Genome-wide CRISPR–Cas9 screening reveals ubiquitous T cell cancer targeting via the monomorphic MHC class I-related protein MR1

Abstract

Human leukocyte antigen (HLA)-independent, T cell–mediated targeting of cancer cells would allow immune destruction of malignancies in all individuals. Here, we use genome-wide CRISPR–Cas9 screening to establish that a T cell receptor (TCR) recognized and killed most human cancer types via the monomorphic MHC class I-related protein, MR1, while remaining inert to noncancerous cells. Unlike mucosal-associated invariant T cells, recognition of target cells by the TCR was independent of bacterial loading. Furthermore, concentration-dependent addition of vitamin B-related metabolite ligands of MR1 reduced TCR recognition of cancer cells, suggesting that recognition occurred via sensing of the cancer metabolome. An MR1-restricted T cell clone mediated in vivo regression of leukemia and conferred enhanced survival of NSG mice. TCR transfer to T cells of patients enabled killing of autologous and nonautologous melanoma. These findings offer opportunities for HLA-independent, pan-cancer, pan-population immunotherapies.

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Fig. 1: MC.7.G5 recognizes multiple cancer types through an HLA-independent mechanism.
Fig. 2: Whole-genome CRISPR–Cas9 library screening reveals MR1 as the candidate target of MC.7.G5.
Fig. 3: MR1 is the cancer cell-expressed target of MC.7.G5.
Fig. 4: MC.7.G5 does not recognize MR1 by known mechanisms.
Fig. 5: MC.7.G5 does not recognize healthy cells.
Fig. 6: MC.7.G5 remained inert to activated, stressed or infected healthy cells.
Fig. 7: MC.7.G5 mediates in vivo regression of leukemia and prolongs the survival of mice.
Fig. 8: Transfer of the MC.7.G5 T cell receptor redirects patient T cells to recognize autologous melanoma.

Data availability

The datasets generated during the current study are available from the corresponding author upon reasonable request.

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Acknowledgements

We thank F. Zhang for deposition of the GeCKO v.2 library at the Addgene plasmid repository (Addgene plasmid no. 1000000048); D. Trono for the deposition of pRRL.sin.cppt.pgk-gfp.wpre (Addgene plasmid no. 12252), envelope plasmid pMD2.G (Addgene plasmid no. 12259), and packaging plasmids pMDLg/pRRE (Addgene plasmid no. 12251) and pRSV-Rev (Addgene plasmid no. 12253); and J. Riley, University of Pennsylvania, who kindly provided the pELNS vector. A.K.S. is a Welcome Senior Investigator (WT100327MA), M.D.C. was funded by the Welsh Assembly Government via a Health and Care Research Wales PhD studentship. M.L. is funded by a Consolidator Award via the Wellcome Institutional Strategic Support Fund to the Cardiff University College of Biomedical and Life Sciences. S.A.E.G. was funded by a Tenovus Cancer Care PhD studentship. J.M. was supported by Program Grant APP1113293 from the National Health and Medical Research Council Australia.

Author information

A.K.S. and G.D. conceived project. M.D.C., G.D., M.E.C., S.A.E.G., M.A., A.L. and C.R. undertook the T cell experiments. M.D.C., M.L., C.P.F., B.S. and J.P. performed the genome-wide CRISPR experiments and/or analyses. A.F. generated lentiviral vectors and edited the manuscript. M.D. and I.M.S. supplied the patient PBMC and melanoma and renal carcinoma cell lines. A.A. provided advice on mouse experiments. A.L.P. provided expertise and ovarian cancer ascites. J.R. and J.M. provided the MR1 tetramer reagents. G.D. and A.K.S. supervised the work. M.D.C., G.D. and A.K.S. wrote and edited the manuscript.

Correspondence to Andrew K. Sewell.

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Cardiff University has filed patents based on these findings.

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Peer review information Zoltan Fehervari was the primary editor on this article and managed its editorial process and peer review in collaboration with the rest of the editorial team.

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Crowther, M.D., Dolton, G., Legut, M. et al. Genome-wide CRISPR–Cas9 screening reveals ubiquitous T cell cancer targeting via the monomorphic MHC class I-related protein MR1. Nat Immunol 21, 178–185 (2020). https://doi.org/10.1038/s41590-019-0578-8

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