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Milona M, Ciechanowicz A, Węsierska K, Gońda-Domin M, Zawiślak A, Jarząbek A, Sobalska-Kwapis M, Jarczak J, Gruszka R, Strapagiel D, Janiszewska-Olszowska J, Grocholewicz K. Association of Three Genetic Loci with Molar Incisor Hypomineralization in Polish Children. J Clin Med 2024; 13:857. [PMID: 38337551 PMCID: PMC10856562 DOI: 10.3390/jcm13030857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 01/23/2024] [Accepted: 01/30/2024] [Indexed: 02/12/2024] Open
Abstract
BACKGROUND Molar incisor hypomineralization (MIH) is a qualitative, demarcated enamel defect of hypomineralization affecting one to four first permanent molars, often with incisor involvement. Its etiology is complex. However, evidence suggests the influence of genetic factors, potentially including the single nucleotide polymorphisms (SNPs) rs2889956, rs4811117 and rs13058467, which were previously linked to MIH in a genome-wide association study of German children. The aim was to replicate analyses of possible associations between the SNPs and molar incisor hypomineralization in Polish children. METHODS The final study group consisted of 778 children aged 126-168 months old. Saliva samples were taken, and genomic DNA was extracted and genotyped using beadchip microarrays. RESULTS Among the 778 subjects, there were 68 (8.7%) subjects with MIH and 710 (91.3%) subjects without MIH. There were no significant differences in distributions in age, sex, or the frequency of caries in permanent dentition between the MIH and non-MIH groups. The rs2889956, rs4811117, and rs13058467 genotype distributions in the studied group conformed to the expected Hardy-Weinberg equilibria, and there were no significant differences in the distributions of their alleles or genotypes between the MIH and non-MIH groups. CONCLUSION Our replication study did not confirm highly significant associations between the single nucleotide polymorphisms rs2889956, rs4811117, and rs13058467 with molar incisor hypomineralization in Polish children.
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Affiliation(s)
- Marta Milona
- Department of Hygiene and Epidemiology, Pomeranian Medical University, 70-111 Szczecin, Poland;
| | - Andrzej Ciechanowicz
- Department of Clinical and Molecular Biochemistry, Pomeranian Medical University, 70-111 Szczecin, Poland
| | | | | | - Alicja Zawiślak
- Department of Interdisciplinary Dentistry, Pomeranian Medical University, 70-111 Szczecin, Poland; (A.Z.); (J.J.-O.); (K.G.)
| | - Anna Jarząbek
- Laboratory of Paediatric Dentistry, Pomeranian Medical University, 70-111 Szczecin, Poland;
| | - Marta Sobalska-Kwapis
- Biobank Lab, Department of Oncobiology and Epigenetics, Faculty of Biology and Environmental Protection, University of Lodz, 90-237 Lodz, Poland; (M.S.-K.); (D.S.)
| | - Justyna Jarczak
- Regenerative Medicine Laboratory, Medical University of Warsaw, 02-097 Warszawa, Poland;
| | - Renata Gruszka
- Department of Molecular Biotechnology and Genetics, Faculty of Biology and Environmental Protection, University of Lodz, 90-237 Lodz, Poland;
| | - Dominik Strapagiel
- Biobank Lab, Department of Oncobiology and Epigenetics, Faculty of Biology and Environmental Protection, University of Lodz, 90-237 Lodz, Poland; (M.S.-K.); (D.S.)
| | - Joanna Janiszewska-Olszowska
- Department of Interdisciplinary Dentistry, Pomeranian Medical University, 70-111 Szczecin, Poland; (A.Z.); (J.J.-O.); (K.G.)
| | - Katarzyna Grocholewicz
- Department of Interdisciplinary Dentistry, Pomeranian Medical University, 70-111 Szczecin, Poland; (A.Z.); (J.J.-O.); (K.G.)
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Beuchel C, Dittrich J, Becker S, Kirsten H, Tönjes A, Kovacs P, Stumvoll M, Loeffler M, Teren A, Thiery J, Isermann B, Ceglarek U, Scholz M. An atlas of genome-wide gene expression and metabolite associations and possible mediation effects towards body mass index. J Mol Med (Berl) 2023; 101:1305-1321. [PMID: 37672078 PMCID: PMC10560167 DOI: 10.1007/s00109-023-02362-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 08/07/2023] [Accepted: 08/15/2023] [Indexed: 09/07/2023]
Abstract
Investigating the cross talk of different omics layers is crucial to understand molecular pathomechanisms of metabolic diseases like obesity. Here, we present a large-scale association meta-analysis of genome-wide whole blood and peripheral blood mononuclear cell (PBMC) gene expressions profiled with Illumina HT12v4 microarrays and metabolite measurements from dried blood spots (DBS) characterized by targeted liquid chromatography tandem mass spectrometry (LC-MS/MS) in three large German cohort studies with up to 7706 samples. We found 37,295 associations comprising 72 amino acids (AA) and acylcarnitine (AC) metabolites (including ratios) and 8579 transcripts. We applied this catalogue of associations to investigate the impact of associating transcript-metabolite pairs on body mass index (BMI) as an example metabolic trait. This is achieved by conducting a comprehensive mediation analysis considering metabolites as mediators of gene expression effects and vice versa. We discovered large mediation networks comprising 27,023 potential mediation effects within 20,507 transcript-metabolite pairs. Resulting networks of highly connected (hub) transcripts and metabolites were leveraged to gain mechanistic insights into metabolic signaling pathways. In conclusion, here, we present the largest available multi-omics integration of genome-wide transcriptome data and metabolite data of amino acid and fatty acid metabolism and further leverage these findings to characterize potential mediation effects towards BMI proposing candidate mechanisms of obesity and related metabolic diseases. KEY MESSAGES: Thousands of associations of 72 amino acid and acylcarnitine metabolites and 8579 genes expand the knowledge of metabolome-transcriptome associations. A mediation analysis of effects on body mass index revealed large mediation networks of thousands of obesity-related gene-metabolite pairs. Highly connected, potentially mediating hub genes and metabolites enabled insight into obesity and related metabolic disease pathomechanisms.
