and Vimentin of each group was shown. Three independent experiments were carried out and quantification of the abundance of these proteins is shown in panel (n=3 in each group). mPTCs were transfected with siNC or siLONP1, and then pre-treated with 84-B10 (10 μM) 2h before TGF-β1 (10ng/mL) treatment for another 24h.</p><p>Data information: Data are presented as mean ± SEM. Student's t-test.</p>
|
https://api.sourcedata.io/file.php?figure_id=51737
|
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"ncbi_gene_id": null,
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"role": "assayed",
"text": "α-SMA",
"type": "geneprod",
"uniprot_ids": [
"P62737"
]
},
{
"ext_dbs": "Uniprot",
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"text": "Collagen III",
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"P08121"
]
},
{
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"ext_ids": "P11276",
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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": "FN1",
"type": "geneprod",
"uniprot_ids": [
"P11276"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P54869",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
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"mapping_status": "mapped",
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"role": "assayed",
"text": "HMGCS2",
"type": "geneprod",
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"P54869"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P20152",
"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": "Vimentin",
"type": "geneprod",
"uniprot_ids": [
"P20152"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "74142",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "74142",
"original_type": "gene",
"role": "intervention",
"text": "LONP1",
"type": "geneprod",
"uniprot_ids": [
"Q8CGK3"
]
},
{
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"ext_ids": "P62737",
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"ext_tax_names": "Mus musculus",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
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"text": "α-SMA",
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]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P11276",
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"ext_tax_names": "Mus musculus",
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"text": "FN1",
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"uniprot_ids": [
"P11276"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q8CGK3",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
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"mapping_status": "mapped",
"ncbi_gene_id": null,
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"text": "LONP1",
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"uniprot_ids": [
"Q8CGK3"
]
},
{
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"ext_ids": "P01137",
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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": "TGF-β1",
"type": "geneprod",
"uniprot_ids": [
"P01137"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "P20152",
"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": "Vimentin",
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"uniprot_ids": [
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]
}
] |
||
23619093
|
10.1038/embor.2013.51
|
Species‐specific impact of the autophagy machinery on Chikungunya virus infection
|
2013
|
Figure 1
|
Autophagy components promote CHIKV infection and control virus‐induced cell death in HeLa cells. Cells were mock infected or infected and immunoblotted for actin, p62 (<b>A</b>) or LC3 (<b>B</b>). Cells were infected for 15 h and labeled using antibodies to p62 and capsid (<b>C</b>). Cells were transfected with GFP‐LC3‐B, infected for 15 h and labeled with anti‐capsid antibody (<b>D</b>). Mice were infected for 3 days, then whole‐cell lysates of muscle were immunoblotted for LC3 or actin (<b>E</b>) and muscle sections were labeled with p62 and capsid antibodies (<b>F</b>). Cells were treated with DMSO (CTRL) or rapamycin and then infected. Viral replication (<b>G</b>) and production (<b>H</b>) were assessed and whole‐cell lysates were immunoblotted for capsid or actin (<b>I</b>). Cells were treated with CTRL, Beclin1 (left) or Atg7 (right) siRNA, then infected for 24 h. Cell mortality (that is, fold change relative to mock‐infected cells) (<b>J</b>), viral replication (<b>K</b>) and production (<b>L</b>) were assessed and whole‐cell lysates of siRNA‐treated cells were immunoblotted for Beclin1, Atg7, capsid and actin (<b>M</b>). Images and graphs shown are representative of at least three independent experiments and data presented in graphs correspond to mean+s.d. (<i>n</i>=3). Scale bar, 10 μm. CHIKV, Chikungunya virus; CTRL, control; GFP, green fluorescent protein; DMSO, dimethylsulphoxide; siRNA, short interfering RNA.
|
https://api.sourcedata.io/file.php?figure_id=1691
|
[
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"ext_tax_ids": "9606///9606///9606",
"ext_tax_names": "Homo sapiens///Homo sapiens///Homo sapiens",
"mapping_source": "unknown",
"mapping_status": "unmapped",
"ncbi_gene_id": null,
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"role": "assayed",
"text": "LC3",
"type": "geneprod",
"uniprot_ids": []
},
{
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"Q13501"
]
},
{
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"text": "p62",
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]
},
{
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"ext_ids": "Q9GZQ8",
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"ext_tax_names": "Homo sapiens",
"mapping_source": "direct",
"mapping_status": "mapped",
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"role": "assayed",
"text": "LC3‐B",
"type": "geneprod",
"uniprot_ids": [
"Q9GZQ8"
]
},
{
"ext_dbs": "Uniprot///Uniprot",
"ext_ids": "Q9CQV6///Q91VR7",
"ext_tax_ids": "10090///10090",
"ext_tax_names": "Mus musculus///Mus musculus",
"mapping_source": "unknown",
"mapping_status": "unmapped",
"ncbi_gene_id": null,
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"text": "LC3",
"type": "geneprod",
"uniprot_ids": []
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q64337",
"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": "p62",
"type": "geneprod",
"uniprot_ids": [
"Q64337"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "10533",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "10533",
"original_type": "gene",
"role": "intervention",
"text": "Atg7",
"type": "geneprod",
"uniprot_ids": [
"O95352",
"B3KQM6"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "8678",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "8678",
"original_type": "gene",
"role": "intervention",
"text": "Beclin1",
"type": "geneprod",
"uniprot_ids": [
"Q14457",
"A0A024R1X5",
"B4DQ36",
"E7EV84",
"W0FFG4"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "O95352",
"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": "Atg7",
"type": "geneprod",
"uniprot_ids": [
"O95352"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q14457",
"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": "Beclin1",
"type": "geneprod",
"uniprot_ids": [
"Q14457"
]
}
] |
|
23619093
|
10.1038/embor.2013.51
|
Species‐specific impact of the autophagy machinery on Chikungunya virus infection
|
2013
|
Figure 2
|
Autophagy receptors p62 and NDP52 localize to distinct pools of capsid and have distinct effects on CHIKV infection in Hela cells. Cells were infected for 15 h and labeled using antibodies to NDP52 and capsid (<b>A</b>), to p62, NDP52 and capsid (<b>B</b>), to NDP52, LC3‐C or capsid (<b>C</b>), to p62, ubiquitin (FK2) and capsid (<b>D</b>), or to NDP52, ubiquitin (FK2), and capsid (<b>E</b>). Cells were treated with CTRL or p62 siRNA, then infected for 24 h. Cell mortality (that is, fold change relative to mock‐infected cells) (<b>F</b>), viral replication (left) and qRT‐PCR (right) (<b>G</b>), and viral production (<b>H</b>) were assessed and whole‐cell lysates were immunoblotted for p62, capsid or actin (<b>I</b>). Cells were treated with CTRL or NDP52 siRNA, then infected for 24 h. Cell mortality (that is, fold change relative to mock‐infected cells) (<b>J</b>), viral replication (left) and qRT‐PCR (right) (<b>K</b>) and production were assessed (<b>L</b>). Whole‐cell lysates of siRNA‐treated cells were immunoblotted for NDP52, capsid or actin (<b>M</b>). Images and graphs shown are representative of at least three independent experiments and data presented in graphs correspond to mean+s.d. (<i>n</i>=3). Scale bar, 10 μm. C, capsid; CHIKV, Chikungunya virus; CTRL, control; NDP52, nuclear dot protein 52 kDa; qRT‐PCR, quantitative reverse transcription polymerase chain reaction; siRNA, short interfering RNA.
|
https://api.sourcedata.io/file.php?figure_id=1692
|
[
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"ext_ids": "Q13137",
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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": "NDP52",
"type": "geneprod",
"uniprot_ids": [
"Q13137"
]
},
{
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"ext_ids": "Q13137",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
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"text": "NDP52",
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"uniprot_ids": [
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]
},
{
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"original_type": "protein",
"role": "assayed",
"text": "NDP52",
"type": "geneprod",
"uniprot_ids": [
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]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q13137",
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"mapping_source": "direct",
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"text": "NDP52",
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]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q13137",
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"mapping_status": "mapped",
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"text": "NDP52",
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]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q9BXW4",
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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": "LC3‐C",
"type": "geneprod",
"uniprot_ids": [
"Q9BXW4"
]
},
{
"ext_dbs": "Uniprot///Uniprot///Uniprot///Uniprot",
"ext_ids": "P62979///P62987///P0CG48///P0CG47",
"ext_tax_ids": "9606///9606///9606///9606",
"ext_tax_names": "Homo sapiens///Homo sapiens///Homo sapiens///Homo sapiens",
"mapping_source": "unknown",
"mapping_status": "unmapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "ubiquitin",
"type": "geneprod",
"uniprot_ids": []
},
{
"ext_dbs": "Uniprot///Uniprot///Uniprot///Uniprot",
"ext_ids": "P62979///P62987///P0CG48///P0CG47",
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"ext_tax_names": "Homo sapiens///Homo sapiens///Homo sapiens///Homo sapiens",
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"mapping_status": "unmapped",
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"role": "assayed",
"text": "ubiquitin",
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"uniprot_ids": []
},
{
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"ncbi_gene_id": null,
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"role": "assayed",
"text": "p62",
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]
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]
},
{
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"text": "NDP52",
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"uniprot_ids": [
"Q13137"
]
}
] |
|
23619093
|
10.1038/embor.2013.51
|
Species‐specific impact of the autophagy machinery on Chikungunya virus infection
|
2013
|
Figure 3
|
p62 associates with ubiquitinated capsid and controls cell death induced by cytotoxic capsid in HeLa cells. Cells were infected for 24 h and immunoprecipitation experiments were performed using antibodies to FK2, capsid or nonspecific IgG controls. Immunoprecipitated proteins were revealed using antibodies to FK2 or capsid (<b>A</b>,<b>B</b>). Cells were transfected with Ub‐HA and capsid‐3XFLAG. Immunoprecipitation experiments were performed 24 h p.i. using antibodies to FLAG or nonspecific IgG controls. Immunoprecipitated proteins were revealed with anti‐HA antibody (<b>C</b>). Immunoprecipitation experiments were performed using antibodies to p62 or nonspecific IgG controls. Immunoprecipitated proteins were revealed using antibodies to p62, FK2 or capsid (<b>D</b>,<b>E</b>). Cells were infected for 3 h and then transfected with empty plasmid (CTRL) or p62<sub>WT</sub>‐3XFLAG or p62delta<sub>UBA</sub>‐3XFLAG. Immunoprecipitation experiments were performed 24 h p.i. with anti‐FLAG antibody. Immunoprecipitated proteins were revealed using antibodies to FLAG or capsid (<b>F</b>). Cells were treated with CTRL or p62 siRNA, then infected for 24 h. Immunoprecipitation experiments were performed using antibodies to FK2 or nonspecific IgG controls. Immunoprecipitated proteins were revealed using anti‐capsid antibody (<b>G</b>). Cells were infected for 15 h and labeled with antibodies to p62, LAMP‐1 or capsid (<b>H</b>). Cells were infected for 9, 15 or 24 h and treated with DMSO (CTRL) or bafilomycin 3 h before the end of experiment. Whole‐cell lysates were immunoblotted for capsid or actin (<b>I</b>). HeLa cells were transfected with empty plasmid (CTRL), control protein (cherry‐3XFLAG) or capsid‐3XFLAG at fixed (750 ng) or at the indicated concentrations. Cell mortality (that is, % of dead cells) was measured 24 h post transfection (<b>J</b>,<b>K</b>). Cells were treated with CTRL or p62 siRNA and transfected with NT or capsid‐3XFLAG. Cell mortality (that is, fold change relative to mock‐infected cells) was measured 48 h post transfection (<b>L</b>). Cells were infected with CHIKV for 3 h and transfected with empty plasmid (CTRL), p62<sub>WT</sub>‐3XFLAG, p62<sub>deltaUBA</sub>‐3XFLAG or p62<sub>deltaLIR</sub>‐3XFLAG. Cell mortality (that is, fold change relative to mock‐infected cells) was measured 24 h post transfection (<b>M</b>). Images and graphs shown are representative of at least three independent experiments and data presented in graphs correspond to mean+s.d. (<i>n</i>=3). Scale bar, 10 μm. CHIKV, Chikungunya virus; CTRL, control; IP, immunoprecipitation; NT, empty plasmid; p.i., post infection; qRT‐PCR, quantitative reverse transcription polymerase chain reaction; siRNA, short interfering RNA; Ub, ubiquitin; WB, western blot.
