Journal Article

Genome-scale screens identify factors regulating tumor cell responses to natural killer cells

Lowry, Emily, Freeman, Samuel S., Dhimolea, Eugen, Bryan, Jordan G., Syrgkanis, Vasilis, Mitsiades, Constantine S., Wang, Li, Romee, Rizwan, Tariq, Ifrah, Fraenkel, Ernest, Mustjoki, Satu, Culhane, Aedin C., Gandolfi, Sara, Wieten, Lotte, Amara, Suha Naffar-Abu, Zhu, Cong, Kamath, Govinda M., Sheffer, Michal, Yu, Channing, Roth, Jennifer A., Simoes, Ricardo De Matos, Mader, Chris C., Giannakis, Marios, Bender, Samantha, Golub, Todd, Beelen, Nicky, Dashevsky, Olga, Borah, Minasri, Tsherniak, Aviad, Dufva, Olli, Hu, Yiguo

2021

Overview

To systematically define molecular features in human tumor cells that determine their degree of sensitivity to human allogeneic natural killer (NK) cells, we quantified the NK cell responsiveness of hundreds of molecularly annotated ‘DNA-barcoded’ solid tumor cell lines in multiplexed format and applied genome-scale CRISPR-based gene-editing screens in several solid tumor cell lines, to functionally interrogate which genes in tumor cells regulate the response to NK cells. In these orthogonal studies, NK cell–sensitive tumor cells tend to exhibit ‘mesenchymal-like’ transcriptional programs; high transcriptional signature for chromatin remodeling complexes; high levels of B7-H6 ( NCR3LG1 ); and low levels of HLA-E /antigen presentation genes. Importantly, transcriptional signatures of NK cell–sensitive tumor cells correlate with immune checkpoint inhibitor (ICI) resistance in clinical samples. This study provides a comprehensive map of mechanisms regulating tumor cell responses to NK cells, with implications for future biomarker-driven applications of NK cell immunotherapies. The use of natural killer (NK) cells in immunotherapy as an alternative to allogeneic T cells is gaining ground. Here, two genome-scale high-throughput platforms are used to identify genes that modulate the sensitivity of multiple solid tumor cell lines to NK-mediated killing.

• Publisher: Nature Publishing Group US,Nature Publishing Group
• Subject: 631/208/191/2018 / 631/250/251 / Agriculture / Allogeneic Cells - physiology / Animal Genetics and Genomics / Animals / Antigen presentation / Antigens / B7 Antigens - genetics / Biomarkers / Biomedical and Life Sciences / Biomedicine / Cancer / Cancer cells / Cancer Research / Cell Line, Tumor / Chromatin Assembly and Disassembly - physiology / Chromatin remodeling / CRISPR / Cytotoxicity / Cytotoxicity Tests, Immunologic - methods / Cytotoxicity, Immunologic - genetics / Cytotoxicity, Immunologic - physiology / Deoxyribonucleic acid / DNA / DNA barcoding / Drug Resistance, Neoplasm - drug effects / Drug Resistance, Neoplasm - genetics / Female / Gene expression / Gene Expression Regulation, Neoplastic / Gene Function / Genes / Genetic aspects / Genetic modification / Genetic transcription / Genome editing / Genome, Human / Genomes / Genomics / Histocompatibility antigen HLA / Histocompatibility Antigens Class I - genetics / Histocompatibility Antigens Class I - immunology / HLA-E Antigens / Human Genetics / Humans / Immune checkpoint inhibitors / Immune Checkpoint Inhibitors - pharmacology / Immunotherapy / Killer cells / Killer Cells, Natural - physiology / Ligands / Mesenchyme / Methods / Mice, Inbred NOD / Mutation / Natural killer cells / Oncology, Experimental / Proteins / Solid tumors / Transcription / Tumor cell lines / Tumor cells / Tumors / Xenograft Model Antitumor Assays