Journal Article

Developing a network view of type 2 diabetes risk pathways through integration of genetic, genomic and functional data

Fernández-Tajes, Juan, Lage, Kasper, Mahajan, Anubha, Torres, Jason, Thurner, Matthias, Gloyn, Anna L., Gaulton, Kyle J., McCarthy, Mark I., van de Bunt, Martijn

2019

Overview

Background 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 a non-coding sequence, complicating the task of defining the effector transcripts through which they operate. Methods 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 sub-networks. 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. Results 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 × 10 − 5 ) when we combine the analysis of the islet-specific PPI network with a focus on the subset of T2D GWAS loci which act through defective insulin secretion. Conclusions These analyses reveal a pattern of non-random functional connectivity between candidate causal genes at T2D GWAS loci and highlight the products of genes including YWHAG , SMAD4 or CDK2 as potential contributors to T2D-relevant islet dysfunction. The approach we describe can be applied to other complex genetic and genomic datasets, facilitating integration of diverse data types into disease-associated networks.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: 14-3-3 Proteins - genetics / 14-3-3 Proteins - metabolism / Algorithms / Analysis / Annotations / Base sequence / Bioinformatics / Biomedical and Life Sciences / Biomedicine / Cancer Research / Cyclin-dependent kinase 2 / Cyclin-Dependent Kinase 2 - genetics / Cyclin-Dependent Kinase 2 - metabolism / Cyclin-dependent kinases / Diabetes / Diabetes mellitus / Diabetes mellitus (non-insulin dependent) / Diabetes Mellitus, Type 2 - genetics / Disease susceptibility / Gene Regulatory Networks / Genes / Genetic Predisposition to Disease / Genetic research / Genome-wide association studies / Genome-Wide Association Study - methods / Genomes / Human Genetics / Humans / Insulin / Insulin secretion / Integration / Kinases / Medicine/Public Health / Metabolomics / Optimization theory / Polymorphism, Single Nucleotide / Prevalence studies (Epidemiology) / Prevention / Protein interaction / Protein-protein interactions / Proteins / Ribonucleic acid / Risk factors / RNA / Secretion / Seeds / Smad4 protein / Smad4 Protein - genetics / Smad4 Protein - metabolism / Systems Biology / Transcriptome / Type 2 diabetes