|
https://api.sourcedata.io/file.php?figure_id=1693
|
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] |
|
23619093
|
10.1038/embor.2013.51
|
Species‐specific impact of the autophagy machinery on Chikungunya virus infection
|
2013
|
Figure 4
|
Human NDP52 binds nsP2, localizes near CHIKV RCs, and restricts cell shutoff promoting cell survival in HeLa cells. Yeast cells expressing Gal4 DNA BD fused alone (empty vector) or to nsP2 were cotransformed with a plasmid encoding the Gal4 AD fused to NDP52 or the indicated NDP52 deletion mutants (top). Yeast cells expressing BD fused to nsP2 or the indicated nsP2 deletion mutants were cotransformed with a plasmid encoding the Gal4 AD fused alone (empty vector) or to NDP52 (bottom) (<b>A</b>). Cells were infected for 15 h, then labeled using antibodies to NDP52 and nsP2 (<b>B</b>), or to TGN46, nsP2 and nsP3 (<b>C</b>). Cells were treated with control (CTRL) (left) or NDP52 (right) siRNA, infected for 15 h, then labeled using antibodies to NDP52, nsP2 and puromycin. Quantitative analysis was performed by counting the percentage of infected cells with TGN‐associated RCs (<i>n</i>=30 cells per experiment) (<b>D</b>). Cells were transfected with empty plasmid (CTRL) or nsP2<sub>wt</sub>‐3XFLAG or nsP2<sub>R606A</sub>‐3XFLAG. Cell mortality (that is, % of dead cells) was measured 24 h post transfection (<b>E</b>). Cells were treated with control (CTRL) or NDP52 siRNA, then mock infected (M) or infected (<b>C</b>) for 24 h. Cytoplasmic and nuclear fractions were isolated and immunoblotted for nsP2 and NDP52. The amounts of the cytoplasmic and nuclear fractions of nsP2 were quantified by densitometry and expressed as the ratio of nuclear to cytoplasmic fraction of nsP2 (<b>F</b>). Cells were treated with control (CTRL) or NDP52 siRNA, infected for 15 and 24 h and treated with puromycin. Whole‐cell lysates of siRNA‐treated cells were immunoblotted for NDP52, capsid or actin. Puromycin incorporation into newly synthesized protein was revealed using antibodies to puromycin (<b>G</b>). Cells were treated with CTRL or NDP52 siRNA, then transfected with NT or nsP2‐3XFLAG. Cell mortality (that is, fold change relative to mock‐infected cells) was measured 48 h post transfection (<b>H</b>). Images and graphs shown are representative of at least three independent experiments and data presented in graphs correspond to mean+s.d. (<i>n</i>=3). Scale bar, 10 μm. AD, transactivation domain; BD, binding domain; CHIKV, Chikungunya virus; CTRL, control; NDP52, nuclear dot protein 52 kDa; nsP, nonstructural protein; NT, empty plasmid; RC, replicative complexes; siRNA, short interfering RNA; TGN, <i>trans</i>‐Golgi network.
|
https://api.sourcedata.io/file.php?figure_id=1694
|
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"Q13137"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q13137",
"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": "NDP52",
"type": "geneprod",
"uniprot_ids": [
"Q13137"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "10241",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "10241",
"original_type": "gene",
"role": "intervention",
"text": "NDP52",
"type": "geneprod",
"uniprot_ids": [
"Q13137"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "956309",
"ext_tax_ids": "37124",
"ext_tax_names": "Chikungunya virus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "956309",
"original_type": "gene",
"role": "intervention",
"text": "nsP2",
"type": "geneprod",
"uniprot_ids": [
"Q8JUX6"
]
}
] |
|
23619093
|
10.1038/embor.2013.51
|
Species‐specific impact of the autophagy machinery on Chikungunya virus infection
|
2013
|
Figure 5
|
NDP52 promotes CHIKV infection in a species‐specific manner. MEF cells were treated with CTRL or NDP52 siRNA, then infected for 24 h. Cell mortality (that is, fold change relative to mock‐infected cells) (<b>A</b>) and viral production (<b>B</b>) were measured. Yeast cells expressing Gal4 DNA BD fused alone (empty vector) or to nsP2 were cotransformed with a plasmid encoding the Gal4 AD fused to hNDP52 or mouse NDP52 (<b>C</b>). MEF cells were infected for 3 h and transfected with empty plasmid (CTRL) or hNDP52‐3XFLAG. Immunoprecipitation experiments were performed 24 h p.i. using antibodies to FLAG or nonspecific IgG controls. Immunoprecipitated proteins were revealed with anti‐nsP2 antibody (<b>D</b>). MEF cells were infected for 3 h and transfected with empty plasmid (CTRL), hNDP52, hLC3‐C or hNDP52 and hLC3‐C. Viral production (<b>E</b>) and cell mortality (<b>F</b>) were assessed 24 h post transfection. Isogenic wt or Atg5−/− MEFs were infected for 24 h and cell mortality (that is, fold change relative to mock‐infected cells) (<b>G</b>) and viral production (<b>H</b>) were assessed. MEF cells were infected and immunoprecipitation experiments were performed 24 h p.i. using antibodies to p62 or nonspecific IgG controls. Immunoprecipitated proteins were revealed with anti‐capsid antibody (<b>I</b>). MEF cells were treated with CTRL or p62 siRNA, then infected for 24 h. Cell mortality (that is, fold change relative to mock‐infected cells) (<b>J</b>) and viral production were assessed. Whole‐cell lysates of siRNA‐treated cells were immunoblotted for p62 or actin (<b>K</b>). Images and graphs shown are representative of at least three independent experiments and data presented in graphs correspond to mean+s.d. (<i>n</i>=3). Scale bar, 10 μm. AD, transactivation domain; BD, binding domain; CHIKV, Chikungunya virus; CTRL, control; hLC3‐C, human LC3‐C; hNDP52, human NDP52; IP, immunoprecipitation; MEF, mouse embryonic fibroblast; mNDP52, mouse NDP52; NDP52, nuclear dot protein 52 kDa; nsP, nonstructural protein; p.i., post infection; siRNA, short interfering RNA; WB, western blot.
|
https://api.sourcedata.io/file.php?figure_id=1695
|
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"ext_ids": "10241",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "10241",
"original_type": "gene",
"role": "intervention",
"text": "NDP52",
"type": "geneprod",
"uniprot_ids": [
"Q13137"
]
},
{
"ext_dbs": "NCBI gene",
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"mapping_status": "mapped",
"ncbi_gene_id": "76815",
"original_type": "gene",
"role": "intervention",
"text": "NDP52",
"type": "geneprod",
"uniprot_ids": [
"A2A6M5"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "F2YI08",
"ext_tax_ids": "37124",
"ext_tax_names": "Chikungunya virus",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "nsP2",
"type": "geneprod",
"uniprot_ids": [
"F2YI08"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "A2A6M5",
"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": "NDP52",
"type": "geneprod",
"uniprot_ids": [
"A2A6M5"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q13137",
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"ext_tax_names": "Homo sapiens",
"mapping_source": "direct",
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"role": "assayed",
"text": "NDP52",
"type": "geneprod",
"uniprot_ids": [
"Q13137"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "10241",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "10241",
"original_type": "gene",
"role": "intervention",
"text": "NDP52",
"type": "geneprod",
"uniprot_ids": [
"Q13137"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "F2YI08",
"ext_tax_ids": "37124",
"ext_tax_names": "Chikungunya virus",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "nsP2",
"type": "geneprod",
"uniprot_ids": [
"F2YI08"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "11793",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "11793",
"original_type": "gene",
"role": "intervention",
"text": "Atg5",
"type": "geneprod",
"uniprot_ids": [
"Q99J83"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "10241",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "10241",
"original_type": "gene",
"role": "intervention",
"text": "NDP52",
"type": "geneprod",
"uniprot_ids": [
"Q13137"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "440738",
"ext_tax_ids": "9606",
"ext_tax_names": "Homo sapiens",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "440738",
"original_type": "gene",
"role": "intervention",
"text": "LC3‐C",
"type": "geneprod",
"uniprot_ids": [
"Q9BXW4"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q13137",
"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": "NDP52",
"type": "geneprod",
"uniprot_ids": [
"Q13137"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q9BXW4",
"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‐C",
"type": "geneprod",
"uniprot_ids": [
"Q9BXW4"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q64337",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "p62",
"type": "geneprod",
"uniprot_ids": [
"Q64337"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "18412",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "18412",
"original_type": "gene",
"role": "intervention",
"text": "p62",
"type": "geneprod",
"uniprot_ids": [
"Q64337"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q64337",
"ext_tax_ids": "10090",
"ext_tax_names": "Mus musculus",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "p62",
"type": "geneprod",
"uniprot_ids": [
"Q64337"
]
}
] |
|
29572529
|
10.1038/nn.2922
|
Drosophila Rae1 controls the abundance of the ubiquitin ligase Highwire in post-mitotic neurons
|
2011
|
figf1
|
<p>(<b>a</b>) The Hiw-associated complex was purified by TAP (see Online <ancref rid="an1">Methods</ancref>) and analyzed by one-dimensional SDS-PAGE gel followed by Sypro Ruby staining. Mass spectrometry identified the full-length Hiw, β-tubulin, Rae1 and Fsn, indicated by arrows. (<b>b</b>) The Rae1-associated complex purified from fly brains by TAP was analyzed by one-dimensional SDS-PAGE gel followed by Coomassie blue G-250 staining. Mass spectrometry identified Hiw, Nup98 and Rae1, indicated by arrows. (<b>c</b>) Larval brain lysate of wild-type (WT), <i>hiw</i> null mutant (<i>hiw</i><super><i>ΔN</i></super>) and <i>Fsn</i> mutant (<i>Fsn</i><super><i>f06595</i></super><i>/Df(2R)7872</i>) flies was subject to co-immunoprecipitation with antibody to Hiw (Hiw2b). Both the input and the immunoprecipitated complexes were analyzed by western blots with antibodies to Hiw or Rae1. The membrane was also blotted with antibody to β-tubulin to ensure equal amount of total proteins in the input samples. Full-length blots are presented in <sir rid="S1" refobjid="nn.2922-S1">Supplementary Figure 8</sir>.</p>
|
https://api.sourcedata.io/file.php?figure_id=3685
|
[
{
"ext_dbs": "Uniprot///Uniprot",
"ext_ids": "P61857///P08841",
"ext_tax_ids": "7227///7227",
"ext_tax_names": "Drosophila melanogaster///Drosophila melanogaster",
"mapping_source": "unknown",
"mapping_status": "unmapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "β-tubulin",
"type": "geneprod",
"uniprot_ids": []
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q9V6L9",
"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": "Fsn",
"type": "geneprod",
"uniprot_ids": [
"Q9V6L9"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q9NB71",
"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": "Hiw",
"type": "geneprod",
"uniprot_ids": [
"Q9NB71"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q9NB71",
"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": "Hiw",
"type": "geneprod",
"uniprot_ids": [
"Q9NB71"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q9W2E7",
"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": "Rae1",
"type": "geneprod",
"uniprot_ids": [
"Q9W2E7"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q9NB71",
"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": "Hiw",
"type": "geneprod",
"uniprot_ids": [
"Q9NB71"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q9VCH5",
"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": "Nup98",
"type": "geneprod",
"uniprot_ids": [
"Q9VCH5"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q9W2E7",
"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": "Rae1",
"type": "geneprod",
"uniprot_ids": [
"Q9W2E7"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q9W2E7",
"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": "Rae1",
"type": "geneprod",
"uniprot_ids": [
"Q9W2E7"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "36460",
"ext_tax_ids": "7227",
"ext_tax_names": "Drosophila melanogaster",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "36460",
"original_type": "gene",
"role": "intervention",
"text": "Fsn",
"type": "geneprod",
"uniprot_ids": [
"Q9V6L9"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "32429",
"ext_tax_ids": "7227",
"ext_tax_names": "Drosophila melanogaster",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "32429",
"original_type": "gene",
"role": "intervention",
"text": "hiw",
"type": "geneprod",
"uniprot_ids": [
"Q9NB71",
"X2JF19"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "32429",
"ext_tax_ids": "7227",
"ext_tax_names": "Drosophila melanogaster",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "32429",
"original_type": "gene",
"role": "intervention",
"text": "hiw",
