Genome-wide association studies (GWAS) are an important way of identifying germline polymorphisms that are associated with a specific trait or disease. However, characterizing the functional effects of disease-associated variants is challenging since many are located in intergenic regions of the genome. We have established a methodological framework to study the functional effects of disease-associated polymorphisms by examining their effect on disease- specific transcriptional pathways. Based on the most recent meta-analysis of GWAS in renal cell cancer (RCC), we show that RCC- associated polymorphisms are statistically enriched for binding sites of the transcriptional enhancer, hypoxia-inducible factor (HIF), as identified by ChIP-seq analysis in kidney cancer cells. HIF orchestrates a major transcriptional pathway and is constitutively activated in kidney cancer through loss of the von Hippel-Lindau (VHL) tumor suppressor. At these loci, RCC-associated polymorphisms quantitatively affect HIF binding in allele-specific assays as well as expression of

the HIF target genes in eQTL analysis. Furthermore, the association between HIF-binding sites and GWAS signal extends to loci below conventional levels of genome-wide significance thereby implicating these sub-threshold loci in the pathogenesis of RCC. In addition we also observe enrichment of RCC-associated polymorphisms close to, but not directly overlapping HIF-binding sites suggesting that they may alter HIF-target gene expression by mechanisms other than directly affecting HIF-binding. As well as emphasizing the importance of the HIF transcriptional pathway in kidney cancer, this analysis helps distinguish HIF key targets that help drive the pathogenesis of RCC from those that are simply co-activated as a consequence of pathway activation. Although focused on the HIF pathway in kidney cancer, this work also forms a paradigm for studying the effect of non-coding variants linked to other cancers originating from other tissue types.

Financial support:

The Ludwig Institute for Cancer Research, Cancer Research UK (A16016), National Institute for Health Research (NIHR-RP-2016-06-004), the Wellcome Trust (088182/Z/09/Z, 078333/Z/05/Z, WT091857MA), the Deanship of Scientific Research (DSR), Department of Nephrology and Hypertension, Universitätsklinikum Erlangen und Friedrich-Alexander-University Erlangen- Nürnberg, Ulmenweg 18, 91054 Erlangen, Germany. King Abdulaziz University, Ministry of High Education for Saudi Arabia. High-Throughput Genomics Group at the Wellcome Trust Centre for Human Genetics is funded by the Wellcome Trust (090532/Z/09/Z).

Citation Format: Virginia Schmid, David Mole. Studying effects of disease associated polymorphism on a transcriptional pathway: A case study in renal cell cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr LB-239.