Publications by authors named "Melina Claussnitzer"

28 Publications

  • Page 1 of 1

Gaining insight into metabolic diseases from human genetic discoveries.

Trends Genet 2021 Dec 24;37(12):1081-1094. Epub 2021 Jul 24.

Department of Medicine and Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA. Electronic address:

Human large-scale genetic association studies have identified sequence variations at thousands of genetic risk loci that are more common in patients with diverse metabolic disease compared with healthy controls. While these genetic associations have been replicated in multiple large cohorts and sometimes can explain up to 50% of heritability, the molecular and cellular mechanisms affected by common genetic variation associated with metabolic disease remains mostly unknown. A variety of new genome-wide data types, in conjunction with novel biostatistical and computational analytical methodologies and foundational experimental technologies, are paving the way for a principled approach to systematic variant-to-function (V2F) studies for metabolic diseases, turning associated regions into causal variants, cell types and states of action, effector genes, and cellular and physiological mechanisms. Identification of new target genes and cellular programs for metabolic risk loci will improve mechanistic understanding of disease biology and identification of novel therapeutic strategies.
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http://dx.doi.org/10.1016/j.tig.2021.07.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8578350PMC
December 2021

Linking the obesity rs1421085 variant circuitry to cellular, metabolic, and organismal phenotypes in vivo.

Sci Adv 2021 Jul 21;7(30). Epub 2021 Jul 21.

Mammalian Genetics Unit, MRC Harwell Institute, Oxfordshire OX11 0RD, UK.

Variants in FTO have the strongest association with obesity; however, it is still unclear how those noncoding variants mechanistically affect whole-body physiology. We engineered a deletion of the rs1421085 conserved cis-regulatory module (CRM) in mice and confirmed in vivo that the CRM modulates and gene expression and mitochondrial function in adipocytes. The CRM affects molecular and cellular phenotypes in an adipose depot-dependent manner and affects organismal phenotypes that are relevant for obesity, including decreased high-fat diet-induced weight gain, decreased whole-body fat mass, and decreased skin fat thickness. Last, we connected the CRM to a genetically determined effect on steroid patterns in males that was dependent on nutritional challenge and conserved across mice and humans. Together, our data establish cross-species conservation of the rs1421085 regulatory circuitry at the molecular, cellular, metabolic, and organismal level, revealing previously unknown contextual dependence of the variant's action.
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http://dx.doi.org/10.1126/sciadv.abg0108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8294759PMC
July 2021

A distribution-centered approach for analyzing human adipocyte size estimates and their association with obesity-related traits and mitochondrial function.

Int J Obes (Lond) 2021 09 25;45(9):2108-2117. Epub 2021 Jun 25.

Technical University of Munich, Else Kröner-Fresenius-Center for Nutritional Medicine, Chair of Nutritional Medicine, School of Life Sciences, Gregor-Mendel-Straße 2, 85354, Freising-Weihenstephan, Germany.

Objective: Cell diameter, area, and volume are established quantitative measures of adipocyte size. However, these different adipocyte sizing parameters have not yet been directly compared regarding their distributions. Therefore, the study aimed to investigate how these adipocyte size measures differ in their distribution and assessed their correlation with anthropometry and laboratory chemistry. In addition, we were interested to investigate the relationship between fat cell size and adipocyte mitochondrial respiratory chain capacity.

Methods: Subcutaneous and visceral histology-based adipocyte size estimates from 188 individuals were analyzed by applying a panel of parameters to describe the underlying cell population. Histology-based adipocyte diameter distributions were compared with adipocyte diameter distributions from collagenase digestion. Associations of mean adipocyte size with body mass index (BMI), glucose, HbA, blood lipids as well as mature adipocyte mitochondrial respiration were investigated.

Results: All adipocyte area estimates derived from adipose tissue histology were not normally distributed, but rather characterized by positive skewness. The shape of the size distribution depends on the adipocyte sizing parameter and on the method used to determine adipocyte size. Despite different distribution shapes histology-derived adipocyte area, diameter, volume, and surface area consistently showed positive correlations with BMI. Furthermore, associations between adipocyte sizing parameters and glucose, HbA, or HDL specifically in the visceral adipose depot were revealed. Increasing subcutaneous adipocyte diameter was negatively correlated with adipocyte mitochondrial respiration.

Conclusions: Despite different underlying size distributions, the correlation with obesity-related traits was consistent across adipocyte sizing parameters. Decreased mitochondrial respiratory capacity with increasing subcutaneous adipocyte diameter could display a novel link between adipocyte hypertrophy and adipose tissue function.
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http://dx.doi.org/10.1038/s41366-021-00883-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8380540PMC
September 2021

Extensive pleiotropism and allelic heterogeneity mediate metabolic effects of and .

Science 2021 06;372(6546):1085-1091

Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA.

Whereas coding variants often have pleiotropic effects across multiple tissues, noncoding variants are thought to mediate their phenotypic effects by specific tissue and temporal regulation of gene expression. Here, we investigated the genetic and functional architecture of a genomic region within the gene that is strongly associated with obesity risk. We show that multiple variants on a common haplotype modify the regulatory properties of several enhancers targeting and from megabase distances. We demonstrate that these enhancers affect gene expression in multiple tissues, including adipose and brain, and impart regulatory effects during a restricted temporal window. Our data indicate that the genetic architecture of disease-associated loci may involve extensive pleiotropy, allelic heterogeneity, shared allelic effects across tissues, and temporally restricted effects.
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http://dx.doi.org/10.1126/science.abf1008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8386003PMC
June 2021

Lipid droplet-size mapping in human adipose tissue using a clinical 3T system.

