Fig. 3: Biological processes operative in genomically instable CLL.

a–d Heatmap showing expression profiles (n = 337) for genes involved in a mismatch repair (MMR), b base excision repair (BER), c nucleotide excision repair (NER), d non-homologous end joining (NHEJ). FDRs of DEGs (GI vs. (I)EMT-L) are indicated (q). Single genes may be involved in multiple processes. e Protein expression in CLL subtypes; p53 (n = 4 each), phospho-p53 (GI/(I)EMT-L: n = 11 each, (I)GI/EMT-L: n = 8 each) (normalized to actin). f, g Models summarizing alterations which contribute to f genomic instability, g activation of MYC family members in GI/(I)GI. Source/method (e.g., mRNA/GISTIC) and significance/frequencies are shown in gray, along with estimated mode of regulation/biological effect (red: increase/activation; blue: decrease/inactivation). h Protein expression in CLL subtypes; PRMT5 (n = 4 each), XPO1/cMYC (GI/(I)EMT-L: n = 11 each, (I)GI/EMT-L: n = 8 each) (normalized to actin). i Heatmap showing CNAs (paired CLL8 cases; before treatment (pre), at relapse (post)). CNAs are frequent at relapse (TP53 wild-type: GI/(I)EMT-L; p < 0.05, Wilcoxon signed-rank test (two-sided)). GI cases show more aberrations (mean) before ((I)EMT-L: 0.83; GI: 1.71) and after treatment ((I)EMT-L: 2.17; GI: 3.43), with considerable increase after treatment when TP53 mutations are included (GI(pre): 1.91, GI(post): 4.36; p < 0.01, Wilcoxon signed-rank test (two-sided)). Arrowheads highlight TP53 inactivation (preexisting: red; acquired: blue). GI alterations often involve chromosomes other than 13, 12, 11, and 17. j Fraction of signature activations in CLL subtypes (EBF1-r n = 6, GI n = 68, EMT-L n = 11, (I)EMT-L n = 52, (I)GI n = 31, NRIP1 n = 3) and k activation levels of mutational signatures (median centered) with order/color code according to clusters and IGHV status (light orange: IGHV mutated, yellow box: GI/(I)GI/(I)EMT-L). IGHV mutated cases show higher activations for signatures 9, 3, 15, and 20. l Alterations in DNA-damage response genes are more frequent in IGHV mutated GI/(I)GI cases (57%/50% ≥ one alteration) vs. IGHV mutated (I)EMT-L cases (11% ≥ one alteration) (p < 0.05, Mann–Whitney (two-sided)). IGHV unmutated cases (either subtype) have similar frequencies (64–70% ≥ one alteration). Only cases with WES for respective genes and known TP53 status (excluding EBF1-r/NRIP1) were used (n = 156). For Fig. 3a–l, data within individual figures derives from biologically independent samples. For boxplots, centerline, box limits, and whiskers represent the median, 25th, and 75th percentiles and 1.5× interquartile range, respectively.