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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.

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Fig. 1: Arrayed CRISPR-Cas9 screen and machine learning classification identify multiple chromosome 7 genes with myeloid tumor suppressor activity, concentrated within 7q CDRs.
Fig. 2: CUX1 and ACHE are potential TSGs in the 7q22.1 CDR, and ACHE loss can be rescued by a muscarinic acetylcholine inhibitor.


  1. Inaba T, Honda H, Matsui H. The enigma of monosomy 7. Blood. 2018;131:2891–8.

    Article  CAS  PubMed  Google Scholar 

  2. Takahashi K, Wang F, Kantarjian H, Song X, Patel K, Neelapu S, et al. Copy number alterations detected as clonal hematopoiesis of indeterminate potential. Blood Adv. 2017;1:1031–6.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Dimitriou M, Woll PS, Mortera-Blanco T, Karimi M, Wedge DC, Doolittle H, et al. Perturbed hematopoietic stem and progenitor cell hierarchy in myelodysplastic syndromes patients with monosomy 7 as the sole cytogenetic abnormality. Oncotarget. 2016;7:72685–98.

    Article  PubMed  PubMed Central  Google Scholar 

  4. McNerney ME, Brown CD, Wang X, Bartom ET, Karmakar S, Bandlamudi C, et al. CUX1 is a haploinsufficient tumor suppressor gene on chromosome 7 frequently inactivated in acute myeloid leukemia. Blood. 2013;121:975–83.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Ernst T, Chase AJ, Score J, Hidalgo-Curtis CE, Bryant C, Jones AV, et al. Inactivating mutations of the histone methyltransferase gene EZH2 in myeloid disorders. Nat Genet. 2010;42:722–6.

    Article  CAS  PubMed  Google Scholar 

  6. Ebert BL, Pretz J, Bosco J, Chang CY, Tamayo P, Galili N, et al. Identification of RPS14 as a 5q- syndrome gene by RNA interference screen. Nature. 2008;451:335–9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Shalem O, Sanjana NE, Zhang F. High-throughput functional genomics using CRISPR-Cas9. Nat Rev Genet. 2015;16:299–311.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Camacho DM, Collins KM, Powers RK, Costello JC, Collins JJ. Next-generation machine learning for biological networks. Cell. 2018;173:1581–92.

    Article  CAS  PubMed  Google Scholar 

  9. Makishima H, Visconte V, Sakaguchi H, Jankowska AM, Abu Kar S, Jerez A, et al. Mutations in the spliceosome machinery, a novel and ubiquitous pathway in leukemogenesis. Blood. 2012;119:3203–10.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Tisserand J, Khetchoumian K, Thibault C, Dembélé D, Chambon P, Losson R. Tripartite motif 24 (Trim24/Tif1α) tumor suppressor protein is a novel negative regulator of interferon (IFN)/signal transducers and activators of transcription (STAT) signaling pathway acting through retinoic acid receptor α (Rarα) inhibition. J Biol Chem. 2011;286:33369–79.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. An N, Khan S, Imgruet MK, Gurbuxani SK, Konecki SN, Burgess MR, et al. Gene dosage effect of CUX1 in a murine model disrupts HSC homeostasis and controls the severity and mortality of MDS. Blood. 2018;131:2682–97.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Taylor P, Radić Z. The cholinesterases: from genes to proteins. Annu Rev Pharmacol Toxicol. 1994;34:281–320.

    Article  CAS  PubMed  Google Scholar 

  13. Chen C, Liu Y, Rappaport AR, Kitzing T, Schultz N, Zhao Z, et al. MLL3 is a haploinsufficient 7q tumor suppressor in acute myeloid leukemia. Cancer Cell. 2014;25:652–65.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Zhang Y, Wong J, Klinger M, Tran MT, Shannon KM, Killeen N. MLL5 contributes to hematopoietic stem cell fitness and homeostasis. Blood. 2009;113:1455–63.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Davidsson J, Puschmann A, Tedgård U, Bryder D, Nilsson L, Cammenga J. SAMD9 and SAMD9L in inherited predisposition to ataxia, pancytopenia, and myeloid malignancies. Leukemia. 2018;32:1106–15.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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The authors are grateful for the services and assistance provided by University of Chicago core facilities supported by the Cancer Center Support Grant (P30 CA014599). In particular, the authors thank William Buikema and the DNA Sequencing and Genotyping Facility Core for special assistance and services (RRID:SCR_019196). We also acknowledge support from the Cytometry and Antibody Technology Core (RRID: SCR_017760) and the Center for Research Informatics Bioinformatics Core.


This work was funded in part by NIH/NHLBI R01 HL142782, NIH/NCI R01 CA231880, American Cancer Society Research Scholar Award 132457-RSG-18-171-01-LIB, American Society of Hematology Junior Faculty Scholar Award, the Brinson Foundation, and The University of Chicago Cancer Research Foundation Women’s Board. The authors gratefully acknowledge the support of Robin and Matthew Patinkin.

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JTB and ICP performed experiments and datamining; WL and SZ performed machine learning analysis; JTB and WL analyzed results and made the figures; JTB, WL, and MEM designed the research and wrote the paper.

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Correspondence to Megan E. McNerney.

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Baeten, J.T., Liu, W., Preddy, I.C. et al. CRISPR screening in human hematopoietic stem and progenitor cells reveals an enrichment for tumor suppressor genes within chromosome 7 commonly deleted regions. Leukemia 36, 1421–1425 (2022).

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