"type": "geneprod",
"uniprot_ids": [
"Q9NB71",
"X2JF19"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q9V6L9",
"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": "Fsn",
"type": "geneprod",
"uniprot_ids": [
"Q9V6L9"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q9NB71",
"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": "Hiw",
"type": "geneprod",
"uniprot_ids": [
"Q9NB71"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q9NB71",
"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": "Hiw",
"type": "geneprod",
"uniprot_ids": [
"Q9NB71"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q9W2E7",
"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": "Rae1",
"type": "geneprod",
"uniprot_ids": [
"Q9W2E7"
]
}
] |
|
29572529
|
10.1038/nn.2922
|
Drosophila Rae1 controls the abundance of the ubiquitin ligase Highwire in post-mitotic neurons
|
2011
|
figf2
|
<p>(<b>a</b>) The gene structure of <i>Rae1</i>. The black-arrowed boxes indicate exons. A transposable element, P{GawB}NP3499, located ∼400 bp upstream of the first exon of <i>Rae1</i> was used to generate imprecise excision mutants of <i>Rae1</i>. PCR analysis indicates that ∼900 bp and a ∼1.5-k bp DNA fragment in the <i>Rae1</i> promoter region are missing in <i>Rae1</i><super><i>EX28</i></super> and <i>Rae1</i><super><i>EXB12</i></super>, respectively. (<b>b</b>) Western blot analysis on Rae1 protein in the brain lysate of wild-type, <i>Df(2R)5764/</i>+, <i>Rae1</i><super><i>EX28</i></super>/+, or late second instar <i>Rae1</i><super><i>EX28</i></super>, <i>Rae1</i><super><i>EX28</i></super>/<i>Df(2R)5764</i>(/<i>Df</i>) and <i>Rae1</i><super><i>EXB12</i></super> /<i>Df(2R)5764</i> larvae. β-tubulin was used as the loading control. Full-length blots are presented in <sir rid="S1" refobjid="nn.2922-S1">Supplementary Figure 9</sir>. (<b>c</b>) Quantification of Rae1 protein levels in the <i>Rae1</i> heterozygous and homozygous mutant brains. Rae1 protein levels were first normalized to β-tubulin protein levels and are presented as percentage of wild-type level. *<i>P</i> 0.05, **<i>P</i> 0.001. Error bars denote s.e.m.</p>
|
https://api.sourcedata.io/file.php?figure_id=3686
|
[
{
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"ext_ids": "37467",
"ext_tax_ids": "7227",
"ext_tax_names": "Drosophila melanogaster",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "37467",
"original_type": "gene",
"role": "intervention",
"text": "Rae1",
"type": "geneprod",
"uniprot_ids": [
"Q9W2E7"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q9W2E7",
"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": "Rae1",
"type": "geneprod",
"uniprot_ids": [
"Q9W2E7"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q9W2E7",
"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": "Rae1",
"type": "geneprod",
"uniprot_ids": [
"Q9W2E7"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q9W2E7",
"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": "Rae1",
"type": "geneprod",
"uniprot_ids": [
"Q9W2E7"
]
},
{
"ext_dbs": "Uniprot",
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"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
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"role": "assayed",
"text": "Rae1",
"type": "geneprod",
"uniprot_ids": [
"Q9W2E7"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q9W2E7",
"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": "Rae1",
"type": "geneprod",
"uniprot_ids": [
"Q9W2E7"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q9W2E7",
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"ext_tax_names": "Drosophila melanogaster",
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},
{
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"ext_tax_names": "Drosophila melanogaster",
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] |
|
29572529
|
10.1038/nn.2922
|
Drosophila Rae1 controls the abundance of the ubiquitin ligase Highwire in post-mitotic neurons
|
2011
|
figf3
|
<p>(<b>a</b>) Representative confocal images of segment A3 muscle 6/7 synapses stained for both DVGLUT (green) and FasII (red), in late 2<super>nd</super>/early 3<super>rd</super> instar wild-type, <i>Rae1</i><super><i>EX28</i></super>, <i>Rae1</i><super><i>EX28</i></super> presynaptic rescue (<i>Rae1</i><super><i>EX28</i></super><i>; elav-Gal4/UAS–NTAP-Rae1</i>) and <i>Rae1</i><super><i>EX28</i></super> <i>wallenda</i> suppression (<i>Rae1</i><super><i>EX28</i></super><i>; wnd<sub>3</sub></i>) larvae. Scale bar represents 10 μm. (<b>b</b>,<b>c</b>) Quantification of bouton number (<b>b</b>) and size (<b>c</b>) in wild-type, <i>Rae1</i><super><i>EX28</i></super><i>/Df</i>, <i>Rae1</i><super><i>EX28</i></super>, <i>Rae1</i><super><i>EX28</i></super> rescue, <i>Rae1</i><super><i>EX28</i></super><i>; wnd<sub>3</sub></i> suppression and <i>hiw</i><super><i>ΔN</i></super> larval NMJs (segment A3 muscle 6/7; <i>n</i> = 20, 21, 18, 20, 20 and 11, respectively, for bouton number; <i>n</i> = 271, 465, 548, 726, 486 and 826, respectively, for bouton size). There was no significant difference in either bouton number or bouton size between <i>Rae1</i><super><i>EX28</i></super> and <i>Rae1</i><super><i>EX28</i></super><i>/Df</i> (<i>P</i> > 0.1 for both comparisons). *<i>P</i> 0.001. Error bars denote s.e.m.</p>
|
https://api.sourcedata.io/file.php?figure_id=3687
|
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"ncbi_gene_id": null,
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] |
|
29572529
|
10.1038/nn.2922
|
Drosophila Rae1 controls the abundance of the ubiquitin ligase Highwire in post-mitotic neurons
|
2011
|
figf4
|
<p>(<b>a</b>) Representative confocal images of muscle 4 synapses stained for both DVGLUT (green) and FasII (red) in wild-type, <i>Rae1</i><super><i>EX28</i></super><i>/</i>+, <i>hiw</i><super><i>ND51</i></super>, <i>hiw</i><super><i>ND51</i></super><i>; Rae1</i><super><i>EX28</i></super><i>/</i>+, <i>hiw</i><super><i>ΔN</i></super> and <i>hiw</i><super><i>ΔN</i></super><i>; Rae1</i><super><i>EX28</i></super><i>/</i>+ larvae. Scale bar represents 10 μm. (<b>b</b>) Quantification of bouton number at muscle 4 NMJs in wild-type, <i>Rae1</i><super><i>EX28</i></super><i>/</i>+, <i>hiw</i><super><i>ND51</i></super>, <i>hiw</i><super><i>ND51</i></super><i>; Rae1</i><super><i>EX28</i></super><i>/</i>+, <i>hiw</i><super><i>ΔN</i></super> and <i>hiw</i><super><i>ΔN</i></super><i>; Rae1</i><super><i>EX28</i></super><i>/</i>+ larvae (<i>n</i> = 27, 23, 42, 46, 23 and 25 cells, respectively). There was a significant increase in the number of boutons formed in <i>hiw</i><super><i>ND51</i></super><i>; Rae1</i><super><i>EX28</i></super><i>/</i>+ compared with <i>hiw</i><super><i>ND51</i></super> 3<super>rd</super> instar larval NMJs (*<i>P</i> 0.001). The number of boutons in the <i>hiw</i><super><i>ΔN</i></super><i>; Rae1</i><super><i>EX28</i></super><i>/</i>+ double mutant was not significantly different from that in <i>hiw</i><super><i>ΔN</i></super> (**<i>P</i> > 0.5), demonstrating a lack of enhancement of the <i>hiw</i><super><i>ΔN</i></super> phenotype by <i>Rae1</i><super><i>EX28</i></super><i>/</i>+. Error bars denote s.e.m.</p>
|
https://api.sourcedata.io/file.php?figure_id=3688
|
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] |
|
29572529
|
10.1038/nn.2922
|
Drosophila Rae1 controls the abundance of the ubiquitin ligase Highwire in post-mitotic neurons
|
2011
|
figf5
|
<p>(<b>a</b>) Schematic presentation of NTAP-tagged (NT-) and HM-tagged (HM-) <i>hiw</i> transgenes encoding full-length, mutated or truncated Hiw proteins. Hiw functional domains are marked with colored boxes. The positions of amino-acid substitution in NT-HiwΔRING and the added amino acid residue necessary to maintain the reading frame in NT-Hiw-RCC1 and NT-Hiw-PHR are indicated. The right column summarizes the ability of the given <i>hiw</i> transgene to rescue the synaptic overgrowth phenotype in <i>hiw</i> mutants, to cause dominant negative overgrowth phenotype when expressed in wild-type background and to bind to Rae1. (<b>b</b>) Western blot analysis of fly brain lysate using antibody to TAP (PAP, Sigma) or Myc revealed the expression of wild-type and mutant <i>hiw</i> transgenes in predicted size. (<b>c</b>) Representative confocal images of muscle 4 synapses stained for DVGLUT (green) and FasII (red) in wild-type (<i>+/hiw</i><super><i>ND8</i></super><i>;</i> +<i>/</i>+<i>; GS-elav-Gal4/</i>+<i>)</i>, NT-Hiw overexpression (+<i>/hiw</i><super><i>ND8</i></super><i>; UAS-NT-hiw/</i>+<i>; GS-elav-Gal4/</i>+), NT-Hiw-NT overexpression (+<i>/hiw</i><super><i>ND8</i></super><i>; UAS-NT-hiw-NT/</i>+<i>; GS-elav-Gal4/</i>+<i>)</i>, NT-Hiw-CT1000 overexpression (+<i>/hiw</i><super><i>ND8</i></super><i>;</i> +<i>/</i>+<i>; GS-elav-Gal4/UAS-NT-hiw-CT1000</i>), NT-Hiw-PHR overexpression (+<i>/hiw</i><super><i>ND8</i></super><i>;</i> +<i>/</i>+<i>; GS-elav-Gal4/UAS-NT-hiw-PHR</i>), HM-Hiw-HindIII overexpression (+<i>/hiw</i><super><i>ND8</i></super><i>; UAS-HW-hiw-HindIII/</i>+<i>; GS-elav-Gal4/</i>+<i>)</i>, NT-Hiw-RCC1 overexpression (<i>NT-hiw-RCC1/hiw</i><super><i>ND8</i></super><i>;</i> +<i>/</i>+<i>; GS-elav-Gal4/</i>+), or NT-Hiw-CT overexpression (+<i>/hiw</i><super><i>ND8</i></super><i>;</i> +<i>/</i>+<i>; GS-elav-Gal4/UAS-NT-hiw-CT</i>) 3<super>rd</super> larval NMJs. Overexpression is indicated by an up arrow. Scale bar represents 10 μm. (<b>d</b>) Quantification of the number of boutons at muscle 4 NMJs in wild-type larvae or larvae overexpressing wild-type or mutant <i>hiw</i> transgenes (<i>n</i> = 23, 24, 26, 27, 26, 21, 25 and 27, respectively; *<i>P</i> 0.001). Error bars denote s.e.m.</p>
|
https://api.sourcedata.io/file.php?figure_id=3689
|
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{
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]
},
{
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"ext_ids": "Q9VQC0",
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"ext_tax_names": "Drosophila melanogaster",
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}
] |
|
29572529
|
10.1038/nn.2922
|
Drosophila Rae1 controls the abundance of the ubiquitin ligase Highwire in post-mitotic neurons
|
2011
|
figf6
|
<p>(<b>a</b>) Indicated NTAP-tagged <i>hiw</i> transgenes (described in <figr rid="f5">Fig. 5</figr>) and a TAP only transgene were expressed in neurons under the control of the <i>BG380-Gal4</i> driver. Larval brain lysates from each sample were subject to IgG pulldown. Both the inputs and the IgG pulldown complexes were analyzed by western blot using antibody to Rae1. Rae1 was present in all of the pulldown complexes except for those from TAP only, NT-Hiw-CT1000 and NT-Hiw-NT. Full-length blots are presented in <sir rid="S1" refobjid="nn.2922-S1">Supplementary Figure 10</sir>. (<b>b</b>) Quantification of the interaction between various Hiw transgenic proteins and Rae1. Rae1 intensities in TAP pulldown blots were normalized to both the intensities and molecular weights of the corresponding TAP pulldown proteins. (<b>c</b>) Representative confocal images of muscle 4 synapses stained for both DVGLUT (green) and FasII (red) in wild-type (<i>BG380/Y;</i>+<i>/</i>+<i>;</i> +<i>/</i>+), NT-Hiw-CT and GAP-GFP (<i>BG380/Y; UAS-GAP-GFP/</i>+<i>; UAS-NT-hiw-CT/</i>+), and NT-Hiw-CT and Rae1 (<i>BG380/Y;</i> +<i>/</i>+<i>; UAS-NT-hiw-CT/UAS-GFP-Rae1</i>) larvae. Scale bar represents 10 μm. (<b>d</b>) Quantification of number of boutons at muscle 4 NMJs in wild-type, NT-Hiw-CT overexpression (<i>BG380/Y;</i> +<i>/</i>+<i>; UAS-NT-hiw-CT/</i>+), NT-Hiw-CT and GAP-GFP, and NT-Hiw-CT and Rae1 (<i>n</i> = 24, 27, 32 and 26, respectively) larvae. Error bars denote s.e.m.; *<i>P</i> 0.001.</p>
|
https://api.sourcedata.io/file.php?figure_id=3690
|
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] |
|
29572529
|
10.1038/nn.2922
|
Drosophila Rae1 controls the abundance of the ubiquitin ligase Highwire in post-mitotic neurons
|
2011
|
figf7
|
<p>(<b>a</b>) Neuronal expression of neither Hiw nor Rae1 rescues the synaptic terminal overgrowth phenotype caused by the loss of function of the other gene. Quantification of the number of boutons in wild-type, <i>Rae1</i><super><i>EX28</i></super>, <i>Rae1</i><super><i>EX28</i></super><i>; Hiw</i> rescue (Res) (<i>Rae1</i><super><i>EX28</i></super><i>; elav-Gal4/UAS-GFP-hiw</i>), <i>hiw</i><super><i>ΔN</i></super> and <i>hiw</i><super><i>ΔN</i></super><i>; Rae1</i> rescue (<i>hiw</i><super><i>ΔN</i></super><i>; elav-Gal4/UAS-NTAP-Rae1</i>) larval NMJs (segment A3 muscle 6/7; <i>n</i> = 12, 12, 12, 7 and 11, respectively). (<b>b</b>) Representative confocal images of wild-type (<i>BG380-Gal4/</i>+<i>;</i> +<i>/</i>+<i>; UAS-GFP-hiw/</i>+) or <i>Rae1</i> mutant (<i>BG380-Gal4/</i>+<i>; Rae1</i><super><i>EX28</i></super><i>; UAS-GFP-hiw/</i>+) ventral ganglions with <i>UAS-GFP-hiw</i> trangene expressed in neurons. The larvae were stained with antibodies to horseradish peroxidase (HRP, red) and GFP (green). Scale bar represents 10 μm. (<b>c</b>) Western blots of total proteins extracted from wild-type, <i>hiw</i><super><i>ΔN</i></super>, <i>Rae1</i><super><i>EX28</i></super> and <i>Rae1</i><super><i>EX28</i></super> rescue (<i>Rae1</i><super><i>EX28</i></super><i>; elav-Gal4/UAS-NTAP-Rae1</i>) larval brains probed with indicated antibodies. Full-length blots are presented in <sir rid="S1" refobjid="nn.2922-S1">Supplementary Figure 11</sir>. (<b>d</b>) Western blot analysis on total proteins extracted from <i>hiw</i><super><i>ΔN</i></super>, wild-type (<i>C155-Gal4/</i>+) and Rae1 expression (<i>C155-Gal4/</i>+<i>; UAS-NTAP-Rae1/</i>+) larval brains. Full-length blots are presented in <sir rid="S1" refobjid="nn.2922-S1">Supplementary Figure 12</sir>. (<b>e</b>) Quantification of Hiw protein levels in the wild-type and the Rae1 expression larval brains (*<i>P</i> 0.001, based on seven independent experiments). Arrows indicate a 38-kDa endogenous Rae1 protein and the arrowheads indicate the 58-kDa transgenic NTAP-Rae1 protein. Error bars denote s.e.m.</p>