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Affiliation(s)
- Carl Beuchel
- Institute for Medical Informatics, Statistics and Epidemiology, Leipzig University, Leipzig, Germany
| | - Julia Dittrich
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, Leipzig University, Leipzig, Germany
| | - Susen Becker
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, Leipzig University, Leipzig, Germany
- Department of Forensic Toxicology, Institute of Legal Medicine, University Leipzig, Leipzig, Germany
| | - Holger Kirsten
- Institute for Medical Informatics, Statistics and Epidemiology, Leipzig University, Leipzig, Germany
- LIFE - Leipzig Research Center for Civilization Diseases, Leipzig University, Leipzig, Germany
| | - Anke Tönjes
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University Hospital Leipzig, Leipzig, Germany
| | - Peter Kovacs
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University Hospital Leipzig, Leipzig, Germany
- Deutsches Zentrum für Diabetesforschung, Neuherberg, Germany
| | - Michael Stumvoll
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University Hospital Leipzig, Leipzig, Germany
| | - Markus Loeffler
- Institute for Medical Informatics, Statistics and Epidemiology, Leipzig University, Leipzig, Germany
- LIFE - Leipzig Research Center for Civilization Diseases, Leipzig University, Leipzig, Germany
| | | | - Joachim Thiery
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, Leipzig University, Leipzig, Germany
- LIFE - Leipzig Research Center for Civilization Diseases, Leipzig University, Leipzig, Germany
| | - Berend Isermann
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, Leipzig University, Leipzig, Germany
- LIFE - Leipzig Research Center for Civilization Diseases, Leipzig University, Leipzig, Germany
| | - Uta Ceglarek
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, Leipzig University, Leipzig, Germany
- LIFE - Leipzig Research Center for Civilization Diseases, Leipzig University, Leipzig, Germany
| | - Markus Scholz
- Institute for Medical Informatics, Statistics and Epidemiology, Leipzig University, Leipzig, Germany.
- LIFE - Leipzig Research Center for Civilization Diseases, Leipzig University, Leipzig, Germany.
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Carracedo S, Lirussi L, Alsøe L, Segers F, Wang C, Bartosova Z, Bohov P, Tekin NB, Kong XY, Esbensen QY, Chen L, Wennerström A, Kroustallaki P, Ceolotto D, Tönjes A, Berge RK, Bruheim P, Wong G, Böttcher Y, Halvorsen B, Nilsen H. SMUG1 regulates fat homeostasis leading to a fatty liver phenotype in mice. DNA Repair (Amst) 2022; 120:103410. [DOI: 10.1016/j.dnarep.2022.103410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 08/08/2022] [Accepted: 10/01/2022] [Indexed: 11/25/2022]
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Genome-wide meta-analysis of phytosterols reveals five novel loci and a detrimental effect on coronary atherosclerosis. Nat Commun 2022; 13:143. [PMID: 35013273 PMCID: PMC8748632 DOI: 10.1038/s41467-021-27706-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 11/22/2021] [Indexed: 12/29/2022] Open
Abstract
Phytosterol serum concentrations are under tight genetic control. The relationship between phytosterols and coronary artery disease (CAD) is controversially discussed. We perform a genome-wide meta-analysis of 32 phytosterol traits reflecting resorption, cholesterol synthesis and esterification in six studies with up to 9758 subjects and detect ten independent genome-wide significant SNPs at seven genomic loci. We confirm previously established associations at ABCG5/8 and ABO and demonstrate an extended locus heterogeneity at ABCG5/8 with different functional mechanisms. New loci comprise HMGCR, NPC1L1, PNLIPRP2, SCARB1 and APOE. Based on these results, we perform Mendelian Randomization analyses (MR) revealing a risk-increasing causal relationship of sitosterol serum concentrations and CAD, which is partly mediated by cholesterol. Here we report that phytosterols are polygenic traits. MR add evidence of both, direct and indirect causal effects of sitosterol on CAD.
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Rønningen T, Dahl MB, Valderhaug TG, Cayir A, Keller M, Tönjes A, Blüher M, Böttcher Y. m6A Regulators in Human Adipose Tissue - Depot-Specificity and Correlation With Obesity. Front Endocrinol (Lausanne) 2021; 12:778875. [PMID: 34950106 PMCID: PMC8689137 DOI: 10.3389/fendo.2021.778875] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 11/15/2021] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND N6-methyladenosine (m6A) is one of the most abundant post-transcriptional modifications on mRNA influencing mRNA metabolism. There is emerging evidence for its implication in metabolic disease. No comprehensive analyses on gene expression of m6A regulators in human adipose tissue, especially in paired adipose tissue depots, and its correlation with clinical variables were reported so far. We hypothesized that inter-depot specific gene expression of m6A regulators may differentially correlate with clinical variables related to obesity and fat distribution. METHODS We extracted intra-individually paired gene expression data (omental visceral adipose tissue (OVAT) N=48; subcutaneous adipose tissue (SAT) N=56) of m6A regulators from an existing microarray dataset. We also measured gene expression in another sample set of paired OVAT and SAT (N=46) using RT-qPCR. Finally, we extracted existing gene expression data from peripheral mononuclear blood cells (PBMCs) and single nucleotide polymorphisms (SNPs) in METTL3 and YTHDF3 from genome wide data from the Sorbs population (N=1049). The data were analysed for differential gene expression between OVAT and SAT; and for association with obesity and clinical variables. We further tested for association of SNP markers with gene expression and clinical traits. RESULTS In adipose tissue we observed that several m6A regulators (WTAP, VIRMA, YTHDC1 and ALKBH5) correlate with obesity and clinical variables. Moreover, we found adipose tissue depot specific gene expression for METTL3, WTAP, VIRMA, FTO and YTHDC1. In PBMCs, we identified ALKBH5 and YTHDF3 correlated with obesity. Genetic markers in METTL3 associate with BMI whilst SNPs in YTHDF3 are associated with its gene expression. CONCLUSIONS Our data show that expression of m6A regulators correlates with obesity, is adipose tissue depot-specific and related to clinical traits. Genetic variation in m6A regulators adds an additional layer of variability to the functional consequences.
