Leukemia-intrinsic determinants of CAR-T response revealed by in vivo genome-wide CRISPR screening.

Ramos, A.; Koch, C. E.; Liu, Y.; Hellinger, R. D.; Kyung, T.; Larson, R. C.; Froese, J.; Goulet, D.; Doench, J. G.; Regev, A.; Maus, M. V.; Birnbaum, M. E.; Hemann, M.

doi:10.1101/2022.02.15.480217

bioRxiv · 10.1101/2022.02.15.480217

Leukemia-intrinsic determinants of CAR-T response revealed by in vivo genome-wide CRISPR screening.

Ramos, A.·Koch, C. E.·Liu, Y.·Hellinger, R. D.·Kyung, T.·Larson, R. C.·Froese, J.·Goulet, D.·Doench, J. G.·Regev, A.·Maus, M. V.·Birnbaum, M. E.·Hemann, M.

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Abstract

CAR-T therapy is a promising new treatment modality for B-cell malignancies. However, the majority of patients inevitably go on to experience disease relapse through largely unknown means. To investigate leukemia-intrinsic CAR-T resistance mechanisms, we performed genome-wide CRISPR-Cas9 loss-of-function screens in an immunocompetent murine model of B-cell acute lymphoblastic leukemia (B-ALL) utilizing a novel, modular guide RNA library. We identified IFN{gamma}/JAK/STAT signaling and components of antigen processing and presentation pathway as key mediators of resistance to CAR-T therapy in vivo, but not in vitro. Transcriptional characterization of this model demonstrated an upregulation of these pathways in CAR-T treated relapsed tumors, and examination of data from CAR-T treated patients with B-ALL revealed an association between poor outcomes and increased expression of JAK/STAT/MHC-I in leukemia cells. Overall, our data identify an unexpected mechanism of resistance to CAR-T therapy in which tumor cell interaction with CAR-T cells in vivo induces expression of an adaptive T-cell resistance program in tumor cells.

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Ramos, A., Koch, C. E., Liu, Y., Hellinger, R. D., Kyung, T., Larson, R. C., Froese, J., Goulet, D., Doench, J. G., Regev, A., Maus, M. V., Birnbaum, M. E., Hemann, M.. 2022-02-17. Leukemia-intrinsic determinants of CAR-T response revealed by in vivo genome-wide CRISPR screening.. https://doi.org/10.1101/2022.02.15.480217

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