|
https://api.sourcedata.io/file.php?figure_id=3691
|
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] |
|
29572529
|
10.1038/nn.2922
|
Drosophila Rae1 controls the abundance of the ubiquitin ligase Highwire in post-mitotic neurons
|
2011
|
figf8
|
<p>(<b>a</b>) Representative confocal images of segment A3 muscle 6/7 synapses stained for both DVGLUT (green) and FasII (red), in wild-type, <i>Rae1</i><super><i>EX28</i></super>, <i>Rae1</i><super><i>EX28</i></super>; <i>atg1/</i>+, <i>Rae1</i><super><i>EX28</i></super>; <i>atg2/</i>+ and <i>Rae1</i><super><i>EX28</i></super>; <i>atg18/</i>+ wandering larvae. Scale bar represents 10 μm. (<b>b</b>) Quantification of the number of boutons in wild-type, <i>atg1/</i>+, <i>atg2/</i>+, <i>atg18/</i>+, <i>Rae1</i><super><i>EX28</i></super>, <i>Rae1</i><super><i>EX28</i></super>; <i>atg1/</i>+, <i>Rae1</i><super><i>EX28</i></super>; <i>atg2/</i>+ and <i>Rae1</i><super><i>EX28</i></super>; <i>atg18/</i>+ larval NMJs (segment A3 muscle 6/7; <i>n</i> = 12, 12, 12, 12, 12, 16, 12 and 21, respectively). (<b>c</b>) Western blot analysis on total proteins extracted from wild-type, <i>Rae1</i><super><i>EX28</i></super>, <i>Rae1</i><super><i>EX28</i></super>; <i>atg1/</i>+, <i>Rae1</i><super><i>EX28</i></super>; <i>atg2/</i>+ and <i>Rae1</i><super><i>EX28</i></super>; <i>atg18/</i>+ larval brains. The neural form of β-catenin (82 kDa, see Online <ancref rid="an1">Methods</ancref>) was used as an internal control of neuronal proteins. Full-length blots are presented in <sir rid="S1" refobjid="nn.2922-S1">Supplementary Figure 13</sir>. (<b>d</b>) Quantification of Hiw protein levels in wild-type, <i>Rae1</i><super><i>EX28</i></super>, <i>Rae1</i><super><i>EX28</i></super>; <i>atg1/</i>+, <i>Rae1</i><super><i>EX28</i></super>; <i>atg2/</i>+ and <i>Rae1</i><super><i>EX28</i></super>; <i>atg18/</i>+ larval brains (based on six independent experiments). (<b>e</b>) Representative confocal images of muscle 4 synapses stained for both DVGLUT (green) and FasII (red) in wandering larvae of wild-type (<i>C155-Gal4/</i>+), Atg1 Gap-GFP (<i>C155-Gal4/</i>+<i>; UAS-Gap-GFP/</i>+<i>; UAS-Atg1</i><super><i>6B</i></super><i>/</i>+), and Atg1 NTAP-Rae1 (<i>C155-Gal4/</i>+<i>; UAS-NTAP-Rae1/</i>+<i>; UAS-Atg1/</i>+). Scale bar represents 10 μm. (<b>f</b>) Quantification of the number of boutons at muscle 4 synapses in wild-type, Rae1 expression (<i>C155-Gal4/</i>+<i>; UAS-NTAP-Rae1/</i>+), Atg1 Gap-GFP and Atg1 NTAP-Rae1 wandering larvae (segment A2–4, <i>n</i> = 28, 27, 33 and 34, respectively). Error bars denote s.e.m. *<i>P</i> 0.001, **<i>P</i> 0.05.</p>
|
https://api.sourcedata.io/file.php?figure_id=3692
|
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|
10.15252/emmm.202012088
|
BAM15 Mediated Mitochondrial Uncoupling Protects Against Obesity and Improves Glycemic Control
|
2020
|
Figure 1
|
<sd-panel> <p><strong>Figure 1</strong>. BAM15 improves cellular respiratory kinetics by sustained mitochondrial uncoupling.</p> <p><strong>(A)</strong> Caspase 3/7 activation ± 16-hour treatment with varying concentrations of BAM15, DNP, or FCCP (N=3 per condition). 5 μM: BAM15 vs. DNP (<em>P</em>=0.030). 10 μM: BAM15 vs. DNP (<em>P</em>=0.013). 20 μM: BAM15 vs. DNP (<em>P</em>=0.0005), BAM15 vs. FCCP (<em>P</em>=0.036). 40 μM: BAM15 vs. DNP (<em>P</em>=0.018), BAM15 vs. FCCP (<em>P</em>=0.021). 80 μM: BAM15 vs. DNP (<em>P</em>=0.018), DNP vs. FCCP (<em>P</em>=0.004).</p> <p><strong>(B-F) (B)</strong> The rate of oxygen consumption (OCR), <strong>(C)</strong> ratio of oxygen consumption to extracellular acidification (OCR/ECAR), <strong>(D)</strong> maximal rate of OCR (BAM15 vs. DNP, <em>P</em><0.0001; DNP vs. FCCP (<em>P</em><0.0001) <strong>(E)</strong> time to maximal uncoupling rate (BAM15 vs. DNP, <em>P</em><0.0001; BAM15 vs. FCCP (<em>P</em><0.0001), and <strong>(F)</strong> mitochondrial respiratory half-life following acute injection of 1 μM BAM15, DNP, or FCCP (BAM15 vs. DNP, <em>P</em><0.0001; BAM15 vs. FCCP (<em>P</em><0.0001) (N=6 per condition).</p> <p><strong>(G, H) (G)</strong> Representative respirometry plot of intact cells ± 16-hour treatment with 20 μM BAM15 sequentially injected with oligomycin, FCCP, and a cocktail of rotenone and antimycin a (N=5 per condition) and <strong>(H)</strong> basal (<em>P</em>=0.002) and ATP-linked respiration, proton leak (<em>P</em>=0.0003), maximal uncoupling, spare respiratory capacity (<em>P</em><0.0001), and non-mitochondrial respiration (N=5 per condition).</p> <p><strong>(I)</strong> Assessment of routine (R) oxygen flux (<em>P</em>=0.030), leak (L) (<em>P</em>=0.010), OXPHOS (P) and ETC (E) capacity in permeabilized C2C12 cells ± 16-hour treatment with BAM15 (N=4 per condition). PM: pyruvate and malate, ADP: adenosine diphosphate, GS: glutamate and succinate, Tm: tetramethyl-p-phenylenediamine.</p> <p>(<strong>J)</strong> Citrate synthase activity ± 16-hour treatment with 20 μM BAM15 (N=10 per condition).</p> <p><strong>(K)</strong> mtDNA (<em>COX2</em>:<em>18S</em>) ± 16-hour treatment with 20 μM BAM15 (N=6 per condition).</p> <p>Data information. Data are shown as the mean ± SEM. *p<0.05, **p<0.01, ***p<0.01, ****p<0.001. Panels A, H, and I were assessed by two-way repeated measures ANOVA with Tukey's multiple comparisons. Panels D, E, and F were assessed by one-way ANOVA with Tukey's multiple comparisons. Panels J and K were assessed by unpaired Student's t-test.</p> </sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=33098
|
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] |
||
10.15252/emmm.202012088
|
BAM15 Mediated Mitochondrial Uncoupling Protects Against Obesity and Improves Glycemic Control
|
2020
|
Figure 3
|
<sd-panel> <p><strong>Figure 3.</strong> BAM15 stimulates insulin signaling and oxidation of glucose and fatty acids in an AMPK dependent manner.</p> <p><strong>A-D (A)</strong> Representative immunoblots and <strong>(B)</strong> quantitative analysis of AKT (1 μM insulin: <em>P</em>=0.038), <strong>(C)</strong> AS160 (- insulin: <em>P</em>=0.036, 1 μM insulin: <em>P</em>=0.0038), and <strong>(D)</strong> AMPK (- insulin: <em>P</em>=0.018) phosphorylation ± 16 hour BAM15 treatment and 15 minute insulin stimulation (N=3 per condition) in C2C12 myotubes.</p> <p><strong>E, F (E)</strong> Representative immunoblots and quantitative analysis of <strong>(F)</strong> plasma membrane GLUT4 translocation (<em>P</em>=0.0139) ± 16-hour BAM15 treatment (N=3 per condition) in C2C12 myotubes.</p> <p><strong>G, H (G)</strong> [3-<sup>3</sup>H]glucose uptake ± 16 hour BAM15 treatment and 30 minute insulin stimulation (N=4 per condition; vehicle vs. vehicle + insulin: <em>P</em>=0.0016, vehicle vs. BAM15: <em>P</em><0.0001, vehicle vs. BAM15 + insulin: <em>P</em><0.0001, vehicle + insulin vs. BAM15 + insulin: <em>P</em>=0.0018, BAM15 vs. BAM15 + insulin: <em>P</em>=0.0024) <strong>and (H)</strong> [1-<sup>14</sup>C]palmitate oxidation ± 16 hour BAM15 treatment and 5 mM glucose and 1 mM pyruvate (N=6 per condition; no glucose/pyruvate: <em>P</em><0.0001) in C2C12 myotubes.</p> <p><strong>(I)</strong> Representative immunoblot and quantitative analysis (N=5 per condition; <em>P</em><0.0001) of AMPK demonstrating loss of function following transfection with an shAMPK construct in C2C12 myotubes.</p> <p><strong>J, K (J)</strong> Representative respirometry plot of intact cells ± shAMPK and 16 hour BAM15 treatment in C2C12 myotubes cells sequentially injected with oligomycin, FCCP, and a cocktail of rotenone and antimycin a (N=5 per condition) and <strong>(K)</strong> basal and ATP-linked respiration, proton leak, maximal uncoupling, and spare respiratory capacity (N=5 per condition). Basal: shEV vs. shEV + BAM15 (<em>P</em>=0.0317), shEV + BAM15 vs. shAMPK (<em>P</em><0.0001), shEV + BAM15 vs. shAMPK + BAM15 (<em>P</em><0.0001). ATP: shEV vs. shAMPK + BAM15 (<em>P</em>=0.0026), shEV + BAM15 vs. shAMPK + BAM15 (<em>P</em>=0.0003), shAMPK vs. shAMPK + BAM15 (<em>P</em>=0.040). Proton leak: shEV vs. shEV + BAM15 (<em>P</em>=0.0052), shAMPK vs. shAMPK + BAM15 (<em>P</em>=0.0394). Maximal: shEV vs. shAMPK + BAM15 (<em>P</em><0.0001), shEV + BAM15 vs. shAMPK + BAM15 (<em>P</em><0.0001), shAMPK vs. shAMPK + BAM15 (<em>P</em><0.0001). Spare Capacity: shEV vs. shAMPK (<em>P</em>=0.0028), shEV vs. shAMPK + BAM15 (<em>P</em><0.0001), shEV + BAM15 vs. shAMPK (<em>P</em><0.0001), shEV + BAM15 vs. shAMPK + BAM15 (<em>P</em><0.0001), shAMPK vs. shAMPK + BAM15 (<em>P</em><0.0001).</p> <p><strong>(L)</strong> [3-<sup>3</sup>H]glucose uptake ± shAMPK, 16 hour BAM15 treatment, and 30 minute insulin stimulation in C2C12 myotubes (N=3 per condition). No insulin: shEV vs. shEV + BAM15 (<em>P</em>=0.0001). Insulin: shEV vs. shEV + BAM15 (<em>P</em>=0.0142).</p> <p><strong>M-O (M)</strong> Representative immunoblots and quantitative analysis of <strong>(N)</strong> AKT (shEV + insulin: <em>P</em>=0.0128, shAMPK - insulin: <em>P</em>=0.0018, shAMPK + insulin, <em>P</em>=0.0124), and <strong>(O)</strong> AS160 (shEV - insulin: <em>P</em>=0.0283, shEV + insulin: <em>P</em>=0.0137) phosphorylation ± shAMPK, 16 hour BAM15 treatment, and 15 minute insulin stimulation in C2C12 myotubes (N=3 per condition).</p> <p>Data information: Data are shown as the mean ± SEM. *p<0.05, **p<0.01, ***p<0.01, ****p<0.001. Panels B, C, D, H, K, L, N, and O were assessed by two-way repeated measures ANOVA with Tukey's multiple comparisons. Panel G was assessed by one-way ANOVA with Tukey's multiple comparisons. Panels F and I were assessed by unpaired Student's t-test.</p> </sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=33102
|
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"uniprot_ids": [
"Q8BYJ6"
]
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] |
||
10.15252/emmm.202012088
|
BAM15 Mediated Mitochondrial Uncoupling Protects Against Obesity and Improves Glycemic Control
|
2020
|
Figure 7
|
<sd-panel> <p><strong>Figure 7.</strong> Increased skeletal muscle fatty acid oxidation is supported by AMPK mediated suppression of lipogenesis in white adipose tissue following treatment with BAM15.</p> <p><strong>A-D (A)</strong> Plasma concentrations of non-esterified fatty acids (NEFA) (CTRL N=7, BAM15 N=8, <em>P</em>=0.0073), <strong>(B)</strong> leptin (N=8 per group, <em>P</em><0.0001), <strong>(C)</strong> GDF15 (N=7 per group, <em>P</em>=0.035), and <strong>(D)</strong> FGF21 (N=7 per group, <em>P</em>=0.0026) after 3-weeks of CTRL or BAM15 treatment.</p> <p><strong>E, F (E)</strong> Total (basal: <em>P</em>=0.015) and <strong>(F)</strong> complete (basal: <em>P</em>=0.0137) oxidation of 200 μM [1-<sup>14</sup>C]palmitate to CO<sub>2</sub> from mixed gastrocnemius muscle homogenates (N=7 per group).</p> <p><strong>(G)</strong> Routine (R) oxygen flux, leak (L), OXPHOS (P) and ETC (E) capacity in permeabilized mixed gastrocnemius fibers (N=6 per group). PM: pyruvate and malate, ADP: adenosine diphosphate, GS: glutamate and succinate, Tm: tetramethyl-p-phenylenediamine, PalM: palmitoylcarnitine and malate, Oct: octanoylcarnitine, and Dur: duroquinol.</p> <p><strong>H-K (H)</strong> Representative immunoblots of phosphorylated and total AMPK and ACC from iWAT, and mixed gastrocnemius muscle and <strong>(I-K)</strong> Densitometric quantification (N=4 per group; iWAT p-AMPK<sup>T172</sup>: <em>P</em>=0.0186, iWAT p-ACC<sup>S79</sup>: <em>P</em>=0.0083, mixed gastrocnemius p-AMPK<sup>T172</sup>: <em>P</em>=0.0286).</p> <p><strong>(L-N)</strong> mRNA expression of transcriptional regulators of lipogenesis and lipolysis in iWAT (N=7 per group). Srebf1 (<em>P</em><0.0001), Mlxipl (<em>P</em>=0.0018), Scd1 (<em>P</em><0.0001), FASN (<em>P</em>=0.0009), LIPE (<em>P</em>=0.0015), Pnpla2 (<em>P</em><0.0001), PPARg (<em>P</em><0.0001).</p> <p>Data information: Data are shown as the mean ± SEM. *p<0.05, **p<0.01, ***p<0.01, ****p<0.001. Panels E, F, and G were assessed by two-way repeated measures ANOVA with Tukey's multiple comparisons. Panels A, B, C, D, I, J, K, L, M, and N were assessed by an unpaired Student's t-test.</p> </sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=33109