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Affiliation(s)
- Torunn Rønningen
- Clinical Molecular Biology (EpiGen), Division of Medicine, Akershus Universitetssykehus, Lørenskog, Norway
| | - Mai Britt Dahl
- Department of Clinical Molecular Biology (EpiGen), Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | | | - Akin Cayir
- Clinical Molecular Biology (EpiGen), Division of Medicine, Akershus Universitetssykehus, Lørenskog, Norway
- Vocational Health College, Canakkale Onsekiz Mart University, Canakkale, Turkey
| | - Maria Keller
- Department of Medicine, University of Leipzig, Leipzig, Germany
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Zentrum München at the University of Leipzig and University Hospital, Leipzig, Germany
| | - Anke Tönjes
- Department of Medicine, University of Leipzig, Leipzig, Germany
| | - Matthias Blüher
- Department of Medicine, University of Leipzig, Leipzig, Germany
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Zentrum München at the University of Leipzig and University Hospital, Leipzig, Germany
| | - Yvonne Böttcher
- Clinical Molecular Biology (EpiGen), Division of Medicine, Akershus Universitetssykehus, Lørenskog, Norway
- Department of Clinical Molecular Biology (EpiGen), Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Zentrum München at the University of Leipzig and University Hospital, Leipzig, Germany
- *Correspondence: Yvonne Böttcher,
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Keller M, Gebhardt C, Huth S, Schleinitz D, Heyne H, Scholz M, Stumvoll M, Böttcher Y, Tönjes A, Kovacs P. Genetically programmed changes in transcription of the novel progranulin regulator. J Mol Med (Berl) 2020; 98:1139-1148. [PMID: 32620998 PMCID: PMC7399677 DOI: 10.1007/s00109-020-01942-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 06/18/2020] [Accepted: 06/18/2020] [Indexed: 01/02/2023]
Abstract
Abstract Progranulin is a glycoprotein marking chronic inflammation in obesity and type 2 diabetes. Previous studies suggested PSRC1 (proline and serine rich coiled-coil 1) to be a target of genetic variants associated with serum progranulin levels. We aimed to identify potentially functional variants and characterize their role in regulation of PSRC1. Phylogenetic module complexity analysis (PMCA) prioritized four polymorphisms (rs12740374, rs629301, rs660240, rs7528419) altering transcription factor binding sites with an overall score for potential regulatory function of Sall > 7.0. The effects of these variants on transcriptional activity and binding of transcription factors were tested by luciferase reporter and electrophoretic mobility shift assays (EMSA). In parallel, blood DNA promoter methylation of two regions was tested in subjects with a very high (N = 100) or a very low (N = 100) serum progranulin. Luciferase assays revealed lower activities in vectors carrying the rs629301-A compared with the C allele. Moreover, EMSA indicated a different binding pattern for the two rs629301 alleles, with an additional prominent band for the A allele, which was finally confirmed with the supershift for the Yin Yang 1 transcription factor (YY1). Subjects with high progranulin levels manifested a significantly higher mean DNA methylation (P < 1 × 10−7) in one promoter region, which was in line with a significantly lower PSRC1 mRNA expression levels in blood (P = 1 × 10−3). Consistently, rs629301-A allele was associated with lower PSRC1 mRNA expression (P < 1 × 10−7). Our data suggest that the progranulin-associated variant rs629301 modifies the transcription of PSRC1 through alteration of YY1 binding capacity. DNA methylation studies further support the role of PSRC1 in regulation of progranulin serum levels. Key messages PSRC1 (proline and serine rich coiled-coil 1) SNPs are associated with serum progranulin levels. rs629301 regulates PSRC1 expression by affecting Yin Yang 1 transcription factor (YY1) binding. PSRC1 is also epigenetically regulated in subjects with high progranulin levels.
Electronic supplementary material The online version of this article (10.1007/s00109-020-01942-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Maria Keller
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Center Munich, University Hospital Leipzig, University of Leipzig, 04103, Leipzig, Germany.,Department of Clinical Sciences, Genetic and Molecular Epidemiology Unit, Lund University, Skåne University Hospital Malmö, 20502, Malmö, Sweden.,Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, 04103, Leipzig, Germany
| | - Claudia Gebhardt
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Center Munich, University Hospital Leipzig, University of Leipzig, 04103, Leipzig, Germany
| | - Sandra Huth
- Institute of Biochemistry, Medical Faculty, University of Leipzig, 04103, Leipzig, Germany
| | - Dorit Schleinitz
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, 04103, Leipzig, Germany
| | - Henrike Heyne
- Institute of Human Genetics, University of Leipzig, 04103, Leipzig, Germany
| | - Markus Scholz
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, 04107, Leipzig, Germany
| | - Michael Stumvoll
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Center Munich, University Hospital Leipzig, University of Leipzig, 04103, Leipzig, Germany.,Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, 04103, Leipzig, Germany
| | - Yvonne Böttcher
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Department of Clinical Molecular Biology, Akershus Universitetssykehus, Lørenskog, Norway
| | - Anke Tönjes
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, 04103, Leipzig, Germany.
| | - Peter Kovacs
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, 04103, Leipzig, Germany.
