Gene set enrichment analysis implicates vascular endothelial growth factor pathway in genetic risk of developing proliferative diabetic retinopathy

Abstract

Purpose : To gain statistical discovery power and biological insight into the genetic architecture of diabetic retinopathy (DR), we tested for enrichment of multiple genetic variant associations with DR in gene sets or pathways related to DR pathophysiology, rather than inspecting variants individually.

Methods : We applied the gene set enrichment analysis (GSEA) method, Meta-Analysis Gene-set Enrichment of variaNT Associations (MAGENTA), to four previously published DR genome-wide association study (GWAS) analyses adjusted for duration of diabetes and glycemic control. These GWAS were performed separately in patients of African American (AA) and European (EU) ancestry, using one of two DR case-control definitions: (1) PDR analysis: cases (n=1495) had proliferative DR (PDR) and controls (n=4362) had any level of non-proliferative DR or no DR and (2) Extremes of DR analysis: cases (n=1495) had PDR and controls (n=2911) had no DR. From a literature review, we identified key DR-associated biological processes including angiogenesis, glial dysregulation, neuronal dysfunction, and inflammation. Gene sets representing these pathways were extracted from four gene set databases: Gene Ontology (n=144 pathways extracted), Kyoto Encyclopedia of Genes and Genomes (KEGG, n=13 pathways extracted), Reactome (n=10 pathways extracted), and Mouse Phenotype Ontology (MGI, n=79 pathways extracted). Multiple hypothesis correction based on false discovery rate (FDR) was applied to gene sets from each database separately.

Results : MAGENTA identified one statistically significant pathway from KEGG, the vascular endothelial growth factor (VEGF) signaling pathway, for the PDR analysis in the AA population. Significance was based on a 75th percentile enrichment cutoff (Gene set enrichment P=0.0015, FDR=0.0159). This analysis suggests 11 new DR-associated genes (1.6 fold-enrichment) based on their confounder-adjusted gene association P values, with the variant DR P values ranging between 2x10^-5 and 0.001. No significant enrichment was found among these genes in the EU extremes of DR analysis.

Conclusions : Genetic variation in the VEGF signaling pathway may be associated with PDR risk in the AA population. Replication of this finding with alternate GSEA analysis methods and in independent DR GWAS are needed to confirm these results and to determine if the significance is AA-specific.

This is a 2020 ARVO Annual Meeting abstract.