|
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"ext_dbs": "NCBI gene",
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"ext_tax_names": "Mus musculus",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "20787",
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"uniprot_ids": [
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] |
||
10.15252/emmm.202013742
|
Repurposing of tamoxifen ameliorates CLN3 and CLN7 disease phenotype
|
2021
|
Figure 1
|
<p>Figure 1. Accumulation of Gb3 in Batten Disease cellular models.</p><p>(A) Representative Opera images of WT and CLN3 KO ARPE 19 cell lines stained using fluorescent-conjugated cholera toxin (to detect GM1), LipidTox (to detect neutral lipids), fluorescent-conjugated Shiga toxin and is quantification (to detect Gb3), Filipin III (to detect cholesterol). Data are presented as mean ± SD ***: <em>P</em> ≤ 0.0001, as determined by Student's <em>t</em>‐test (n=3 biological replicas in duplicate). Scale bars: 50 µm.</p><p>(B-C) Representative confocal images and their quantification of Gb3 accumulation within the lysosome, detected by fluorescent-conjugated Shiga toxin, from WT, CLN3-KO and CLN7-KO ARPE-19 cells treated with PDMP or silenced for Gb3 synthase (siGb3S) (*** vs WT, °°° vs DMSO). Data are presented as mean ± SD, °°°/***: <em>P</em> ≤ 0.0001, as determined by ANOVA (n=3 biological replicas in duplicate). Scale bars: 20 µm.</p><p>(D) Lipidomic analysis of ARPE-19CLN3KO and ARPE-19CLN7KO. Data are presented as mean ± SD, *: <em>P</em> ≤ 0.01, **: <em>P</em> ≤ 0.001, ***: <em>P</em> ≤ 0.0001, as determined by ANOVA (n=4 technical replicas).</p>
|
https://api.sourcedata.io/file.php?figure_id=42561
|
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"A0A286YF45",
"A0A286YF72",
"A0A286YF73",
"A0A286YFB5",
"A0A286YFC6",
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"A0A286YFI8",
"A0A286YFM2",
"B7Z2B2",
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] |
||
10.15252/emmm.202013742
|
Repurposing of tamoxifen ameliorates CLN3 and CLN7 disease phenotype
|
2021
|
Figure 2
|
<p>Figure 2. Neural accumulation of Gb3 in brain areas of the CLN7<sup>Δex2</sup> mouse.</p><p>(A-B) Representative confocal images of Gb3 accumulation, revealed by STX staining, in brain sections from CLN7<sup>Δex2</sup> mice at 3 and 7.5 months of age compared with CLN7 WT mice. Scale bars: 80 µm.</p><p>(C-D) Gb3, NeuN, and GFAP distribution in brain areas of CLN7<sup>Δex2</sup> mice at 7.5 months of age. Scale bars: 40 µm, 20 µm.</p><p>(E) Lipidomic analysis of neurons isolated from CLN7 WT and CLN7<sup><span class="underline">Δex2</span></sup> mouse forebrain. Data are presented as mean ± SD, **: <em>P</em> ≤ 0.001, ***: <em>P</em> ≤ 0.0001, as determined by ANOVA (n= 3 biological replicas)</p>
|
https://api.sourcedata.io/file.php?figure_id=42562
|
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"mapping_status": "mapped",
"ncbi_gene_id": "72175",
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] |
||
10.15252/emmm.202013742
|
Repurposing of tamoxifen ameliorates CLN3 and CLN7 disease phenotype
|
2021
|
Figure 3
|
<p>Figure 3. Role of Gb3 in Batten Disease and identification of correctors of Gb3 accumulation.</p><p>(A) Representative confocal images and quantification of SCMAS staining within the lysosome of ARPE-19 WT and CLN3 KO upon depletion of Gb3S (siGb3S), LacCer (siLCS), and GM3s (siGM3S). (*** vs WT, °°° vs CLN3 KO siSCR). Data are presented as mean ± SD, °°°/***: <em>P</em> ≤ 0.0001, as determined by ANOVA (n=3 biological replicas in duplicate). Scale bars: 20 µm.</p><p>(B) Identification of FDA-compounds reducing Gb3 accumulation: Plot showing the ability of compound hits to reduce Gb3 within the lysosomal compartment compared with DMSO treated mutant cells. Data are presented as mean ± SD, ***: <em>P</em> ≤ 0.0001, as determined by ANOVA (n=3 biological replicas in duplicate).</p><p>(C) Table showing the EC50s (Half maximal effective concentration) from the dose-response curves of compound hits. EC50s were calculated using the Prism software.</p><p>(D) Representative confocal images and quantification of STX staining within the lysosome of ARPE-19 WT and CLN7 KO in DMSO or treated 48h with Tamoxifen. (*** vs WT, °°° vs CLN3 KO DMSO). Data are presented as mean ± SD, °°°/***: <em>P</em> ≤ 0.0001, as determined by ANOVA (n=3 biological replicas in duplicate). Scale bars: 20 µm.</p><p>(E) Representative confocal images and quantification of STX staining within the lysosome of NPCs WT and derived from CLN7<sup>Pa474</sup> patient IPSCs in DMSO or treated with Tamoxifen for 48h. (*** vs WT, °°° vs CLN7<sup>Pa474</sup> DMSO). Data are presented as mean ± SD, °°°/***: <em>P</em> ≤ 0.0001, as determined by ANOVA (n=3 biological replicas in duplicate). Scale bars: 20 µm.</p>
|
https://api.sourcedata.io/file.php?figure_id=42564
|
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"A0A286YFM2",
"B7Z2B2",
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]
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] |
||
10.15252/emmm.202013742
|
Repurposing of tamoxifen ameliorates CLN3 and CLN7 disease phenotype
|
2021
|
Figure 4
|
<p>Figure 4. Tamoxifen-mediated clearance of Gb3 is ER-independent but TFEB-dependent.</p><p>(A) Representative confocal images and Quantification of STX within the lysosome in U2-OS and HeLa cells after acute silencing of CLN3 (siCLN3) in DMSO or treated 48h with Tamoxifen. (*** vs siSCR DMSO, °°° vs siCLN3 DMSO). Data are presented as mean ± SD, °°°/***: <em>P</em> ≤ 0.0001, as determined by ANOVA (n=3 biological replicas in duplicate). Scale bars: 20 µm.</p><p>(B) Representative confocal image and quantification of Gb3 in ARPE-19 CLN3 KO cells silenced with siRNA against scramble sequence and TFEB (siTFEB) for 72h and treated for the last 48h with DMSO or Tamoxifen. Data are presented as mean ± SD, ***: <em>P</em> ≤ 0.0001, as determined by ANOVA (n=3 biological replicas in duplicate). Scale bars: 20 µm.</p><p>(C) Representative confocal image and quantification of TFEB in U2-OS cells silenced with siRNA against scramble sequence and CLN3 (siCLN3) for 72h and treated for the last 48h with DMSO or Tamoxifen (5 µM and 10 µM). Data are presented as mean ± SD, ***: <em>P</em> ≤ 0.0001, as determined by ANOVA (n=3 biological replicas in duplicate). Scale bars: 20 µm.</p>
|
https://api.sourcedata.io/file.php?figure_id=42566
|
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] |
||
10.15252/emmm.202013742
|
Repurposing of tamoxifen ameliorates CLN3 and CLN7 disease phenotype
|
2021
|
Figure 5
|
<p>Figure 5. Tamoxifen dephosphorylates TFEB.</p><p>(A) Immunoblot analysis and quantification of pTFEB S211 in HeLa cells stably expressing TFEB-GFP. Data are presented as mean ± SD, ***: P ≤ 0.0001, as determined by ANOVA (n=3 biological replicas ). GAPDH immunoblotting was performed as a loading control.</p><p>(B) Immunoblot analysis of TFEB shift in ARPE-19 CLN3 KO cells. β-actin immunoblotting were performed as a loading control.</p><p>(C) Representative confocal image and quantification of TFEB localization in HeLa TFEB-GFP transfected with RagC for 48h and treated for the last 3h with DMSO, Torin1, Tamoxifen or Ospemifene. Ratios of nuclear to cytosolic TFEB localization in RagC non-expressing (RagC-) and RagC-expressing cells (RagC+) are presented as mean ± SD, ***: P ≤ 0.0001, as determined by ANOVA (n=3 biological replicas in duplicate). Scale bars: 20 µm.</p><p>D) Representative <del>c</del>onfocal images and quantification of STX in ARPE-19 CLN3 KO cells transfected with empty vector or HA-RagC for 48h and treated for 48h with DMSO or Tamoxifen. STX average spot area presented as mean ± SD, ***: <em>P</em> ≤ 0.0001, as determined by ANOVA (n=3 biological replicas in duplicate). Scale bars: 20 µm.</p>
|
https://api.sourcedata.io/file.php?figure_id=42568
|
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||
10.15252/emmm.202013742
|
Repurposing of tamoxifen ameliorates CLN3 and CLN7 disease phenotype
|
2021
|
Figure 6
|
<p>Figure 6. Tamoxifen reduce Gb3 accumulation in brain of CLN7<sup>Δex2</sup> mice.</p><p>Representative confocal images of STX in the Cortex, Hippocampus, and Cerebellum brain section derived from 7.5 months-old mouse WT or CLN7<sup>Δex2</sup> injected with vehicle or Tamoxifen (Tamox). Quantification of confocal images, the plot shows the quantification of the STX average spot area normalized for the number of Hoechst positive cells. (*** vs WT, °°°/°° vs CLN7<sup>Δex2</sup> Vehicle). Data are presented as mean ± SD, **/<sup>oo</sup>: <em>P</em> ≤ 0.001, ***/<sup>ooo</sup>: <em>P</em> ≤ 0.0001, as determined by ANOVA (N≥3 biological replicas). Scale bars: 60 µm.</p>
|
https://api.sourcedata.io/file.php?figure_id=42570
|
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] |
||
10.15252/emmm.202013742
|
Repurposing of tamoxifen ameliorates CLN3 and CLN7 disease phenotype
|
2021
|
Figure 7
|
<p>Figure 7. Tamoxifen reduces SCMAS accumulation in the brains of CLN7<sup>Δex2</sup> mice.</p><p>Representative confocal images of SCMAS in the Cortex, Hippocampus, and Cerebellum brain section derived from mouse WT or CLN7<sup>Δex2</sup> injected with vehicle or Tamoxifen. Quantification of confocal images, the plot shows the quantification of the SCMAS average spot area normalized for the number of Hoechst positive cells. (*** vs WT, °°° vs CLN7<sup>Δex2</sup> Vehicle). Data are presented as mean ± SD, ***: <em>P</em> ≤ 0.0001, as determined by ANOVA (N≥3 biological). Scale bars: 60 µm.</p>
|
https://api.sourcedata.io/file.php?figure_id=42571
|
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||
10.15252/emmm.202013742
|
Repurposing of tamoxifen ameliorates CLN3 and CLN7 disease phenotype
|
2021
|
Figure 8
|
<p>Figure 8. Tamoxifen ameliorates CLN7<sup>Δex2</sup> phenotype.</p><p>(A-B) Representative confocal images and quantification of IBA-1 in the Cortex, Hippocampus, and Cerebellum brain section derived from WT or CLN7<sup>Δex2</sup> mice injected with the vehicle or Tamoxifen. (***/**/* vs WT, °°°/°°/° vs CLN7<sup>Δex2</sup> Vehicle). Data are presented as mean ± SD, *<sup>/o</sup>: <em>P</em> ≤ 0.01, **<sup>/oo</sup>: <em>P</em> ≤ 0.001, ***: <em>P</em> ≤ 0.0001, as determined by ANOVA (N≥3 biological replicas). Scale bars: 50 µm.</p><p>(C) Plots show the quantification latency to fall from the rotarod. Data are presented as mean ± SD, *: <em>P</em> ≤ 0.01, as determined by ANOVA (N≥3 biological replicas).</p><p>(D) Representative Images of hindlimb clasping test in mouse WT or CLN7Δex2 injected with vehicle or Tamoxifen.</p><p><strong>Expanded View Legends</strong></p>
|
https://api.sourcedata.io/file.php?figure_id=42572
|
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||
27242363
|
10.15252/embj.201593265
|
WRNIP1 protects stalled forks from degradation and promotes fork restart after replication stress
|
2016
|
Figure 1
|
<p><strong>Fig</strong><strong>ure</strong><strong> 1.</strong> <strong>Loss of</strong> <strong>WRNIP1 leads to nascent DNA strand degradation after HU-induced replication stress</strong></p>
<p>(<strong>A</strong>) Western blot analysis showing the expression of the WRNIP1 protein in wild-type cells (shWRNIP1<sup>WT</sup>) and WRNIP1-deficient (shWRNIP1) or mutant (shWRNIP1<sup>T294A</sup>) cells. MRC5SV fibroblasts were used as a positive control. The membrane was probed with an anti-FLAG or anti-WRNIP1. GAPDH was used as a loading control. Below each lane of the blot the ratio of WRNIP1 protein to total protein, then normalised to MRC5SV, is reported.</p>
<p>(<strong>B</strong>) Experimental scheme of dual labelling of DNA fibers in shWRNIP1<sup>WT</sup>, shWRNIP1 and shWRNIP1<sup>T294A</sup> cells. Cells were pulse-labelled with CldU, and then subjected to a pulse-labelling with IdU.</p>
<p>(<strong>C</strong>) Analysis of replication fork velocity (fork speed) in the cells under unperturbed conditions. The length of the green tracks were measured. Mean values are represented as horizontal black lines (ns, not significant; Student’s t-test).</p>
<p>(<strong>D</strong>) Cells were treated as in (B). For each replication origin, the length of the right-fork signal was measured and plotted against the length of the left-fork signal. A schematic representation of symmetric and asymmetric forks is given. If the ratio between the left-fork length and the right-fork length deviated by more than 33% from 1 (that is, outside the violet dashed lines in the graphs), the fork was considered asymmetric. The percentage of asymmetric forks was calculated for all cell lines. N= number of forks counted for each cell line. R represents linear correlation coefficient.</p>
<p>(<strong>E</strong>) Experimental scheme of dual labelling of DNA fibers in shWRNIP1<sup>WT</sup>, shWRNIP1 and shWRNIP1<sup>T294A</sup> cells. Cells were pulse-labelled with CldU, treated with 4mM HU and then subjected to a pulse-labelling with IdU.</p>
