CRISPR screening in hematology research: from bulk to single-cell level

Mohr S, Bakal C, Perrimon N. Genomic screening with RNAi: results and challenges. Annu Rev Biochem. 2010;79:37. https://doi.org/10.1146/ANNUREV-BIOCHEM-060408-092949.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA, Charpentier E. A programmable dual-RNA–guided DNA endonuclease in adaptive bacterial immunity. Science. 1979;2012(337):816–21. https://doi.org/10.1126/science.1225829.

Article  CAS  Google Scholar 

Makarova KS, Wolf YI, Iranzo J, Shmakov SA, Alkhnbashi OS, Brouns SJJ, et al. Evolutionary classification of CRISPR–Cas systems: a burst of class 2 and derived variants. Nat Rev Microbiol. 2020;18:67. https://doi.org/10.1038/S41579-019-0299-X.

Article  CAS  PubMed  Google Scholar 

Cox DBT, Gootenberg JS, Abudayyeh OO, Franklin B, Kellner MJ, Joung J, et al. RNA editing with CRISPR-Cas13. Science. 2017;358:1019–27. https://doi.org/10.1126/SCIENCE.AAQ0180.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Ran FA, Hsu PD, Lin CY, Gootenberg JS, Konermann S, Trevino AE, et al. Double nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity. Cell. 2013. https://doi.org/10.1016/J.CELL.2013.08.021.

Article  PubMed  PubMed Central  Google Scholar 

Kleinstiver BP, Sousa AA, Walton RT, Tak YE, Hsu JY, Clement K, et al. Engineered CRISPR-Cas12a variants with increased activities and improved targeting ranges for gene, epigenetic and base editing. Nat Biotechnol. 2019;37:276–82. https://doi.org/10.1038/S41587-018-0011-0.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Zetsche B, Gootenberg JS, Abudayyeh OO, Slaymaker IM, Makarova KS, Essletzbichler P, et al. Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system. Cell. 2015;163:759–71. https://doi.org/10.1016/J.CELL.2015.09.038.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kim HK, Lee S, Kim Y, Park J, Min S, Choi JW, et al. High-throughput analysis of the activities of xCas9, SpCas9-NG and SpCas9 at matched and mismatched target sequences in human cells. Nat Biomed Eng. 2020. https://doi.org/10.1038/s41551-019-0505-1.

Article  PubMed  PubMed Central  Google Scholar 

Shmakov S, Abudayyeh OO, Makarova KS, Wolf YI, Gootenberg JS, Semenova E, et al. Discovery and functional characterization of diverse class 2 CRISPR-Cas systems. Mol Cell. 2015;60:385–97. https://doi.org/10.1016/J.MOLCEL.2015.10.008.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Anzalone AV, Randolph PB, Davis JR, Sousa AA, Koblan LW, Levy JM, et al. Search-and-replace genome editing without double-strand breaks or donor DNA. Nature. 2019;576:149–57. https://doi.org/10.1038/s41586-019-1711-4.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Komor AC, Kim YB, Packer MS, Zuris JA, Liu DR. Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage. Nature. 2016;533:420–4. https://doi.org/10.1038/nature17946.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bock C, Datlinger P, Chardon F, Coelho MA, Dong MB, Lawson KA, et al. High-content CRISPR screening. Nature Reviews Methods Primers. 2022;2:1–23. https://doi.org/10.1038/s43586-021-00093-4.

Article  CAS  Google Scholar 

Anzalone AV, Koblan LW, Liu DR. Genome editing with CRISPR–Cas nucleases, base editors, transposases and prime editors. Nat Biotechnol. 2020;38:824–44. https://doi.org/10.1038/s41587-020-0561-9.

Article  CAS  PubMed  Google Scholar 

Pickar-Oliver A, Gersbach CA. The next generation of CRISPR–Cas technologies and applications. Nat Rev Mol Cell Biol. 2019;20:490–507. https://doi.org/10.1038/s41580-019-0131-5.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Doench JG. Am I ready for CRISPR? A user’s guide to genetic screens. Nat Rev Genet. 2018;19:67–80. https://doi.org/10.1038/nrg.2017.97.

Article  CAS  PubMed  Google Scholar 

Joung J, Konermann S, Gootenberg JS, Abudayyeh OO, Platt RJ, Brigham MD, et al. Genome-scale CRISPR-Cas9 knockout and transcriptional activation screening. Nat Protoc. 2017;12:828–63. https://doi.org/10.1038/nprot.2017.016.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hart T, Tong AHY, Chan K, van Leeuwen J, Seetharaman A, Aregger M, et al. Evaluation and design of genome-wide CRISPR/SpCas9 knockout screens. G3 Genes Genomes Genet. 2017;7:2719–27. https://doi.org/10.1534/G3.117.041277/-/DC1.

