Genome-wide association study on 13,167 individuals identifies regulators of blood CD34+ cell levels

Stem cell transplantation is a cornerstone in the treatment of blood malignancies. The most common method to harvest stem cells for transplantation is by leukapheresis, requiring mobilization of CD34+ hematopoietic stem and progenitor cells (HSPC) from the bone marrow into the blood. Identifying the genetic factors that control blood CD34+ cell levels could expose new drug targets for HSPC mobilization. Here, we report the first large-scale genome-wide association study on blood CD34+ cell levels. Across 13,167 individuals, we identify 9 significant and 2 suggestive associations, accounted for by 8 loci (PPM1H, CXCR4, ENO1-RERE, ITGA9, ARHGAP45, CEBPA, TERT and MYC). Notably, 4 of the identified associations map to CXCR4, demonstrating that bona fide regulators of blood CD34+ cell levels can be identified through genetic variation. Further, the most significant association maps to PPM1H, encoding a serine/threonine phosphatase never previously implicated in HSPC biology. PPM1H is expressed in HSPCs, and the allele that confers higher blood CD34+ cell levels downregulates PPM1H. Through functional fine-mapping, we find that this downregulation is caused by the variant rs772557-A, which abrogates a MYB transcription factor binding site in PPM1H intron 1 that is active in specific HSPC subpopulations, including hematopoietic stem cells, and interacts with the promoter by chromatin looping. Furthermore, PPM1H knockdown increases the proportion of CD34+ and CD34+90+ cells in cord blood assays. Our results provide first large-scale analysis of the genetic architecture of blood CD34+ cell levels, and warrant further investigation of PPM1H as a potential inhibition target for stem cell mobilization.