Table 1 CRISPR screens in T cells to identify genes for cancer immunotherapy
From: Functional CRISPR screens in T cells reveal new opportunities for cancer immunotherapies
Conditions | Cells | Libraries | Methods | Purpose | Hit genes | References |
|---|---|---|---|---|---|---|
ex vivo | IL13Rα2-targeted CAR T cells | Addgene #73179 | CRISPR loss of function screens | CAR-T effector activity, cytotoxic potency | TLE4 IKZF2 | Wang, D., et al. (2021)[113] |
ex vivo | Primary human T cells | Addgene #73178 | CRISPR loss of function screens | T cell proliferation | SOCS1 TCEB2 RASA2 CBLB | Shifrut, E., et al. (2018)[114] |
ex vivo | Primary human T cells | lentiSAM v2 | Coupled CRISPR activation and CRISPR interference screen | Gene networks controlling IL-2 and IFN-g production | VAV1 CD28 LCP2 LAT MALT1 BCL10 TRAF6 | Schmidt, R., et al. (2022)[115] |
ex vivo | Primary mouse CD8+ T cells | mm10dgLib | dead-guide RNA (dgRNA)-based CRISPR activation screen | CAR-T killing and in vivo efficacy in cancers | PRODH2 | Ye, L., et al. (2022)[116] |
in vivo | P14-transgenic Cas9-expressing CD45.1+ LSK cells (mouse) | A library of 110 sgRNAs targeting 21 genes relevant to T cell biology and 50 non-targeting control sgRNAs | CHIME: CHimeric IMmune Editing, | CD8+ T cell responses to LCMV Clone 13 infection | Ptpn2 | LaFleur, M. W., et al. (2019)[96] |
in vivo and ex vivo | Primary mouse CD8+ T cells | The genome-scale mouse T cell CRISPR library (MKO) | CRISPR loss of function screens | T cell activation, tumour infiltration and degranulation | Dhx37 | Dong, M. B., et al. (2019)[117] |
in vivo | Primary mouse CD8+ T cells | sgRNA library targeting 1658 genes, with 6628 sgRNAs and 1000 nontargeting controls | AAV–SB-CRISPR screens | T cells effector functions, and potent of killing tumour cells | Lag3 Mgat5 Pdia3 Emp1 | Ye, L., et al. (2019)[118] |
ex vivo | Primary human CD4+ T cells | Human genome-wide sgRNA library targeting 18,360 protein-coding genes | Guide Swap pooled CRISPR enrichment and depletion screens | Validation of guide swap in depletion and enrichment screens in CD4 + T cells | MDM2 WEE1 EEF2 TOP2A | Ting, P. Y., et al. (2018)[119] |
ex vivo | 68–41 murine T cell line | Lentiviral gRNA library (87,898 gRNAs/19,150 genes) | CRISPR loss of function screens | T cell activation | Fut8 | Okada, M., et al. (2017)[120] |
ex vivo | Primary mouse T helper cells | Addgene #67988 | CRISPR loss of function screens | T helper cell activation and differentiation | PPARG | Henriksson, J., et al. (2019) [121] |
in vivo | Mouse CD8+ T cells | Pooled gRNA library of 3017 metabolism-associated genes | CRISPR loss of function screens | CD8+ T cell fate decision | Pofut1 | Huang, H., et al. (2021)[122] |
in vivo | Mouse CD8+ T cells | Two lentiviral sub-libraries of single-guide sgRNAs targeting 3017 metabolic enzymes, small molecule transporters and metabolism-related transcriptional regulators | CRISPR loss of function screens | T cell longevity and antitumour response | REGNASE-1 | Wei, J., et al. (2019)[123] |
in vivo | Antigen-experienced mouse CD4+ T cells | A genome-wide knockout (GWKO) sgRNA lentiviral library (18,400 genes, 90,000 sgRNAs) | CRISPR loss of function screens | The expansion of activated CD4+ T cells | SOCS1 | Sutra Del Galy, A., et al. (2021)[97] |
in vivo | Primary mouse CD8+ T cells | Retroviral sgRNA library targeting 271 transcription factors | CRISPR loss of function screens (OpTICS) | T cell effector activity | Fli1 | Chen, Z., et al. (2021)[124] |
