Distinct NK cell subsets in HGSC: scRNAseq insights and microenvironmental features
Sarah Nersesian1,2,3, Celine M Laumont4,5, Lauren P Westhaver6, Stacey N Lee1,2, Morgan Pugh-Toole3,6, Anna P Nicolela6, Riley J Arseneau2,6, Shreena Kalaria4,5, Julian Smazynski4,5, Alex Miranda4,5, Phineas T Hamilton4,5, Daniel Gaston2,6,7, Brad H Nelson4,5, Jeanette E Boudreau6.
1Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, Canada; 2Beatrice Hunter Cancer Research Institute, Halifax, NS, Canada; 3Ovarian Cancer Expert Alliance of Nova Scotia, Halifax, NS, Canada; 4Deeley Research Centre, BC Cancer, Victoria, BC, Canada; 5Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada; 6Department of Pathology, Dalhousie University, Halifax, NS, Canada; 7Department of Pathology and Laboratory Medicine, Nova Scotia Health, Halifax, NS, Canada
Introduction. Immunotherapies have had little success in HGSC. Natural killer (NK) cells are attractive targets for cellular therapies because they have diverse anti-tumour functions: cytokine production to recruit and direct immunity, and cytotoxicity activated by signals from stress, DNA damage, HLA loss or antibodies bound to target cells.
Methods. We characterized NK cells in HGSC using single-cell RNA sequencing from 21 treatment-naive HGSC tumours. To validate predicted NK cell subtypes, we developed a high-parameter flow cytometry panel to study ascites samples. Next, we performed differential RNA-seq gene expression analyses within our dataset and the HGSC TCGA dataset to understand transcriptional features associated with HGSC-infiltrating NK cells.
Results. We identified five transcriptionally distinct NK cell populations, predicted to have unique functions and phenotypes. The proportions of NK cell subsets vary between tumours, with corresponding changes in RNA-seq predicted activities. Tumours with high NK cell proportions had transcriptional features of humoral immunity, immune cell chemotaxis and cell senescence; while NK cell low tumours were associated with high metabolic activity and collagen-rich environments.
Conclusions. NK cell subsets differ in proportion between patient tumours, with each subset associating with unique transcriptional signatures, suggesting distinct functions. Effective NK cell-based immunotherapy will likely require consideration and understanding of how the HGSC microenvironment impacts NK cell reactivity.