Whole-Exome Sequencing for Identification of Genetic Variants Involved in Vitamin D Metabolic Pathways in Families With Vitamin D Deficiency in Saudi Arabia.

Shatha Alharazy,Adeel G Chaudhary,Susan Lanham-New,Margaret Denise Robertson,Eman Alissa,Muhammad Imran Naseer

doi:10.3389/fgene.2021.677780

Shatha Alharazy, Adeel G Chaudhary + Show 4 more

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https://doi.org/10.3389/fgene.2021.677780

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Abstract

BackgroundNumerous research studies have found an association between vitamin D (vitD) status and single-nucleotide polymorphisms (SNPs) in genes involved in vitD metabolism. It is notable that the influence of these SNPs on 25-hydroxyvitamin D [25(OH)D] levels might vary in different populations. In this study, we aimed to explore for genetic variants in genes related to vitD metabolism in families with vitD deficiency in Saudi Arabia using whole-exome sequencing (WES).MethodsThis family-based WES study was conducted for 21 families with vitD deficiency (n = 39) in Saudi Arabia. WES was performed for DNA samples, then resulting WES data was filtered and a number of variants were prioritized and validated by Sanger DNA sequencing.ResultsSeveral missense variants in vitD-related genes were detected in families. We determined two variants in low-density lipoprotein 2 gene (LRP2) with one variant (rs2075252) observed in six individuals, while the other LRP2 variant (rs4667591) was detected in 13 subjects. Single variants in 7-dehydrocholesterol reductase (DHCR7) (rs143587828) and melanocortin-1 receptor (MC1R) (rs1805005) genes were observed in two subjects from two different families. Other variants in group-specific component (GC), cubilin (CUBN), and calcium-sensing receptor (CASR) gene were found in index cases and controls. Polymorphisms in GC (rs9016) and CASR (rs1801726) were found in the majority of family cases (94 and 88%), respectively.ConclusionIn vitD-deficient families in Saudi Arabia, we were able to detect a number of missense exonic variants including variants in GC (rs9016), CUBN (rs1801222), CASR (rs1801726), and LRP2 (rs4667591). However, the existence of these variants was not different between affected family members and non-affected controls. Additionally, we were able to find a mutation in DHCR7 (rs143587828) and a polymorphism in LRP2 (rs2075252), which may affect vitD levels and influence vitD status. Further studies are now required to confirm the association of these variants with vitD deficiency.

Highlights

Vitamin D plays an important role in maintaining skeletal calcium (Ca) homeostasis by stimulating intestinal absorption of Ca and phosphate (PO4), stimulating bone resorption and inducing Ca reabsorption by the kidney, sustaining the level of calcium and phosphate necessary for bone formation and supporting appropriate functioning of parathyroid hormone (PTH) to maintain Ca levels in serum (Holick, 2007; Holick et al, 2011).Clinically, serum 25-hydroxyvitamin D [25(OH)D] has been identified as the most effective predictor of vitD status, to date
VitD is produced mainly in the skin epidermis under the effect of ultraviolet-B radiation which activates 7-dehydrocholesterol (7-DHC) in the skin to form pre-vitD (Datta et al, 2017). 7-DHC is converted to cholesterol by the enzyme 7-dehydrocholesterol reductase (DHCR7) and the presence of the reduced coenzyme nicotinamide adenine dinucleotide phosphate (NAD-P) which is activated by nicotinamide adenine dinucleotide synthetase 1 (NADSYN1) (Ahn et al, 2010)
The active form of vitD, 1,25(OH)2D, initiates its genomic action by binding to the vitamin D receptor (VDR) (Pike and Meyer, 2012). In addition to these genes that can be directly implicated in vitD metabolism, additional genes such as the calcium-sensing receptor (CASR) that contributes in vitD metabolism by regulating PTH and Ca levels (Brown, 2013) may be clinically important in determining vitD status

Summary

Introduction

Vitamin D (vitD) plays an important role in maintaining skeletal calcium (Ca) homeostasis by stimulating intestinal absorption of Ca and phosphate (PO4), stimulating bone resorption and inducing Ca reabsorption by the kidney, sustaining the level of calcium and phosphate necessary for bone formation and supporting appropriate functioning of parathyroid hormone (PTH) to maintain Ca levels in serum (Holick, 2007; Holick et al, 2011).Clinically, serum 25-hydroxyvitamin D [25(OH)D] has been identified as the most effective predictor of vitD status, to date. VitD (from all sources) is hydroxylated in the liver mainly by cytochrome p450 enzyme (CYP2R1/25hydroxylase) to form 25(OH)D, with further hydroxylation in the kidney distal tubule by cytochrome p450 enzyme (CYP27B1/1α-hydroxylase) producing 1,25-dihydroxyvitamin D [1,25(OH)2D], the active form of vitD (Eyles et al, 2005) Both 25(OH)D and l,25(OH)2D are eliminated under the effect of another cytochrome P450 enzyme (CYP24A1/24-hydroxylase), transforming them into inactive waste calcitroic acid products [24,25(OH)2D and 1,24,25(OH)3D] (McGrath et al, 2010). The active form of vitD, 1,25(OH)2D, initiates its genomic action by binding to the vitamin D receptor (VDR) (Pike and Meyer, 2012) In addition to these genes that can be directly implicated in vitD metabolism, additional genes such as the calcium-sensing receptor (CASR) that contributes in vitD metabolism by regulating PTH and Ca levels (Brown, 2013) may be clinically important in determining vitD status. We aimed to explore for genetic variants in genes related to vitD metabolism in families with vitD deficiency in Saudi Arabia using whole-exome sequencing (WES)

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