Recurrent pre-leukemic deletions are the result of microhomology-mediated end joining DNA repair

The mechanisms underlying myeloid malignancies deletions are not well understood, nor is it clear why specific genomic hotspots are predisposed to particular deletions. Inspecting the genomic regions around recurrent deletions in myeloid malignancies, we identified microhomology-mediated end-joining (MMEJ) signatures in recurrent pre-leukemic deletions. Introducing CRISPR Cas9 double-strand breaks (DSBs) into exon 12 of ASXL1, we successfully generated recurrent ASXL1 deletion in human hematopoietic stem and progenitor cells (HSPCs). Our further analyses show that deletions with MMEJ signature enrich myeloid malignancies and can be detected in multipotent HSCs. Gene expression analysis in single human adult bone marrow HSPCs exposed differences between myeloid and lymphoid biased progenitors. Overall we provide evidence that somatic deletions in pre-leukemic HSCs are associated with specific DSBs followed by MMEJ repair. A better understanding of the source of these DSBs and the regulation of the HSC MMEJ repair pathway might aid with preventing recurrent deletions in human pre-leukemia.