A candidate-gene based approach for assessing genetic predisposition to childhood obesity

The main aim of the present series of experiments was to assess the influence of selected candidate genes on several adiposity-related phenotypes in a large cohort of toddlers and preschoolers from Greece using both genotype- and haplotype-based approaches. Investigating the impact of genetic polymorphisms on adiposity in the young may reveal stronger associations than in older ages since the environment has had less time to take effect. Anthropometric measurements and buccal cell samples, from where genomic DNA was extracted, were obtained from 2374 children aged 1-6 years, all in public and private nurseries in Greece. The aim of the first experiment (Chapter 3) was to assess developmental changes in adiposity in the present population of Greek toddlers and preschoolers. This was achieved by determining the prevalence of overweight and obesity in this population using specific BMI cut-off points based on UK and US national reference data. The aim of the second experiment (Chapter 4) was to assess the potential influences of ACE I/D polymorphism and its interaction with age and/or gender on adiposity-related phenotypes in the cohort of Greek toddlers and preschoolers. A significant main effect of the ACE I/D polymorphism on BMI and significant interactions between I/D genotype and age for the same phenotype were revealed. The aim of the third experiment (Chapter 5) was to investigate the potential influence of five genetic polymorphisms in ADRB genes on adiposity-related phenotypes in the Greek children and their potential interactions with age and/or gender. Significant main effects of ADRB2 C16 on waist and hip circumferences and significant interactions between Cl6 genotypes and age for the same phenotypes were revealed. The aim of the fourth and final experiment (Chapter 6) was to assess the influence of two polymorphisms in PPAR? gene on adiposity-related phenotypes in the Greek toddlers and preschoolers. Genetic analysis based on Prol2Ala genotypes revealed that the rare Alal2 and T1431 alleles had no significant main effect on adiposity-related phenotypes. Interactions with age and/or gender were either not significant. A synergistic effect of PPAR? Pro 12Ala and ADRB3 Arg64Trp polymorphisms, as well as a modulating effect of BMI on the establishment of associations previously observed in adults was not confirmed in this study. Haplotype-based analysis including both PPAR? polymorphisms revealed no stronger associations of PPAR? diplotypes with adiposity-related indices compared to individual genotypes. Variation in the PPAR? seems not to contribute significantly to the high prevalence of early-onset obesity possibly due to differences in the dietary composition between children and adults. The findings from the genetic analyses suggested that allelic variations in candidate genes simply predispose to the obesity phenotype. With well-conducted genetic studies and with thorough examination of the information with respect to genetic associations, progress in understanding and management of obesity can be foreseen. (Abstract shortened by ProQuest.)

FTO variant rs9939609 is associated with body mass index and waist circumference, but not with energy intake or physical activity in European- and African-American youth

<p>Abstract</p> <p>Background</p> <p>Genome-wide association studies found common variants in the fat mass and obesity-associated (<it>FTO</it>) gene associated with adiposity in Caucasians and Asians but the association was not confirmed in African populations. Association of <it>FTO </it>variants with insulin resistance and energy intake showed inconsistent results in previous studies. This study aimed to assess the influence of <it>FTO </it>variant rs9939609 on adiposity, insulin resistance, energy intake and physical activity in European - (EA) and African-American (AA) youth.</p> <p>Methods</p> <p>We conducted a cross-sectional study in EA and AA youths. One thousand, nine hundred and seventy-eight youths (48.2% EAs, 47.1% male, mean age 16.5 years) had measures of anthropometry. Percent body fat (%BF) was measured by dual-energy X-ray absorptiometry, visceral adipose tissue (VAT) and subcutaneous abdominal adipose tissue (SAAT) by magnetic resonance imaging. Energy intake and physical activity were based on self report from up to 7 24-hour recalls. Physical activity was also measured by accelerometry.</p> <p>Results</p> <p><it>FTO </it>rs9939609 was significantly associated with body mass index (BMI) (<it>P </it>= 0.01), weight (<it>P </it>= 0.03) and waist circumference (<it>P </it>= 0.04), with per-allele effects of 0.4 kg/m², 1.3 kg and 0.8 cm, respectively. No significant association was found between rs9939609 and %BF, VAT, SAAT or insulin resistance (<it>P </it>> 0.05), or between rs9939609 and energy intake or vigorous physical activity (<it>P </it>> 0.05). No significant interactions of rs9939609 with ethnicity, gender, energy intake or physical activity were observed (<it>P </it>> 0.05).</p> <p>Conclusions</p> <p>The <it>FTO </it>variant rs9939609 is modestly associated with BMI and waist circumference, but not with energy intake or physical activity. Moreover, these effects were similar for EAs and AAs. Improved understanding of the effect of the <it>FTO </it>variant will offer new insights into the etiology of excess adiposity.</p

