Extended Data Fig. 9: Single cell gene expression and T cell receptor (TCR) repertoire characteristics of post-treatment tumor infiltrating lymphocytes from patient OT6. | Nature Immunology

Extended Data Fig. 9: Single cell gene expression and T cell receptor (TCR) repertoire characteristics of post-treatment tumor infiltrating lymphocytes from patient OT6.

From: Immunotherapy response induces divergent tertiary lymphoid structure morphologies in hepatocellular carcinoma

Extended Data Fig. 9

a, Uniform Manifold Approximation and Projection (UMAP) for 562 T cells identified by single-cell sequencing of CD3+CD19+ FACS-sorted tumor infiltrating lymphocytes. B cells excluded from analysis. b, Barplot showing number of single cells per cluster. c, Violin plots showing expression of subset specific marker genes across clusters. d, UMAP showing clonality of tumor infiltrating lymphocytes according to T cell receptor beta chain (TCRβ) sequence. e, Heatmap showing gene expression of the top 3 differentially expressed genes per cluster. Rows represent single genes and columns represent individual cells. Annotation bar indicates cluster identity, whether each cell had a sequenced TCR, the clonality of the TCR, and whether the TCR was identified in microdissected TLS from the same patient. f-h, Volcano plots showing differentially expressed genes in the CD8 TEM_GZMK (f), CD8 TEM_GZMB (g), and CD4 Tph (h) clusters compared to all other cells. Vertical dotted lines indicate a fold change of greater or less than 1.4 and horizontal line indicates a P value of 0.05.

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