Figure 4.
RNA-seq analysis identifies aberrant regulation of immune system and upregulation of AP-1 complex genes associated with NrasG12D/+;Asxl1−/− AML. Lin–c-Kit+ cells were sorted from moribund NA mice with CMML (NA-CMML) or AML (NA-AML) and age-matched controls (Vav-Cre), Asxl1−/−, and Nras mice for RNA-seq analysis. (A-D) RNA-seq analysis of NA-CMML cells. (A) Heatmap of DEGs in NA-CMML cells compared with control cells (fold change ≥2 and false discovery rate [FDR] <0.05). (B) Gene Ontology (GO) analysis of DEGs in NA-CMML cells. The representative biological processes are shown with numbers of genes in each category and corresponding FDR in parentheses. (C) Gene set enrichment analysis (GSEA) identified dysregulated gene signatures in NA-CMML vs control. (D) Venn diagrams of up- or downregulated DEGs among NA-CMML, Nras, and Asxl1−/− cells. (E-J) RNA-seq analysis of NA-AML cells. (E) Heatmap of DEGs in NA-AML cells compared with control cells (fold change ≥2; FDR <0.05). (F) GO analysis of DEGs in NA-AML cells. The representative biological processes are shown with numbers of genes in each category and corresponding FDR in parentheses. (G) GSEA identified dysregulated gene signatures in NA-AML vs control. (H) Venn diagrams of up- or downregulated DEGs among NA-AML, Nras, and Asxl1−/− cells. (I) Volcano plot illustrating DEGs in NA-AML vs control, highlighting AP-1 complex genes and Flt3. (J) Quantification of AP-1 complex genes (Fos, Fosb, Jun, Junb, Jund, and Atf3) and Flt3 messenger RNA (mRNA) levels using quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) in sorted Lin–c-Kit+ cells (n = 5 in each group). Data are presented as mean + SD. *P < .05; **P < .01; ***P < .001. NES, normalized enrichment score.

RNA-seq analysis identifies aberrant regulation of immune system and upregulation of AP-1 complex genes associated with NrasG12D/+;Asxl1−/− AML. Lin–c-Kit+ cells were sorted from moribund NA mice with CMML (NA-CMML) or AML (NA-AML) and age-matched controls (Vav-Cre), Asxl1−/−, and Nras mice for RNA-seq analysis. (A-D) RNA-seq analysis of NA-CMML cells. (A) Heatmap of DEGs in NA-CMML cells compared with control cells (fold change ≥2 and false discovery rate [FDR] <0.05). (B) Gene Ontology (GO) analysis of DEGs in NA-CMML cells. The representative biological processes are shown with numbers of genes in each category and corresponding FDR in parentheses. (C) Gene set enrichment analysis (GSEA) identified dysregulated gene signatures in NA-CMML vs control. (D) Venn diagrams of up- or downregulated DEGs among NA-CMML, Nras, and Asxl1−/− cells. (E-J) RNA-seq analysis of NA-AML cells. (E) Heatmap of DEGs in NA-AML cells compared with control cells (fold change ≥2; FDR <0.05). (F) GO analysis of DEGs in NA-AML cells. The representative biological processes are shown with numbers of genes in each category and corresponding FDR in parentheses. (G) GSEA identified dysregulated gene signatures in NA-AML vs control. (H) Venn diagrams of up- or downregulated DEGs among NA-AML, Nras, and Asxl1−/− cells. (I) Volcano plot illustrating DEGs in NA-AML vs control, highlighting AP-1 complex genes and Flt3. (J) Quantification of AP-1 complex genes (Fos, Fosb, Jun, Junb, Jund, and Atf3) and Flt3 messenger RNA (mRNA) levels using quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) in sorted Lin–c-Kit+ cells (n = 5 in each group). Data are presented as mean + SD. *P < .05; **P < .01; ***P < .001. NES, normalized enrichment score.

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