Magn Reson Med 2021 09 1;86(3):1256-1270. Epub 2021 Apr 1.

Department of Diagnostic and Interventional Radiology, School of Medicine, Technical University of Munich, Munich, Germany.

Purpose: To develop a methodology for probing lipid droplet sizes with a clinical system based on a diffusion-weighted stimulated echo-prepared turbo spin-echo sequence and to validate the methodology in water-fat emulsions and show its applicability in ex vivo adipose-tissue samples.

Methods: A diffusion-weighted stimulated echo-prepared preparation was combined with a single-shot turbo spin-echo readout for measurements at different b-values and diffusion times. The droplet size was estimated with an analytical expression, and three fitting approaches were compared: magnitude-based spatial averaging with voxel-wise residual minimization, complex-based spatial averaging with voxel-wise residual minimization, and complex-based spatial averaging with neighborhood-regularized residual minimization. Simulations were performed to characterize the fitting residual landscape and the approaches' noise performance. The applicability was assessed in oil-in-water emulsions in comparison with laser deflection and in ten human white adipose tissue samples in comparison with histology.

Results: The fitting residual landscape showed a minimum valley with increasing extent as the droplet size increased. In phantoms, a very good agreement of the mean droplet size was observed between the diffusion-weighted MRI-based and the laser deflection measurements, showing the best performance with complex-based spatial averaging with neighborhood-regularized residual minimization processing (R /P: 0.971/0.014). In the human adipose-tissue samples, complex-based spatial averaging with neighborhood-regularized residual minimization processing showed a significant correlation (R /P: 0.531/0.017) compared with histology.

Conclusion: The proposed acquisition and parameter-estimation methodology was able to probe restricted diffusion effects in lipid droplets. The methodology was validated using phantoms, and its feasibility in measuring an apparent lipid droplet size was demonstrated ex vivo in white adipose tissue.
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http://dx.doi.org/10.1002/mrm.28755DOI Listing
September 2021

A regulatory variant at 3q21.1 confers an increased pleiotropic risk for hyperglycemia and altered bone mineral density.

Cell Metab 2021 03 28;33(3):615-628.e13. Epub 2021 Jan 28.

Metabolism Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Cell Circuits and Epigenomics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02131, USA; University of Hohenheim, Institute of Nutritional Science, Stuttgart 70599, Germany. Electronic address:

Skeletal and glycemic traits have shared etiology, but the underlying genetic factors remain largely unknown. To identify genetic loci that may have pleiotropic effects, we studied Genome-wide association studies (GWASs) for bone mineral density and glycemic traits and identified a bivariate risk locus at 3q21. Using sequence and epigenetic modeling, we prioritized an adenylate cyclase 5 (ADCY5) intronic causal variant, rs56371916. This SNP changes the binding affinity of SREBP1 and leads to differential ADCY5 gene expression, altering the chromatin landscape from poised to repressed. These alterations result in bone- and type 2 diabetes-relevant cell-autonomous changes in lipid metabolism in osteoblasts and adipocytes. We validated our findings by directly manipulating the regulator SREBP1, the target gene ADCY5, and the variant rs56371916, which together imply a novel link between fatty acid oxidation and osteoblast differentiation. Our work, by systematic functional dissection of pleiotropic GWAS loci, represents a framework to uncover biological mechanisms affecting pleiotropic traits.
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http://dx.doi.org/10.1016/j.cmet.2021.01.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7928941PMC
March 2021

Role of the Neutral Amino Acid Transporter SLC7A10 in Adipocyte Lipid Storage, Obesity, and Insulin Resistance.

Diabetes 2021 03 6;70(3):680-695. Epub 2021 Jan 6.

Mohn Nutrition Research Laboratory, Department of Clinical Science, University of Bergen, Bergen, Norway

Elucidation of mechanisms that govern lipid storage, oxidative stress, and insulin resistance may lead to improved therapeutic options for type 2 diabetes and other obesity-related diseases. Here, we find that adipose expression of the small neutral amino acid transporter SLC7A10, also known as alanine-serine-cysteine transporter-1 (ASC-1), shows strong inverse correlates with visceral adiposity, insulin resistance, and adipocyte hypertrophy across multiple cohorts. Concordantly, loss of Slc7a10 function in zebrafish in vivo accelerates diet-induced body weight gain and adipocyte enlargement. Mechanistically, SLC7A10 inhibition in human and murine adipocytes decreases adipocyte serine uptake and total glutathione levels and promotes reactive oxygen species (ROS) generation. Conversely, SLC7A10 overexpression decreases ROS generation and increases mitochondrial respiratory capacity. RNA sequencing revealed consistent changes in gene expression between human adipocytes and zebrafish visceral adipose tissue following loss of SLC7A10, e.g., upregulation of (lipid storage) and downregulation of (lipid oxidation). Interestingly, ROS scavenger reduced lipid accumulation and attenuated the lipid-storing effect of SLC7A10 inhibition. These data uncover adipocyte SLC7A10 as a novel important regulator of adipocyte resilience to nutrient and oxidative stress, in part by enhancing glutathione levels and mitochondrial respiration, conducive to decreased ROS generation, lipid accumulation, adipocyte hypertrophy, insulin resistance, and type 2 diabetes.
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http://dx.doi.org/10.2337/db20-0096DOI Listing
March 2021

A MicroRNA Linking Human Positive Selection and Metabolic Disorders.

Cell 2020 10 14;183(3):684-701.e14. Epub 2020 Oct 14.

Departments of Internal Medicine and Cellular & Molecular Physiology, Yale School of Medicine, New Haven, CT 06510, USA.