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Bartels MS, Scheffler L, Chakaroun R, Dietrich A, Blüher M, Stumvoll M, Tönjes A, Breitfeld J, Kovacs P. Increased circulating cell-free DNA in insulin resistance. DIABETES & METABOLISM 2020; 46:249-252. [DOI: 10.1016/j.diabet.2018.06.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 06/07/2018] [Accepted: 06/09/2018] [Indexed: 12/12/2022]
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Adipocytokines are not associated with gestational diabetes mellitus but with pregnancy status. Cytokine 2020; 131:155088. [PMID: 32283441 DOI: 10.1016/j.cyto.2020.155088] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 03/12/2020] [Accepted: 04/01/2020] [Indexed: 02/08/2023]
Abstract
AIMS Adipose tissue-secreted proteins, i.e. adipocytokines, have been identified as potential mediators linking fat mass and adipose tissue dysfunction with impaired glucose homeostasis, alterations in the inflammatory status, and risk of diabetes. The aim of this study was to determine whether seven circulating adipocytokines are associated with gestational diabetes mellitus (GDM) or are altered by metabolic and weight changes during pregnancy itself. METHODS A panel of seven adipocytokines (i.e. adiponectin, adipocyte fatty acid-binding protein, chemerin, leptin, Pro-Enkephalin, progranulin, and Pro-Neurotensin) was quantified in serum in a cross-sectional cohort of 222 women with the following three groups matched for age and body mass index: (i) 74 pregnant women with GDM; (ii) 74 pregnant women without GDM; and (iii) 74 non-pregnant and healthy women. A stepwise statistical approach was used by performing pairwise comparisons, principal component analysis (PCA), and partial least square discriminant analysis (PLS-DA). RESULTS Five out of seven adipocytokines were dysregulated between pregnant and non-pregnant women, i.e. adiponectin, chemerin, leptin, Pro-Enkephalin, and progranulin. None of the adipocytokines significantly differed between GDM and non-GDM status during pregnancy. The same five adipocytokines clustered in a principal component representing pregnancy-induced effects. Fasting insulin was the most relevant parameter in the discrimination of GDM as compared to pregnant women without GDM, whereas chemerin and adiponectin were most relevant factors to discriminate pregnancy status. CONCLUSIONS Pregnancy status but not presence of GDM can be distinguished by the seven investigated adipocytokines in discrimination analyses.
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Beuchel C, Becker S, Dittrich J, Kirsten H, Toenjes A, Stumvoll M, Loeffler M, Thiele H, Beutner F, Thiery J, Ceglarek U, Scholz M. Clinical and lifestyle related factors influencing whole blood metabolite levels - A comparative analysis of three large cohorts. Mol Metab 2019; 29:76-85. [PMID: 31668394 PMCID: PMC6734104 DOI: 10.1016/j.molmet.2019.08.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 08/13/2019] [Accepted: 08/13/2019] [Indexed: 12/31/2022] Open
Abstract
Objective Human blood metabolites are influenced by a number of lifestyle and environmental factors. Identification of these factors and the proper quantification of their relevance provides insights into human biological and metabolic disease processes, is key for standardized translation of metabolite biomarkers into clinical applications, and is a prerequisite for comparability of data between studies. However, so far only limited data exist from large and well-phenotyped human cohorts and current methods for analysis do not fully account for the characteristics of these data. The primary aim of this study was to identify, quantify and compare the impact of a comprehensive set of clinical and lifestyle related factors on metabolite levels in three large human cohorts. To achieve this goal, we improve current methodology by developing a principled analysis approach, which could be translated to other cohorts and metabolite panels. Methods 63 Metabolites (amino acids, acylcarnitines) were quantified by liquid chromatography tandem mass spectrometry in three cohorts (total N = 16,222). Supported by a simulation study evaluating various analytical approaches, we developed an analysis pipeline including preprocessing, identification, and quantification of factors affecting metabolite levels. We comprehensively identified uni- and multivariable metabolite associations considering 29 environmental and clinical factors and performed metabolic pathway enrichment and network analyses. Results Inverse normal transformation of batch corrected and outlier removed metabolite levels accompanied by linear regression analysis proved to be the best suited method to deal with the metabolite data. Association analyses revealed numerous uni- and multivariable significant associations. 15 of the analyzed 29 factors explained >1% of variance for at least one of the metabolites. Strongest factors are application of steroid hormones, reticulocytes, waist-to-hip ratio, sex, haematocrit, and age. Effect sizes of factors are comparable across studies. Conclusions We introduced a principled approach for the analysis of MS data allowing identification, and quantification of effects of clinical and lifestyle factors with metabolite levels. We detected a number of known and novel associations broadening our understanding of the regulation of the human metabolome. The large heterogeneity observed between cohorts could almost completely be explained by differences in the distribution of influencing factors emphasizing the necessity of a proper confounder analysis when interpreting metabolite associations. Amino-acids and acylcarnitines analyzed in three studies with >16,000 individuals. Develop a generic and adaptable bioinformatics workflow. Analysis of the impact of 29 clinical and life-style factors on blood metabolites. Analysis of network between factors and metabolites. Comparison of results between studies.
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Affiliation(s)
- Carl Beuchel
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
| | - Susen Becker
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, Leipzig University, Leipzig, Germany; Department of Pediatric Surgery, University of Leipzig, Leipzig, Germany
| | - Julia Dittrich
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, Leipzig University, Leipzig, Germany
| | - Holger Kirsten
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany; LIFE - Leipzig Research Center for Civilization Diseases, Leipzig University, Leipzig, Germany
| | - Anke Toenjes
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University Hospital Leipzig, Leipzig, Germany
| | - Michael Stumvoll
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University Hospital Leipzig, Leipzig, Germany
| | - Markus Loeffler
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany; LIFE - Leipzig Research Center for Civilization Diseases, Leipzig University, Leipzig, Germany
| | | | | | - Joachim Thiery
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, Leipzig University, Leipzig, Germany; LIFE - Leipzig Research Center for Civilization Diseases, Leipzig University, Leipzig, Germany
| | - Uta Ceglarek
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, Leipzig University, Leipzig, Germany; LIFE - Leipzig Research Center for Civilization Diseases, Leipzig University, Leipzig, Germany
| | - Markus Scholz
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany; LIFE - Leipzig Research Center for Civilization Diseases, Leipzig University, Leipzig, Germany; IFB Adiposity Diseases, University Hospital Leipzig, Leipzig, Germany.
