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

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 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.publishedVersionPeer reviewe

From GWAS to gene : Zebrafish as a model system for large-scale studies of obesity and comorbidities

Obesity increases the risk of developing comorbidities such as cardiovascular and metabolic diseases. However, not all obese individuals develop comorbidities, and those that do not are referred to as “metabolically healthy obesity” individuals. These contrast with lean individuals that display the metabolic profile of unhealthy obese individuals and are classified as “metabolically obese normal weight” individuals. The mechanisms underlying the variability in susceptibility to metabolic diseases are not fully understood and suggest the presence of biological and genetic components. This project aims to identify and characterize causal genes in loci identified by genome-wide association studies (GWAS) that are associated with higher adiposity and lower risk of comorbidities, or vice versa. In Study I, I integrated results from several bioinformatic approaches to prioritize candidate genes in loci identified in a genome-wide cross-phenotype meta-analysis of adiposity and cardiometabolic trait pairs. I prioritized 61 candidate genes in 42 of the 62 identifies loci, of which 39 genes were located in 25 novel loci. In Study II, I developed an experimental pipeline and validated 10-day old zebrafish larvae as a model system for image and CRISPR/Cas9-based characterization of candidate genes for obesity. I examined the effect of overfeeding and the effect of CRISPR/Cas9-induced mutations in 15 zebrafish orthologues of 12 established human obesity genes and of 16 human genes with an anticipated role in food intake. I show that 10 days is too early to see an effect of the genetic perturbation on lipid accumulation in adipocytes, but that such experiments can be used to see an effect on other cardiometabolic traits. In Study III, I described a framework to functionally characterize candidate genes in CRISPR/Cas9 founders by targeting the housekeeping kita gene in both mutagenized larvae for a candidate gene and sibling controls. By targeting both cases and controls at kita, the framework ensures that both groups undergo micro-injections, DNA editing, and DNA repair, and that any differences in phenotype can be attributed to mutations in the candidate gene. In Study IV, I applied the approach developed in Study III to examine the effect of mutations in five genes prioritized in Study I and in five additional genes for their effect on adiposity and cardiometabolic traits in crispants. I show that while 10 days is too early to see an effect on adiposity, effects on the cardiometabolic traits the genes were anticipated to affect can be observed

Identification and characterization of causal genes for LDL cholesterol levels and downstream effects on atherosclerosis

Coronary artery disease is the leading cause of death worldwide and results from progression of atherosclerosis, which is triggered in part by elevated plasma concentrations of LDL cholesterol. Genome-wide association studies have identified many loci that are associated with circulating lipid levels and bioinformatics tools have been implemented to prioritize positional candidate genes. This project aims to better understand the genetics underlying the regulation of plasma LDL levels and their effect of atherosclerosis using a zebrafish (Danio rerio) model system. A multiplex line with the genes abcg5, abcg8, myrf, col4a3bpa, col4a3bpb, st3gal3, ywhaqa and ywhaqb targeted by CRISPR/Cas9 technique was established using zebrafish with fluorescently labeled macrophages (Tg[mpeg1:mCherry]) and neutrophils (Tg[mpo:EGFP]). Monodansylpentane cadaverase was used to visualize lipids droplets, together with macrophages and neutrophils, in 384 overfed larvae, allowing the visualization and quantification of vascular atherogenic traits at 10 days post-fertilization. Euthanized larvae were homogenized for the quantification of triglycerides, total cholesterol, LDL, HDL, glucose and protein levels. DNA was extracted and larvae were paired-end sequenced for the CRISPR-targeted sites. Linear regression analysis to compare the wild-type larvae against homozygous mutants and additive models for orthologous genes were performed. The lower accumulation of lipids and the lower co-localization of macrophages and neutrophils in the vasculature suggested that the larvae with mutations in the gene abcg5, abcg8, col4a3bpb, and ywhaqb resulted in larvae more protected against atherosclerotic phenotype. The study suggested that loss of function of the targeted genes was associated with atherogenic traits, helping to understand the pathophysiology of atherosclerosis

Translating GWAS-identified loci for cardiac rhythm and rate using an in vivo image- and CRISPR/Cas9-based approach

A meta-analysis of genome-wide association studies (GWAS) identified eight loci that are associated with heart rate variability (HRV), but candidate genes in these loci remain uncharacterized. We developed an image- and CRISPR/Cas9-based pipeline to systematically characterize candidate genes for HRV in live zebrafish embryos. Nine zebrafish orthologues of six human candidate genes were targeted simultaneously in eggs from fish that transgenically express GFP on smooth muscle cells (Tg[acta2:GFP]), to visualize the beating heart. An automated analysis of repeated 30 s recordings of beating atria in 381 live, intact zebrafish embryos at 2 and 5 days post-fertilization highlighted genes that influence HRV (hcn4 and si:dkey-65j6.2 [KIAA1755]); heart rate (rgs6 and hcn4); and the risk of sinoatrial pauses and arrests (hcn4). Exposure to 10 or 25 mu M ivabradine-an open channel blocker of HCNs-for 24 h resulted in a dose-dependent higher HRV and lower heart rate at 5 days post-fertilization. Hence, our screen confirmed the role of established genes for heart rate and rhythm (RGS6 and HCN4); showed that ivabradine reduces heart rate and increases HRV in zebrafish embryos, as it does in humans; and highlighted a novel gene that plays a role in HRV (KIAA1755)

Loss of RREB1 in pancreatic beta cells reduces cellular insulin content and affects endocrine cell gene expression

AIMS/HYPOTHESIS: Genome-wide studies have uncovered multiple independent signals at the RREB1 locus associated with altered type 2 diabetes risk and related glycaemic traits. However, little is known about the function of the zinc finger transcription factor Ras-responsive element binding protein 1 (RREB1) in glucose homeostasis or how changes in its expression and/or function influence diabetes risk. METHODS: A zebrafish model lacking rreb1a and rreb1b was used to study the effect of RREB1 loss in vivo. Using transcriptomic and cellular phenotyping of a human beta cell model (EndoC-βH1) and human induced pluripotent stem cell (hiPSC)-derived beta-like cells, we investigated how loss of RREB1 expression and activity affects pancreatic endocrine cell development and function. Ex vivo measurements of human islet function were performed in donor islets from carriers of RREB1 type 2 diabetes risk alleles. RESULTS: CRISPR/Cas9-mediated loss of rreb1a and rreb1b function in zebrafish supports an in vivo role for the transcription factor in beta cell mass, beta cell insulin expression and glucose levels. Loss of RREB1 also reduced insulin gene expression and cellular insulin content in EndoC-βH1 cells and impaired insulin secretion under prolonged stimulation. Transcriptomic analysis of RREB1 knockdown and knockout EndoC-βH1 cells supports RREB1 as a novel regulator of genes involved in insulin secretion. In vitro differentiation of RREB1KO/KO hiPSCs revealed dysregulation of pro-endocrine cell genes, including RFX family members, suggesting that RREB1 also regulates genes involved in endocrine cell development. Human donor islets from carriers of type 2 diabetes risk alleles in RREB1 have altered glucose-stimulated insulin secretion ex vivo, consistent with a role for RREB1 in regulating islet cell function. CONCLUSIONS/INTERPRETATION: Together, our results indicate that RREB1 regulates beta cell function by transcriptionally regulating the expression of genes involved in beta cell development and function

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 II 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

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