Positive selection in Europeans at the 2q21.3 locus harboring the lactase gene has been attributed to selection for the ability of adults to digest milk to survive famine in ancient times. However, the 2q21.3 locus is also associated with obesity and type 2 diabetes in humans, raising the possibility that additional genetic elements in the locus may have contributed to evolutionary adaptation to famine by promoting energy storage, but which now confer susceptibility to metabolic diseases. We show here that the miR-128-1 microRNA, located at the center of the positively selected locus, represents a crucial metabolic regulator in mammals. Antisense targeting and genetic ablation of miR-128-1 in mouse metabolic disease models result in increased energy expenditure and amelioration of high-fat-diet-induced obesity and markedly improved glucose tolerance. A thrifty phenotype connected to miR-128-1-dependent energy storage may link ancient adaptation to famine and modern metabolic maladaptation associated with nutritional overabundance.
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http://dx.doi.org/10.1016/j.cell.2020.09.017DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8092355PMC
October 2020

A lead candidate functional single nucleotide polymorphism within the WARS2 gene associated with waist-hip-ratio does not alter RNA stability.

Biochim Biophys Acta Gene Regul Mech 2020 11 30;1863(11):194640. Epub 2020 Sep 30.

MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire OX11 0RD, UK. Electronic address:

We have prioritised a single nucleotide polymorphism (SNP) rs2645294 as one candidate functional SNP in the TBX15-WARS2 waist-hip-ratio locus using posterior probability analysis. This SNP is located in the 3' untranslated region of the WARS2 (tryptophanyl tRNA synthetase 2, mitochondrial) gene with which it has an expression quantitative trait in subcutaneous white adipose tissue. We show that transcripts of the WARS2 gene in a human white adipose cell line, heterozygous for the rs2645294 SNP, showed allelic imbalance. We tested whether the rs2645294 SNP altered WARS2 RNA stability using three different methods: actinomycin-D inhibition and RNA decay, mature and nascent RNA analysis and luciferase reporter assays. We found no evidence of a difference in RNA stability between the rs2645294 alleles indicating that the allelic expression imbalance was likely due to transcriptional regulation.
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http://dx.doi.org/10.1016/j.bbagrm.2020.194640DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7695619PMC
November 2020

Machine Learning based histology phenotyping to investigate the epidemiologic and genetic basis of adipocyte morphology and cardiometabolic traits.

PLoS Comput Biol 2020 08 14;16(8):e1008044. Epub 2020 Aug 14.

Big Data Institute, University of Oxford, Oxford, United Kingdom.

Genetic studies have recently highlighted the importance of fat distribution, as well as overall adiposity, in the pathogenesis of obesity-associated diseases. Using a large study (n = 1,288) from 4 independent cohorts, we aimed to investigate the relationship between mean adipocyte area and obesity-related traits, and identify genetic factors associated with adipocyte cell size. To perform the first large-scale study of automatic adipocyte phenotyping using both histological and genetic data, we developed a deep learning-based method, the Adipocyte U-Net, to rapidly derive mean adipocyte area estimates from histology images. We validate our method using three state-of-the-art approaches; CellProfiler, Adiposoft and floating adipocytes fractions, all run blindly on two external cohorts. We observe high concordance between our method and the state-of-the-art approaches (Adipocyte U-net vs. CellProfiler: R2visceral = 0.94, P < 2.2 × 10-16, R2subcutaneous = 0.91, P < 2.2 × 10-16), and faster run times (10,000 images: 6mins vs 3.5hrs). We applied the Adipocyte U-Net to 4 cohorts with histology, genetic, and phenotypic data (total N = 820). After meta-analysis, we found that mean adipocyte area positively correlated with body mass index (BMI) (Psubq = 8.13 × 10-69, βsubq = 0.45; Pvisc = 2.5 × 10-55, βvisc = 0.49; average R2 across cohorts = 0.49) and that adipocytes in subcutaneous depots are larger than their visceral counterparts (Pmeta = 9.8 × 10-7). Lastly, we performed the largest GWAS and subsequent meta-analysis of mean adipocyte area and intra-individual adipocyte variation (N = 820). Despite having twice the number of samples than any similar study, we found no genome-wide significant associations, suggesting that larger sample sizes and a homogenous collection of adipose tissue are likely needed to identify robust genetic associations.
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http://dx.doi.org/10.1371/journal.pcbi.1008044DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7449405PMC
August 2020

Gender Differences in the Response to Short-term Cold Exposure in Young Adults.

J Clin Endocrinol Metab 2020 05;105(5)

Else Kröner-Fresenius-Zentrum für Ernährungsmedizin, ZIEL-Institute for Food and Health, Technical University of Munich, Freising-Weihenstephan, Germany.

Context: Cold exposure (CE) has been shown to enhance energy expenditure by activating brown adipose tissue thermogenesis and metabolism in humans. However, it remains to be elucidated if there are gender-specific differences in cold-induced thermogenesis and metabolism.

Objective: To study the impact of mild CE on resting energy expenditure (REE) and metabolism in males compared with females.

Setting: A cross-sectional study.

Participants: 117 healthy young Caucasians participated in this study (58 males). Mean age was 25.1 ± 3.6 years and mean body mass index 22.3 ± 1.7 kg/m2.

Intervention: Participants underwent a short-term CE using water perfused mattresses to activate nonshivering thermogenesis.

Main Outcome Measures: REE was assessed before and 2 hours after CE followed by blood sampling. Selected metabolites and hormones were measured. Skin temperatures were monitored at various sites throughout the experiment.

