Functional analysis of low-moderate risk susceptibility genes emerging from pathway based approaches and genome wide association studies in epithelial ovarian cancer

Pathway based and genome wide association studies aim to identify alleles of low/moderate risk that may account for the development of EOC not attributed to high risk susceptibility genes. The aim of this study was to investigate the functional role of low/moderate susceptibility SNPs and candidate genes that emerge from candidate gene approaches and GWAS using tumour tissues or appropriate models from the proposed cells of origin for EOC, normal Ovarian Surface Epithelium (NOSE), Fallopian Tube Epithelium (FTE) respectively. Part of this study focused in establishing NOSE, FTE and EOC cell lines to study differential expression of candidate genes in post-GWAS functional characterisation studies. Additionally, I have established 3D FTE cultures and propose they more closely resemble the in vivo characteristics than 2D cultures. A candidate gene approach has identified nine candidate genes. I tested 301 invasive EOC tumours and found frequent LOH for tagging SNPs in those genes. LOH was associated with worse survival for AXIN2, CASP5, RRBBP8 and AIFM2 but the result for AXIN2, CASP5 and AIFM2 were associated with stage. Additionally, one SNP in STAG3 showed significant preferential loss of the common allele. Six loci containing susceptibility SNPs were identified in an ovarian cancer GWAS. I found compelling evidence for the somatic role of several genes within these loci in EOC development based on their differential expression between normal (NOSE & FTE) and EOC cell lines. These genes included PVT1, SP2, CBX1, PNPO, HAUS8, USE1, SKAP1, MERIT40 and members of the HOXB family of genes with an observed gain of function role and TIPARP and BNC2 with an observed loss of function role in EOC development. Additionally, I found weak associations of susceptibility SNPs’ genotypes with CBX1, SNX11, SP2 and HOXD1 expression and compelling evidence of genotype specific methylation of HOXB5 using non tumour samples. I further knocked down MERIT40 in EOC cell lines to study the potential role of the gene in EOC development. I found that MERIT40 depletion led to increased accumulation of spontaneous DNA damage and cell cycle arrest characterised by reduction in ploidy of the mucinous EOC cell line EFO27. This study provides functional evidence that GWAS are powerful tools for identifying novel genes implicated with EOC and that further functional investigation of GWAS identified loci leads to a better understanding of the molecular players involved in EOC initiation, development and survival

Genetic Variants in TGF-β Pathway Are Associated with Ovarian Cancer Risk

The transforming growth factor-β (TGF-β) signaling pathway is involved in a diverse array of cellular processes responsible for tumorigenesis. In this case-control study, we applied a pathway-based approach to evaluate single-nucleotide polymorphisms (SNPs) in the TGF-β signaling pathway as predictors of ovarian cancer risk. We systematically genotyped 218 SNPs from 21 genes in the TGF-β signaling pathway in 417 ovarian cancer cases and 417 matched control subjects. We analyzed the associations of these SNPs with ovarian cancer risk, performed haplotype analysis and identified potential cumulative effects of genetic variants. We also performed analysis to identify higher-order gene-gene interactions influencing ovarian cancer risk. Individual SNP analysis showed that the most significant SNP was SMAD6: rs4147407, with an adjusted odds ratio (OR) of 1.60 (95% confidence interval [CI], 1.14–2.24, P = 0.0066). Cumulative genotype analysis of 13 SNPs with significant main effects exhibited a clear dose-response trend of escalating risk with increasing number of unfavorable genotypes. In gene-based analysis, SMAD6 was identified as the most significant gene associated with ovarian cancer risk. Haplotype analysis further revealed that two haplotype blocks within SMAD6 were significantly associated with decreased ovarian cancer risk, as compared to the most common haplotype. Gene-gene interaction analysis further categorized the study population into subgroups with different ovarian cancer risk. Our findings suggest that genetic variants in the TGF-β signaling pathway are associated with ovarian cancer risk and may facilitate the identification of high-risk subgroups in the general population

Immunosuppression overcomes insulin- and vector-specific immune responses that limit efficacy of AAV2/8-mediated insulin gene therapy in NOD mice

10.1038/s41434-018-0052-5GENE THERAPY261-Feb40-56complete

Common variants at 19p13 are associated with susceptibility to ovarian cancer.

Epithelial ovarian cancer (EOC) is the leading cause of death from gynecological malignancy in the developed world, accounting for 4% of the deaths from cancer in women. We performed a three-phase genome-wide association study of EOC survival in 8,951 individuals with EOC (cases) with available survival time data and a parallel association analysis of EOC susceptibility. Two SNPs at 19p13.11, rs8170 and rs2363956, showed evidence of association with survival (overall P = 5 × 10⁻⁴ and P = 6 × 10⁻⁴, respectively), but they did not replicate in phase 3. However, the same two SNPs demonstrated genome-wide significance for risk of serous EOC (P = 3 × 10⁻⁹ and P = 4 × 10⁻¹¹, respectively). Expression analysis of candidate genes at this locus in ovarian tumors supported a role for the BRCA1-interacting gene C19orf62, also known as MERIT40, which contains rs8170, in EOC development