Evaluation of a Role for NPY and NPY2R in the Pathogenesis of Obesity by Mutation and Copy Number Variation Analysis in Obese Children and Adolescents.

Neuropeptide Y (NPY) and its G protein-coupled NPY Y2 Receptor (NPY2R) are highly expressed in orexigenic NPY/Agouti-related peptide neurons within the arcuate nucleus, a major integrator of appetite control in the hypothalamus. As NPY and NPY2R are interesting candidate genes for obesity, we hypothesized that a genetic variation in these genes might be implicated in the pathogenesis of obesity. In the first part of this study, we performed a mutation analysis of the coding region of NPY and NPY2R with high-resolution melting curve analysis. For the highly conserved NPY gene, an extended population of 436 obese children and adolescents was screened, while for NPY2R, a smaller subset of 306 patients was used. A control population of 300 healthy individuals was screened for NPY2R to determine the general prevalence of the variants found among patients. Direct sequencing was performed for samples with melting patterns deviating from wild-type. In the second part of this study, Multiplex Amplicon Quantification (MAQ) analysis was performed in 308 obese children and adolescents to detect copy number variation (CNV) in the NPY2R region. Mutation analysis of the NPY gene led to the identification of one common missense variant (L7P; MAF 0.04), while the screening of the NPY2R gene resulted in the identification of one rare missense variant F87I in the patient population. In our CNV analysis, we could not identify copy number variation in the NPY2R region among obese children and adolescents. In summary, this study clearly indicates that genetic variation in NPY and NPY2R is at low frequency and thus does not make a major contribution to the obese phenotype in the general population.

Genetic and structural variation in the SH2B1 gene in the Belgian population.

OBJECTIVE: Animal studies, genome-wide association and genomic structural variation studies have identified the SH2B1 gene as a candidate gene for obesity. Therefore, we have designed an extensive mutation and copy number variation (CNV) analysis investigating the prevalence of genetic and structural variations in SH2B1 in the Belgian population. DESIGN AND METHODS: In the first part of this study, we performed a mutation screen for variants in the SH2B1 coding region in 581 obese children and adolescents and 433 healthy, lean individuals with high-resolution melting curve analysis followed by direct sequencing. In the second part of this study, Multiplex Amplicon Quantification (MAQ) analysis was used to identify CNVs in the distal SH2B1-containing chr.16p11.2 region in 421 obese children and adolescents with no developmental delay or behavioral phenotype. RESULTS: Mutation analysis resulted in the identification of fifteen rare non-synonymous heterozygous variants. Several of these were found both in lean and obese subjects, suggesting that these are neutral polymorphisms. However, six private, heterozygous, non-synonymous variations were present in obese children only. Furthermore, we also identified six missense variants solely in lean individuals. CNV analysis could not identify carriers of the distal 16p11.2 deletion in our population. CONCLUSION: Our mutation analysis has demonstrated that variation in the SH2B1 gene is frequent in both lean and obese groups, with distinctive variations being present on either side of the weight spectrum. Although the equal variation frequency does not immediately support disease causality, it cannot be excluded that some variations are weight-increasing or -decreasing. Further functional testing of the variants will be necessary to fully understand the impact of these variants on SH2B1. We were not able to detect carriers of the distal 16p11.2 deletion in our study population. As we excluded patients with developmental or behavioral problems, we suggest that in addition to obesity, the distal deletion might predispose for these traits. Further characterization of the phenotype is therefore necessary to clearly identify the phenotype of the distal 16p11.2 microdeletion syndrome.

DNA sequencing and copy number variation analysis of MCHR2 in a cohort of Prader Willi like (PWL) patients.

BACKGROUND: Prader Willi Syndrome (PWS) is a syndromic form of obesity caused by a chromosomal aberration on chromosome 15q11.2-q13. Patients with a comparable phenotype to PWS not carrying the 15q11.2-q13 defect are classified as Prader Willi like (PWL). In literature, PWL patients do frequently harbor deletions at 6q16, which led to the identification of the single-minded 1 (SIM1) gene as a possible cause for the presence of obesity in these patients. However, our previous work in a PWL cohort showed a rather limited involvement of SIM1 in the obesity phenotype. In this paper, we investigated the causal role of the melanin-concentrating hormone receptor 2 (MCHR2) gene in PWL patients, as most of the reported 6q16 deletions also encompass this gene and it is suggested to be active in the control of feeding behavior and energy metabolism. METHODS: Copy number variation analysis of the MCHR2 genomic region followed by mutation analysis of MCHR2 was performed in a PWL cohort. RESULTS: Genome-wide microarray analysis of 109 patients with PWL did not show any gene harboring deletions on chromosome 6q16. Mutation analysis in 92 patients with PWL demonstrated three MCHR2 variants: p.T47A (c.139A>G), p.A76A (c.228T>C) and c.*16A>G. We identified a significantly higher prevalence of the c.228T>C C allele in our PWL cohort compared to previously published results and controls of the ExAC Database. CONCLUSION: Overall, our results are in line with some previously performed studies suggesting that MCHR2 is not a major contributor to human obesity and the PWL phenotype.