<p>(<strong>F</strong>) Graphs show the percentage of red (CldU) tracts (stalled forks) or red-green (CldU-IdU) contiguous tracts (restarting forks) in the cells. Mean shown, n = 3. Error bars represent standard error. (*, p < 0.05; **, p < 0.01; Student’s t test). Representative DNA fiber images are shown. Scale bars, 10 µm.</p>
<p>(<strong>G</strong>) Experimental scheme of dual labelling of DNA fibers in shWRNIP1<sup>WT</sup>, shWRNIP1 and shWRNIP1<sup>T294A</sup> cells. Cells were sequentially pulse-labelled with CldU and IdU as indicated, then treated or not with 4 mM HU.</p>
<p>(<strong>H</strong>) Representative IdU tract length distributions in all cell lines under unperturbed conditions (left graph) or after HU treatment (right graph). Median tract lengths are given in parentheses. See also Tables S1 and S2 for details on the data sets and statistical test. Representative DNA fiber images are shown. Scale bars, 10 µm.</p>
|
https://api.sourcedata.io/file.php?figure_id=8326
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] |
|
27242363
|
10.15252/embj.201593265
|
WRNIP1 protects stalled forks from degradation and promotes fork restart after replication stress
|
2016
|
Figure 2
|
<p><strong>Fig</strong><strong>ure</strong> <strong>2.</strong> <strong>Inhibition of MRE11 exonuclease activity prevents nascent DNA strand degradation after replication stress </strong></p>
<p>(<strong>A</strong>) Experimental scheme of dual labelling of DNA fibers in wild-type cells (shWRNIP1<sup>WT</sup>) or WRNIP1-deficient cells (shWRNIP1). Cells were sequentially pulse-labelled with CldU and IdU as indicated, then left untreated or treated with 4 mM HU in combination or not with 50 µM Mirin.</p>
<p>(<strong>B</strong>) Representative IdU tract length distributions in shWRNIP1<sup>WT</sup> (left graph) or shWRNIP1 cells (right graph) after treatment. Median tract lengths are given in parentheses. See Tables S1 and S2 for details on the data sets and statistical test. Representative DNA fiber images are shown. Scale bars, 10 µm.</p>
|
https://api.sourcedata.io/file.php?figure_id=8327
|
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] |
|
27242363
|
10.15252/embj.201593265
|
WRNIP1 protects stalled forks from degradation and promotes fork restart after replication stress
|
2016
|
Figure 3
|
<p><strong>Fig</strong><strong>ure</strong> <strong>3. Analysis of parental ssDNA formation and RAD51 destabilization at stalled replication forks</strong></p>
<p>(<strong>A</strong>) Evaluation of ssDNA accumulation at parental-strand by immunofluorescence analysis in wild-type (shWRNIP1<sup>WT</sup>) or WRNIP1-deficient (shWRNIP1) cells. Experimental design of ssDNA assay is shown. Cells were labelled with IdU for 24 h, as indicated, washed and left to recover for 2 h, then treated or not with 4 mM HU. In parallel samples, the MRE11 activity is chemically inhibited with 50 µM Mirin, alone or in combination with HU-induced replication stress. After treatment, cells were fixed and stained with an anti-IdU antibody without denaturing the DNA to specifically detect parental ssDNA. Horizontal black lines represent the mean SE; n = 3. Error bars represent standard error (ns, not significant; **, p<0.01; ****, p<0.0001; two-tailed Student’s t test). Representative images are shown. DNA was counterstained with DAPI (blue).</p>
<p>(<strong>B</strong>) Analysis of chromatin binding of MRE11 and RAD51 in shWRNIP1<sup>WT</sup> and shWRNIP1 cells. Chromatin fractions of cells, treated or not with 4 mM HU, were analysed by immunoblotting. The membrane was probed with the anti-WRNIP1, anti-MRE11 and anti-RAD51 antibodies. LAMIN B1 was used as a loading for the chromatin fraction. Total amount of RAD51 and MRE11 (Input) in the cells was determined with the relevant antibodies. LAMIN B1 was used as a loading control. In the graph, the fold increase respect to the wild-type untreated of the normalized ratio of the chromatin-bound RAD51 (or MRE11)/ total RAD51 (or MRE11) is reported for each cell line.</p>
<p>(<strong>C</strong>) Analysis of DNA-protein interactions between ssDNA and endogenous RAD51 in shWRNIP1<sup>WT </sup>and shWRNIP1 cells by <em>in situ</em> PLA assay. Experimental designed used for the assay is given. Cells were labelled with IdU for 24 h, as indicated, washed and left to recover for 2 h, then treated or not with 4 mM HU for 4 h. Next, cells were fixed, stained with an anti-IdU antibody without denaturing the DNA to specifically detect parental-strand ssDNA, and subjected to PLA assay as described in the “Experimental procedures” section. Antibodies raised against IdU or RAD51 were used to reveal ssDNA or endogenous RAD51 respectively. Each red spot represents a single interaction between ssDNA and RAD51. No spot has been revealed in cells stained with each single antibody (negative control). DNA was counterstained with DAPI (blue). Representative images of the PLA assay are given. Graph shows the number of PLA spots per cell. Horizontal black lines represent the mean value (ns, not significant; **, p < 0.01; two-tailed Student’s t test); n = 3.</p>
<p>(<strong>D</strong>) Localization of WRNIP1, MRE11 and RAD51 to stalled replication forks. Forks were isolated by CldU-co-immunoprecipitation (CldU-IP). shWRNIP1<sup>WT</sup> or shWRNIP1 cells were pulse-labelled with CldU, then fixed or treated with HU. Cells were cross-linked, and the nuclear extracts were isolated (Input) and subjected to CldU-IP using an anti-CldU antibody (CldU-IP). The membranes were probed with the anti-WRNIP1 or anti-RAD51 antibodies. After stripping, the membranes were probed with an anti-MRE11 antibody. LAMIN B1 and GAPDH were used as loading controls (Input). Ponceau S was used as a loading control of CldU-IP. Dot blot analysis was performed to confirm that equal amounts of immunoprecipitated DNA from each sample. 10% of each IP was loaded on a nitrocellulose membrane. The membrane was probed with an anti-CldU antibody. The graph shows the normalized ratio of the proteins co-immunoprecipitated with CldU (CldU Co-IP proteins)/ the total of labelled DNA immunoprecipitated with CldU (CldU IP) for each cell line after replication stress from two independent experiments. The dots in the graph represent the individual data points from each single experiment. Horizontal black line represents the mean value from two replicates; n = 2.</p>
|
https://api.sourcedata.io/file.php?figure_id=8328
|
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] |
|
27242363
|
10.15252/embj.201593265
|
WRNIP1 protects stalled forks from degradation and promotes fork restart after replication stress
|
2016
|
Figure 4
|
<p><strong>Fig</strong><strong>ure</strong><strong> 4.</strong> <strong>RAD51 protects nascent DNA strand from degradation after fork stalling in the absence of WRNIP1 </strong></p>
<p>(<strong>A</strong>) Experimental scheme of pulse-labelling of DNA fibers in wild-type cells (shWRNIP1<sup>WT</sup>) or WRNIP1-deficient cells (shWRNIP1). Cells were labelled with IdU and exposed or not to 25 μM RAD51 inhibitor, then treated or not with 4 mM HU.</p>
<p>(<strong>B</strong>) Representative IdU tract length distributions in shWRNIP1<sup>WT</sup> cells (left graph) or shWRNIP1 cells (right graph). Median tract lengths are reported in parentheses. See Tables S1 and S2 for details on the data sets and statistical test. Representative DNA fiber images are reported. Scale bars, 10 µm.</p>
<p>(<strong>C</strong>) Scheme of DNA fiber tract analysis in shWRNIP1 cells. Cells were transfected with an empty vector or a plasmid expressing a wild-type human RAD51, and 48 h thereafter labelled with IdU and treated or not with 4 mM HU.</p>
<p>(<strong>D</strong>) Representative IdU tract length distributions in shWRNIP1 cells or shWRNIP1 cells expressing exogenous wild-type RAD51 after HU exposure. Median tract lengths are given in parentheses. See Tables S1 and S2 for details on the data sets and statistical test. Representative DNA fiber images are given. Scale bars, 10 µm. Western blot shows the expression of the RAD51 protein in shWRNIP1 cells. The membrane was probed with an anti-RAD51. LAMIN B1 was used as a loading control.</p>
|
https://api.sourcedata.io/file.php?figure_id=8329
|
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|
27242363
|
10.15252/embj.201593265
|
WRNIP1 protects stalled forks from degradation and promotes fork restart after replication stress
|
2016
|
Figure 5
|
<p><strong>Fig</strong><strong>ure</strong><strong> 5.</strong> <strong>WRNIP1 stabilizes RAD51 on stalled forks</strong></p>
<p>(<strong>A</strong>) Co-immunoprecipitation experiments in HEK293T cells transfected with empty vector or FLAG-WRNIP1 plasmid. Cells were treated or not with HU. After treatment, cell lysates were immunoprecipitated (FLAG IP) using anti-FLAG antibody. The presence of WRNIP1, BRCA2 and RAD51 was assessed by immunoblotting using the anti-FLAG, anti-RAD51 and anti-BRCA2 antibodies, respectively. Whole cell extracts were analysed (Input). The membrane was probed with the same antibodies used for IP. GAPDH was used as a loading control.</p>
<p>(<strong>B</strong>) Analysis of protein-protein interactions between WRNIP1 and endogenous RAD51 in wild-type (shWRNIP1<sup>WT</sup>) or WRNIP1-mutant (shWRNIP1<sup>T294A</sup>) cells by <em>in situ</em> PLA assay. Cells were labelled with IdU for 24 h, washed and left to recover for 2 h, then treated or not with 4 mM HU. Antibodies raised against FLAG-Tag and RAD51 were used to reveal FLAG-WRNIP1 or endogenous RAD51 respectively. Each red spot represents a single interaction between WRNIP1 and RAD51. No spot has been revealed in cells stained with each single antibody (negative control). DNA was counterstained with DAPI (blue). Representative images of the PLA assay are shown. Graph shows the mean number of PLA spots per cell SE. Error bars represent standard error (ns, not significant; two-tailed Student’s t test); n = 3.</p>
<p>(<strong>C</strong>) Experimental scheme of pulse-labelling of DNA fibers in wild-type cells (shWRNIP1<sup>WT</sup>) or WRNIP1-deficient cells (shWRNIP1). Cells were transfected with <em>BRCA2</em> siRNA (siBRCA2), and 48 h thereafter labelled with IdU, then treated or not with 4 mM HU.</p>
<p>(<strong>D</strong>) Representative IdU tract length distributions in shWRNIP1<sup>WT/siBRCA2</sup> or shWRNIP1<sup>siBRCA2</sup> cells treated or not with HU. Median tract lengths are given in parentheses. See Tables S1 and S2 for details on the data sets and statistical test. Representative DNA fiber images are reported. Scale bars, 10 µm. Western blot shows BRCA2 depletion in shWRNIP1<sup>WT</sup> and shWRNIP1 cells. The membrane was probed with an anti-BRCA2 or anti-WRNIP1. GAPDH was used as a loading control.</p>
<p>(<strong>E</strong>) Experimental scheme of pulse-labelling of DNA fibers in shWRNIP1 cells. Cells were transfected with control siRNA (shWRNIP1<sup>siCtrl</sup>) or <em>FBH1</em> siRNA (shWRNIP1<sup>siFBH1</sup>), and 48 h thereafter labelled with IdU, then treated or not with 4 mM HU.</p>
<p>(<strong>F</strong>) Representative IdU tract length distributions in shWRNIP1<sup>siCtrl</sup> or shWRNIP1<sup>siFBH1</sup> cells with or without HU treatment. Representative DNA fiber images are reported. Scale bars, 10 µm. Western blot shows FBH1 depletion in the cells. The membrane was probed with an anti-FBH1. GAPDH was used as a loading control. Median tract lengths are given in parentheses. See Tables S1 and S2 for details on the data sets and statistical test.</p>
<p>(<strong>G</strong>) Analysis of chromatin binding of RAD51 in shWRNIP1 cells depleted for FBH1. Cells were transfected with control siRNA (shWRNIP1<sup>siCtrl</sup>) or <em>FBH1</em> siRNA (shWRNIP1<sup>siFBH1</sup>), and 48 h treated or not with HU for 4h. Chromatin fractions of cells were analysed by immunoblotting. The membrane was probed with the anti-FBH1 and anti-RAD51 antibodies. LAMIN B1 was used as a loading for the chromatin fraction. Total amount of RAD51 (Input) in the cells was determined with the relevant antibodies. GAPDH was used as a loading control. The ratio of the RAD51/LAMIN B1 signal (chromatin) is reported below each lane.</p>
|
https://api.sourcedata.io/file.php?figure_id=8330
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|
27242363
|
10.15252/embj.201593265
|
WRNIP1 protects stalled forks from degradation and promotes fork restart after replication stress
|
2016
|
Figure 6
|
<p><strong>Fig</strong><strong>ure</strong><strong> 6.</strong> <strong>Loss of</strong> <strong>WRNIP1 or its ATPase activity results in DNA damage accumulation and enhanced chromosomal instability in response to fork stalling </strong></p>
<p>(<strong>A</strong>) Analysis of DNA damage accumulation. Wild-type (shWRNIP1<sup>WT</sup>), WRNIP1-deficient (shWRNIP1) or mutant (shWRNIP1<sup>T294A</sup>) cells were treated or not with 4 mM HU for 4 h, then subjected to -H2AX immunofluorescence. Graph shows data presented as mean of -H2AX-positive cells SE from three independent experiments; n = 3. Error bars represent standard error (*, p < 0.1; **, p < 0.01; two-tailed Student’s t test). Representative images of nuclei showing the different number of foci per nucleus are reported.</p>