Results: Participants showed a significant increase in REE after CE (6.5%, P < .001). This increase did not differ between genders (P = .908). However, there were differences between males and females in changes of plasma glucose (-5.1% versus -7.4%, P = .024), leptin (-14.3% versus -30.1%, P < .001) and adiponectin (5.4% versus 12.8%, P = .018) after CE. We observed a significant decrease of the supraclavicular skin temperature in men (-0.3%, P = .034), but not in women (0.3%, P = .326)(P = .019 between genders).

Conclusions: We did not observe a difference in the thermogenic response, measured as change of REE, to CE in women compared with men. However, we found that some metabolic and hormonal changes were more pronounced in women than in men suggesting a gender-specific response to cold.
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http://dx.doi.org/10.1210/clinem/dgaa110DOI Listing
May 2020

A brief history of human disease genetics.

Nature 2020 01 8;577(7789):179-189. Epub 2020 Jan 8.

Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK.

A primary goal of human genetics is to identify DNA sequence variants that influence biomedical traits, particularly those related to the onset and progression of human disease. Over the past 25 years, progress in realizing this objective has been transformed by advances in technology, foundational genomic resources and analytical tools, and by access to vast amounts of genotype and phenotype data. Genetic discoveries have substantially improved our understanding of the mechanisms responsible for many rare and common diseases and driven development of novel preventative and therapeutic strategies. Medical innovation will increasingly focus on delivering care tailored to individual patterns of genetic predisposition.
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http://dx.doi.org/10.1038/s41586-019-1879-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7405896PMC
January 2020

High-resolution genome-wide functional dissection of transcriptional regulatory regions and nucleotides in human.

Nat Commun 2018 12 19;9(1):5380. Epub 2018 Dec 19.

Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.

Genome-wide epigenomic maps have revealed millions of putative enhancers and promoters, but experimental validation of their function and high-resolution dissection of their driver nucleotides remain limited. Here, we present HiDRA (High-resolution Dissection of Regulatory Activity), a combined experimental and computational method for high-resolution genome-wide testing and dissection of putative regulatory regions. We test ~7 million accessible DNA fragments in a single experiment, by coupling accessible chromatin extraction with self-transcribing episomal reporters (ATAC-STARR-seq). By design, fragments are highly overlapping in densely-sampled accessible regions, enabling us to pinpoint driver regulatory nucleotides by exploiting differences in activity between partially-overlapping fragments using a machine learning model (SHARPR-RE). In GM12878 lymphoblastoid cells, we find ~65,000 regions showing enhancer function, and pinpoint ~13,000 high-resolution driver elements. These are enriched for regulatory motifs, evolutionarily-conserved nucleotides, and disease-associated genetic variants from genome-wide association studies. Overall, HiDRA provides a high-throughput, high-resolution approach for dissecting regulatory regions and driver nucleotides.
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http://dx.doi.org/10.1038/s41467-018-07746-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6300699PMC
December 2018

Large meta-analysis of genome-wide association studies identifies five loci for lean body mass.

Nat Commun 2017 07 19;8(1):80. Epub 2017 Jul 19.

Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St Louis, MO, 63110, USA.

Lean body mass, consisting mostly of skeletal muscle, is important for healthy aging. We performed a genome-wide association study for whole body (20 cohorts of European ancestry with n = 38,292) and appendicular (arms and legs) lean body mass (n = 28,330) measured using dual energy X-ray absorptiometry or bioelectrical impedance analysis, adjusted for sex, age, height, and fat mass. Twenty-one single-nucleotide polymorphisms were significantly associated with lean body mass either genome wide (p < 5 × 10) or suggestively genome wide (p < 2.3 × 10). Replication in 63,475 (47,227 of European ancestry) individuals from 33 cohorts for whole body lean body mass and in 45,090 (42,360 of European ancestry) subjects from 25 cohorts for appendicular lean body mass was successful for five single-nucleotide polymorphisms in/near HSD17B11, VCAN, ADAMTSL3, IRS1, and FTO for total lean body mass and for three single-nucleotide polymorphisms in/near VCAN, ADAMTSL3, and IRS1 for appendicular lean body mass. Our findings provide new insight into the genetics of lean body mass.Lean body mass is a highly heritable trait and is associated with various health conditions. Here, Kiel and colleagues perform a meta-analysis of genome-wide association studies for whole body lean body mass and find five novel genetic loci to be significantly associated.
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http://dx.doi.org/10.1038/s41467-017-00031-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5517526PMC
July 2017

Allele-specific quantitative proteomics unravels molecular mechanisms modulated by cis-regulatory PPARG locus variation.

Nucleic Acids Res 2017 04;45(6):3266-3279

Else Kroener-Fresenius-Center for Nutritional Medicine, Chair of Nutritional Medicine, Technische Universität München, 85354 Freising-Weihenstephan, Germany.

Genome-wide association studies identified numerous disease risk loci. Delineating molecular mechanisms influenced by cis-regulatory variants is essential to understand gene regulation and ultimately disease pathophysiology. Combining bioinformatics and public domain chromatin information with quantitative proteomics supports prediction of cis-regulatory variants and enabled identification of allele-dependent binding of both, transcription factors and coregulators at the type 2 diabetes associated PPARG locus. We found rs7647481A nonrisk allele binding of Yin Yang 1 (YY1), confirmed by allele-specific chromatin immunoprecipitation in primary adipocytes. Quantitative proteomics also found the coregulator RING1 and YY1 binding protein (RYBP) whose mRNA levels correlate with improved insulin sensitivity in primary adipose cells carrying the rs7647481A nonrisk allele. Our findings support a concept with diverse cis-regulatory variants contributing to disease pathophysiology at one locus. Proteome-wide identification of both, transcription factors and coregulators, can profoundly improve understanding of mechanisms underlying genetic associations.
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http://dx.doi.org/10.1093/nar/gkx105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5389726PMC
April 2017

Novel Genetic Variants Associated With Increased Vertebral Volumetric BMD, Reduced Vertebral Fracture Risk, and Increased Expression of SLC1A3 and EPHB2.

