Journal: bioRxiv

Article Title: Fibroblast-derived Collagen VI shapes the structure and function of the tumor-immune microenvironment in clear cell renal cell carcinoma

doi: 10.64898/2026.03.19.712351

Figure Lengend Snippet: ( A ) Survival analysis for high or low expression of COL6A1 and COL6A2 in the CheckMate 025 study cohort of Nivolumab (anti-PD-1) or everolimus (mTOR inhibitor) treated patients . Graphs show Kaplan-Meier plots and Log-rank (Mantel-Cox) tests. (B-D) Analysis of COL6 deposition in CDMs treated with cabozantinib (Cabo.), sunitinib (Suni.), temsirolimus (Temsi.), or DMSO (Ctrl.) treated TK173 cells. (B) Dot plot depicting relative median fluorescence intensities (MFI) of COL6 in CDMs of respectively treated cells in the screening experiment (N=10 regions of interest, one-way ANOVA with Tukey’s multiple comparison test). (C) Dot plot depicting mean relative MFI of COL6 in CDMs of respectively treated TK173 cells (dots indicate mean of N=4 independent experiments, unpaired t test). (D) IF images stained for FN (green) and COL6 (violet) of synthesized CDMs of TK173 cells treated with the indicated drugs. (E) Schematic description of RNA sequencing analysis of cabozantinib or DMSO control-treated TK173 fibroblasts and acute organotypic slice cultures (OTSCs) of ccRCCs (Created in BioRender. Schell, C. (2026) https://BioRender.com/x5sqb3y ). (F&G) Volcano plot of differential gene expression analysis of matrisome genes in cabozantinib-treated TK173 cells and ccRCC OTSCs. The inserts depict a volcano plot of all genes. Red dots indicate significantly regulated genes with adjusted p<0.01 and log 2 fold change (FC) > |1|). (H) Heatmap analysis of significantly regulated matrisome genes in cabozantinib-treated TK173 cells and ccRCC OTSCs (genes with adjusted p<0.0001 and fold change > |2| are depicted for TK173 cells or with adjusted p<0.01 and fold change > |1.5| for OTSCs). (I) Heatmap analysis of log 2 expression fold changes (FC) of immunomodulatory genes in TK173 cells and ccRCC OTSCs (N/A – not announced). (J&K) IF validation of COL6 regulation in cabozantinib-treated ccRCC OTSCs. Images show IF staining for Nuclei by Hoechst (blue), CK (yellow) and COL6A1 (violet) of OTSCs treated with the indicated drugs. Quantification of COL6A1-positive areas in OTSCs of 10 ccRCC patients (dots indicate individual patients analyzed, ratio paired t test). (L) Schematic summary illustrating the findings of the study, highlighting COL6 expression in tumor stroma as well as the remodeling of the ECM architecture in dependence of COL6 abundance and the subsequent implications for cancer and immune cells (Created in BioRender. Schell, C. (2026) https://BioRender.com/x5sqb3y ).

Article Snippet: Inhibitors used and respective working concentrations are 5 μM cabozantinib (S1119, Selleck Chemicals, Houston, TX, USA), 10 μM sunitinib (S1042, Selleck Chemicals, Houston, TX, USA) and 10 μM temsirolimus (S1044, Selleck Chemicals, Houston, TX, USA), medium was changed every second day.

Techniques: Expressing, Fluorescence, Comparison, Staining, Synthesized, RNA Sequencing, Control, Gene Expression, Biomarker Discovery

Journal: Communications Biology

Article Title: TGFBI promotes liver fibrosis through remodeling the profibrotic microenvironment by a positive feedback regulatory loop

doi: 10.1038/s42003-026-09601-2

Figure Lengend Snippet: A Western blot analyses of PDGF-B in BMDM or RAW264.7 treated with rTGFBI (ng/mL) with the indicated concentrations ( n = 3 independent experiments). B RT-qPCR analyses of PDGF-B in BMDM or RAW264.7 treated with rTGFBI (ng/mL) with the indicated concentrations ( n = 3 independent experiments). C Western blot analysis of the indicated proteins in BMDM or RAW264.7 treated with or without rTGFBI (200 ng/mL) for 6 h. D RT-qPCR analysis of Pdgfb in BMDM or RAW264.7 treated with rTGFBI (200 ng/mL) alone or in combination with integrin αvβ3 or αvβ5 neutralizing antibody ( n = 3 independent experiments). E Flow cytometry analysis and statistical analysis of the percentage of Trem2 + CD9 + subpopulation in BMDM or RAW264.7 transfected with the indicated siRNAs for 24 h and treated with or without rTGFBI (200 ng/mL) for 24 h ( n = 3 independent experiments). F RT-qPCR and Western blot analysis of α-SMA in HSCs cocultured with BMDMs transfected the indicated siRNAs for 24 h and treated with or without rTGFBI (200 ng/mL) for 24 h ( n = 3 independent experiments). G RT-qPCR and Western blot analyses of α-SMA in HSCs treated with rTGFBI or in combination with SU11248 ( n = 3 independent experiments). Mice samples ( n = 4–6 per group). Data were presented as the mean ± SDs; scale bars, 50 µm; * p < 0.05, ** p < 0.01, *** p < 0.001, **** p < 0.0001; ns not significant (Student’s t test).

Article Snippet: SU11248 (PDGFR inhibitor, sunitinib, #HY-10255A, MedChemExpress) and Imatinib Mesylate (PDGFR inhibitor, #HY-50946, MedChemExpress) .

Techniques: Western Blot, Quantitative RT-PCR, Flow Cytometry, Transfection