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. 2023 Mar;54(3):800-809.
doi: 10.1161/STROKEAHA.122.040883. Epub 2023 Feb 10.

Whole-Exome Sequencing Analyses Support a Role of Vitamin D Metabolism in Ischemic Stroke

Yuhan Xie #  1 , Julián N Acosta #  2 , Yixuan Ye  3 , Zachariah S Demarais  4 , Carolyn J Conlon  4 , Ming Chen  1 , Hongyu Zhao  1   3 , Guido J Falcone  2
Affiliations

Whole-Exome Sequencing Analyses Support a Role of Vitamin D Metabolism in Ischemic Stroke

Yuhan Xie et al. Stroke. 2023 Mar.

Abstract

Background: Ischemic stroke (IS) is a highly heritable trait, and genome-wide association studies have identified several commonly occurring susceptibility risk loci for this condition. However, there are limited data on the contribution of rare genetic variation to IS.

Methods: We conducted an exome-wide study using whole-exome sequencing data from 152 058 UK Biobank participants, including 1777 IS cases. We performed single-variant analyses for rare variants and gene-based analyses for loss-of-function and deleterious missense rare variants. We validated these results through (1) gene-based testing using summary statistics from MEGASTROKE-a genome-wide association study of IS that included 67 162 IS cases and 454 450 controls, (2) gene-based testing using individual-level data from 1706 IS survivors, including 142 recurrent IS cases, enrolled in the VISP trial (Vitamin Intervention for Stroke Prevention); and (3) gene-based testing against neuroimaging phenotypes related to cerebrovascular disease using summary-level data from 42 310 UK Biobank participants with available magnetic resonance imaging data.

Results: In single-variant association analyses, none of the evaluated variants were associated with IS at genome-wide significance levels (P<5×10-8). In the gene-based analysis focused on loss-of-function and deleterious missense variants, rare genetic variation at CYP2R1 was significantly associated with IS risk (P=2.6×10-6), exceeding the Bonferroni-corrected threshold for 16 074 tests (P<3.1×10-6). Validations analyses indicated that CYP2R1 was associated with IS risk in MEGASTROKE (gene-based test, P=0.003), with IS recurrence in the VISP trial (gene-based test, P=0.001) and with neuroimaging traits (white matter hyperintensity, mean diffusivity, and fractional anisotropy) in the UK Biobank neuroimaging study (all gene-based tests, P<0.05).

Conclusions: Because CYP2R1 plays an important role in vitamin D metabolism and existing observational evidence suggests an association between vitamin D levels and cerebrovascular disease, our results support a role of this pathway in the occurrence of IS.

Keywords: genomics; ischemic stroke; vitamin D; whole exome sequencing.

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Conflict of interest statement

Disclosures

J.N.A. was a postdoc at Yale when this work was conducted, and he has since transitioned to RadAI. Y.Y. was a Ph.D. student at Yale when this work was conducted, and she has since transitioned to Google. M.C. was a Ph.D. student at Yale when this work was conducted, and she has since transitioned to Johnson & Johnson. The other authors declare no competing interests.

Figures

Figure 1.
Figure 1.. Manhattan plot for the exome-wide gene-based association analysis.
The genome coordinates of each variant are displayed along the x-axis, and the negative logarithm of the association p-values for each variant are displayed on the y-axis. The blue line represents the threshold of 1×10−4, and the red line represents the threshold of 2.5×10−6. Genes that passed the thresholds in our gene-based tests are annotated with gene symbols.
Figure 2.
Figure 2.. Vitamin D levels in all participants and CYP2R1 carriers.
(A) Histogram of serum vitamin D levels in all participants included in the analysis. (B) Histogram of serum vitamin D levels in carriers of CYP2R1 variants; in red non-CV carriers, in blue CV carriers.
Figure 3.
Figure 3.. Locus Zoom plots of the association analysis of CYP2R1 variants in GARNET by treatment arm.
The genome coordinates of each variant are displayed along the x-axis, and the negative logarithm of the association p-values for each variant are displayed on the y-axis. (A) Low-dose group. (B) High-dose group.
See this image and copyright information in PMC

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