J Bone Miner Res 2016 12 6;31(12):2085-2097. Epub 2016 Sep 6.

Center for Diabetes Research, Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA.

Genome-wide association studies (GWASs) have revealed numerous loci for areal bone mineral density (aBMD). We completed the first GWAS meta-analysis (n = 15,275) of lumbar spine volumetric BMD (vBMD) measured by quantitative computed tomography (QCT), allowing for examination of the trabecular bone compartment. SNPs that were significantly associated with vBMD were also examined in two GWAS meta-analyses to determine associations with morphometric vertebral fracture (n = 21,701) and clinical vertebral fracture (n = 5893). Expression quantitative trait locus (eQTL) analyses of iliac crest biopsies were performed in 84 postmenopausal women, and murine osteoblast expression of genes implicated by eQTL or by proximity to vBMD-associated SNPs was examined. We identified significant vBMD associations with five loci, including: 1p36.12, containing WNT4 and ZBTB40; 8q24, containing TNFRSF11B; and 13q14, containing AKAP11 and TNFSF11. Two loci (5p13 and 1p36.12) also contained associations with radiographic and clinical vertebral fracture, respectively. In 5p13, rs2468531 (minor allele frequency [MAF] = 3%) was associated with higher vBMD (β = 0.22, p = 1.9 × 10 ) and decreased risk of radiographic vertebral fracture (odds ratio [OR] = 0.75; false discovery rate [FDR] p = 0.01). In 1p36.12, rs12742784 (MAF = 21%) was associated with higher vBMD (β = 0.09, p = 1.2 × 10 ) and decreased risk of clinical vertebral fracture (OR = 0.82; FDR p = 7.4 × 10 ). Both SNPs are noncoding and were associated with increased mRNA expression levels in human bone biopsies: rs2468531 with SLC1A3 (β = 0.28, FDR p = 0.01, involved in glutamate signaling and osteogenic response to mechanical loading) and rs12742784 with EPHB2 (β = 0.12, FDR p = 1.7 × 10 , functions in bone-related ephrin signaling). Both genes are expressed in murine osteoblasts. This is the first study to link SLC1A3 and EPHB2 to clinically relevant vertebral osteoporosis phenotypes. These results may help elucidate vertebral bone biology and novel approaches to reducing vertebral fracture incidence. © 2016 American Society for Bone and Mineral Research.
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http://dx.doi.org/10.1002/jbmr.2913DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5477772PMC
December 2016

Whole-genome sequencing identifies EN1 as a determinant of bone density and fracture.

Nature 2015 Oct 14;526(7571):112-7. Epub 2015 Sep 14.

Institute for Aging Research, Hebrew SeniorLife, Boston, Massachusetts 02131, USA.

The extent to which low-frequency (minor allele frequency (MAF) between 1-5%) and rare (MAF ≤ 1%) variants contribute to complex traits and disease in the general population is mainly unknown. Bone mineral density (BMD) is highly heritable, a major predictor of osteoporotic fractures, and has been previously associated with common genetic variants, as well as rare, population-specific, coding variants. Here we identify novel non-coding genetic variants with large effects on BMD (ntotal = 53,236) and fracture (ntotal = 508,253) in individuals of European ancestry from the general population. Associations for BMD were derived from whole-genome sequencing (n = 2,882 from UK10K (ref. 10); a population-based genome sequencing consortium), whole-exome sequencing (n = 3,549), deep imputation of genotyped samples using a combined UK10K/1000 Genomes reference panel (n = 26,534), and de novo replication genotyping (n = 20,271). We identified a low-frequency non-coding variant near a novel locus, EN1, with an effect size fourfold larger than the mean of previously reported common variants for lumbar spine BMD (rs11692564(T), MAF = 1.6%, replication effect size = +0.20 s.d., Pmeta = 2 × 10(-14)), which was also associated with a decreased risk of fracture (odds ratio = 0.85; P = 2 × 10(-11); ncases = 98,742 and ncontrols = 409,511). Using an En1(cre/flox) mouse model, we observed that conditional loss of En1 results in low bone mass, probably as a consequence of high bone turnover. We also identified a novel low-frequency non-coding variant with large effects on BMD near WNT16 (rs148771817(T), MAF = 1.2%, replication effect size = +0.41 s.d., Pmeta = 1 × 10(-11)). In general, there was an excess of association signals arising from deleterious coding and conserved non-coding variants. These findings provide evidence that low-frequency non-coding variants have large effects on BMD and fracture, thereby providing rationale for whole-genome sequencing and improved imputation reference panels to study the genetic architecture of complex traits and disease in the general population.
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http://dx.doi.org/10.1038/nature14878DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4755714PMC
October 2015

FTO Obesity Variant Circuitry and Adipocyte Browning in Humans.

N Engl J Med 2015 Sep 19;373(10):895-907. Epub 2015 Aug 19.

