CRISPR screening in human hematopoietic stem and progenitor cells reveals an enrichment for tumor suppressor genes within chromosome 7 commonly deleted regions

Monosomy 7 and del(7q) are among the most common cytogenetic abnormalities in myeloid malignancies, yet their underlying pathogenesis remains unclear. Using an array-based CRISPR screen and orthogonal machine learning approach, we identify potential chromosome 7 tumor suppressor genes (TSGs). We selected candidate TSGs via datamining of genome-scale studies, individually CRISPR-edited 108 candidates, and measured the subsequent impact on the proliferation and erythroid differentiation of primary, human CD34+ hematopoietic stem and progenitor cells (HSPCs). An unexpected 39% of genes increased proliferation when edited and were significantly enriched in commonly deleted regions. The only two genes that both increased proliferation and decreased erythroid differentiation when edited were the CUX1 transcription factor and ACHE, encoding acetylcholinesterase, both located in the 7q22.1 commonly deleted region. We demonstrate a novel role for ACHE in regulating erythropoiesis through acetylcholine receptor signaling. The defects stemming from loss of ACHE were corrected by a muscarinic receptor inhibitor, implicating muscarinic antagonists as potential treatments for −7/del(7q)-associated anemia. While chromosome-level deletions were historically thought to harbor a single TSG, the significant enrichment of TSGs within commonly deleted regions suggests a contiguous gene syndrome, wherein combinatorial loss of multiple neighboring genes drives disease.