Poster Presentation 41st Lorne Genome Conference 2020

Systematic identification, validation, and evaluation of breast cancer risk genes through follow-up of genome-wide association studies (#258)

Natasha K Tuano 1 , Jonathan Beesley 2 , Murray Manning 1 , Wei Shi 2 , Juliet French 3 , Stacey Edwards 4 , Georgia Chenevix-Trench 2 , Joseph Rosenbluh 1
  1. Cancer Functional Genomics Laboratory, Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
  2. Cancer Genetics Laboratory, QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
  3. Functional Genetics Laboratory, QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
  4. Functional Cancer Genomics Laboratory, QIMR Berghofer Medical Research Institute, Herston, QLD, Australia

Genome-wide association studies (GWAS) has been extensively useful in identification of low penetrance genetic risk variants that contribute to disease progression or susceptibility. Breast cancer (BC) risk is linked to susceptibility genes such as BRCA1, however most of the BC risk variants still remain unknown.  GWAS of breast cancer has identified 179 loci associated with BC risk. In order to direct functional follow-up studies of BC risk loci, INQUISIT (integrated expression quantitative trait and in-silico prediction of GWAS targets), is a heuristic scoring system  that ranks predicted target genes at these BC risk loci based on multiple features derived from in-silico breast tissue data. INQUISIT analysis in combination with eQTL (expression quantitative trait loci) analysis and Transcriptome Wide-Association Study (TWAS) predicted 1648 (1107 coding and 541 non-coding) candidate genes, which include known cancer driver genes and many genes with no known role in BC aetiology.

To systematically study these candidate BC risk genes we performed large-scale CRISPR suppression screens in an unbiased approach by generation of a pooled lentiviral library containing single guide RNAs (sgRNA) targeting the predicted 1648 genes and transduced this library into immortalized mammary epithelial cells and stem/progenitor cells. Cells were propagated for 21 days, genomic DNA isolated and used for next generation sequencing to quantify sgRNA abundance. CRISPR suppression screens identified well-validated tumor suppressor genes (NF2 and PTEN) and novel tumor suppressor genes such as ATXN7, DHX29 and LPAR2, which were strongly predicted as risk genes by INQUISIT that upon suppression are able to promote proliferation.

This systematic approach enables further understanding of BC aetiology and identification of novel BC risk genes, which will allow the development of strategies for BC chemoprevention and risk reduction. The ultimate aim of post-GWAS is to translate evidence of genetic association into molecular mechanisms and effective clinical interventions.