Extended Data Fig. 8: Gene expression and scRNA-seq analysis of immune infiltration in LLC tumours.

a–c, Transcriptional profiling with RNA-seq performed on bulk tumour tissue from control (n = 8 untreated and n = 6 ICB-treated) and Setdb1 KO (n = 10 untreated and n = 6 ICB-treated) LLC tumours. Data represent 1 experiment. a, Running enrichment scores by GSEA for immune gene sets significantly (FDR <0.01) upregulated in Setdb1 KO LLC tumours treated with ICB relative to controls. b, Volcano plot depicts expression fold-change (x-axis) and statistical significance (y-axis) of cytotoxicity genes (red) and all other genes (grey) in Setdb1 KO LLC tumours treated with ICB relative to controls. c, TCR repertoire profiling with targeted sequencing of alpha and beta-chain variable regions from Setdb1 KO LLC tumours (untreated and ICB-treated) relative to controls. Variation in clonotype abundance (skewing) is represented by the Gini index (left, higher number indicates greater skewness) and Shannon entropy (right, lower number indicates greater skewness). Data are mean ± s.e.m. Statistics by two-sided Student’s t-test. d–h, scRNA-seq (3′) analysis of immune cells (CD45⁺ enrichment) from control (n = 3 untreated, n = 4 ICB-treated) or Setdb1 KO (n = 3 untreated, n = 4 ICB-treated) LLC tumours. Data are from 1 experiment. d, UMAP plots highlight 4,497 cells and associated clusters identified in the lymphoid compartment. e, Representative marker genes used to identify and annotate cell clusters in d. f, Changes in lymphoid populations in ICB-treated tumours (n = 4 control, n = 4 Setdb1 KO) as a proportion of the total lymphoid population. Data are mean ± s.e.m. Statistics by two-sided Student’s t-test. g, Ratio of NK-2 to NK-1 cells in ICB-treated samples. Data are mean ± s.e.m. Statistics by Mann–Whitney U test. h, Differentially expressed genes (log₂(fold-change)) in NK-2 vs NK-1 cells. Circle sizes indicate statistical significance (FDR). *P < 0.05. ****P < 0.0001.