Table S4 . (E) Expression of genes significantly upregulated by ccRCC2 compared two-by-two to all other non-tumoral cell clusters of the TME. Color corresponds to the intensity of average expression, and dot size to the percentage of cells expressing the gene in the cluster. (F) Expression of VEGFα, EGFR, TGFα, ANG, CD70, OPN, PLXNB2 by two ccRCC cell lines (786-O, Caki2), and a proximal tubule primary cell line (RPTEC), at protein levels. Expression of surface markers is quantified by flow cytometry using specific mean fluorescence intensity (MFI), corresponding to the MFI obtained with specific antibody subtracted by those with the corresponding isotype (n = 5 up to 7 biologically independent replicates). Secreted molecules were measured from cell lines supernatants (n = 8 biologically independent replicates). Data are represented as mean values ±SEM. Conditions were compared using Kruskal–Wallis statistical tests combined with a Dunn’s post-hoc. ns, not significant; ∗p < 0.05; ∗∗p < 0.01; ∗∗∗p < 0.001; ∗∗∗∗p < 0.0001. See also
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Journal: iScience
Article Title: Large-scale analysis of cell-cell communication reveals angiogenin-dependent tumor progression in clear cell renal cell carcinoma
doi: 10.1016/j.isci.2023.108367
Figure Lengend Snippet: Characterization of ccRCC cancer cell-specific vocabulary within the TME (A) UMAP of the cancer cells from tumor samples. Two sub-clusters were identified at a resolution of 0.1: ccRCC1 (pink), and ccRCC2 (blue). Proportions of each sub-cluster among the 3 patients are represented later in discussion the UMAP. (B) Proportion of expressed genes belonging to the ribosomal gene family (in percentage), in the function of the total number of expressed genes, for each cancer cell subcluster. (C) Expression of CA9 (ccRCC cancer cell marker) for each cancer cell subcluster (left), and enrichment score of communication genes in each cancer cell subcluster (right). The scores were compared by Wilcoxon tests. (D) Functional enrichment analysis of ccRCC1 compared to ccRCC2 cells (left), or conversely (right). Genes differentially expressed between ccRCC1 and ccRCC2 cells and filtered for minimum log2FC of 0.5 and p < 0.05 were considered. See also Table S4 . (E) Expression of genes significantly upregulated by ccRCC2 compared two-by-two to all other non-tumoral cell clusters of the TME. Color corresponds to the intensity of average expression, and dot size to the percentage of cells expressing the gene in the cluster. (F) Expression of VEGFα, EGFR, TGFα, ANG, CD70, OPN, PLXNB2 by two ccRCC cell lines (786-O, Caki2), and a proximal tubule primary cell line (RPTEC), at protein levels. Expression of surface markers is quantified by flow cytometry using specific mean fluorescence intensity (MFI), corresponding to the MFI obtained with specific antibody subtracted by those with the corresponding isotype (n = 5 up to 7 biologically independent replicates). Secreted molecules were measured from cell lines supernatants (n = 8 biologically independent replicates). Data are represented as mean values ±SEM. Conditions were compared using Kruskal–Wallis statistical tests combined with a Dunn’s post-hoc. ns, not significant; ∗p < 0.05; ∗∗p < 0.01; ∗∗∗p < 0.001; ∗∗∗∗p < 0.0001. See also Figure S2 .
Article Snippet: BUV737 Mouse anti-human CD70 (Clone Ki-24) , BD , Cat# 612856; RRID: AB_2739193.
Techniques: Expressing, Marker, Functional Assay, Flow Cytometry, Fluorescence