Article  CAS  Google Scholar 

Wang T, Wei JJ, Sabatini DM, Lander ES. Genetic screens in human cells using the CRISPR-Cas9 system. Science. 1979;2014(343):80–4. https://doi.org/10.1126/science.1246981.

Article  CAS  Google Scholar 

Shalem O, Sanjana NE, Hartenian E, Shi X, Scott DA, Mikkelson T, et al. Genome-scale CRISPR-Cas9 knockout screening in human cells. Science. 2014;343:84–7. https://doi.org/10.1126/science.1247005.

Article  CAS  PubMed  Google Scholar 

Soares F, Chen B, Lee JB, Ahmed M, Ly D, Tin E, et al. CRISPR screen identifies genes that sensitize AML cells to double-negative T-cell therapy. Blood. 2021;137:2171–81. https://doi.org/10.1182/blood.2019004108.

Article  CAS  PubMed  Google Scholar 

Zou X, Koh GCC, Nanda AS, Degasperi A, Urgo K, Roumeliotis TI, et al. A systematic CRISPR screen defines mutational mechanisms underpinning signatures caused by replication errors and endogenous DNA damage. Nat Cancer. 2021;2:643–57. https://doi.org/10.1038/s43018-021-00200-0.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Wei L, Lee D, Law C-T, Zhang MS, Shen J, Chin DW-C, et al. Genome-wide CRISPR/Cas9 library screening identified PHGDH as a critical driver for Sorafenib resistance in HCC. Nat Commun. 2019;10:4681. https://doi.org/10.1038/s41467-019-12606-7.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bajaj J, Hamilton M, Shima Y, Chambers K, Spinler K, Van Nostrand EL, et al. An in vivo genome-wide CRISPR screen identifies the RNA-binding protein Staufen2 as a key regulator of myeloid leukemia. Nat Cancer. 2020;1:410–22. https://doi.org/10.1038/s43018-020-0054-2.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Dai M, Yan G, Wang N, Daliah G, Edick AM, Poulet S, et al. In vivo genome-wide CRISPR screen reveals breast cancer vulnerabilities and synergistic mTOR/Hippo targeted combination therapy. Nat Commun. 2021;12:3055. https://doi.org/10.1038/s41467-021-23316-4.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Fu G, Guy CS, Chapman NM, Palacios G, Wei J, Zhou P, et al. Metabolic control of TFH cells and humoral immunity by phosphatidylethanolamine. Nature. 2021;595:724–9. https://doi.org/10.1038/s41586-021-03692-z.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Yan F, Li J, Milosevic J, Petroni R, Liu S, Shi Z, et al. KAT6A and ENL form an epigenetic transcriptional control module to drive critical leukemogenic gene-expression programs. Cancer Discov. 2022;12:792–811. https://doi.org/10.1158/2159-8290.CD-20-1459.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Khan DH, Mullokandov M, Wu Y, Voisin V, Gronda M, Hurren R, et al. Mitochondrial carrier homolog 2 is necessary for AML survival. Blood. 2020;136:81–92. https://doi.org/10.1182/BLOOD.2019000106/454408/MITOCHONDRIAL-CARRIER-HOMOLOG-2-MTCH2-IS-NECESSARY.

Article  PubMed  Google Scholar 

Lee D, Kang S-H, Choi D, Ko M, Choi E, Ahn H, et al. Genome wide CRISPR screening reveals a role for sialylation in the tumorigenesis and chemoresistance of acute myeloid leukemia cells. Cancer Lett. 2021;510:37–47. https://doi.org/10.1016/j.canlet.2021.04.006.

Article  CAS  PubMed  Google Scholar 

Oshima K, Zhao J, Pérez-Durán P, Brown JA, Patiño-Galindo JA, Chu T, et al. Mutational and functional genetics mapping of chemotherapy resistance mechanisms in relapsed acute lymphoblastic leukemia. Nat Cancer. 2020;1:1113–27. https://doi.org/10.1038/s43018-020-00124-1.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Autry RJ, Paugh SW, Carter R, Shi L, Liu J, Ferguson DC, et al. Integrative genomic analyses reveal mechanisms of glucocorticoid resistance in acute lymphoblastic leukemia. Nat Cancer. 2020;1:329. https://doi.org/10.1038/S43018-020-0037-3.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Zhang P, Brinton LT, Gharghabi M, Sher S, Williams K, Cannon M, et al. Targeting OXPHOS de novo purine synthesis as the nexus of FLT3 inhibitor–mediated synergistic antileukemic actions. Sci Adv. 2022;8:9005. https://doi.org/10.1126/SCIADV.ABP9005/SUPPL_FILE/SCIADV.ABP9005_DATA_FILES_S1_TO_S6.ZIP.

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