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. 2019 Jun 21;216(9):2128–2149. doi: 10.1084/jem.20190249

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© 2019 Clarke et al.

This article is distributed under the terms of an Attribution–Noncommercial–Share Alike–No Mirror Sites license for the first six months after the publication date (see http://www.rupress.org/terms/). After six months it is available under a Creative Commons License (Attribution–Noncommercial–Share Alike 4.0 International license, as described at https://creativecommons.org/licenses/by-nc-sa/4.0/).

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Figure 2. — Tumor T_RM cells were clonally expanded. (A) RNA-seq analysis of transcripts (one per row) differentially expressed by tumor T_RM relative to lung T_RM, lung non-T_RM, and tumor non-T_RM (pairwise comparison; change in expression of twofold with an adjusted P value of ≤0.05 [DESeq2 analysis; Benjamini–Hochberg test]), presented as row-wise z-scores of TPM counts; each column represents an individual sample (lung non-T_RM = 21, lung T_RM = 20, tumor non-T_RM = 25, and tumor T_RM = 19). (B) Summary of overrepresentation analysis (using Reactome) of genes involved in the cell cycle that are differentially expressed by lung tumor T_RM cells relative to the other lung CTLs; q values represent FDR. (C) Shannon–Wiener diversity and inverse Simpson indices obtained using V(D)J tools following TCR-seq analysis of β chains in tumor T_RM and tumor non-T_RM populations. Bars represent the mean, t-lines represent SEM, and symbols represent individual data points (*, P ≤ 0.05; **, P ≤ 0.01; n = 10 patients; Wilcoxon rank-sum test). (D) Left: Bar graphs show the percentage of total TCRβ chains that were expanded (≥3 clonotypes). Bars represent the mean, t-lines represent SEM, and dots represent individual data points (*, P ≤ 0.05; n = 10 patients). Right: Pie charts show the distribution of TCRβ clonotypes based on clonal frequency. (E) Spearman coexpression analysis of the 77 genes up-regulated (A) in tumor T_RM cells; values are clustered with complete linkage. (F) WGCNA visualized in Gephi; the nodes are colored and sized according to the number of edges (connections), and the edge thickness is proportional to the edge weight (strength of correlation). (G) Correlation of the expression of HAVCR2 (TIM-3) transcripts and the indicated transcripts in the tumor T_RM population; r indicates Spearman correlation value (*, P ≤ 0.05; ***, P ≤ 0.001; ****, P ≤ 0.0001; n = 19 patients).