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Rohde K, Keller M, la Cour Poulsen L, Rønningen T, Stumvoll M, Tönjes A, Kovacs P, Horstmann A, Villringer A, Blüher M, Böttcher Y. (Epi)genetic regulation of CRTC1 in human eating behaviour and fat distribution. EBioMedicine 2019; 44:476-488. [PMID: 31153815 PMCID: PMC6606956 DOI: 10.1016/j.ebiom.2019.05.050] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 05/14/2019] [Accepted: 05/24/2019] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND In brain, CREB-regulated transcription co-activator 1 (CRTC1) is involved in metabolic dysregulation. In humans a SNP in CRTC1 was associated to body fat percentage and two SNPs affected RNA Pol II binding and chromatin structure, implying epigenetic regulation of CRTC1. We sought to understand the relevance of CRTC1 SNPs, DNA methylation and expression in human eating behaviour and its relationship to clinical variables of obesity in blood and adipose tissue. METHODS 13 CRTC1 SNPs were included to analyze eating behaviour. For rs7256986, follow up association analyses were applied on DNA methylation, CRTC1 expression and clinical parameters. Linear regression was used throughout the study adjusted for age, sex and BMI. Besides data extraction from previous work, rs7256986 was de-novo genotyped and DNA methylation was evaluated by using pyrosequencing. FINDINGS We found several SNPs in the CRTC1 locus nominally associated with human eating behaviour or 2hr postprandial insulin levels and observed a correlation with alcohol and coffee intake (all P < 0.05). G-allele carriers of rs7256986 showed slightly increased hip circumference. We showed that rs7256986 represents a methylation quantitative trait locus (meQTL) in whole blood and adipose tissue. The presence of the SNP and/or DNA methylation correlated with CRTC1 gene expression which in turn, related to BMI and fat distribution. INTERPRETATION Our data support the known role of CRCT1 regulating energy metabolism in brain. Here, we highlight relevance of CRTC1 regulation in blood and adipose tissue. FUND: IFB AdiposityDiseases (BMBF); n609020-Scientia Fellows; Helse-SørØst; DFG: CRC 1052/1 and/2; Kompetenznetz Adipositas, German Diabetes Association.
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Affiliation(s)
- Kerstin Rohde
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Department of Clinical Molecular Biology, Akershus Universitetssykehus, Lørenskog, Norway; IFB Adiposity Diseases, University of Leipzig, Leipzig, Germany.
| | - Maria Keller
- IFB Adiposity Diseases, University of Leipzig, Leipzig, Germany.
| | - Lars la Cour Poulsen
- Department of Clinical Molecular Biology, Akershus Universitetssykehus, Lørenskog, Norway.
| | - Torunn Rønningen
- Department of Clinical Molecular Biology, Akershus Universitetssykehus, Lørenskog, Norway.
| | - Michael Stumvoll
- Department of Medicine, University of Leipzig, Leipzig, Germany.
| | - Anke Tönjes
- Department of Medicine, University of Leipzig, Leipzig, Germany.
| | - Peter Kovacs
- IFB Adiposity Diseases, University of Leipzig, Leipzig, Germany.
| | - Annette Horstmann
- Department for Neurology, Max-Planck-Institute for Human Cognitive and Brain Sciences, Leipzig, Germany.
| | - Arno Villringer
- Department for Neurology, Max-Planck-Institute for Human Cognitive and Brain Sciences, Leipzig, Germany; Clinic of Cognitive Neurology, University of Leipzig, Leipzig, Germany.
| | - Matthias Blüher
- IFB Adiposity Diseases, University of Leipzig, Leipzig, Germany; Department of Medicine, University of Leipzig, Leipzig, Germany.
| | - Yvonne Böttcher
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Department of Clinical Molecular Biology, Akershus Universitetssykehus, Lørenskog, Norway; IFB Adiposity Diseases, University of Leipzig, Leipzig, Germany.
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11
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Breitfeld J, Wiele N, Gutsmann B, Stumvoll M, Blüher M, Scholz M, Kovacs P, Tönjes A. Circulating Adipokine
VASPIN
Is Associated with Serum Lipid Profiles in Humans. Lipids 2019; 54:203-210. [DOI: 10.1002/lipd.12139] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 02/08/2019] [Accepted: 02/09/2019] [Indexed: 01/14/2023]
Affiliation(s)
- Jana Breitfeld
- IFB Adiposity DiseasesUniversity of Leipzig Liebigstrasse 21, 04103, Leipzig Germany
| | - Norman Wiele
- Department of Medicine, Division of Endocrinology and NephrologyUniversity of Leipzig Liebigstrasse 21, 04103, Leipzig Germany
| | - Beate Gutsmann
- Department of Medicine, Division of Endocrinology and NephrologyUniversity of Leipzig Liebigstrasse 21, 04103, Leipzig Germany
| | - Michael Stumvoll
- IFB Adiposity DiseasesUniversity of Leipzig Liebigstrasse 21, 04103, Leipzig Germany
- Department of Medicine, Division of Endocrinology and NephrologyUniversity of Leipzig Liebigstrasse 21, 04103, Leipzig Germany
| | - Matthias Blüher
- IFB Adiposity DiseasesUniversity of Leipzig Liebigstrasse 21, 04103, Leipzig Germany
- Department of Medicine, Division of Endocrinology and NephrologyUniversity of Leipzig Liebigstrasse 21, 04103, Leipzig Germany
| | - Markus Scholz
- Institute for Medical Informatics, Statistics and EpidemiologyUniversity of Leipzig Härtelstrasse 16‐18, 04103, Leipzig Germany
- LIFE Research CenterUniversity of Leipzig Philipp‐Rosenthal‐Straβe 27, 04103, Leipzig Germany
| | - Peter Kovacs
- Department of Medicine, Division of Endocrinology and NephrologyUniversity of Leipzig Liebigstrasse 21, 04103, Leipzig Germany
| | - Anke Tönjes
- Department of Medicine, Division of Endocrinology and NephrologyUniversity of Leipzig Liebigstrasse 21, 04103, Leipzig Germany
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12
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Tönjes A, Scholz M, Krüger J, Krause K, Schleinitz D, Kirsten H, Gebhardt C, Marzi C, Grallert H, Ladenvall C, Heyne H, Laurila E, Kriebel J, Meisinger C, Rathmann W, Gieger C, Groop L, Prokopenko I, Isomaa B, Beutner F, Kratzsch J, Fischer-Rosinsky A, Pfeiffer A, Krohn K, Spranger J, Thiery J, Blüher M, Stumvoll M, Kovacs P. Genome-wide meta-analysis identifies novel determinants of circulating serum progranulin. Hum Mol Genet 2019; 27:546-558. [PMID: 29186428 DOI: 10.1093/hmg/ddx413] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 11/22/2017] [Indexed: 11/14/2022] Open