Integrative genomic analyses in adipocytes implicate DNA methylation in human obesity and diabetes

DNA methylation variations are prevalent in human obesity but evidence of a causative role in disease pathogenesis is limited. Here, we combine epigenome-wide association and integrative genomics to investigate the impact of adipocyte DNA methylation variations in human obesity. We discover extensive DNA methylation changes that are robustly associated with obesity (N = 190 samples, 691 loci in subcutaneous and 173 loci in visceral adipocytes, P 500 target genes, and identify putative methylation-transcription factor interactions. Through Mendelian Randomisation, we infer causal effects of methylation on obesity and obesity-induced metabolic disturbances at 59 independent loci. Targeted methylation sequencing, CRISPR-activation and gene silencing in adipocytes, further identifies regional methylation variations, underlying regulatory elements and novel cellular metabolic effects. Our results indicate DNA methylation is an important determinant of human obesity and its metabolic complications, and reveal mechanisms through which altered methylation may impact adipocyte functions

Homozygous DBF4 mutation as a cause for severe congenital neutropenia

Background Severe congenital neutropenia presents with recurrent infections early in life due to arrested granulopoiesis. Multiple genetic defects are known to block granulocyte differentiation, however a genetic cause remains unknown in approximately 40% of cases. Objective We aimed to characterize a patient with severe congenital neutropenia and syndromic features without a genetic diagnosis. METHODS: Whole exome sequencing results were validated using flow cytometry, Western blotting, co-immunoprecipitation, quantitative PCR, cell cycle and proliferation analysis of lymphocytes and fibroblasts and granulocytic differentiation of primary CD34+ and HL-60 cells. Results We identified a homozygous missense mutation in DBF4 in a patient with mild extra-uterine growth retardation, facial dysmorphism and severe congenital neutropenia. DBF4 is the regulatory subunit of the CDC7 kinase, together known as DBF4-dependent kinase (DDK), the complex essential for DNA replication initiation. The variant allele demonstrated impaired ability to bind CDC7, resulting in decreased DDK-mediated phosphorylation, defective S phase entry and progression and impaired differentiation of granulocytes associated with activation of the p53-p21 pathway. The introduction of WT DBF4 into patient CD34+ cells rescued the promyelocyte differentiation arrest. Conclusion Hypomorphic DBF4 mutation causes autosomal recessive severe congenital neutropenia with syndromic features

Genome-wide association analyses of physical activity and sedentary behavior provide insights into underlying mechanisms and roles in disease prevention

Although physical activity and sedentary behavior are moderately heritable, little is known about the mechanisms that influence these traits. Combining data for up to 703,901 individuals from 51 studies in a multi-ancestry meta-analysis of genome-wide association studies yields 99 loci that associate with self-reported moderate-to-vigorous intensity physical activity during leisure time (MVPA), leisure screen time (LST) and/or sedentary behavior at work. Loci associated with LST are enriched for genes whose expression in skeletal muscle is altered by resistance training. A missense variant in ACTN3 makes the alpha-actinin-3 filaments more flexible, resulting in lower maximal force in isolated type IIA muscle fibers, and possibly protection from exercise-induced muscle damage. Finally, Mendelian randomization analyses show that beneficial effects of lower LST and higher MVPA on several risk factors and diseases are mediated or confounded by body mass index (BMI). Our results provide insights into physical activity mechanisms and its role in disease prevention. Multi-ancestry meta-analyses of genome-wide association studies for self-reported physical activity during leisure time, leisure screen time, sedentary commuting and sedentary behavior at work identify 99 loci associated with at least one of these traits