<p>(<strong>B</strong>) Analysis of DNA breakage accumulation. shWRNIP1<sup>WT</sup>, shWRNIP1 and shWRNIP1<sup>T294A</sup> cells were treated as in (A), then subjected to alkaline Comet assay. Graph shows data presented as mean tail moment SE from three independent experiments; n = 3. Error bars represent standard error (*, p < 0.1; **, p < 0.01; two-tailed Student’s t test). Representative images are shown.</p>
<p>(<strong>C</strong>) Evaluation of cell death. shWRNIP1<sup>WT</sup> shWRNIP1 and shWRNIP1<sup>T294A </sup>cells were treated or not with 4 mM HU for 16 h. Cell viability was evaluated by LIVE/DEAD fluorescent assay. Data are expressed as mean of dead cells SE from three independent experiments; n = 3. Error bars represent standard error (*, p < 0.1; **, p < 0.01; two-tailed Student’s t test). Representative images of double-staining of viable (green) and dead (red) cells are shown.</p>
<p>(<strong>D</strong>) Experimental scheme for evaluation of the chromosomal aberrations is shown. shWRNIP1<sup>WT</sup> shWRNIP1 and shWRNIP1<sup>T294A </sup>cells were treated or not with 4 mM HU, then left to recover for 16h in drug-free medium and metaphases collected with colcemid. Next, cells were fixed and processed as reported in “Supplemental information” section. Dot plot shows the number of chromosomal aberrations per cell. Horizontal black lines represent the mean SE. Error bars represent standard error (ns, not significant; **, p < 0.01; two-tailed Student’s t test). Representative Giemsa-stained metaphases of cells treated or not with 4 mM HU. Arrows indicate chromosomal aberrations.</p>
<p>(<strong>E</strong>) Experimental scheme of the chromosomal aberration analysis is given. The experiment was carried out as in (D) but cells were pre-treated or not with 50 µM Mirin. Dot plot shows the effect of Mirin exposure on the number of chromosome aberrations per cell in shWRNIP1 cells. Horizontal black lines represent the mean SE. Error bars represent standard error (ns, not significant; **, p < 0.01; two-tailed Student’s t test). Representative Giemsa-stained metaphases of shWRNIP1 cells treated with Mirin alone or in combination with HU. Arrows indicate chromosomal aberrations.</p>
<p>(<strong>F</strong>) Experimental design of the chromosomal aberration assay is reported. shWRNIP1 cells were transfected with control siRNAs (siCtrl) or <em>FBH1</em> siRNA (siFBH1). Fourth-eight hours thereafter, cells were treated or not with 4 mM HU and then left to recover for 16 h. Metaphases were collected with colcemid and prepared as reported in “Supplemental information” section. Dot plot shows the number of chromosomal aberrations per cell. Western blot shows FBH1 depletion in the cells. The membrane was probed with an anti-FBH1. GAPDH was used as a loading control. Horizontal black lines represent the mean SE. Error bars represent standard error. (**, p < 0.01; two-tailed Student’s t test).</p>
|
https://api.sourcedata.io/file.php?figure_id=8331
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|
10.15252/embr.202256271
|
ABCB-mediated shootward auxin transport feeds into the root clock
|
2023
|
Figure 2
|
<p><strong>Figure 2. The <em>amiR-2572</em> line has reduced auxin oscillation amplitude and LR density defects</strong>.</p><p><strong>A Luciferase image of the whole <em>WT and amiR-2572</em> seedlings after 10 min exposure to visualize the pre-branch sites in the root</strong> by <em>DR5:LUC</em> luminescence.</p><p><strong>B</strong> Quantification of pre-branch site density in 10-day-old WT and <em><strong>amiR-2572</strong></em> determined by <em>DR5:LUC</em> luminescence, n= 26 (WT and <em><strong>amiR-2572</strong></em>).</p><p><strong>C</strong> Confocal images of root tips in 5-day-old Col-0, <em>amiR-2572</em> and <em>syn-tasi-1522A#1</em> seedlings. LRC cells were indicated by white asterisks. The distal LRC cells were indicated by white arrows The scale bar represents 50 µm.</p><p><strong>D-F</strong> Quantification of meristem size (<strong>D</strong>), LRC cell number (<strong>E</strong>), and distal LRC cell length (<strong>F</strong>) in 5-day-old Col-0, <em>amiR-2572</em> and <em>syn-tasi-1522A#1</em> seedlings. The meristem size was measured along the yellow dashed lines in (<strong>C)</strong>, as estimated by the distance from the QC to the first elongating cortical cell, n<sub>D/E/F</sub>= 33/30/22 (WT), 34/30/26 (<em>amiR-2572</em>) and 37/30/23 (<em>syn-tasi-1522</em>) from 3 independent biological repeats.</p><p><strong>G</strong> Macroview stereo microscopic view of DR5:VENUS expression in root tips of 3-day-old WT, <em>amiR-2572</em> and <em>syn-tasi-1522A#1</em> seedlings, red arrows indicate DR5 stripes in the lateral root cap. Scale bar = 50 µm</p><p><strong>H</strong> Quantifications of the time interval(s) between the consecutive disappearance of DR5:VENUS stripes in the most-distal lateral root cap in 3-day-old WT, <em>amiR-2572</em> and <em>syn-tasi-1522A#1</em>. n= 15 (WT), 18 (<em>amiR-2572</em>) and 17 (<em>syn-tasi-1522A#1</em>)</p><p><strong>I, J</strong> Quantification of the oscillation period (<strong>I</strong>) and amplitude (<strong>J</strong>) of <em>DR5::LUC</em> in 3-day-old WT and <em>amiR-2572, n= 21 (</em>WT and <em>amiR-2572).</em></p><p>Data information: For (B, I, J), Unpaired two-tailed Student's t-test with Welch's correction, P<0.05 (*), P<0.001(***). For (D-F, H), One-way ANOVA in combination with Tukey's multiple comparisons test, significant differences (P ≤ 0.05) are indicated by different lowercase letters. Central bands in the box plots show the medians; box limits indicate the 25th and 75th percentiles as determined by R software; whiskers extend 1.5 times the interquartile range from the 25th and 75th percentiles, outliers are represented by dots.</p>
|
https://api.sourcedata.io/file.php?figure_id=52094
|
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"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "DR5",
"type": "geneprod",
"uniprot_ids": [
"F4KG58"
]
}
] |
||
10.15252/embr.202256271
|
ABCB-mediated shootward auxin transport feeds into the root clock
|
2023
|
Figure 3
|
<p><strong>Figure 3. Analysis of plasma membrane localisation and cellular transport activities.</strong></p><p><em><strong>A Co-localisation of</strong> YFP-ABCB15 with P</em>ropidium Iodide (PI) in root epidermal cells of 3-day-old seedlings. A plot of the fluorescence intensity of YFP and PI along the dashed lines shows the colocalization of the YFP and PI intensity peaks. Scale bars = 10 µm.</p><p><strong>B</strong> Presence of <em>YFP-ABCB15</em> on Hechtian strands of epidermal cells of 3-day-old seedlings after 10min 0.8M mannitol treatment. Cell walls are counterstained by Propidium Iodide (PI). The white arrow indicated the Hechtian strands. Scale bars = 10 µm.</p><p><strong>C IAA export assay. Export of [<sup>3</sup>H]-IAA, assayed in parallel from tobacco mesophyll protoplasts expressing ABCB1, ABCB15-22 and ABCB17<sup>P980G</sup> against vector control. mean ± SE; n = 26 (vector control), 44 (ABCB1), 5 (ABCB15), 4 (ABCB16), 9 (ABCB17), 5 (ABCB18), 9 (ABCB22) and 8 (ABCB17<sup>P980G</sup>),transport experiments generated from independent tobacco transfections.</strong></p><p><strong>D Export assay of plant hormones IAA (n<sub>VC/ABCB17</sub> = 26/9), IBA (n<sub>VC/ABCB17</sub> =6/6), BA (n<sub>VC/ABCB17</sub> =7/7), ABA (n<sub>VC/ABCB17</sub> =6/6), tZ (n<sub>VC/ABCB17</sub> =7/6) and malate (n<sub>VC/ABCB17</sub> =6/16) in parallel from <em>N. benthamiana</em> mesophyll protoplasts expressing ABCB17 against vector control. mean ± SE; transport experiments generated from independent tobacco transfections.</strong></p><p><strong>E [<sup>3</sup>H]-IAA export from WT, <em>abcb15-1</em>, <em>abcb16-1</em>, <em>abcb17-1</em>, <em>abcb18-1</em>, <em>abcb22-1, amiR-2572</em> and <em>syn-tasi-1522A#1</em> Arabidopsis leaf mesophyll protoplasts, mean ± SE; n= 9 (WT), 4 (<em>abcb15-1)</em>, 3 (<em>abcb16-, abcb17-1, abcb18-1</em>) and 4 (<em>abcb22-1</em>)<em>,</em> n = 4 (WT, <em>amiR-2572)</em> and 6 (<em>syn-tasi-1522A#1)</em></strong></p><p>Data information: For (C-E), Unpaired two-tailed Student's t-test with Welch's correction, P<0.05 (*), P<0.01 (**).</p>
|
https://api.sourcedata.io/file.php?figure_id=52095
|
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"Q9LHD1"
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"Q9ZR72"
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"mapping_status": "mapped",
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"role": "intervention",
"text": "ABCB1",
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"Q9ZR72"
]
},
{
"ext_dbs": "NCBI gene",
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"ext_tax_names": "Arabidopsis thaliana",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "822463",
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"role": "intervention",
"text": "ABCB15",
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"uniprot_ids": [
"Q9LHD1"
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{
"ext_dbs": "NCBI gene",
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"ext_tax_names": "Arabidopsis thaliana",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "822463",
"original_type": "gene",
"role": "intervention",
"text": "ABCB15",
"type": "geneprod",
"uniprot_ids": [
"Q9LHD1"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "822465",
"ext_tax_ids": "3702",
"ext_tax_names": "Arabidopsis thaliana",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "822465",
"original_type": "gene",
"role": "intervention",
"text": "ABCB16",
"type": "geneprod",
"uniprot_ids": [
"Q9LSJ8"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "822467",
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"ext_tax_names": "Arabidopsis thaliana",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "822467",
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"text": "ABCB17",
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},
{
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"original_type": "gene",
"role": "intervention",
"text": "ABCB17",
"type": "geneprod",
"uniprot_ids": [
"Q9LSJ6"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "822468",
"ext_tax_ids": "3702",
"ext_tax_names": "Arabidopsis thaliana",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "822468",
"original_type": "gene",
"role": "intervention",
"text": "ABCB18",
"type": "geneprod",
"uniprot_ids": [
"Q9LSJ5"
]
},
{
"ext_dbs": "NCBI gene",
"ext_ids": "822471",
"ext_tax_ids": "3702",
"ext_tax_names": "Arabidopsis thaliana",
"mapping_source": "ncbi_gene",
"mapping_status": "mapped",
"ncbi_gene_id": "822471",
"original_type": "gene",
"role": "intervention",
"text": "ABCB22",
"type": "geneprod",
"uniprot_ids": [
"Q9LSJ2"
]
}
] |
||
10.15252/embr.202256271
|
ABCB-mediated shootward auxin transport feeds into the root clock
|
2023
|
Figure 4
|
<p><strong><em>Figure 4.</em> ABCB15-22 contribute to shootward auxin transport for LR induction.</strong></p><p><strong>A Shootward auxin transport assay of [<sup>3</sup>H]-IAA and [<sup>14</sup>C]-BA in WT (Col-0) and <em>amiR-2572 roots</em>, mean ± SE; n = 3 (Col-0 and <em>amiR-2572; IAA</em>); n=4 (Col-0; BA) and 3 (<em>amiR-2572</em>; BA)</strong></p><p><strong>B Analysis of <em>DR5::VENUS</em> expression in the root elongation zone of 4-day-old <em>pWOX5:XVE>>YUC1-2A-TAA1</em>, in Control and <em>amiR-2572</em> treated with β-estradiol (5 µM) for 0, 7.5 and 9h. Images are composed of several tiles generated in a single snap with automatic assembly, PI in gray. The zoomed images of the yellow squares are presented below each root showing the accumulation of the DR5::VENUS signal in the elongation zone. Scale bar = 100µm.</strong></p><p><strong>C Quantification of <em>DR5::VENUS</em> signals in the epidermis of the elongation zone shown in (B). n<sub>0h</sub>=40/40, n<sub>7.5h</sub>=70/70, n<sub>9h</sub>=140/160 (WT/<em>amiR-2572</em>) from at least 4 (0h), 7 (7.5h), 14 (9h) seedlings of each treatment</strong></p><p><strong>D LR density of <em>pWOX5:XVE>>YUC1-2A-TAA1,</em> in control and <em>amiR-2572</em> treated with β-estradiol. 7-day-old seedlings were transferred to MS plates containing 500 nM β-estradiol. The primary root length and the total number of emerged LRs were recorded after 5 and 8 days of treatment.n = 9 (Col-0; Mock), 7 (<em>amiR-2572;</em> Mock), 11 (Col-0; Estradiol) and 10 ( <em>amiR-2572;</em> Estradiol)</strong></p><p>Data information: For (A, C, D), Unpaired two-tailed Student's t-test with Welch's correction, P<0.05 (*), P<0.001 (***). Central bands in the box plots show the medians; box limits indicate the 25th and 75th percentiles as determined by R software; whiskers extend 1.5 times the interquartile range from the 25th and 75th percentiles, outliers are represented by dots.</p>
|