From Beth Israel Deaconess Medical Center and Hebrew SeniorLife, Gerontology Division, Harvard Medical School, Boston (M.C., Y.-H.H.); Massachusetts Institute of Technology (MIT) Computer Science and Artificial Intelligence Laboratory (M.C., G.Q., W.M., N.A.A., M.K.), and Broad Institute of MIT and Harvard, Cambridge (M.C., G.Q., W.M., M.K.); Clinical Cooperation Group "Nutrigenomics and Type 2 Diabetes," Helmholtz Center Munich (M.C., H.H.), and Else Kröner-Fresenius Center for Nutritional Medicine, Klinikum rechts der Isar, ZIEL-Institute for Food and Health, Technische Universität München (M.C., V.G., I.S.S., H.H.), Munich, Germany; KG Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, and Hormone Laboratory, Haukeland University Hospital, Bergen, Norway (S.N.D., C.H., G.M.); Program in Developmental and Stem Cell Biology, Hospital for Sick Children, and Department of Molecular Genetics, University of Toronto (K.-H.K., V.P., J.L., C.-C.H.), and Department of Medicine, Lunenfeld-Tanenbaum Research Institute, Mt. Sinai Hospital (J.L.B., D.J.D.), Toronto; and the Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden (P.-A.S.).

Background: Genomewide association studies can be used to identify disease-relevant genomic regions, but interpretation of the data is challenging. The FTO region harbors the strongest genetic association with obesity, yet the mechanistic basis of this association remains elusive.

Methods: We examined epigenomic data, allelic activity, motif conservation, regulator expression, and gene coexpression patterns, with the aim of dissecting the regulatory circuitry and mechanistic basis of the association between the FTO region and obesity. We validated our predictions with the use of directed perturbations in samples from patients and from mice and with endogenous CRISPR-Cas9 genome editing in samples from patients.

Results: Our data indicate that the FTO allele associated with obesity represses mitochondrial thermogenesis in adipocyte precursor cells in a tissue-autonomous manner. The rs1421085 T-to-C single-nucleotide variant disrupts a conserved motif for the ARID5B repressor, which leads to derepression of a potent preadipocyte enhancer and a doubling of IRX3 and IRX5 expression during early adipocyte differentiation. This results in a cell-autonomous developmental shift from energy-dissipating beige (brite) adipocytes to energy-storing white adipocytes, with a reduction in mitochondrial thermogenesis by a factor of 5, as well as an increase in lipid storage. Inhibition of Irx3 in adipose tissue in mice reduced body weight and increased energy dissipation without a change in physical activity or appetite. Knockdown of IRX3 or IRX5 in primary adipocytes from participants with the risk allele restored thermogenesis, increasing it by a factor of 7, and overexpression of these genes had the opposite effect in adipocytes from nonrisk-allele carriers. Repair of the ARID5B motif by CRISPR-Cas9 editing of rs1421085 in primary adipocytes from a patient with the risk allele restored IRX3 and IRX5 repression, activated browning expression programs, and restored thermogenesis, increasing it by a factor of 7.

Conclusions: Our results point to a pathway for adipocyte thermogenesis regulation involving ARID5B, rs1421085, IRX3, and IRX5, which, when manipulated, had pronounced pro-obesity and anti-obesity effects. (Funded by the German Research Center for Environmental Health and others.).
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http://dx.doi.org/10.1056/NEJMoa1502214DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4959911PMC
September 2015

Integrative analysis of 111 reference human epigenomes.

Nature 2015 Feb;518(7539):317-30

1] Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, Moores Cancer Center, Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA. [2] Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, California 92093, USA.

The reference human genome sequence set the stage for studies of genetic variation and its association with human disease, but epigenomic studies lack a similar reference. To address this need, the NIH Roadmap Epigenomics Consortium generated the largest collection so far of human epigenomes for primary cells and tissues. Here we describe the integrative analysis of 111 reference human epigenomes generated as part of the programme, profiled for histone modification patterns, DNA accessibility, DNA methylation and RNA expression. We establish global maps of regulatory elements, define regulatory modules of coordinated activity, and their likely activators and repressors. We show that disease- and trait-associated genetic variants are enriched in tissue-specific epigenomic marks, revealing biologically relevant cell types for diverse human traits, and providing a resource for interpreting the molecular basis of human disease. Our results demonstrate the central role of epigenomic information for understanding gene regulation, cellular differentiation and human disease.
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http://dx.doi.org/10.1038/nature14248DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4530010PMC
February 2015

COL6A3 expression in adipocytes associates with insulin resistance and depends on PPARγ and adipocyte size.

Obesity (Silver Spring) 2014 Aug 10;22(8):1807-13. Epub 2014 Apr 10.

Department of Clinical Science, University of Bergen, Bergen, Norway; KG Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway; Hormone Laboratory, Haukeland University Hospital, Bergen, Norway.

Objective: COL6A3 may modulate adipose tissue function in obesity and insulin resistance. A role for human adipocytes linking COL6A3 with insulin resistance warrants exploration.

Methods: COL6A3 mRNA in abdominal subcutaneous adipose samples was compared between (1) BMI-matched obese subjects resistant or sensitive to insulin (surgical whole tissue biopsies, n = 30/group), (2) lean/overweight and obese subjects (isolated adipocytes from collagenase-treated surgical biopsies, n = 11/group), (3) developing primary human adipocytes with/without knockdown of the insulin-sensitizing adipogenic gene PPARG (collagenase-treated lipoaspirate, n = 5), and (4) small and large adipocytes from lean/overweight subjects (collagenase-treated surgical biopsies or lipoaspirate, n = 10). Insulin resistance and sensitivity were assessed by euglycemic-hyperinsulinemic clamp (glucose infusion rate <60 and >70 μmol kg(-1) min(-1) , respectively) (1), or by HOMA-IR and TG/HDL ratio (2).

