Exome sequencing in Thai patients with familial obesity.

Obesity is a major worldwide health issue, with increasing prevalence in adults and children from developed and developing countries. Obesity causes several chronic diseases, including cardiovascular and respiratory diseases, osteoarthritis, hypertension, stroke, type II diabetes, obstructive sleep apnea, and several types of cancer. Previous genome-wide association studies have identified several genes associated with obesity, including LEP, LEPR, POMC, PCSK1, FTO, MC3R, MC4R, GNPDA2, TMEM18, QPCTL/GIPR, BDNF, ETV5, MAP2K5/SKOR1, SEC16B, SIM1, and TNKS/MSRA. However, most of these variants are found in the intronic or intergenic regions, making it difficult to elucidate the underlying mechanisms. Therefore, in this study, we performed a whole exome sequencing of the protein-coding regions in the total genome (exome) of two obese and one normal subject belonging to the same Thai family to identify the genes responsible for obesity. We identified 709 functional variants that were differentially expressed between obese and normal subjects; of these, 65 were predicted to be deleterious to protein structure or function. The minor allele frequency of 14 of these genes (ALOX5AP, COL9A2, DEFB126, GDPD4, HCRTR1, MLL3, OPLAH, OR4C45, PRIM2, RXFP2, TIGD6, TRPM8, USP49, and ZNF596) was low, indicating causal variants that could be associated with complex traits or diseases. Genotyping revealed HCRTR1, COL9A2, and TRPM8 to be associated with the regulation of feeding behavior and energy expenditure. These genes constituted a network of pathways, including lipid metabolism, signaling transduction, immune, membrane transport, and gene regulation pathways, and seemed to play important roles in obesity.

Association between rs155971 in the PCSK1 gene and the lipid profile of obese Thai children: a family-based study.

Genetic variants of the POMC and PCSK1 genes cause severe obesity among patients in the early stages of childhood. This family-based study analyzed the links between single nucleotide polymorphisms (SNPs) in either the POMC or PCSK1 genes and obesity, as well as obesity-related traits among obese Thai children and their families. The variants rs1042571 and rs6713532 in the POMC gene in a sample of 83 obese children and their family members were investigated using polymerase chain reaction (PCR)-restriction fragment length polymorphism. In addition, the SNPs rs6232, rs155971, rs3762986, rs3811942, and rs371897784 of PCSK1 were analyzed in all samples using PCR and gene sequencing methods. Participants with the homozygous variant genotype in rs155971 had significantly elevated cholesterol and low-density lipoprotein cholesterol (LDL-C) levels (P = 0.011, OR = 1.025, 95%CI = 1.006-1.045; and P = 0.006, OR = 1.030, 95%CI = 1.009-1.053, respectively) after adjustment for age, gender, and body mass index (BMI). In addition, patients with the heterozygous variant genotype in rs371897784 of PCSK1 had a 1.249- fold higher risk (95%CI = 1.081-1.444, P = 0.027) of increased waist circumference than patients with the normal genotype, after adjustment for age, gender, and BMI. However, this analysis did not find any correlation between obesity and SNPs in PCSK1 and POMC. Therefore, these common variants in PCSK1 and POMC were not the major cause of obesity in the Thai subjects sampled. However, variants in PCSK1 did affect cholesterol level, LDL-C level, and waist circumference.

Genetic variant screening of MC3R and MC4R genes in early-onset obese children and their relatives among a Thai population: family-based study.

MC3R (melanocortin-3 receptor) and MC4R (melanocortin-4 receptor) play important roles in energy homeostasis. Severe early-onset obesity, known as monogenic obesity when it is the consequence of a mutation in a single-gene product, may result when energy homeostasis is disrupted. The purpose of our study was to screen for variations of the MC3R and MC4R genes and observe the mode of inheritance of variations in affected families. We used polymerase chain reaction and direct sequencing to analyze the 11 early-onset obese children (probands) with their 71 family members, together with DNA from 100 healthy subjects used as controls. No novel mutations were found in the MC3R gene. Two previously described polymorphisms, rs3746619 and rs3827103, were detected in the MC3R gene. It was not associated with any obesity-related phenotypes. Three heterozygous variations of the MC4R gene were detected in 3 of 11 probands. The rs34114122 and rs61741819 variations have previously been reported, but rs182455344 was novel. Moreover, each MC4R variant was also found in a number of family members, indicating that this molecular analysis of a family-based study showed an autosomal dominant pattern. Our study indicated that MC4R variations in early-onset obese Thai children were found, and transmission of these variations in each family is in the dominant pattern. These variants could possibly contribute to a genetic influence of early-onset obesity in Thais. There is no evidence of any association between MC3R variations and obesity.