in vivo and ex vivo | Chronic stimulated CD8+ T cells | Addgene #104861 | CRISPR loss of function screens | T cell exhaustion | Arid1a | Belk, J. A., et al. (2022)[125] |
ex vivo | Jurkat T cells | sgRNA library consists of over 250,000 total sgRNAs targeting every unique Refseq annotated (hg19) protein coding isoform with up to 12 sgRNAs, plus 7700 NTCs | CRISPR loss of function screens | T cell activation | FAM49B | Shang, W., et al. (2018)[126] |
ex vivo | Human CD4+ and CD8+ T cells | Lentiviral library of human ORFs containing nearly 12,000 full-length genes | CRISPR gain of function screens | T cell proliferation | LTBR | Legut, M., et al. (2022)[127] |
in vivo | Mouse OT-1 CD8+ T cells | scCRISPR library containing 180 TFs with 720 sgRNAs and 80 NTC sgRNAs | CRISPR loss of function screens | CD8+ cytotoxic T cells differentiation and Tex cell reinvigoration | IKZF1 ETS1 | Zhou, P., et al. (2023)[128] |
ex vivo | Primary human CD8+ T cells | Published highly optimized library that encodes gRNAs and Cas9 (Wang et al. 2017) | CRISPR loss of function screens | T cell exhaustion | SNX9 | Trefny, M. P., et al. (2023)[129] |
ex vivo | Primary mouse CD8+ T cells | sgRNA library from Benchling or Brie, adding up to a total of 2298 sgRNAs | CRISPR loss of function screens | T cell adhesion, migration, homeostasis | RASA3 | Johansen, K. H., et al. (2022)[130] |
ex vivo | Primary human T cells | Brunello sgRNA library | CRISPR loss of function screens (SLICE) | T cell dysfunction | RASA2 | Carnevale, J., et al. (2022)[131] |
ex vivo | Primary mouse Treg cells | A library of 489 nuclear factors on the basis of optimized sgRNA sequences from the Brie library | CRISPR loss of function screens | Treg instability | Usp22 Rnf20 | Cortez, J. T., et al. (2020)[98] |
in vivo | Primary mouse CD4+ T cells | Addgene, PooledLibrary #73632 | CRISPR loss of function screens | T cell differentiation and function | MTHFD2 | Sugiura, A., et al. (2022)[132] |
ex vivo | Primary mouse Treg cells | LentiCRISPRv2-Brie | CRISPR loss of function screens | Treg cell function and anti-tumour immunity | Brd9-containing ncBAF complex | Loo, C. S., et al. (2020)[133] |
ex vivo | Primary human Treg cells | Cas9 RNPs pooled containing 40 selected candidate TFs of Treg cell identity | CRISPR loss of function screens | Treg cell function | HIVEP2 SATB1 | Schumann, K., et al. (2020)[134] |
in vivo | Primary mouse CD4+ T cells | sgRNA metabolic library | CRISPR loss of function screens | Tfh cell differentiation | ETNK1 PCYT2 SELENOI | Fu, G., et al. (2021)[135] |
ex vivo | Primary mouse CD4+ T cells | Lentiviral Brie sgRNA library (78,633 sgRNAs targeting 19,674 genes) | CRISPR loss of function screens | T cell priming and Treg suppressive function | SEC31A CCDC101 | Long, L., et al. (2021)[136] |
in vivo | Primary mouse CD4+ T cells |  ~ 400 SgRNAs from Brie library targeting ~ 80 genes | CRISPR loss of function screens | Tfh cell development, Tfh versus Th1 decisions | HIF-1α | Huang, B., et al. (2022)[137] |
ex vivo | Human T cells | sgRNA library targeting 829 genes | CRISPR loss of function screens | T cell exhaustion | IKZF1 | Gayathri, B., et al. (2022)[138] |
in vivo and ex vivo | Primary mouse CD8+ T cells | sgRNA library with 78,633 sgRNAs targeting 19,674 genes | CRISPR loss of function screens | CD8+ T cell expansion and anti-tumour immunity | Roquin | Zhao, H., et al. (2021)[139] |