Analysis of Genes Involved in Body Weight Regulation by Targeted Re-Sequencing

Abstract

IntroductionGenes involved in body weight regulation that were previously investigated in genome-wide association studies (GWAS) and in animal models were target-enriched followed by massive parallel next generation sequencing.MethodsWe enriched and re-sequenced continuous genomic regions comprising FTO, MC4R, TMEM18, SDCCAG8, TKNS, MSRA and TBC1D1 in a screening sample of 196 extremely obese children and adolescents with age and sex specific body mass index (BMI) ≥ 99th percentile and 176 lean adults (BMI ≤ 15th percentile). 22 variants were confirmed by Sanger sequencing. Genotyping was performed in up to 705 independent obesity trios (extremely obese child and both parents), 243 extremely obese cases and 261 lean adults.Results and ConclusionWe detected 20 different non-synonymous variants, one frame shift and one nonsense mutation in the 7 continuous genomic regions in study groups of different weight extremes. For SNP Arg695Cys (rs58983546) in TBC1D1 we detected nominal association with obesity (pTDT = 0.03 in 705 trios). Eleven of the variants were rare, thus were only detected heterozygously in up to ten individual(s) of the complete screening sample of 372 individuals. Two of them (in FTO and MSRA) were found in lean individuals, nine in extremely obese. In silico analyses of the 11 variants did not reveal functional implications for the mutations. Concordant with our hypothesis we detected a rare variant that potentially leads to loss of FTO function in a lean individual. For TBC1D1, in contrary to our hypothesis, the loss of function variant (Arg443Stop) was found in an obese individual. Functional in vitro studies are warranted.

Glucose transporters in adipose tissue, liver, and skeletal muscle in metabolic health and disease

“…Mutations in TBC1D1 have been associated with obesity-related traits in human [ 157 , 223 , 247 ] and mice [ 29 , 55 , 88 ]. In addition, mutations in TBC1D4 have been linked with insulin resistance in humans [ 40 ].…”

Structural variants caused byAluinsertions are associated with risks for many human diseases

“…Although the effect has been attributed to the transmembrane protein 18 (TMEM18), a transcriptional repressor that sequesters sequences at the membrane, there is debate concerning whether TMEM18 is involved in obesity regulation through expression in adipose tissue or the central nervous system (38). The causative variant(s) remain unclear even after targeted resequencing efforts that focused mainly on the TMEM18 coding sequence (39)(40)(41); it is presumed that the risk haplotype contains a noncoding regulatory variant. Seven TASs occur over a 23.5-kb interval, mapping ∼15-70 kb downstream of TMEM18 (e.g., refs.…”

Rab28 is a TBC1D1/TBC1D4 substrate involved in GLUT4 trafficking

“…Both proteins are phosphorylated in response to insulin, AMP-activated protein kinase, and exercise/muscle contraction, and mutation of specific phosphorylation sites has been shown to abrogate insulin-stimulated glucose transport [3]. Interestingly, in humans, mutations in TBC1D4 (R363X, R684X) and TBC1D1 (R125W, R443X) have been linked to severe postprandial hyperinsulinemia and obesity, respectively [4][5][6][7]. Consistently, knockout mice lacking either Tbc1d1 or Tbc1d4 display altered energy Abbreviations EDL, Extensor digitorum longus; GAPs, GTPase-activating proteins; KHB, Krebs-Henseleit buffer; TA, tibialis anterior.…”