Abstract
Progranulin is a secreted protein with important functions in processes including immune and inflammatory response, metabolism and embryonic development. The present study aimed at identification of genetic factors determining progranulin concentrations. We conducted a genome-wide association meta-analysis for serum progranulin in three independent cohorts from Europe: Sorbs (N = 848) and KORA (N = 1628) from Germany and PPP-Botnia (N = 335) from Finland (total N = 2811). Single nucleotide polymorphisms (SNPs) associated with progranulin levels were replicated in two additional German cohorts: LIFE-Heart Study (Leipzig; N = 967) and Metabolic Syndrome Berlin Potsdam (Berlin cohort; N = 833). We measured mRNA expression of genes in peripheral blood mononuclear cells (PBMC) by micro-arrays and performed mRNA expression quantitative trait and expression-progranulin association studies to functionally substantiate identified loci. Finally, we conducted siRNA silencing experiments in vitro to validate potential candidate genes within the associated loci. Heritability of circulating progranulin levels was estimated at 31.8% and 26.1% in the Sorbs and LIFE-Heart cohort, respectively. SNPs at three loci reached study-wide significance (rs660240 in CELSR2-PSRC1-MYBPHL-SORT1, rs4747197 in CDH23-PSAP and rs5848 in GRN) explaining 19.4%/15.0% of the variance and 61%/57% of total heritability in the Sorbs/LIFE-Heart Study. The strongest evidence for association was at rs660240 (P = 5.75 × 10-50), which was also associated with mRNA expression of PSRC1 in PBMC (P = 1.51 × 10-21). Psrc1 knockdown in murine preadipocytes led to a consecutive 30% reduction in progranulin secretion. In conclusion, the present meta-GWAS combined with mRNA expression identified three loci associated with progranulin and supports the role of PSRC1 in the regulation of progranulin secretion.
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Affiliation(s)
- Anke Tönjes
- Department of Medicine, University of Leipzig, Leipzig 04103, Germany
| | - Markus Scholz
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig 04107, Germany.,LIFE Research Center, University of Leipzig, Leipzig 04103, Germany
| | - Jacqueline Krüger
- Leipzig University Medical Center, IFB AdiposityDiseases, University of Leipzig, Leipzig 04103, Germany
| | - Kerstin Krause
- Department of Medicine, University of Leipzig, Leipzig 04103, Germany
| | - Dorit Schleinitz
- Department of Medicine, University of Leipzig, Leipzig 04103, Germany
| | - Holger Kirsten
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig 04107, Germany.,LIFE Research Center, University of Leipzig, Leipzig 04103, Germany
| | - Claudia Gebhardt
- Department of Medicine, University of Leipzig, Leipzig 04103, Germany
| | - Carola Marzi
- Research Unit of Molecular Epidemiology, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg 85764, Germany.,German Research Center for Environmental Health, Institute of Epidemiology II, Helmholtz Center Munich, Neuherberg 85764, Germany.,German Center for Diabetes Research (DZD e.V.), Neuherberg 85764, Germany
| | - Harald Grallert
- Research Unit of Molecular Epidemiology, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg 85764, Germany.,German Research Center for Environmental Health, Institute of Epidemiology II, Helmholtz Center Munich, Neuherberg 85764, Germany.,German Center for Diabetes Research (DZD e.V.), Neuherberg 85764, Germany
| | - Claes Ladenvall
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University and Lund University Diabetes Centre, CRC at Skåne University Hospital, Malmö 20502, Sweden
| | - Henrike Heyne
- Institute of Human Genetics, University of Leipzig, Leipzig 04103, Germany
| | - Esa Laurila
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University and Lund University Diabetes Centre, CRC at Skåne University Hospital, Malmö 20502, Sweden
| | - Jennifer Kriebel
- Research Unit of Molecular Epidemiology, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg 85764, Germany.,German Research Center for Environmental Health, Institute of Epidemiology II, Helmholtz Center Munich, Neuherberg 85764, Germany.,German Center for Diabetes Research (DZD e.V.), Neuherberg 85764, Germany
| | - Christa Meisinger
- German Research Center for Environmental Health, Institute of Epidemiology II, Helmholtz Center Munich, Neuherberg 85764, Germany.,German Center for Diabetes Research (DZD e.V.), Neuherberg 85764, Germany
| | - Wolfgang Rathmann
- German Diabetes Center, Institute of Biometrics and Epidemiology, Leibniz Center for Diabetes Research at Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany
| | - Christian Gieger
- Research Unit of Molecular Epidemiology, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg 85764, Germany.,German Research Center for Environmental Health, Institute of Epidemiology II, Helmholtz Center Munich, Neuherberg 85764, Germany
| | - Leif Groop
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University and Lund University Diabetes Centre, CRC at Skåne University Hospital, Malmö 20502, Sweden
| | - Inga Prokopenko
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK.,Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford OX3 7LE, UK.,Department of Genomics of Common Diseases, Imperial College London, London SW7 2AZ, UK
| | - Bo Isomaa
- Department of Social Services and Healthcare, Jakobstad 68601, Finland.,Folkhälsan Research Centre, Helsinki 00290, Finland
| | - Frank Beutner
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig 04103, Germany
| | - Jürgen Kratzsch
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig 04103, Germany
| | - Antje Fischer-Rosinsky
- Department of Endocrinology, Diabetes and Nutrition, Charité-Universitätsmedizin, Berlin 10117, Germany
| | - Andreas Pfeiffer
- Department of Endocrinology, Diabetes and Nutrition, Charité-Universitätsmedizin, Berlin 10117, Germany.,Department of Clinical Nutrition, German Institute of Human Nutrition, Nuthetal 14558, Germany
| | - Knut Krohn
- Interdisciplinary Centre for Clinical Research, University of Leipzig, Leipzig 04103, Germany
| | - Joachim Spranger
