Single-cell functional genomics of natural killer cell evasion in blood cancers

Natural killer (NK) cells are emerging as a promising therapeutic option in cancer. To better understand how cancer cells evade NK cells, we studied interacting NK and blood cancer cells using single-cell and genome-scale functional genomics screens. At single-cell resolution, interaction of NK and cancer cells induced distinct activation states in both cell types depending on the cancer cell lineage and molecular phenotype, ranging from more sensitive myeloid to more resistant B-lymphoid cancers. CRISPR screens uncovered cancer cell-intrinsic genes driving sensitivity and resistance, including antigen presentation and death receptor signaling mediators, adhesion molecules, protein fucosylation genes, and transcriptional regulators. CRISPR screens with a single-cell transcriptomic readout revealed how these cancer cell genes influenced the gene expression landscape of both cell types, including regulation of activation states in both cancer and NK cells by IFNγ signaling. Our findings provide a resource for rational design of NK cell-based therapies in blood cancers. HIGHLIGHTS ### Competing Interest Statement M.S. and C.S.M. are authors of a patent application related to antitumor activity of NK cells. C.S.M. is a member of the Scientific Advisory Board of Adicet Bio and also discloses consultant honoraria from Fate Therapeutics, Ionis Pharmaceuticals, FIMECS, Secura Bio, Oncopeptides; and research funding from Sanofi, Merck KGaA/EMD Serono, Arch Oncology, Karyopharm, Nurix, H3 Biosciences, Novartis, BMS, Abcuro, and Springworks. S.M. has received honoraria and research funding from Novartis, Pfizer and Bristol-Myers Squibb (not related to this study).