CRISPR Screens Identify Targets Modulating Breast Cancer Vulnerabilities to NK Cells   — ASN Events
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  2. Poster Session One
  3. CRISPR Screens Identify Targets Modulating Breast Cancer Vulnerabilities to NK Cells  

CRISPR Screens Identify Targets Modulating Breast Cancer Vulnerabilities to NK Cells   (#162)

Yi Luo 1 , Debra Black 1 , Melissa R Elliott 2 , Christos Xiao 1 , Fernando Guimaraes 2 , Georgia Chenevix-Trench 1 , Jonathan Beesley 1
  1. Cancer Research Program, QIMR Berghofer, Brisbane, Queensland, Australia
  2. Frazer Institute, Faculty of Medicine, The University of Queensland, Woolloongabba, Queensland, Australia

Background:

Breast cancer (BC) remains the most prevalent cancer among women worldwide. While genome-wide association studies (GWAS) have identified over 230 genetic loci associated with BC risk, translating these findings into actionable therapeutic targets remains a challenge. Recurrence and metastasis, particularly due to immune evasion mechanisms, are largely incurable with current therapies. Notably, natural killer (NK) cells play a crucial role in eliminating tumour cells, yet many BC cells develop resistance to NK-mediated cytotoxicity. Here, we aim to identify BC risk genes that regulate resistance to NK cell killing with the goal of improving immunotherapeutic strategies.

Methods:

We performed in vitro CRISPR knockout screens targeting BC GWAS-predicted genes to identify tumour-intrinsic modulators of NK-mediated cytotoxicity. The screens were conducted by co-culturing pooled breast cell lines (MCF7, B80T5, and MDA-MB-231), transduced with the GWAS library, with either primary NK or NK92 cells. Candidate genes conferring resistance to NK cell cytotoxicity were selected for validation using in vitro NK-mediated cytotoxicity assays and in vivo orthotopic tumour models.

Results:

Our CRISPR screens identified 79 genes mediating tumour resistance to NK cytotoxicity (genes depleted in at least one screen with Beta < 0 and FDR < 0.25). We selected 10 for validation, including genes belonging to distinct functional pathways, such as chromatin modification (MAU2, BRD9), mitochondrial function and energy metabolism (ATP5ME, SDHA, FH, HSCB), protein folding (CALR), protein glycosylation (DPM3), and proteasomal degradation (RNF7). In vitro NK cytotoxicity assays further confirmed their effects detected in the screens. In vivo experiments are underway to confirm their role in NK evasion. 

Conclusion:

Our study identifies novel BC risk genes that contribute to NK cell resistance through distinct cellular pathways. Mechanistic investigation of these genes may identify novel vulnerabilities that may be exploited to enhance NK-mediated tumour clearance to improve immunotherapies for breast cancer.