CMTM6 regulates hematopoietic stem cell homeostasis through modulating IFNRs-STAT1-KLF4 signaling axis

CMTM6 is known to stabilize PD-L1 on cancer cells, facilitating immune evasion, but its role in normal hematopoiesis remains unexplored. Hematopoietic stem cell (HSC) homeostasis is tightly regulated by interferon (IFN) signaling, yet the mechanisms controlling IFN receptor stability are unclear.

In this study we investigated whether CMTM6 regulates HSC maintenance and elucidated the underlying molecular pathways.

Using a conditional Cmtm6 knockout mouse model (Vav-Cre), we performed flow cytometry, competitive transplantation, single-cell RNA sequencing, co-immunoprecipitation, and functional assays on bone marrow HSCs.

Cmtm6 deficiency led to increased HSC proliferation but impaired reconstitution capacity, accompanied by elevated DNA damage and disrupted cell polarity. Single-cell analysis revealed a marked reduction in IFN response pathways. Mechanistically, CMTM6 directly interacted with IFNAR1 and IFNGR1, stabilizing their protein expression. Downstream, Cmtm6 deletion impaired STAT1 phosphorylation and reduced KLF4 expression; single-cell analysis revealed a significant positive correlation between Stat1 activity and Klf4 expression, and STAT1 inhibition in HSCs confirmed that STAT1 activity is required for maintaining KLF4 expression. Notably, KLF4 overexpression partially rescued colony-forming defects and reduced γH2AX foci in Cmtm6-deficient HSCs, identifying KLF4 as a key downstream effector. Additionally, we observed accompanying molecular changes including reduced SIAH2, elevated DYRK2, decreased c-MYC, and increased P53, which may contribute to the observed phenotypes.

These findings demonstrate that CMTM6 maintains HSC homeostasis by stabilizing IFN receptors and regulating the IFNR-STAT1-KLF4 signaling axis, revealing a novel physiological function for CMTM6 in hematopoiesis.