CRISPR Screens for Functional Interrogation of Immunity

Overview

Journal Nat Rev Immunol

Specialty Allergy & Immunology

Date 2022 Dec 9

PMID 36481809

Authors

Hao Shi

John G Doench

Hongbo Chi

Affiliations

Soon will be listed here.

Abstract

CRISPR-based technologies represent a major breakthrough in biomedical science as they offer a powerful platform for unbiased screening and functional genomics in various fields, including immunology. Pooled and arrayed CRISPR screens have uncovered previously unknown intracellular drivers in innate and adaptive immune cells for immune regulation as well as intercellular regulators mediating cell-cell interactions. Recent single-cell CRISPR screening platforms expand the readouts to the transcriptome and enable the inference of gene regulatory networks for better mechanistic insights. CRISPR screens also allow for mapping of genetic interactions to identify genes that synergize or alleviate complex immune phenotypes. Here, we review the progress in and emerging adaptation of CRISPR technologies to advance our fundamental immunological knowledge and identify novel disease targets for immunotherapy of infection, inflammation and cancer.

Citing Articles

Paracrine rescue of MYR1-deficient mutants reveals limitations of pooled CRISPR screens.

Torelli F, da Fonseca D, Butterworth S, Young J, Treeck M Elife. 2024; 13.

PMID: 39654402 PMC: 11630813. DOI: 10.7554/eLife.102592.

Synthetic lethal strategies for the development of cancer therapeutics.

Ngoi N, Gallo D, Torrado C, Nardo M, Durocher D, Yap T Nat Rev Clin Oncol. 2024; 22(1):46-64.

PMID: 39627502 DOI: 10.1038/s41571-024-00966-z.

Kinome-wide CRISPR-Cas9 screens revealed as a positive regulator of TGF-β signaling.

Wang D, Zhang X, Guo J, Liu W, Zhou Y, Wang R Biochem Biophys Rep. 2024; 40:101864.

PMID: 39619656 PMC: 11605321. DOI: 10.1016/j.bbrep.2024.101864.

Spatially Resolved CRISPR Screen Sequencing via Perturb-DBiT.

Baysoy A, Tian X, Zhang F, Renauer P, Bai Z, Shi H bioRxiv. 2024; .

PMID: 39605490 PMC: 11601513. DOI: 10.1101/2024.11.18.624106.

Leveraging CRISPR gene editing technology to optimize the efficacy, safety and accessibility of CAR T-cell therapy.

Lei T, Wang Y, Zhang Y, Yang Y, Cao J, Huang J Leukemia. 2024; 38(12):2517-2543.

PMID: 39455854 PMC: 11588664. DOI: 10.1038/s41375-024-02444-y.

References

Cho S, Kim S, Kim J, Kim J . Targeted genome engineering in human cells with the Cas9 RNA-guided endonuclease. Nat Biotechnol. 2013; 31(3):230-2. DOI: 10.1038/nbt.2507. View

Jinek M, East A, Cheng A, Lin S, Ma E, Doudna J . RNA-programmed genome editing in human cells. Elife. 2013; 2:e00471. PMC: 3557905. DOI: 10.7554/eLife.00471. View

Cong L, Ran F, Cox D, Lin S, Barretto R, Habib N . Multiplex genome engineering using CRISPR/Cas systems. Science. 2013; 339(6121):819-23. PMC: 3795411. DOI: 10.1126/science.1231143. View

Mali P, Yang L, Esvelt K, Aach J, Guell M, DiCarlo J . RNA-guided human genome engineering via Cas9. Science. 2013; 339(6121):823-6. PMC: 3712628. DOI: 10.1126/science.1232033. View

Klompe S, Vo P, Halpin-Healy T, Sternberg S . Transposon-encoded CRISPR-Cas systems direct RNA-guided DNA integration. Nature. 2019; 571(7764):219-225. DOI: 10.1038/s41586-019-1323-z. View

Schumann K, Raju S, Lauber M, Kolb S, Shifrut E, Cortez J . Functional CRISPR dissection of gene networks controlling human regulatory T cell identity. Nat Immunol. 2020; 21(11):1456-1466. PMC: 7577958. DOI: 10.1038/s41590-020-0784-4. View