- Department of Endocrinology, Diabetes and Nutrition, Charité-Universitätsmedizin, Berlin 10117, Germany
| | - Joachim Thiery
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig 04103, Germany
| | - Matthias Blüher
- Department of Medicine, University of Leipzig, Leipzig 04103, Germany.,Leipzig University Medical Center, IFB AdiposityDiseases, University of Leipzig, Leipzig 04103, Germany
| | - Michael Stumvoll
- Department of Medicine, University of Leipzig, Leipzig 04103, Germany.,Leipzig University Medical Center, IFB AdiposityDiseases, University of Leipzig, Leipzig 04103, Germany
| | - Peter Kovacs
- Leipzig University Medical Center, IFB AdiposityDiseases, University of Leipzig, Leipzig 04103, Germany
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13
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Tönjes A, Kralisch S, Hoffmann A, Schleinitz D, Kratzsch J, Blüher M, Stumvoll M, Kovacs P, Fasshauer M, Ebert T. Circulating Pro-Neurotensin in gestational diabetes mellitus. Nutr Metab Cardiovasc Dis 2019; 29:23-29. [PMID: 30527352 DOI: 10.1016/j.numecd.2018.09.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 09/21/2018] [Accepted: 09/24/2018] [Indexed: 11/24/2022]
Abstract
BACKGROUND AND AIMS Pro-Neurotensin (NT), a stable surrogate parameter of NT, has recently been introduced as a peptide predicting the development of obesity, diabetes mellitus, cardiovascular diseases, and cardiovascular mortality. However, regulation of Pro-NT in gestational diabetes mellitus (GDM) remains uninvestigated. METHODS AND RESULTS Pro-NT was quantified in 74 women with GDM, 74 healthy, gestational age-matched, pregnant controls, as well as in a second cohort comprising of 74 healthy, non-pregnant control women, using a chemiluminometric sandwich immunoassay. Pro-NT was correlated to measures of obesity, hypertension, glucose and lipid metabolism, renal function, and inflammation. Mean ± standard deviation of circulating Pro-NT levels were not significantly different in women with GDM (100.2 ± 75.7 pmol/l) as compared to healthy, pregnant controls (103.2 ± 37.4 pmol/l) and healthy, non-pregnant female controls (105.9 ± 38.9 pmol/l) (p = 0.661). Homeostasis model assessment of insulin resistance (HOMA-IR) and creatinine positively correlated with serum Pro-NT in multivariate regression analysis. In contrast, free fatty acids (FFA) were inversely correlated with circulating Pro-NT. Results sustained adjustment for pregnancy status. CONCLUSIONS Circulating Pro-NT is not independently associated with GDM, but is with HOMA-IR, creatinine, and FFA even after adjustment for pregnancy status.
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Affiliation(s)
- A Tönjes
- University of Leipzig, Department of Endocrinology and Nephrology, 04103, Leipzig, Germany
| | - S Kralisch
- University of Leipzig, Department of Endocrinology and Nephrology, 04103, Leipzig, Germany; Leipzig University Medical Center, IFB AdiposityDiseases, 04103, Leipzig, Germany
| | - A Hoffmann
- University of Leipzig, Department of Endocrinology and Nephrology, 04103, Leipzig, Germany
| | - D Schleinitz
- Leipzig University Medical Center, IFB AdiposityDiseases, 04103, Leipzig, Germany
| | - J Kratzsch
- University of Leipzig, Institute of Laboratory Medicine, 04103, Leipzig, Germany
| | - M Blüher
- University of Leipzig, Department of Endocrinology and Nephrology, 04103, Leipzig, Germany
| | - M Stumvoll
- University of Leipzig, Department of Endocrinology and Nephrology, 04103, Leipzig, Germany
| | - P Kovacs
- Leipzig University Medical Center, IFB AdiposityDiseases, 04103, Leipzig, Germany
| | - M Fasshauer
- University of Leipzig, Department of Endocrinology and Nephrology, 04103, Leipzig, Germany; Leipzig University Medical Center, IFB AdiposityDiseases, 04103, Leipzig, Germany; Justus-Liebig-University, Institute of Nutritional Science, 35390, Giessen, Germany
| | - T Ebert
- University of Leipzig, Department of Endocrinology and Nephrology, 04103, Leipzig, Germany; Leipzig University Medical Center, IFB AdiposityDiseases, 04103, Leipzig, Germany.
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14
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Karafet TM, Osipova LP, Savina OV, Hallmark B, Hammer MF. Siberian genetic diversity reveals complex origins of the Samoyedic-speaking populations. Am J Hum Biol 2018; 30:e23194. [PMID: 30408262 DOI: 10.1002/ajhb.23194] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2018] [Revised: 08/26/2018] [Accepted: 09/23/2018] [Indexed: 12/21/2022] Open
Abstract
OBJECTIVES We examined autosomal genome-wide SNPs and Y-chromosome data from 15 Siberian and 12 reference populations to study the affinities of Siberian populations, and to address hypotheses about the origin of the Samoyed peoples. METHODS Samples were genotyped for 567 096 autosomal SNPs and 147 Y-chromosome polymorphic sites. For several analyses, we used 281 093 SNPs from the intersection of our data with publicly available ancient Siberian samples. To examine genetic relatedness among populations, we applied PCA, FST , TreeMix, and ADMIXTURE analyses. To explore the potential effect of demography and evolutionary processes, the distribution of ROH and IBD sharing within population were studied. RESULTS Analyses of autosomal and Y-chromosome data reveal high differentiation of the Siberian groups. The Siberian populations have a large proportion of their genome in ROH and IBD segments. Several populations (ie, Nganasans, Evenks, Yukagirs, and Koryaks) do not appear to have experienced admixture with other Siberian populations (ie, producing only positive f3), while for the other tested populations the composition of mixing sources always included Nganasans or Evenks. The Nganasans from the Taymyr Peninsula demonstrate the greatest level of shared shorter ROH and IBD with nearly all other Siberian populations. CONCLUSIONS Autosomal SNP and Y-chromosome data demonstrate that Samoyedic populations differ significantly in their genetic composition. Genetic relationship is observed only between Forest and Tundra Nentsi. Selkups are affiliated with the Kets from the Yenisey River, while the Nganasans are separated from their linguistic neighbors, showing closer affinities with the Evenks and Yukagirs.
