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. 2023 Sep 27;73(3):496–508. doi: 10.1136/gutjnl-2023-330748

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© Author(s) (or their employer(s)) 2024. Re-use permitted under CC BY. Published by BMJ.

This is an open access article distributed in accordance with the Creative Commons Attribution 4.0 Unported (CC BY 4.0) license, which permits others to copy, redistribute, remix, transform and build upon this work for any purpose, provided the original work is properly cited, a link to the licence is given, and indication of whether changes were made. See: https://creativecommons.org/licenses/by/4.0/.

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Histopathological and transcriptomic profiles of diagnostic biopsies from the RPLS cohort. (A) Representative H&E images (scale bars: 2 mm—top; 200 µm—bottom), characterisation of the epithelial component of diagnostic biopsies in each region of interest, and differential composition in tumourous, stromal and immune cells following cell segmentation (LS: n=6; RP: n=7; Welch t-test). (B) Heatmap of 504 differentially expressed genes (≥2 fold change, p<0.05; Wilcoxon) between LS and RP biopsies. (C) KEGG pathway over-representation analysis of LS-high and RP-high genes using EnrichmentMap. Overlapping pathways are connected by lines and annotated under a common theme using AutoAnnotate. KEGG: Kyoto Encyclopaedia of Genes and Genomes. (D) Heatmap and differential expression analysis of the RPLS score and previously published metrics of gemcitabine sensitivity in the RPLS cohort. P values were derived by Wilcoxon test. (E) Representative H&E stain of a diagnostic biopsy, indicating histological regions targeted by macrodissection. (F) Differentially expressed genes (≥2 fold change, p<0.05; Wilcoxon), differentially active transcription factors (p<0.05, Wilcoxon test; DoRothEA), differentially expressed pathways (p<0.05, Wilcoxon test; ssGSEA of KEGG and Hallmarks gene lists), and differentially active cytokines (p<0.05, Wilcoxon test; CytoSig) between RP and LS tumour cores (TCs; 11 LS, 9 RP). (G) Differential expression of the bulk tissue RPLS signature in TCs, tumour stroma (TSs; 5 LS, 6 RP), invasive fronts (IFs; 3 LS, 3 RP) and non-malignant regions (NRs; 4 LS, 4 RP) from RP and LS biopsies (Wilcoxon test). LS, long survivor; RP, rapid progressor.