Fig. 4. Deconvoluting consequences of subclonal SV heterogeneity in a CLL primary sample.

a, Single-cell SV discovery in CLL_24. All cells exhibiting deletions (10q-Del) shown in Supplementary Fig. 18. 10q-Ref, cells bearing a not rearranged 10q. b, Minimal deleted region (chr10:101615000-103028000; hg38), displaying recurrent deletions in a separate cohort of CLLs⁶². c, Heatmap of genes with altered activity in 10q-Del based on scNOVA (alternative mode; 10% FDR). Genes from all significant pathways reported in d are highlighted. d, Pathway modules with differential activity, in cells exhibiting 10q-Del (10% FDR). e, Minimal deleted region-bearing CLL samples from the International Cancer Genome Consortium (ICGC) demonstrate overexpression of Wnt signaling genes compared with 10q-Ref (P = 0.0098; two-sided likelihood ratio test; n = 174 and n = 4 independent CLL samples for 10q-Ref and 10q-Del, respectively). f, Pathway activities ((–1) × Z score of NO) derived from jointly modeled NO at the gene bodies of Wnt signaling pathway genes for each SV-bearing CLL_24 cell. SIa-SId correspond to single cells exhibiting a deletion at 10q24 not shared by any other cell. n = 2, 3, 2 and 1 cells are depicted in the plot for SCa, SCb, SCc and SIa-SId, respectively. g, Single-cell gene set enrichment scores for five leukemia-related pathways from CITE-seq. Enrichment scores for 10q-terDel (n = 82) and 10q-Ref (n = 2,381) cells were compared using two-sided t-tests. h, Chart depicting 43 differentially active TFs between 10q-terDel and 10q-Ref cells based on DoRothEA⁶⁸. Genes involved in the pathways over-represented by these TFs are annotated using colored dots. i, Differentially expressed surface protein CD279 (PD-1) in 10q-terDel (n = 82) compared with 10q-Ref (n = 2,381) cells based on a two-sided Wilcoxon rank sum test. j, Wnt pathway diagram showing the altered genes or TFs in SCb (10q-terDel) identified by scNOVA (blue nodes) and CITE-seq (red borders). Gray, known (see PubmedIDs) and computationally predicted regulators (based on Gene Ontology Biological Process (GOBP)) of Wnt signaling that are deleted in SCb. Throughout the figure, boxplots were defined by minima = 25th percentile – 1.5× IQR, maxima = 75th percentile + 1.5× IQR, center = median and bounds of box = 25th and 75th percentile.