Abstract
Endometrial cancer is the most common gynaecological cancer in New Zealand, with Māori and Pasifika women under the age of 50 experiencing increased prevalence and mortality over the past 20 years. Obesity rates have increased alongside rates of endometrial cancer, with women who have a body mass index of ≥25 accounting for 33% of cases in New Zealand. Women with first and/or second-degree family history of endometrial cancer have a two-to-three-fold increased risk of developing the disease. Inherited genetic variants associated with endometrial cancer provide evidence of genes or functional domains that lead to disease predisposition. DNA copy number variants (CNVs) have been identified as a common source of variation between individuals, though the functional impact of CNVs on the development of endometrial cancer remains relatively unknown.
This project aimed to functionally characterise candidate genes overlapping CNVs that were recently found to be associated with endometrial cancer from a large genome-wide association study (GWAS) conducted in A/Prof Walker’s laboratory by PhD student Cassie Stylianou. A total of 68 candidate risk genes were assessed, including 21 genes that were encompassed by a risk associated CNV deletion at the 16p11.2 region. Pathway analysis of the GWAS candidate risk genes indicated a significant enrichment with previous SNP-based GWAS results relating to body fat distribution. Expression analysis of the 68 candidate risk genes using tissue specific RNA-seq data from The Cancer Genome Atlas Uterine Corpus Endometrial Carcinoma dataset (TCGA UCEC) showed that 37 genes exhibited dosage sensitivity in endometrial cells. Cell-based functional assays were conducted in the endometrial cancer cell-line AN3-CA and the immortalized “normal” cell-line EM-E6/E7/hTERT. Assessment of two candidate risk genes, BARD1 and PTGIS showed that their expression levels was too low for analysis for knockdown experiments. Successful knockdown of a third candidate gene, KCTD13, was achieved in the AN3-CA cell-line, but analysis of cell viability and proliferation (a hallmark of cancer) showed no significant change with reduced KCTD13 expression. Additionally, RNA expression and CNV profiles of 507 tumour samples were extracted from TCGA UCEC dataset to compare the expression profile of tumours with deletions overlapping candidate risk genes to those without. Differentially expressed genes from deletions overlapping the 16p11.2 region showed an association with body fat distribution, weight, and body fat percentage. Preliminary results from this study provide evidence that genes overlapping deletions associated with endometrial cancer are enriched for obesity and cancer-related pathways.