Fig. 3: Senescent CAFs express elevated levels of immune regulatory genes.

a Gene sets up- and down-regulated in SA-βGal+ CAFs isolated from Kras-activated mouse pancreata, compared to matched SA-βGal- CAFs, as measured by mRNA-seq. x axis indicates -Log₁₀ Padj values, calculated by Metascape with Bonferroni method multiple hypothesis correction. b Selected upregulated genes in the same SA-βGal+ CAFs. y axis indicates fold change relative to SA-βGal- CAFs, as measured by mRNA-seq. Mean of n = 5 tumors ± SEM, differences for all are under a threshold of Padj < 0.1 calculated by DESeq2 (Benjamini-Hochberg FDR correction). c Gene sets upregulated in SA-βGal+ CAFs isolated from human subjects, relative to matched SA-βGal- CAFs. x axis indicates −Log₁₀ Padj values, calculated by Metascape with Bonferroni method multiple hypothesis correction. d SA-βGal staining marking senescence of primary cultured human PDAC CAFs following activation of CreER by 4-OHT (TAM) to eliminate hTERT and LT expression. Scale bar = 20 μm. e Percentage of SA-βGal+ cells in cultured mouse and human CAFs treated or untreated with TAM. Mean of n = 3 replicates ± SEM. t test. f Gene sets enriched in five analyzed datasets comparing senescent to non-senescent CAFs: cells isolated directly from Kras-induced mice, from Kras+p53 mice, or from human patients, and mouse and human CAFs induced to undergo senescence in culture. Colors indicate normalized enrichment scores calculated by GSEA, with positive values indicating increased expression in senescent CAFs. Shown are sets with Padj < 0.25 (Benjamini-Hochberg FDR correction) in at least 3 out of the 5 datasets. NES normalized enrichment score. g Gene sets upregulated in CAFs within the scRNA-seq dataset which score positive for the senescence signature. x axis indicates −Log₁₀ Padj values, calculated by Metascape with Bonferroni method multiple hypothesis correction.