Developing a network view of type 2 diabetes risk pathways through integration of genetic, genomic and functional data
Authors: Fernéndez-Tajes Juan , Gaulton Kyle J , van de Bunt Martijn , Torres Jason , Thurner Matthias , Mahajan Anubha , Gloyn Anna L , Lage Kasper , McCarthy Mark I 
Published: June 2018

Genome wide association studies (GWAS) have identified several hundred susceptibility loci for Type 2 Diabetes (T2D). One critical, but unresolved, issue concerns the extent to which the mechanisms through which these diverse signals influencing T2D predisposition converge on a limited set of biological processes. However, the causal variants identified by GWAS mostly fall into non-coding sequence, complicating the task of defining the effector transcripts through which they operate. Here, we describe implementation of an analytical pipeline to address this question. First, we integrate multiple sources of genetic, genomic, and biological data to assign positional candidacy scores to the genes that map to T2D GWAS signals. Second, we introduce genes with high scores as seeds within a network optimization algorithm (the asymmetric prize-collecting Steiner Tree approach) which uses external, experimentally-confirmed protein-protein interaction (PPI) data to generate high confidence subnetworks. Third, we use GWAS data to test the T2D-association enrichment of the “non-seed” proteins introduced into the network, as a measure of the overall functional connectivity of the network. We find: (a) non-seed proteins in the T2D protein-interaction network so generated (comprising 705 nodes) are enriched for association to T2D (p=0.0014) but not control traits; (b) stronger T2D-enrichment for islets than other tissues when we use RNA expression data to generate tissue-specific PPI networks; and (c) enhanced enrichment (p=3.9×l0−5) when we combine analysis of the islet-specific PPI network with a focus on the subset of T2D GWAS loci which act through defective insulin secretion. These analyses reveal a pattern of non-random functional connectivity between causal candidate genes atT2D GWAS loci, and highlight the products of genes including YWHAG, SMAD4 or CDK2 as contributors to T2D-relevant islet dysfunction. The approach we describe can be applied to other complex genetic and genomic data sets, facilitating integration of diverse data types into disease-associated networks.

Author summary

We were interested in the following question: as we discover more and more genetic variants associated with a complex disease, such as type 2 diabetes, will the biological pathways implicated by those variants proliferate, or will the biology converge onto a more limited set of aetiological processes? To address this, we first took the 1895 genes that map to ~100 type 2 diabetes association signals, and pruned these to a set of 451 for which combined genetic, genomic and biological evidence assigned the strongest candidacy with respect to type 2 diabetes pathogenesis. We then sought to maximally connect these genes within a curated protein-protein interaction network. We found that proteins brought into the resulting diabetes interaction network were themselves enriched for diabetes association signals as compared to appropriate control proteins. Furthermore, when we used tissue-specific RNA abundance data to filter the generic protein-protein network, we found that the enrichment for type 2 diabetes association signals was enhanced within a network filtered for pancreatic islet expression, particularly when we selected the subset of diabetes association signals acting through reduced insulin secretion. Our data demonstrate convergence of the biological processes involved in type 2 diabetes pathogenesis and highlight novel contributors.