Expression of risk genes linked to vitamin D receptor super-enhancer regions and their association with phenotype severity in multiple sclerosis

Abstract

Multiple sclerosis (MS) is a chronic debilitating neurological condition with a wide range of phenotype variability. A complex interplay of genetic and environmental factors contributes to disease onset and progression in MS patients. Vitamin D deficiency is a known susceptibility factor for MS, however the underlying mechanism of vitamin D-gene interactions in MS etiology is still poorly understood. Vitamin D receptor super-enhancers (VSEs) are enriched in MS risk variants and may modulate these environment-gene interactions. mRNA expression in total of 64 patients with contrasting MS severity was quantified in select genes. First, RNA-seq was performed on a discovery cohort (10 mild, 10 severe MS phenotype) and ten genes regulated by VSEs that have been linked to MS risk were analyzed. Four candidates showed a significant positive association (GRINA, PLEC, PARP10, and LRG1) in the discovery cohort and were then quantified using digital droplet PCR (ddPCR) in a validation cohort (33 mild, 11 severe MS phenotype). A significant differential expression persisted in the validation cohort for three of the VSE-MS genes: GRINA (p = 0.0138), LRG1 (p = 0.0157), and PLEC (p = 0.0391). In summary, genes regulated by VSE regions that contain known MS risk variants were shown to have differential expression based on disease severity (p<0.05). The findings implicate a role for vitamin D super-enhancers in modulating disease activity. In addition, expression levels may have some utility as prognostic biomarkers in the future.

Keywords: multiple sclerosis; super-enhancers; vitamin D; vitamin D deficiency; vitamin D receptor (VDR).

Figure 1

Heat map visualizing differential expression in MS-VSE genes in the extremes of MS phenotype discovery cohort. The color legend illustrates the coding by log-fold difference in expression (P1 = Patient 1).

Figure 2

Scatter plots displaying the number of gene copies normalized to the expression of HPRT1 and B2M (normalized counts) in the validation cohort for the following VSE-MS-linked candidates: (A) GRINA, (B) PLEC, (C) PARP10, (D) LRG1. The mean and standard deviation are shown. The asterisks (*) indicate statistically significant results (p < 0.05).