Single-cell functional genomics reveals determinants of sensitivity and resistance to natural killer cells in blood cancers

Olli Dufva; Sara Gandolfi; Jani Huuhtanen; Olga Dashevsky; Hanna Duàn; Khalid Saeed; Jay Klievink; Petra Nygren; Jonas Bouhlal; Jenni Lahtela; Anna Näätänen; Bishwa R Ghimire; Tiina Hannunen; Pekka Ellonen; Hanna Lähteenmäki; Pauliina Rumm; Jason Theodoropoulos; Essi Laajala; Jouni Härkönen; Petri Pölönen; Merja Heinäniemi; Maija Hollmén; Shizuka Yamano; Ryosuke Shirasaki; David A Barbie; Jennifer A Roth; Rizwan Romee; Michal Sheffer; Harri Lähdesmäki; Dean A Lee; Ricardo De Matos Simoes; Matti Kankainen; Constantine S Mitsiades; Satu Mustjoki

doi:10.1016/j.immuni.2023.11.008

Single-cell functional genomics reveals determinants of sensitivity and resistance to natural killer cells in blood cancers

Immunity. 2023 Dec 12;56(12):2816-2835.e13. doi: 10.1016/j.immuni.2023.11.008.

Authors

Olli Dufva¹, Sara Gandolfi², Jani Huuhtanen³, Olga Dashevsky⁴, Hanna Duàn¹, Khalid Saeed⁵, Jay Klievink¹, Petra Nygren¹, Jonas Bouhlal¹, Jenni Lahtela⁶, Anna Näätänen⁶, Bishwa R Ghimire⁶, Tiina Hannunen⁶, Pekka Ellonen⁶, Hanna Lähteenmäki⁵, Pauliina Rumm⁵, Jason Theodoropoulos⁵, Essi Laajala¹, Jouni Härkönen⁷, Petri Pölönen⁸, Merja Heinäniemi⁷, Maija Hollmén⁹, Shizuka Yamano⁴, Ryosuke Shirasaki⁴, David A Barbie⁴, Jennifer A Roth¹⁰, Rizwan Romee¹¹, Michal Sheffer⁴, Harri Lähdesmäki¹², Dean A Lee¹³, Ricardo De Matos Simoes⁴, Matti Kankainen¹⁴, Constantine S Mitsiades¹⁵, Satu Mustjoki¹⁶

Affiliations

¹ Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, 00290 Helsinki, Finland.
² Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, 00290 Helsinki, Finland; Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
³ Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, 00290 Helsinki, Finland; Department of Computer Science, Aalto University, 02150 Espoo, Finland.
⁴ Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA 02215, USA; Ludwig Center, Harvard Medical School, Boston, MA 02215, USA.
⁵ Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland.
⁶ Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, 00014 Helsinki, Finland.
⁷ Faculty of Health Sciences, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211 Kuopio, Finland.
⁸ Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
⁹ Medicity Research Laboratory, University of Turku, 20014 Turku, Finland.
¹⁰ Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
¹¹ Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; Department of Medicine, Harvard Medical School, Boston, MA 02215, USA; Ludwig Center, Harvard Medical School, Boston, MA 02215, USA.
¹² Department of Computer Science, Aalto University, 02150 Espoo, Finland.
¹³ Hematology/Oncology/BMT, Center for Childhood Cancer and Blood Diseases, Nationwide Children's Hospital, Columbus, OH 43205, USA.
¹⁴ Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, 00290 Helsinki, Finland; Laboratory of Genetics, HUS Diagnostic Center, Hospital District of Helsinki and Uusima (HUS), 00290 Helsinki, Finland.
¹⁵ Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA 02215, USA; Ludwig Center, Harvard Medical School, Boston, MA 02215, USA. Electronic address: [email protected].
¹⁶ Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, 00290 Helsinki, Finland. Electronic address: [email protected].

PMID: 38091953
DOI: 10.1016/j.immuni.2023.11.008

Abstract

Cancer cells can evade natural killer (NK) cell activity, thereby limiting anti-tumor immunity. To reveal genetic determinants of susceptibility to NK cell activity, we examined interacting NK cells and blood cancer cells using single-cell and genome-scale functional genomics screens. Interaction of NK and cancer cells induced distinct activation and type I interferon (IFN) states in both cell types depending on the cancer cell lineage and molecular phenotype, ranging from more sensitive myeloid to less sensitive B-lymphoid cancers. CRISPR screens in cancer cells uncovered genes regulating sensitivity and resistance to NK cell-mediated killing, including adhesion-related glycoproteins, protein fucosylation genes, and transcriptional regulators, in addition to confirming the importance of antigen presentation and death receptor signaling pathways. CRISPR screens with a single-cell transcriptomic readout provided insight into underlying mechanisms, including regulation of IFN-γ signaling in cancer cells and NK cell activation states. Our findings highlight the diversity of mechanisms influencing NK cell susceptibility across different cancers and provide a resource for NK cell-based therapies.

Keywords: CRISPR screening; CROP-seq; NK cell; cancer; functional genomics; immunotherapy resistance; leukemia; lymphoma; myeloma; single-cell RNA sequencing.

MeSH terms

Antigen Presentation
Cell Line, Tumor
Cytotoxicity, Immunologic / genetics
Genomics
Hematologic Neoplasms*
Humans
Killer Cells, Natural
Neoplasms* / genetics