Results: Whole tissue COL6A3 mRNA was 2.6-fold higher in insulin resistant compared to sensitive subjects (P < 0.001). In isolated adipocytes, COL6A3 mRNA correlated positively with BMI (P = 0.007), HOMA-IR (P = 0.039), and TG/HDL (P = 0.004). PPARG knockdown in developing adipocytes increased COL6A3 mRNA 1.5-fold (P = 0.043). The inverse relationship with adipocyte development was further supported by 2.8-fold higher COL6A3 mRNA in small compared to large adipocytes (P = 0.004).

Conclusion: Increased adipocyte COL6A3 expression associates with insulin resistance in humans, which may involve impaired PPARγ-mediated adipocyte development.
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http://dx.doi.org/10.1002/oby.20758DOI Listing
August 2014

Restless legs syndrome-associated intronic common variant in Meis1 alters enhancer function in the developing telencephalon.

Genome Res 2014 Apr 18;24(4):592-603. Epub 2014 Mar 18.

Institute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany;

Genome-wide association studies (GWAS) identified the MEIS1 locus for Restless Legs Syndrome (RLS), but causal single nucleotide polymorphisms (SNPs) and their functional relevance remain unknown. This locus contains a large number of highly conserved noncoding regions (HCNRs) potentially functioning as cis-regulatory modules. We analyzed these HCNRs for allele-dependent enhancer activity in zebrafish and mice and found that the risk allele of the lead SNP rs12469063 reduces enhancer activity in the Meis1 expression domain of the murine embryonic ganglionic eminences (GE). CREB1 binds this enhancer and rs12469063 affects its binding in vitro. In addition, MEIS1 target genes suggest a role in the specification of neuronal progenitors in the GE, and heterozygous Meis1-deficient mice exhibit hyperactivity, resembling the RLS phenotype. Thus, in vivo and in vitro analysis of a common SNP with small effect size showed allele-dependent function in the prospective basal ganglia representing the first neurodevelopmental region implicated in RLS.
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http://dx.doi.org/10.1101/gr.166751.113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3975059PMC
April 2014

Leveraging cross-species transcription factor binding site patterns: from diabetes risk loci to disease mechanisms.

Cell 2014 Jan;156(1-2):343-58

Department of Medicine, University of Leipzig, 04103 Leipzig, Germany.

Genome-wide association studies have revealed numerous risk loci associated with diverse diseases. However, identification of disease-causing variants within association loci remains a major challenge. Divergence in gene expression due to cis-regulatory variants in noncoding regions is central to disease susceptibility. We show that integrative computational analysis of phylogenetic conservation with a complexity assessment of co-occurring transcription factor binding sites (TFBS) can identify cis-regulatory variants and elucidate their mechanistic role in disease. Analysis of established type 2 diabetes risk loci revealed a striking clustering of distinct homeobox TFBS. We identified the PRRX1 homeobox factor as a repressor of PPARG2 expression in adipose cells and demonstrate its adverse effect on lipid metabolism and systemic insulin sensitivity, dependent on the rs4684847 risk allele that triggers PRRX1 binding. Thus, cross-species conservation analysis at the level of co-occurring TFBS provides a valuable contribution to the translation of genetic association signals to disease-related molecular mechanisms.
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http://dx.doi.org/10.1016/j.cell.2013.10.058DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7116609PMC
January 2014

Plasma metabolomics reveal alterations of sphingo- and glycerophospholipid levels in non-diabetic carriers of the transcription factor 7-like 2 polymorphism rs7903146.

PLoS One 2013 24;8(10):e78430. Epub 2013 Oct 24.

Medizinische Klinik und Poliklinik IV, Diabetes Zentrum - Campus Innenstadt, Klinikum der Universität München, Munich, Germany ; Clinical Cooperation Group Diabetes, Ludwig-Maximilians-Universität München and Helmholtz Zentrum München, Munich, Germany.

Aims/hypothesis: Polymorphisms in the transcription factor 7-like 2 (TCF7L2) gene have been shown to display a powerful association with type 2 diabetes. The aim of the present study was to evaluate metabolic alterations in carriers of a common TCF7L2 risk variant.

Methods: Seventeen non-diabetic subjects carrying the T risk allele at the rs7903146 TCF7L2 locus and 24 subjects carrying no risk allele were submitted to intravenous glucose tolerance test and euglycemic-hyperinsulinemic clamp. Plasma samples were analysed for concentrations of 163 metabolites through targeted mass spectrometry.

Results: TCF7L2 risk allele carriers had a reduced first-phase insulin response and normal insulin sensitivity. Under fasting conditions, carriers of TCF7L2 rs7903146 exhibited a non-significant increase of plasma sphingomyelins (SMs), phosphatidylcholines (PCs) and lysophosphatidylcholines (lysoPCs) species. A significant genotype effect was detected in response to challenge tests in 6 SMs (C16:0, C16:1, C18:0, C18:1, C24:0, C24:1), 5 hydroxy-SMs (C14:1, C16:1, C22:1, C22:2, C24:1), 4 lysoPCs (C14:0, C16:0, C16:1, C17:0), 3 diacyl-PCs (C28:1, C36:6, C40:4) and 4 long-chain acyl-alkyl-PCs (C40:2, C40:5, C44:5, C44:6).

Discussion: Plasma metabolomic profiling identified alterations of phospholipid metabolism in response to challenge tests in subjects with TCF7L2 rs7903146 genotype. This may reflect a genotype-mediated link to early metabolic abnormalities prior to the development of disturbed glucose tolerance.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0078430PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3813438PMC
February 2015

Octamer-dependent transcription in T cells is mediated by NFAT and NF-κB.