Genome-Wide Association Study Identifies Two Novel Regions at 11p15.5-p13 and 1p31 with Major Impact on Acute-Phase Serum Amyloid A

Elevated levels of acute-phase serum amyloid A (A-SAA) cause amyloidosis and are a risk factor for atherosclerosis and its clinical complications, type 2 diabetes, as well as various malignancies. To investigate the genetic basis of A-SAA levels, we conducted the first genome-wide association study on baseline A-SAA concentrations in three population-based studies (KORA, TwinsUK, Sorbs) and one prospective case cohort study (LURIC), including a total of 4,212 participants of European descent, and identified two novel genetic susceptibility regions at 11p15.5-p13 and 1p31. The region at 11p15.5-p13 (rs4150642; p = 3.20×10−111) contains serum amyloid A1 (SAA1) and the adjacent general transcription factor 2 H1 (GTF2H1), Hermansky-Pudlak Syndrome 5 (HPS5), lactate dehydrogenase A (LDHA), and lactate dehydrogenase C (LDHC). This region explains 10.84% of the total variation of A-SAA levels in our data, which makes up 18.37% of the total estimated heritability. The second region encloses the leptin receptor (LEPR) gene at 1p31 (rs12753193; p = 1.22×10−11) and has been found to be associated with CRP and fibrinogen in previous studies. Our findings demonstrate a key role of the 11p15.5-p13 region in the regulation of baseline A-SAA levels and provide confirmative evidence of the importance of the 1p31 region for inflammatory processes and the close interplay between A-SAA, leptin, and other acute-phase proteins

Integrative genomic analyses in adipocytes implicate DNA methylation in human obesity and diabetes

DNA methylation variations are prevalent in human obesity but evidence of a causative role in disease pathogenesis is limited. Here, we combine epigenome-wide association and integrative genomics to investigate the impact of adipocyte DNA methylation variations in human obesity. We discover extensive DNA methylation changes that are robustly associated with obesity (N = 190 samples, 691 loci in subcutaneous and 173 loci in visceral adipocytes, P 500 target genes, and identify putative methylation-transcription factor interactions. Through Mendelian Randomisation, we infer causal effects of methylation on obesity and obesity-induced metabolic disturbances at 59 independent loci. Targeted methylation sequencing, CRISPR-activation and gene silencing in adipocytes, further identifies regional methylation variations, underlying regulatory elements and novel cellular metabolic effects. Our results indicate DNA methylation is an important determinant of human obesity and its metabolic complications, and reveal mechanisms through which altered methylation may impact adipocyte functions

Impact of Type 2 Diabetes Susceptibility Variants on Quantitative Glycemic Traits Reveals Mechanistic Heterogeneity

Patients with established type 2 diabetes display both β-cell dysfunction and insulin resistance. To define fundamental processes leading to the diabetic state, we examined the relationship between type 2 diabetes risk variants at 37 established susceptibility loci, and indices of proinsulin processing, insulin secretion, and insulin sensitivity. We included data from up to 58,614 nondiabetic subjects with basal measures and 17,327 with dynamic measures. We used additive genetic models with adjustment for sex, age, and BMI, followed by fixed-effects, inverse-variance meta-analyses. Cluster analyses grouped risk loci into five major categories based on their relationship to these continuous glycemic phenotypes. The first cluster (PPARG, KLF14, IRS1, GCKR) was characterized by primary effects on insulin sensitivity. The second cluster (MTNR1B, GCK) featured risk alleles associated with reduced insulin secretion and fasting hyperglycemia. ARAP1 constituted a third cluster characterized by defects in insulin processing. A fourth cluster (TCF7L2, SLC30A8, HHEX/IDE, CDKAL1, CDKN2A/2B) was defined by loci influencing insulin processing and secretion without a detectable change in fasting glucose levels. The final group contained 20 risk loci with no clear-cut associations to continuous glycemic traits. By assembling extensive data on continuous glycemic traits, we have exposed the diverse mechanisms whereby type 2 diabetes risk variants impact disease predisposition