Rare Variant Association Analysis Uncovers Involvement of VNN2 in Stroke Outcome

A stroke's functional outcome presents vast variability among patients, which is influenced by age, sex, characteristics of the lesion, and genetic factors. However, there is little knowledge about stroke recovery genetics. Recently, some GWAS (Genome-Wide Association Studies) have highlighted the involvement of common or low-frequency variants near or within PATJ, PPP1R21, PTCH1, NTN4, and TEK genes, whereas the role of rare variants is still unclear. This study aims to identify the genetic contributions to differences in stroke outcomes by analyzing the effect of rare variants.

We performed a pilot study analyzing 90 exomes of extreme good and bad recovery (modified Rankin Scale score at 3 months, 0-1 versus 4-5) to select target genes involved in stroke recovery. To expand this study, 702 additional samples were sequenced by targeted next-generation sequencing capturing loci selected from the pilot study, GWASs, and literature input. Here, we performed continuous (modified Rankin Scale score, 0-6) and dichotomous (modified Rankin Scale score, 0-1 versus 3-6) analyses, yielding 1 candidate gene. All samples were selected by a retrospective cohort study from incidental stroke cases collected at Spanish Hospitals between 2000 and 2018. The identified VNN2 variants were assessed for protein structure and stability analysis, and an analysis of their effect on basal inflammation levels was performed using UK Biobank data.

Our work identified rare coding variants in VNN2 associated with patients with better stroke recovery (∆ deviance information criterion >10, equivalent to P<0.001). Six rare variants were predicted to significantly affect protein stability (∆∆G >1.6 kcal/mol); meanwhile, another variant, located in the active site, could affect the electrostatic surface.

We propose that VNN2 might play a role in stroke outcomes by modulating poststroke inflammation. A potentially affected function would be neutrophil cell adhesion and migration.