Nucleic Acids Res 2013 Feb 4;41(4):2138-54. Epub 2013 Jan 4.

Institute of Physiological Chemistry, University Ulm, D-89081 Ulm, Germany, Institute of Pathology, University Ulm, D-89081 Ulm, Germany.

The transcriptional co-activator BOB.1/OBF.1 was originally identified in B cells and is constitutively expressed throughout B cell development. BOB.1/OBF.1 associates with the transcription factors Oct1 and Oct2, thereby enhancing octamer-dependent transcription. In contrast, in T cells, BOB.1/OBF.1 expression is inducible by treatment of cells with PMA/Ionomycin or by antigen receptor engagement, indicating a marked difference in the regulation of BOB.1/OBF.1 expression in B versus T cells. The molecular mechanisms underlying the differential expression of BOB.1/OBF.1 in T and B cells remain largely unknown. Therefore, the present study focuses on mechanisms controlling the transcriptional regulation of BOB.1/OBF.1 and Oct2 in T cells. We show that both calcineurin- and NF-κB-inhibitors efficiently attenuate the expression of BOB.1/OBF.1 and Oct2 in T cells. In silico analyses of the BOB.1/OBF.1 promoter revealed the presence of previously unappreciated combined NFAT/NF-κB sites. An array of genetic and biochemical analyses illustrates the involvement of the Ca(2+)/calmodulin-dependent phosphatase calcineurin as well as NFAT and NF-κB transcription factors in the transcriptional regulation of octamer-dependent transcription in T cells. Conclusively, impaired expression of BOB.1/OBF.1 and Oct2 and therefore a hampered octamer-dependent transcription may participate in T cell-mediated immunodeficiency caused by the deletion of NFAT or NF-κB transcription factors.
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http://dx.doi.org/10.1093/nar/gks1349DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3575799PMC
February 2013

Effect of flavonoids on basal and insulin-stimulated 2-deoxyglucose uptake in adipocytes.

Mol Nutr Food Res 2011 May 31;55 Suppl 1:S26-34. Epub 2011 Jan 31.

Else-Kröner-Fresenius Center for Nutritional Medicine, Technische Universität München, Freising, Germany.

Scope: The adipose tissue is a major site of insulin action and contributes substantially to energy homeostasis. Insulin increases the extraction of glucose from circulation into adipose tissue by recruiting the glucose transporter GLUT4 to the plasma membrane. It has been proposed that dietary flavonoids may interfere with glucose transport processes.

Methods And Results: We have used murine 3T3-L1 adipocytes and isolated mature human adipocytes to assess the interaction of selected flavonoids with glucose uptake, both in the basal state and after insulin stimulation. Kinetic characterization of 2-deoxyglucose uptake in the basal state revealed in both cell types an apparent K(m) of around 8 mM with no change in affinity but a significant increase in maximal influx in the presence of insulin. A screening of representative flavonoids of different structural classes revealed the flavanone naringenin and the isoflavone daidzein to affect glucose transport significantly with half-maximal inhibition at concentrations of around 60-80 μM for basal and 70-110 μM for insulin-stimulated glucose uptake in both 3T3-L1 adipocytes and mature human adipocytes.

Conclusion: Considering attainable plasma concentrations of flavonoids in vivo, we assume that even under physiological conditions naringenin and daidzein could impair glucose removal from plasma, which may pose a risk to patients with diabetes mellitus.
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http://dx.doi.org/10.1002/mnfr.201000372DOI Listing
May 2011

Functional characterization of promoter variants of the adiponectin gene complemented by epidemiological data.

Diabetes 2009 Apr 15;58(4):984-91. Epub 2008 Dec 15.

Else Kröner-Fresenius-Center for Nutritional Medicine, Technische Universität München, Munich, Germany.

Objective: Adiponectin (APM1, ACDC) is an adipocyte-derived protein with downregulated expression in obesity and insulin-resistant states. Several potentially regulatory single nucleotide polymorphisms (SNPs) within the APM1 gene promoter region have been associated with circulating adiponectin levels. None of them have been functionally characterized in adiponectin-expressing cells. Hence, we investigated three SNPs (rs16861194, rs17300539, and rs266729) for their influence on adiponectin promoter activity and their association with circulating adiponectin levels.

Research Design And Methods: Basal and rosiglitazone-induced promoter activity of different SNP combinations (haplotypes) was analyzed in 3T3-L1 adipocytes using luciferase reporter gene assays and DNA binding studies comparing all possible APM1 haplotypes. This functional approach was complemented with analysis of epidemiological population-based data of 1,692 participants of the MONICA/KORA S123 cohort and 696 participants from the KORA S4 cohort for SNP and haplotype association with circulating adiponectin levels.

Results: Major to minor allele replacements of the three SNPs revealed significant effects on promoter activity in luciferase assays. Particularly, a minor variant in rs16861194 resulted in reduced basal and rosiglitazone-induced promoter activity and hypoadiponectinemia in the epidemiological datasets. The haplotype with the minor allele in all three SNPs showed a complete loss of promoter activity, and no subject carried this haplotype in either of the epidemiological samples (combined P value for statistically significant difference from a random sample was 0.006).

Conclusions: Our results clearly demonstrate that promoter variants associated with hypoadiponectinemia in humans substantially affect adiponectin promoter activity in adipocytes. Our combination of functional experiments with epidemiological data overcomes the drawback of each approach alone.
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http://dx.doi.org/10.2337/db07-1646DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2661577PMC
April 2009
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