Fig. 1: Transcriptomic profiling of chemo-naive and post-CTX PDAC-HD samples.
From: Persister cell phenotypes contribute to poor patient outcomes after neoadjuvant chemotherapy in PDAC
a, The PDAC-HD cohort included 171 unique samples representing 115 chemo-naive and 56 post-CTX resections. Post-CTX samples received either GEM (n = 23) or mFFX (n = 33). These samples were analyzed by RNA-seq or multiplexed IF. The RNA-seq set was composed of a total of n = 97 samples, including n = 64 chemo-naive and n = 33 post-CTX samples. LCM was performed on chemo-naive samples (n = 32). Chemo-naive individuals received adjuvant GEM (n = 54) and mFFX (n = 5). Post-CTX individuals received neoadjuvant GEM (n = 10) and mFFX (n = 23). b, WGCNA of RNA-seq data showing significantly enriched GPs between chemo-naive and post-CTX PDAC-HD samples. Significance was determined by two-sided Wilcoxon rank-sum test adjusted for multiple testing (P ≤ 0.05). The heat map shows relative module eigengene expression between chemo-naive and post-CTX samples, with red (positive) values associated with increased GP expression and blue (negative) values associated with decreased GP expression. Molecular function and biological processes associated with GPs and enriched in chemo-naive or post-CTX samples are shown; Y, yes; N, no; TNF, tumor necrosis factor; MHC, major histocompatibility complex. c, t-distributed stochastic neighbor embedding (t-SNE) plots showing samples clustered according to the 2,000 top variably expressed genes. Sample clustering is identical between plots, with Moffitt classification and PurIST scores indicated for each sample. d, Heat map showing the classification of chemo-naive and post-CTX PDAC-HD samples by Moffitt subtype. e, Kaplan–Meier survival analysis of chemo-naive and post-CTX PDAC-HD samples. The log-rank P values are annotated on the plots. P values were not adjusted for multiple testing.
