CRISPR screens in the context of immune selection identify CHD1 and MAP3K7 as mediators of cancer immunotherapy resistance

Watterson, A.; Picco, G.; Veninga, V.; Samarakoon, Y.; Cattaneo, C. M.; Vieira, S. F.; Karakoc, E.; Bhosle, S.; Battaglia, T. W.; Consonni, S.; Halim, T. Y. F.; Voest, E. E.; Garnett, M. J.; Coelho, M. A.

doi:10.1101/2025.04.15.648737

bioRxiv · 10.1101/2025.04.15.648737

CRISPR screens in the context of immune selection identify CHD1 and MAP3K7 as mediators of cancer immunotherapy resistance

Watterson, A.·Picco, G.·Veninga, V.·Samarakoon, Y.·Cattaneo, C. M.·Vieira, S. F.·Karakoc, E.·Bhosle, S.·Battaglia, T. W.·Consonni, S.·Halim, T. Y. F.·Voest, E. E.·Garnett, M. J.·Coelho, M. A.

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Abstract

Cancer immunotherapy is only effective in a subset of patients, highlighting the need for effective biomarkers and combination therapies. Here we systematically identify genetic determinants of cancer cell sensitivity to anti-tumor immunity by performing whole-genome CRISPR/Cas9 knock-out screens in autologous tumoroid-T cell co-cultures, isogenic cancer cell models deficient in interferon signaling, and in the context of four cytokines. We discover that loss of CHD1 and MAP3K7 potentiates the transcriptional response to IFN-{gamma}, thereby creating an acquired vulnerability through sensitizing cancer cells to tumor-reactive T cells. Immune checkpoint blockade was more effective in a syngeneic mouse model of melanoma deficient in Chd1 and Map3k7 and was associated with elevated intra-tumoral CD8+ T cell numbers and activation. CHD1 and MAP3K7 are recurrently mutated in cancer and reduced expression in tumors correlates with response to immune checkpoint inhibitors in patients, nominating these genes as potential biomarkers of immunotherapy response.

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Watterson, A., Picco, G., Veninga, V., Samarakoon, Y., Cattaneo, C. M., Vieira, S. F., Karakoc, E., Bhosle, S., Battaglia, T. W., Consonni, S., Halim, T. Y. F., Voest, E. E., Garnett, M. J., Coelho, M. A.. 2025-04-18. CRISPR screens in the context of immune selection identify CHD1 and MAP3K7 as mediators of cancer immunotherapy resistance. https://doi.org/10.1101/2025.04.15.648737

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