DNA repair pathways are uniquely active in ERV re-expressing Asxl1^–/–Ezh2^–/– dKO cells. (A) Venn diagram showing the overlaps of differentially expressed genes (adjusted P < .05) identified in the data set derived from the BM of mice that received primary transplant with the indicated genotype, by comparing each genotype, Asxl1^–/–, Ezh2^–/– MDS/MPN LPD, and Asxl1^–/–Ezh2^–/– dKO MDS/MPN LPD mice with WT. (B) The bar charts show example pathways identified in gene ontology analysis comparing Asxl1^–/– vs WT or Ezh2^–/– vs WT (top) and Asxl1^–/–Ezh2^–/– dKO vs WT (bottom). (C) Example GSEA plots for the indicated pathways in the indicated comparisons are shown. (D-G) Gene set variant analysis (GSVA) for the indicated samples was performed and mean scores for Reactome and Hallmark DNA repair gene sets for each genotype are plotted in the heat map. Different RNA-seq data sets were used for the analysis, c-kit⁺ 5 days after start of in vivo deletion (D), c-kit⁺ 3 months after in vivo deletion (E), BM (F), and CD19⁺ splenocytes (G). (H) Dot plots show selected results for Kyoto Encyclopedia of Genes and Genomes pathway analysis using genes expressed in CLL in the indicated comparisons (WT vs tertiary Asxl1^–/–Ezh2^–/– dKO CLL or WT vs tertiary TCL1 CLL). DNA repair pathways are marked with a star. (I) GSEA results for selected DNA repair gene sets for tertiary Asxl1^–/–Ezh2^–/– dKO CLL vs tertiary TCL1 CLL are shown. (J) Dot plot showing the differential expression of the indicated TE families in BM RNA-seq data from mice that received primary transplant, comparing KO vs WT and dKO vs single KO as indicated. (K) Similar dot plot as shown in panel J but using CD19⁺ splenocyte RNA-seq data from mice that received primary transplant. (L) Dot plot showing the differential expression of the indicated TE families using CD19⁺ splenocytes isolated from tertiary Asxl1^–/–Ezh2^–/– dKO CLL, tertiary TCL1 CLL mice, or WT mice as control. (M) The plot shows the integration of differential expression analysis using CD19⁺ RNA-seq data and quantitative H3K27me3 and H3K27ac CUT&RUN data for the indicated TE families in CD19⁺ splenocytes isolated from tertiary Asxl1^–/–Ezh2^–/– dKO CLL mice or WT mice as control. (N) The genome tracks show examples of differentially expressed individual ERVs (RNA-seq top 2 tracks) and the H3K27me3 and H3K27ac levels in WT and tertiary Asxl1^–/–Ezh2^–/– dKO CLL mice as indicated. The last 2 tracks show control IgG enrichment. H3K27ac, H3K27 acetylation; H3K27me3, H3K27 trimethylation; IgG, immunoglobulin G.