ICOS+ and activated CD4+ T cells are dominant, tumour tissue-specific T cell populations in both mismatch repair-deficient and repair-proficient colorectal.

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ICOS+ and activated CD4+ T cells are dominant, tumour tissue-specific T cell populations in both mismatch repair-deficient and repair-proficient colorectal cancers. ICOS+ and activated CD4+ T cells are dominant, tumour tissue-specific T cell populations in both mismatch repair-deficient and repair-proficient colorectal cancers. (A) HSNE embedding of 3.1×105 landmarks representing the memory CD4+ T cell compartment (2.0×106 cells) from the discovery cohort of patients with CRC coloured by tissue type (first plot) and relative expression of indicated markers. (B) A heatmap showing median marker expression values (left) and frequencies of selected memory CD4+ T cell clusters (right). Hierarchical clustering was performed on cluster frequencies using Spearman’s rank correlation. Colour bars indicate tissue type. (C) Frequencies of selected memory CD4+ T cell clusters among CRC tissues (n=35, MMR-deficient (n=13) and MMR-proficient (n=22)), colorectal healthy mucosa (n=17), tumour-associated lymph nodes (n=26) and peripheral blood (n=19) as percentage of total CD45+ cells (upper panel) and memory CD4+ T cells (lower panel). Cluster IDs correspond to the ones in (B). Bars indicate median±IQR. Each dot represents an individual sample. Data from 22 independent experiments with mass cytometry. *P<0.05, ***p<0.001, ****p<0.0001 by Kruskal-Wallis test with Dunn’s test for multiple comparisons. (D) Violin plot showing log-transformed expression levels of the top 20 differentially expressed genes within CD4+ T cells (n=245) analysed by single-cell RNA-sequencing on CD45+ cells from CRC tissues (n=7) (figure 1D). Each dot represents a single cell. CRC, colorectal cancer; HSNE, hierarchical stochastic neighbour embedding; LN, lymph node; MMR-d, mismatch repair-deficient; MMR-p, mismatch repair-proficient; PBMC, peripheral blood mononuclear cell . Natasja L de Vries et al. Gut doi:10.1136/gutjnl-2019-318672 Copyright © BMJ Publishing Group Ltd & British Society of Gastroenterology. All rights reserved.