Targeted sequencing of candidate genes of dyslipidemia in Punjabi Sikhs: Population-specific rare variants in GCKR promote ectopic fat deposition

Abstract

Dyslipidemia is a well-established risk factor for cardiovascular diseases. Although, advances in genome-wide technologies have enabled the discovery of hundreds of genes associated with blood lipid phenotypes, most of the heritability remains unexplained. Here we performed targeted resequencing of 13 bona fide candidate genes of dyslipidemia to identify the underlying biological functions. We sequenced 940 Sikh subjects with extreme serum levels of hypertriglyceridemia (HTG) and 2,355 subjects were used for replication studies; all 3,295 participants were part of the Asian Indians Diabetic Heart Study. Gene-centric analysis revealed burden of variants for increasing HTG risk in GCKR (p = 2.1x10 -5 ), LPL (p = 1.6x10 -3 ) and MLXIPL (p = 1.6x10 -2 ) genes. Of these, three missense and damaging variants within GCKR were further examined for functional consequences in vivo using a transgenic zebrafish model. All three mutations were South Asian population-specific and were largely absent in other multiethnic populations of Exome Aggregation Consortium. We built different transgenic models of human GCKR with and without mutations and analyzed the effects of dietary changes in vivo . Despite the short-term of feeding, profound phenotypic changes were apparent in hepatocyte histology and fat deposition associated with increased expression of GCKR in response to a high fat diet (HFD). Liver histology of the GCKR mut showed severe fatty metamorphosis which correlated with ~7 fold increase in the mRNA expression in the GCKR mut fish even in the absence of a high fat diet. These findings suggest that functionally disruptive GCKR variants not only increase the risk of HTG but may enhance ectopic lipid/fat storage defects in absence of obesity and HFD. To our knowledge, this is the first transgenic zebrafish model of a putative human disease gene built to accurately assess the influence of genetic changes and their phenotypic consequences in vivo .

Pleiotropic Effects of Common and Rare GCKR Exonic Mutations on Cardiometabolic Traits

“…However, rare loss-of-function GCKR variants do not co-segregate with increased plasma triglyceride levels in families [ 29 ]. By contrast, in two South Asian population-specific, functionally disruptive, rare GCKR non-synonymous mutations, rs774930016 (p.Ser105Asn) and rs55537970 (p.Arg553Trp), significantly increased risks of hypertriglyceridemia have been reported [ 39 ]. Rees et al [ 28 ] subdivided rare GCKR variants into three classes according to cellular localization, cellular interaction with GCK, and kinetic effects.…”

A haplotype-resolved genome assembly of the Nile rat facilitates exploration of the genetic basis of diabetes

“…Gckr encodes glucokinase regulatory protein, which forms an inhibitory complex with glucokinase thereby regulating uptake and storage of dietary glucose [78]. Mammalian Gckr is composed of two sugar isomerase (SIS) domains which contain binding sites for fructose-6-phosphate (F6P) or fructose-1-phosphate (F1P) and glucokinase, where the fructose metabolites alter the affinity of Gckr for glucokinase [79]. Human GCKR has been reported as a diabetic susceptibility gene by several studies [80][81][82][83][84].…”

A haplotype-resolved genome assembly of the Nile rat facilitates exploration of the genetic basis of diabetes

“…Gckr encodes glucokinase regulatory protein, which forms an inhibitory complex with glucokinase thereby regulating uptake and storage of dietary glucose (Raimondo, Rees, and Gloyn 2015). Mammalian Gckr is composed of two sugar isomerase (SIS) domains which contain binding sites for fructose-6-phosphate (F6P) or fructose-1-phosphate (F1P) and glucokinase, where the fructose metabolites alter the affinity of Gckr for glucokinase (Sanghera et al 2019). Human GCKR has been reported as a diabetic susceptibility gene by several studies (Vaxillaire et al 2008) (Sparsø et al 2008) (Chen et al 2021).…”