Chow R, Guzman C, Wang G, Schmidt F, Youngblood M, Ye L . AAV-mediated direct in vivo CRISPR screen identifies functional suppressors in glioblastoma. Nat Neurosci. 2017; 20(10):1329-1341. PMC: 5614841. DOI: 10.1038/nn.4620. View

Ye L, Park J, Dong M, Yang Q, Chow R, Peng L . In vivo CRISPR screening in CD8 T cells with AAV-Sleeping Beauty hybrid vectors identifies membrane targets for improving immunotherapy for glioblastoma. Nat Biotechnol. 2019; 37(11):1302-1313. PMC: 6834896. DOI: 10.1038/s41587-019-0246-4. View

Shifrut E, Carnevale J, Tobin V, Roth T, Woo J, Bui C . Genome-wide CRISPR Screens in Primary Human T Cells Reveal Key Regulators of Immune Function. Cell. 2018; 175(7):1958-1971.e15. PMC: 6689405. DOI: 10.1016/j.cell.2018.10.024. View

10.

Doench J . Am I ready for CRISPR? A user's guide to genetic screens. Nat Rev Genet. 2017; 19(2):67-80. DOI: 10.1038/nrg.2017.97. View

11.

Joung J, Konermann S, Gootenberg J, Abudayyeh O, Platt R, Brigham M . Genome-scale CRISPR-Cas9 knockout and transcriptional activation screening. Nat Protoc. 2017; 12(4):828-863. PMC: 5526071. DOI: 10.1038/nprot.2017.016. View

12.

Platt R, Chen S, Zhou Y, Yim M, Swiech L, Kempton H . CRISPR-Cas9 knockin mice for genome editing and cancer modeling. Cell. 2014; 159(2):440-55. PMC: 4265475. DOI: 10.1016/j.cell.2014.09.014. View

13.

Chu V, Weber T, Graf R, Sommermann T, Petsch K, Sack U . Efficient generation of Rosa26 knock-in mice using CRISPR/Cas9 in C57BL/6 zygotes. BMC Biotechnol. 2016; 16:4. PMC: 4715285. DOI: 10.1186/s12896-016-0234-4. View

14.

Parnas O, Jovanovic M, Eisenhaure T, Herbst R, Dixit A, Ye C . A Genome-wide CRISPR Screen in Primary Immune Cells to Dissect Regulatory Networks. Cell. 2015; 162(3):675-86. PMC: 4522370. DOI: 10.1016/j.cell.2015.06.059. View

15.

Jost M, Jacobson A, Hussmann J, Cirolia G, Fischbach M, Weissman J . CRISPR-based functional genomics in human dendritic cells. Elife. 2021; 10. PMC: 8104964. DOI: 10.7554/eLife.65856. View

16.

Yeung A, Choi Y, Lee A, Hale C, Ponstingl H, Pickard D . A Genome-Wide Knockout Screen in Human Macrophages Identified Host Factors Modulating Infection. mBio. 2019; 10(5). PMC: 6786873. DOI: 10.1128/mBio.02169-19. View

17.

Lai Y, Cui L, Babunovic G, Fortune S, Doench J, Lu T . High-Throughput CRISPR Screens To Dissect Macrophage- Interactions. mBio. 2021; 12(6):e0215821. PMC: 8689513. DOI: 10.1128/mBio.02158-21. View

18.

Sedlyarov V, Eichner R, Girardi E, Essletzbichler P, Goldmann U, Nunes-Hasler P . The Bicarbonate Transporter SLC4A7 Plays a Key Role in Macrophage Phagosome Acidification. Cell Host Microbe. 2018; 23(6):766-774.e5. PMC: 6002608. DOI: 10.1016/j.chom.2018.04.013. View

19.

Haney M, Bohlen C, Morgens D, Ousey J, Barkal A, Tsui C . Identification of phagocytosis regulators using magnetic genome-wide CRISPR screens. Nat Genet. 2018; 50(12):1716-1727. PMC: 6719718. DOI: 10.1038/s41588-018-0254-1. View

20.

Swanson K, Deng M, Ting J . The NLRP3 inflammasome: molecular activation and regulation to therapeutics. Nat Rev Immunol. 2019; 19(8):477-489. PMC: 7807242. DOI: 10.1038/s41577-019-0165-0. View