Association of HTTLPR and 5-HT2A T102C polymorphisms with smoking characteristics and anthropometric profiles of Thai males.

Nicotine increases serotonin release in the brain. Gene polymorphisms in the serotonergic system have been suggested to be associated with smoking behavior. We investigated a possible association between two polymorphisms in the serotonergic system - HTTLPR of a serotonin transporter gene and 5-HT(2A) at position T102C - with biochemical and anthropometric parameters, and with cigarette smoking in an investigation of 200 smokers and 111 non-smokers. The two polymorphisms, HTTLPR and 5-HT(2A) at position T102C, were genotyped by PCR-RFLP. They were not significantly associated with smoking status in these Thai males. Among the smokers, thiocyanate concentrations and quantity of cigarettes smoked (cigarette pack-years) were significantly higher for individuals with LL/LS genotypes than SS genotypes of 5-HTTLPR (all P < 0.05), whereas "age at starting smoking" and "duration of smoking" were not significantly different between these two genotypes. Moreover, anthropometric variables, comprising triceps skinfold thickness, arm circumference, waist circumference, hip circumference, and waist-to-hip ratio, were significantly higher for the CC/TC genotypes of 5-HT(2A) than the TT genotype (all P < 0.05), except for body mass index. HTTLPR and 5-HT(2A) T102C polymorphisms were not significantly associated with smoking status among Thai males; however, the HTTLPR polymorphism among smokers appears to be an indicator of increased smoking intensity consisting of cigarette pack-years and thiocyanate concentrations. The 5-HT(2A) T102C polymorphism plays a role in the anthropometric profiles, triceps skinfold thickness, arm circumference, waist circumference, hip circumference, and waist-to-hip ratio, but not smoking status in Thai subjects.

Association of T869C gene polymorphism of transforming growth factor-ß1 with low protein levels and anthropometric indices in osteopenia/osteoporosis postmenopausal Thai women.

Osteoporosis is the most common metabolic bone disease; it is an important health problem among postmenopausal women. We evaluated the association of three polymorphisms, T869C, C-509T and G915C, of the TGF-ß1 gene with bone mineral density (BMD) serum TGF-ß1 levels in 278 postmenopausal female osteopenia/osteoporosis subjects and 95 postmenopausal female control subjects. Serum TGF-ß1 levels were significantly lower in osteopenia/osteoporosis subjects than in control subjects. Serum TGF-ß1 levels of the CT+CC (T869C) genotype group were significantly lower in osteopenia/osteoporosis subjects than in control subjects (11.3 vs 15.8 ng/mL). There was a significant difference in the CT+CC (T869C) genotype frequencies between the osteopenia/osteoporosis and control subjects (74.18 vs 60.22%; OR = 1.90, 95%CI = 1.16-3.12). In the age group of more than 50 years, subjects with the TC+CC genotype of T869C polymorphism had significantly increased risk of osteopenic/ osteoporotic bones at L1 (OR = 2.36, 95%CI = 1.37-4.07), L2 (OR = 1.71, 95%CI = 1.01-2.90), L3 (OR = 2.21, 95%CI = 1.23-3.98), L4 (OR = 1.74, 95%CI = 1.00-3.03) and the femoral neck (OR = 1.80, 95%CI = 1.04-3.12). The CT+CC genotype of the T869C polymorphism of the TGF-ß1 gene was found to be associated with lower serum TGF-ß1 in osteopenia/osteoporosis subjects and increased risk of osteopenic and osteoporotic fracture at L1-4, femoral neck and total hip in postmenopausal Thai women. Logistic regression analysis showed that T869C polymorphism is a significant risk factor for osteopenia/ osteoporosis. We concluded that T869C polymorphism of the TGF-ß1 gene has an impact on decreased serum TGF-ß1 levels and influences susceptibility to osteopenia/osteoporosis in Thai women.