MS4A3/Ms4a3 transcription is regulated by BCR-ABL1, MECOM-C/EBPε axis, and epigenetic factors in CML. (A) Relative Ms4a3 mRNA in 32D-cl3 cells transfected with wild-type p210^BCR-ABL1, the kinase inactive K271R mutant of p210^BCR-ABL1, or an EV control, after culturing ±1 μM IM for 1 to 4 days. (B) Relative expression of Ms4a3 and BCR-ABL1 mRNA after BCR-ABL1 induction for 72 hours in Lin⁻ BM cells from Scl-tTA⁺;TRE-BCR-ABL1⁺ mice. (C) Relative MS4A3 mRNA expression in CD34⁺ cells from CP-CML or BP-CML patients cultured ±1 μM IM for 24 hours. (D) Correlations between the expression of MECOM, CEBPE, and MS4A3 in CML CD34⁺ cells from a cohort of CP-, BP-, and AP-CML patients. Analysis was performed using log2 transformed microarray data. (E) Gene expression after overexpression of MECOM (EVI1). (F) Gene expression after overexpression of CEBPE. (G) Relative MS4A3 expression in CP-CML CD34⁺ cells treated with an epigenetic inhibitor library. Drug targets are color-coded. # and ## denote the classes of interest. (H-I) The heat map and diagram representing CpG methylation levels in the MS4A3 promoter region as detected by DNA bisulfite conversion and patch PCR sequencing on DNA of CD34⁺ cells from CB, adult BM, CP-CML, and BP-CML samples. (J) H3K27me3 ChIP‐seq signal is shown at the indicated MS4A3 locus in CD34⁺ cells from CB, adult BM, CP‐CML, and BP‐CML patients. Each ChIP‐seq track is normalized and scaled to the same scale. (K) Relative MS4A3 expression in CD34⁺ cells from 2 BP-CML patients, after treatment with indicated EZH2 inhibitors. M033 sample had elevated H3K27me3 reads at MS4A3 locus, while M050 had no obvious change compared with CB and adult BM.