Fig. 6. Deficiency of autophagy reprograms α-SMA⁺ CAFs towards an “inflammatory” phenotype.

a Volcano plot showing distribution p-value (−log₁₀ p-value) and fold change (log₂ fold change) distribution of genes identified in CAFs isolated from αSMA^cre (n = 2) and αSMA^creAtg5^fl/fl (n = 2) mice. b Heatmap with scaled expression values (row z-score) of selected differentially expressed genes (DEGs) between αSMA^cre (n = 2) and αSMA^creAtg5^fl/fl (n = 2) mice. Gene names are depicted on the heatmap. For DEG analysis, the thresholds FDR < 0.05 and −1.5 < log₂FC < 1.5 were used. c Bubble plot of enriched pathways determined from transcriptomic data. The size of the dot represents gene count, and the colour represents the p-value. d Gene set enrichment analysis (GSEA) plots showing the enrichment of “Phagocytosis” (NES 1.305275675, FDR 0.517387464), “mTOR signalling” (NES 1.372658556, FDR 0.288520886), “Cytokine production” (NES 1.279629696, FDR 0.000037360), “Positive regulation of MHC II biosynthetic process” (NES −0.816304866, FDR 0.028912909) gene sets. e Bubble plots of enriched pathways determined from proteomic data of CAFs lysates (left) and CAF supernatants (right, SNs). The size of the dot represents protein count, and the colour represents the −log₁₀(p-value).