Whole-genome sequencing identifies variants in ANK1, LRRN1, HAS1, and other genes and regulatory regions for stroke in type 1 diabetes

Abstract

AimsIndividuals with type 1 diabetes (T1D) carry a markedly increased risk of stroke, with distinct clinical and neuroimaging characteristics as compared to those without diabetes. Using whole-genome sequencing (WGS) and whole-exome sequencing (WES), we aimed to find rare and low-frequency genomic variants associated with stroke in T1D. The lead findings were followed up in various datasets to replicate the findings and to assess their specificity to diabetes. Methods and ResultsWe studied stroke genetics in 1,051 individuals with T1D using WGS or WES. We analysed the genome with single-variant analyses, gene aggregate analyses, and aggregate analyses on genomic windows, enhancers and promoters. Furthermore, we attempted replication in T1D using a genome-wide association study (N=3,945) and direct genotyping (N=3,600), and in the general population from the FinnGen project and UK Biobank summary statistics. We identified a rare missense mutation on SREBF1 associated with hemorrhagic stroke (rs114001633, p.Pro227Leu, p-value=8.96x10-9), which further replicated in T1D. Using gene aggregate analysis with protein altering or protein truncating variants, we identified exome-wide significant genes: ANK1 and LRRN1 displayed replication evidence in T1D, while LRRN1, HAS1 and UACA replicated in the general population (UK Biobank). Furthermore, we performed sliding-window analyses and identified 14 genome-wide significant windows for stroke on 4q33-34.1, of which two replicated in T1D, and a suggestive genomic window on LINC01500, which replicated in T1D. Finally, with the regulatory region aggregate analyses, we identified a stroke-associated TRPM2-AS promoter (p-value=5.78x10-6), which we validated with an in vitro cell-based assay. TRPM2 has been previously linked to ischemic stroke. ConclusionsHere, we report the first genome-wide analysis on stroke in individuals with diabetes. We identified multiple stroke risk loci with evidence of replication: 4q33-34.1, SREBF1, and ANK1 for stroke in T1D; and HAS1, UACA, LRRN1, LINC01500, and TRPM2-AS promoter for stroke potentially generalizable to the non-diabetic population.