Extended Data Fig. 9: Defining cell state-specific gene and surface protein signatures of TRM and TR-TEX cells. | Nature Immunology

Extended Data Fig. 9: Defining cell state-specific gene and surface protein signatures of TRM and TR-TEX cells.

From: Tissue-resident exhausted and memory CD8+ T cells have distinct ontogeny, function and roles in disease

Extended Data Fig. 9: Defining cell state-specific gene and surface protein signatures of TRM and TR-TEX cells.The alt text for this image may have been generated using AI.

a, Relative RNA expression of genes comprising TRM cell-specific or TR-TEX cell-specific signatures. b, Seurat enrichment for Mackay 2016 TRM core4 and Giles 202263 TEX-TERM signatures in TRM and TR-TEX compared to newly derived TRM and TR-TEX cell-state-specific signatures in LCMV TEA-seq clusters. c, Cliff’s delta effect size and fold change of Seurat enrichment for Mackay 2016 TRM core4 and Giles 202263 TEX-TERM signatures and newly derived TRM and TR-TEX cell-state-specific signatures in LCMV TEA-seq clusters. d, Seurat enrichment for cell-state-specific TRM or TR-TEX signature scores within CD8+ T cells isolated from human SI epithelium or non-naive CD8+ T cells from healthy donor blood65 or GSEA enrichment for cell-state-specific signatures within CD39+PD-1+ TEX cells compared to all non-naive CD8+ T cells from healthy donor blood66. δ = Cliff’s delta, FC = fold change. Boxes = interquartile range (25th–75th percentile), center line = median, whiskers = 1.5x the IQR. e, RNA expression of genes encoding indicated surface proteins in LCMV TEA-seq clusters. Size = proportion of cells expressing each gene; scale bar = relative expression. f, Marker expression in Arm Spl TCIRCM, Cl13 Spl TEX-PROG or Cl13 Spl TEX-TERM cells or TRM and TR-TEX cells from SI (CD69+CD103+) or Liv (CD69+CXCR6+) 30–40 dpi with Arm or Cl13. g, Proportion of TRM or TR-TEX cells expressing CD73 and CD200R in Liv (CD69+CXCR6+) or SG (CD69+CD103+) after Arm or Cl13 infection (left and middle panel) or proportion of TRM-like cells in human epidermal or melanoma samples (KLRG1−CD69+CD103+) expressing CD73 and CD200R (right panel). h, IR expression by total P14 Arm TCIRCM (Spl) or by CD69+CD103+CD73+ TRM cells or CD69+CD103+CD73−CD200R+ TR-TEX cells 30–40 dpi with Arm or Cl13. i, IR expression by KLRG1−CD69+CD103+CD73+ TRM-like cells from human tonsil or epidermis or KLRG1−CD69+CD103+CD73−CD200R+ TRM-like TIL from HNSCC or melanoma. Data pooled from 3–6 human donors (g, i) or representative of at least 2 experiments with 4 or 5 mice per group (e, f, g). TEA-seq data pooled from 20-25 mice per infection per tissue. * p < 0.05, two-tailed Mann–Whitney test. Bars represent the mean.

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