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: ANG (BD 558328), VEGFα (BD 558336), IL-6 (BD 558276), IL-8 (BD 558277), MCP-1 (BD 558287), IL-1β (BD 558279), and TNFα (BD 558273) levels were assessed by Cytometry Bead Array on a BD LSR Fortessa, whereas TGFα, and OPN concentrations were measured by Luminex assay (R&D Systems, LXSAHM) on a Luminex Magpix instrument, according to manufacturer’s instructions.

Techniques: Expressing, Marker, Functional Assay, Flow Cytometry, Fluorescence

Journal: PLoS ONE

Article Title: IL-22R Ligands IL-20, IL-22, and IL-24 Promote Wound Healing in Diabetic db/db Mice

doi: 10.1371/journal.pone.0170639

Figure Lengend Snippet: Skins were harvested on day 7 after treatment with control Fc, IL-22-Fc, PDGF or VEGF (n = 3–5). Microarray analysis was done with purified skin RNA. (A) Heat map of genes that were differentially regulated with treatments. (B) GO enrichment analysis of IL-22-Fc-specific gene expression, yielding several enriched GO categories. Genes from these categories are plotted as nodes in the network diagram, with edges indicating shared membership in an enriched GO category. (C-J) Gene expression. (C) Defb1 , (D) S100a9 , (E) Spink12 , (F) Serpinb3a , (G) Cxcr2 , (H) Areg , (I) Alox8 , (J) Pla2g4e . Error bars, s.e.m. ** P < 0.01, *** P < 0.001. Student’s t-test (C-J).

Article Snippet: On day 4, mice were topically applied with 30ug Fc proteins, recombinant PDGF-BB (Peprotech), or VEGFα (Genentech).

Techniques: Control, Microarray, Purification, Gene Expression

Journal: PLoS ONE

Article Title: IL-22R Ligands IL-20, IL-22, and IL-24 Promote Wound Healing in Diabetic db/db Mice

doi: 10.1371/journal.pone.0170639

Figure Lengend Snippet: (A-B) C57BL/6 mice were i.p. injected with control or IL-22-Fc (n = 6), shaved skins on the back were harvested in 24 hours. mRNA expression of s100a9 (A), and Defb1 (B). (C) Wound closure of wounds infected with control (n = 8) or with S.aureus (n = 9). (D-F) S . aureus infected wounds were topically applied with control, IL-22-Fc, VEGF, or PDGF (n = 9). (D) Wound closure. (E) Representative wound images. (F) AUC of the wound closure. Error bars, s.e.m. ** P < 0.01, *** P < 0.001. Unpaired Student’s t-test (A, B, F). 2-way ANOVA (C). Data shown are representative of two independent experiments.

Article Snippet: On day 4, mice were topically applied with 30ug Fc proteins, recombinant PDGF-BB (Peprotech), or VEGFα (Genentech).

Techniques: Injection, Control, Expressing, Infection