Fig. 2: Increased intratumoral T cells following RT and RT + CTLA4i treatment.
Bulk RNA-sequencing was performed on whole 4T1 tumors (n = 4 biologically independent mice for control, CTLA4, and RT groups, n = 6 biologically independent mice for RT + CTLA4). a Gene expression (scaled DEseq2 counts) of a selection of canonical T cell markers in post-treatment tumors. Each column represents an individual mouse. b Linear regression between Cd3e and Cd4 or Cd8 expression in post-treatment tumors. R2 and p indicate linear regression model R-squares and p-values for the models, respectively, shaded area represents the 95% confidence interval. Each dot represents an individual mouse. c Volcano plots of differentially expressed genes. CTLA4i, radiation therapy (RT), and RT+CTLA4i treated tumors were compared with untreated tumors (using DEseq2 on GEX counts data). Genes with adjusted p-value < 0.01 and |fold change| > 2 were considered differentially expressed (number of genes shown with up- or down-arrows indicating increased or decreased expression, respectively). d Heatmap showing normalized and scaled expression of all differentially expressed genes (for any comparison). Each column represents an individual mouse. e Principal component (PC) analysis of the global gene expression profiles. The proportion of variation explained by PC dimensions 1 and 2 are shown in parentheses. Each dot represents an individual mouse. f, g Ingenuity Pathway Analysis Canonical Pathway and Upstream Regulation analysis. Z-scores indicate predicted activation (>2) or inhibition (<−2) of pathways and upstream regulators. Source data are provided as a Source Data file.