https://api.sourcedata.io/file.php?figure_id=52096
|
[
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"ext_tax_names": "Arabidopsis thaliana",
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"role": "assayed",
"text": "DR5",
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"F4KG58"
]
},
{
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"ext_tax_names": "Arabidopsis thaliana",
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"F4KG58"
]
}
] |
||
10.15252/embr.202256271
|
ABCB-mediated shootward auxin transport feeds into the root clock
|
2023
|
Figure 5
|
<p><strong>Figure 5. ABCB15-22 expressed <em>in the outer layers of the root meristem.</em></strong></p><p><strong>A, B</strong> Expression pattern of <em>proABCB15:NLS-GFP-GUS</em>, <em>proABCB16:NLS-GFP-GUS</em>, <em>proABCB17:NLS-GFP-GUS</em>, <em>proABCB18:NLS-GFP-GUS</em>, and <em>proABCB22:NLS-GFP-GUS</em> expression in roots of 3-day-old seedlings, using confocal microscopy showing longitudinal overview pictures (Propidium iodide in magenta), and images zoomed on the epidermis and LRC corresponding to yellow squares <strong>(A)</strong>; cytological sections of GUS stained roots of 3-day-old seedlings, counterstained with ruthenium red (<strong>B</strong>). Scale bars represent 20 µm for both graphs.</p><p><strong>C</strong> Root annotation schematic representation of the summary expression pattern of ABCB15-22 in the root meristem.</p>
|
https://api.sourcedata.io/file.php?figure_id=52097
|
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{
"ext_dbs": "Uniprot",
"ext_ids": "Q9LHD1",
"ext_tax_ids": "3702",
"ext_tax_names": "Arabidopsis thaliana",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "ABCB15",
"type": "geneprod",
"uniprot_ids": [
"Q9LHD1"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q9LSJ8",
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"ext_tax_names": "Arabidopsis thaliana",
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"ncbi_gene_id": null,
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"role": "assayed",
"text": "ABCB16",
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"uniprot_ids": [
"Q9LSJ8"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q9LSJ6",
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"ext_tax_names": "Arabidopsis thaliana",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "ABCB17",
"type": "geneprod",
"uniprot_ids": [
"Q9LSJ6"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q9LSJ5",
"ext_tax_ids": "3702",
"ext_tax_names": "Arabidopsis thaliana",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "ABCB18",
"type": "geneprod",
"uniprot_ids": [
"Q9LSJ5"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "Q9LSJ2",
"ext_tax_ids": "3702",
"ext_tax_names": "Arabidopsis thaliana",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "ABCB22",
"type": "geneprod",
"uniprot_ids": [
"Q9LSJ2"
]
}
] |
||
10.15252/embr.202256271
|
ABCB-mediated shootward auxin transport feeds into the root clock
|
2023
|
Figure 6
|
<p><strong>Figure 6. Tissue-specific silencing of ABCB15-22 impairs auxin oscillation amplitude and LR density.</strong></p><p><strong>A</strong> <em>Fluorescence of YFP-ABCB17 in the r</em>oot meristem and leaf in 3-day-old F1 crosses with WT, <em>syn-tasi-1522A#1</em> and <em>amiR-2572,</em> propidium iodide (PI) in magenta. Red arrows highlight the position of the epidermis . Scale bars = 50 µm.</p><p><strong>B</strong> Schematic representation of root geometry with the indication of regions of interest for <em>YFP-ABCB17</em> signal quantification. Red (Stele), and black (epidermis/LRC).</p><p><strong>C, D</strong> Quantification of <em>YFP-ABCB17</em> fluorescence intensity in the stele (<strong>C</strong>) and epidermis/LRC (<strong>D</strong>) of <strong>A,</strong> measured at regions of interest corresponding to colors shown in panel <strong>B.</strong> n= 16 (WT, <em>syn-tasi-1522A#1</em>) and 14 (<em>amiR-2572,</em>)</p><p><strong>E</strong> Quantification of <em>YFP-ABCB17</em> fluorescence intensity in the leaf epidermis. The average fluorescence intensity of 5 cells per leaf was measured as one sample. n= 16 (WT, <em>syn-tasi-1522A#1</em>) and 14 (<em>amiR-2572,</em>)</p><p><strong>F</strong> Quantification of pre-branch site density in 10-day-old WT and <em>syn-tasi-1522A#1</em> determined by <em>DR5:LUC</em> luminescence, n= 15 (WT) and 14 (<em>syn-tasi-1522A#1</em>).</p><p><strong>G,H</strong> Quantification of the oscillation period (<strong>G</strong>) and amplitude (<strong>H</strong>) of <em>DR5::LUC</em> in 3-day-old WT and <em>syn-tasi-1522A#1,</em> n= 27 (WT) and 23 (<em>syn-tasi-1522A#1</em>).</p><p>Data information: For (C-E), One-way ANOVA in combination with Tukey's multiple comparisons tests; significant differences (P ≤ 0.01) are indicated by different lowercase letters; For (F-H), Unpaired two-tailed Student's t-test with Welch's correction, P<0.001 (***). Central bands in the box plots show the medians; box limits indicate the 25th and 75th percentiles as determined by R software; whiskers extend 1.5 times the interquartile range from the 25th and 75th percentiles, outliers are represented by dots.</p>
|
https://api.sourcedata.io/file.php?figure_id=52098
|
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"mapping_status": "mapped",
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"original_type": "protein",
"role": "assayed",
"text": "ABCB17",
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{
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"text": "ABCB17",
"type": "geneprod",
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]
},
{
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"ext_tax_names": "Arabidopsis thaliana",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
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"role": "assayed",
"text": "ABCB17",
"type": "geneprod",
"uniprot_ids": [
"Q9LSJ6"
]
},
{
"ext_dbs": "Uniprot",
"ext_ids": "F4KG58",
"ext_tax_ids": "3702",
"ext_tax_names": "Arabidopsis thaliana",
"mapping_source": "direct",
"mapping_status": "mapped",
"ncbi_gene_id": null,
"original_type": "protein",
"role": "assayed",
"text": "DR5",
"type": "geneprod",
"uniprot_ids": [
"F4KG58"
]
}
] |
||
10.15252/embr.201948483
|
MicroRNA-195 controls MICU1 expression and tumor growth in ovarian cancer
|
2020
|
Figure 1
|
<sd-panel> <p><strong>Figure 1. miR-195 and MICU1 levels are inversely related in ovarian cancer cell lines</strong></p> <p><strong>(A)</strong> CP20 and OVCAR4 cells were transfected with either non-target miRNA control (miR-CTL), miR-15a, or miR-195. 72h following transfection, cells were lysed and immunoblotted for detection of MICU1, BMI1, BCL2, and MFN2. GAPDH and VDAC were used as loading control.</p> <p><strong>(B)</strong> miR-195 expression in FTE188 and ovarian cell lines as determined by RT-qPCR normalized with U6. Data are mean ± S.D., n=3 (Biological repeats). *P<0.05, Student's <em>t</em>-test.</p> <p><strong>(C)</strong> Expression of MICU1 in FTE188 and various ovarian cell lines as determined by immunoblotting. Actin is used as the loading control.</p> <p><strong>(D)</strong> Anti-miR-195 was transfected in the FTE188 cell line, level of miR-195 was measured using RT-qPCR (left) and MICU1 levels were measured using immunoblotting (right). Data are mean ± S.D., n=3 (Biological repeats). *P<0.05, Student's <em>t</em>-test.</p> </sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=34620
|
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"ncbi_gene_id": "406948",
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"text": "miR-15a",
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"text": "miR-195",
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{
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"original_type": "protein",
"role": "assayed",
"text": "MICU1",
"type": "geneprod",
"uniprot_ids": [
"Q9BPX6"
]
}
] |
||
10.15252/embr.201948483
|
MicroRNA-195 controls MICU1 expression and tumor growth in ovarian cancer
|
2020
|
Figure 2
|
<sd-panel> <p><strong>Figure 2. Ectopic expression of miR-195 suppresses ovarian cancer clonal growth, migration and invasion</strong></p> <p><strong>(A, B)</strong> CP20, OVCAR4, and OVSAHO cells were transfected with non-target micro RNA control (miR-CTL) or miR-195, 24 h post-transfection, cells were recounted and plated as single cells for anchorage-dependent <strong>(A)</strong> or anchorage-independent <strong>(B)</strong> clonal growth. After 10 (CP20) or 14 (OVCAR4 and OVSAHO) days, colonies were quantified using an Optronix GelCount colony counter. The left panel shows representative images of the colonies and the right panel depicts a graphical representation of data presented as percent clonal growth relative to the control (miR-CTL).</p> <p><strong>(C)</strong> Migration of miR-CTL, miR-195, and miR-195+ MICU1 (pLYS1-MICU1-Flag) transfected cells, towards serum gradient was examined and the number of cells per field was counted. The left panel shows representative images and the right panel depicts a graphical representation of relative migration compared to the control (miR-CTL).</p> <p><strong>(D)</strong> Invasion of miR-CTL, miR-195, and miR-195 + MICU1 cells through fibronectin-coated filters was examined using Boyden chamber and number of cells per field was counted. Left panel shows representative images and the right panel depicts a graphical representation of relative invasion compared to the control (miR-CTL).</p> <p><strong>Data information:</strong> Data are mean ± S.D. n=3 (Biological repeats). *P<0.05 when comparing with miR-CTL, <sup>#</sup>P<0.05 when comparing with miR-195 by Student's t-test. Scale Bar = 0.1 mm.</p> </sd-panel>
|
https://api.sourcedata.io/file.php?figure_id=34622
|
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"original_type": "gene",
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"text": "miR-195",
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},
{
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"ext_tax_ids": "9606",
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"mapping_status": "unmapped",
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"role": "intervention",
"text": "miR-195",
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{
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"mapping_source": "unmapped",
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"text": "miR-195",
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||
10.15252/embr.201948483
|
MicroRNA-195 controls MICU1 expression and tumor growth in ovarian cancer
|
2020
|
Figure 3
|
<sd-panel> <p><strong>Figure 3. MICU1 is a direct target of miR-195</strong></p> <p><strong>(A)</strong> The miR-195 binding site as predicted by TargetScan.</p> <p><strong>(B)</strong> MICU1 3'UTR in LightSwitch™ 3′UTR Reporter Vector (wild type or miR-195 binding site deleted) was co-transfected with either non- target miR control (miR-CTL) or different concentrations of miR-195. Post 24h transfection luciferase (Renilla) activity was measured. Relative light units (RLU) compared to miR-CTL were plotted. Data are mean ± S.D. n=3 (Biological repeats). *P<0.05, Student's t-test.</p> <p><strong>(C&D)</strong> CP20 cells were transfected as indicated, 48 h post transfection 4x10<sup>6</sup> cells were permeabilized, and extra-mitochondrial calcium ([Ca<sup>2+</sup>]<sub>out)</sub> clearance was measured, representative traces of [Ca<sup>2+</sup>]<sub>out</sub>‑ clearance in miR-CTL and miR-195 or control siRNA (siCTL) and siMICU1 transfected cells. [Ca2+]<sub>out</sub> pulses and FCCP were delivered as indicated.</p> <p><strong>(E)</strong> Bar graph illustrating the number of Ca<sup>2+</sup> pulses handled by control miR, miR-195, siCTL and siMICU1 transfected cells. Mean ±SEM; n=3-4 (Biological repeats). *P<0.05, Student's t-test.</p> <p><strong>(F)</strong> Representative [Ca<sup>2+</sup>](m) traces after addition of FCCP (10 µM) in permeabilized CP20 cells transfected with non-target miR-CTL or miR-195.</p> <p><strong>(G)</strong> Quantification of resting matrix [Ca<sup>2+</sup>](m) after addition of FCCP. n=5 (Biological repeats) *P<0.05, Student's t-test,</p> <p><strong>(H)</strong> Representative traces of mitochondrial membrane potential (∆Ψ<sub>μ</sub>) in CP20 cells transfected with miR-CTL or miR-195.</p> <p><strong>(I)</strong> Quantification of relative ∆Ψ<sub>μ.</sub> (n=5, Biological repeats).</p> <p><strong>(J)</strong> Intracellular lactate was measured in miR-CTL, miR-195, siCTL, and siMICU1 expressing OVCAR4, CP20, and OVSAHO cells. n=3, biological repeats *P<0.05, Student's t-test.</p> <p><strong>(K&L)</strong> miR-CTL, miR-195, or miR-195 + pLYS1-MICU1-Flag transfected cells were stained with MitoSOX Red, and mitochondrial ROS levels were determined by flow cytometry. The histogram shows representative staining and bar graph (right) shows results of three independent experiments. Mean ± SEM; . 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=34624
|
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