Extended Data Fig. 4: T cell subsets and clonal composition.
From: Peripheral T cell expansion predicts tumour infiltration and clinical response
a, Characterizing clusters of T cell clusters with reference gene signatures. Heat maps show cross-labelling of T cell clusters (columns) to reference gene signatures (rows), taken from the analyses in Guo et al.3, Zhang et al.4 and Yost et al.5, with intensities indicating normalized frequency. CD8 and CD4 clusters from Guo et al.3 and Zhang et al.4 are separated by an extra space to aid visualization. b, Expression of selected genes. Box plots show distributions of gene expression on all T cells in the dataset, with cells grouped by their clusters, coloured as in Fig. 2a. Tops and bottoms of boxes indicate interquartile ranges, and lines within boxes indicate medians. Whiskers extend an additional 1.5 × the interquartile range from the median. c–f, Characterization of T cell clusters. Bar plots show mean values across clusters of various measures on T cells. ‘PD1 expr’ denotes expression of PD1 (d); ‘Term ex’ denotes a published signature of terminal versus stem-like exhaustion9 (e); ‘Trm sig’ denotes a published signature of Trm cells8 (c); and ‘Tumour pct’ denotes the fraction of cells sampled from tumour versus NAT (f). Horizontal lines in d and f indicate mean values over all cells. g, Gene set enrichment analysis for selected clusters and gene sets. The expression of selected gene sets (columns) is shown for clusters (rows) by plotting each gene in the gene set that was assayed in the integrated dataset as a dot according to its t-statistic from a logistic regression analysis to identify biomarkers for each cluster. Gene Ontology gene sets shown are: histone demethylase activity (HDM); histone methyltransferase activity (HMT); mitotic cell cycle (mitosis); and mitochondrial chromosome genes (MT). A predominance of dots to the right of the vertical line (t = 0) indicates overexpression of the gene set relative to the expected zero mean. Statistically significant cases of overexpression are shown in red with the associated genes when a one-sided P < 0.001 from a one-sample z-test on the t-statistics. h, Transcriptional heterogeneity of T cell clones. Each pie chart represents one of the 20 largest clonotypes in this study, as measured by total clone size across tumour, NAT and blood. Each clone represents a set of cells, indicating its total clone size, used to order clonotypes. The area of each pie is proportional to the clone size. Regions of each pie chart indicate the fractions of cells in the given clone assigned to each cluster. i, Composition of clones by T cell cluster and compartment. Heat map shows the unit-normalized cellular composition of 770 clones with a tumour + NAT clone size ≥ 10 (columns) across T cell clusters and tumour or NAT compartment (rows). Clones are integrated from all patients and grouped by their primary cluster. Within each primary cluster, clones are ordered to show a gradation of cell fraction from tumour to NAT. Each clone is further characterized by its clone size (top) and tissue expansion pattern (coloured bars above the heat map).