CNV analysis and mutation screening indicate an important role for the NPY4R gene in human obesity.

OBJECTIVE: Genome-wide copy number variation (CNV) analyses have associated the 10q11.22 CNV with obesity. As the NPY4R gene is the most interesting candidate gene in this region, it was hypothesized that both genetic and structural variation in NPY4R might be implicated in the pathogenesis of obesity. METHODS: In the first part of this study, 326 children and adolescents with obesity and 298 healthy lean individuals were screened for CNV in the NPY4R-containing chr.10q11.22 region. In the second part of this study, a mutation screen for variants in the NPY4R coding region was performed in 356 children and adolescents with obesity and 337 healthy lean adults. RESULTS: Our CNV analysis demonstrated a significantly higher frequency of NPY4R containing 10q11.22 CNV loss in the patient population (P = 0.0003), while CNV gain in this region was more prevalent in the control population (P = 0.031). Mutation analysis resulted in the identification of 15 rare non-synonymous heterozygous variants. For two variants that could only be identified in the patient population, receptor dysfunction and thus a pathogenic effect were demonstrated. CONCLUSIONS: In conclusion, these data support an essential role for genetic and structural variation within the NPY4R gene in the pathogenesis of obesity.

Association study of PNPLA2 gene with histological parameters of NAFLD in an obese population.

INTRODUCTION: The prevalence of non-alcoholic fatty liver disease (NAFLD) and the closely associated metabolic syndrome is high and is related to risk factors such as obesity and type 2 diabetes. A genetic basis for NAFLD has been suggested, but only few causal genes have been identified. The most significant association reported to date is the robust association of the PNPLA3 I148M variant with susceptibility to NAFLD. We therefore hypothesized that the PNPLA2 gene might also be involved in NAFLD pathogenesis, because of its close sequence similarity with PNPLA3 and its possible involvement in ectopic fat accumulation. METHODS: In this study, we investigated the association of PNPLA2 polymorphisms with the development of non-alcoholic fatty liver disease in a prospectively recruited Belgian obese population comprising 633 individuals with varying degrees of fatty liver disease. We selected 3 PNPLA2 SNPs for genotyping, including 2 tagSNPs that cover most information on common genetic variation in the selected region. RESULTS: After performing linear regression analysis, we found that 2 of the analyzed PNPLA2 SNPs were associated with anthropometric and metabolic parameters. In our subcohort of patients that underwent liver biopsy (n=372/633 or 58.7%), we assessed the influence of the PNPLA2 variants on the severity of histologically determined liver damage, but we did not find convincing evidence for association. CONCLUSION: Although we found evidence for moderate association between PNPLA2 tagSNPs and anthropometric and metabolic parameters in our cohort, no evidence for association between polymorphisms in the PNPLA2 gene and the presence and severity of NAFLD was identified.

Screening for rare variants in the PNPLA3 gene in obese liver biopsy patients.

BACKGROUND: Previous research has clearly implicated the PNPLA3 gene in the etiology of nonalcoholic fatty liver disease as a polymorphism in the gene was found to be robustly associated to the disease. However, data on the involvement of rare PNPLA3 variants in the development of nonalcoholic fatty liver disease (NAFLD) is currently limited. Therefore, we performed an extensive mutation analysis study on a cohort of obese liver biopsy patients to determine PNPLA3 variation and its correlation with fatty liver disease. METHODS: We screened the entire coding region of the PNPLA3 gene in DNA samples of 393 obese liver biopsy patients with varying degrees of fatty liver disease. Mutation analysis was performed by high-resolution melting curve analysis in combination with direct sequencing. RESULTS: We identified several common polymorphisms as well as one rare synonymous variant (c.867G>A rs139896256), one rare intronic variant (c.979+13C>T) and 3 nonsynonymous coding variants (p.A76T, p.A104V and p.T200M) in the PNPLA3 gene. In silico analysis indicated that the p.A104V variant will probably have no functional effect, whereas for the p.A76T and p.T200M variant a possible pathogenic effect is suggested. CONCLUSION: Overall, we showed that novel variants in PNPLA3 are very rare in our liver biopsy cohort, thereby indicating that their impact on the etiology of NAFLD is probably limited. Nevertheless, for the three rare coding variants that were identified in patients with advanced liver disease, further functional characterization will be essential to verify their potential disease causality.