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Affiliation(s)
- Tatiana M Karafet
- ARL Division of Biotechnology, University of Arizona, Tucson, Arizona
| | - Ludmila P Osipova
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia
| | - Olga V Savina
- ARL Division of Biotechnology, University of Arizona, Tucson, Arizona
| | - Brian Hallmark
- Interdisciplinary Program in Statistics, University of Arizona, Tucson, Arizona
| | - Michael F Hammer
- ARL Division of Biotechnology, University of Arizona, Tucson, Arizona.,Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona
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15
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Krüger J, Berger C, Weidle K, Schleinitz D, Tönjes A, Stumvoll M, Blüher M, Kovacs P, Klöting N. Metabolic effects of genetic variation in the human REPIN1 gene. Int J Obes (Lond) 2018; 43:821-831. [PMID: 29915365 DOI: 10.1038/s41366-018-0123-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 04/06/2018] [Accepted: 04/17/2018] [Indexed: 12/11/2022]
Abstract
BACKGROUND Replication initiator 1 (Repin1) is a zinc finger protein highly expressed in liver and adipose tissue. The Repin1 resides within a quantitative trait locus (QTL) for body weight and triglyceride levels in the rat, and its hepatic deletion in mice results in improved insulin sensitivity and lower body weight. Here, we analyzed whether genetic variation within the Repin1 affects parameters of glucose and lipid metabolism. METHODS We sequenced REPIN1 in 48 non-related Caucasian subjects. We discovered a 12 base pair deletion (12 bp del; rs3832490), which was subsequently genotyped in two well-characterized cohorts (N = 3013) to test for associations with metabolic traits. Functional consequences of the variant were investigated in HepG2 cells in vitro. RESULTS In human cohorts, we show that the 12 bp del associates with improved glucose metabolism (lower fasting plasma glucose, fasting plasma insulin, and HOMA IR). Cells transfected with the plasmid carrying the 12 bp del variant are characterized by increased GLUT2 and fatty acid translocase CD36 expression and more lipid droplets. CONCLUSION Our data suggest that genetic variation in human REPIN1 plays a role in glucose and lipid metabolism by differentially affecting the expression of REPIN1 target genes including glucose and fatty acid transporters.
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Affiliation(s)
- Jacqueline Krüger
- Leipzig University Medical Center, IFB Adiposity Diseases, University of Leipzig, 04103, Leipzig, Germany
| | - Claudia Berger
- Leipzig University Medical Center, IFB Adiposity Diseases, University of Leipzig, 04103, Leipzig, Germany.,German Diabetes Center Leipzig, University of Leipzig, 04103, Leipzig, Germany
| | - Kerstin Weidle
- Leipzig University Medical Center, IFB Adiposity Diseases, University of Leipzig, 04103, Leipzig, Germany
| | - Dorit Schleinitz
- Leipzig University Medical Center, IFB Adiposity Diseases, University of Leipzig, 04103, Leipzig, Germany
| | - Anke Tönjes
- Department of Medicine, University of Leipzig, 04103, Leipzig, Germany
| | - Michael Stumvoll
- Department of Medicine, University of Leipzig, 04103, Leipzig, Germany
| | - Matthias Blüher
- Department of Medicine, University of Leipzig, 04103, Leipzig, Germany
| | - Peter Kovacs
- Leipzig University Medical Center, IFB Adiposity Diseases, University of Leipzig, 04103, Leipzig, Germany.
| | - Nora Klöting
- Leipzig University Medical Center, IFB Adiposity Diseases, University of Leipzig, 04103, Leipzig, Germany.
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16
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Scheffler L, Crane A, Heyne H, Tönjes A, Schleinitz D, Ihling CH, Stumvoll M, Freire R, Fiorentino M, Fasano A, Kovacs P, Heiker JT. Widely Used Commercial ELISA Does Not Detect Precursor of Haptoglobin2, but Recognizes Properdin as a Potential Second Member of the Zonulin Family. Front Endocrinol (Lausanne) 2018; 9:22. [PMID: 29459849 PMCID: PMC5807381 DOI: 10.3389/fendo.2018.00022] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 01/18/2018] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND There is increasing evidence for the role of impaired intestinal permeability in obesity and associated metabolic diseases. Zonulin is an established serum marker for intestinal permeability and identical to pre-haptoglobin2. Here, we aimed to investigate the relationship between circulating zonulin and metabolic traits related to obesity. METHODS Serum zonulin was measured by using a widely used commercial ELISA kit in 376 subjects from the metabolically well-characterized cohort of Sorbs from Germany. In addition, haptoglobin genotype was determined in DNA samples from all study subjects. RESULTS As zonulin concentrations did not correlate to the haptoglobin genotypes, we investigated the specificity of the zonulin ELISA assay using antibody capture experiments, mass spectrometry, and Western blot analysis. Using serum samples that gave the highest or lowest ELISA signals, we detected several proteins that are likely to be captured by the antibody in the present kit. However, none of these proteins corresponds to pre-haptoglobin2. We used increasing concentrations of recombinant pre-haptoglobin2 and complement C3 as one of the representative captured proteins and the ELISA kit did not detect either. Western blot analysis using both the polyclonal antibodies used in this kit and monoclonal antibodies rose against zonulin showed a similar protein recognition pattern but with different intensity of detection. The protein(s) measured using the ELISA kit was (were) significantly increased in patients with diabetes and obesity and correlated strongly with markers of the lipid and glucose metabolism. Combining mass spectrometry and Western blot analysis using the polyclonal antibodies used in the ELISA kit, we identified properdin as another member of the zonulin family. CONCLUSION Our study suggests that the zonulin ELISA does not recognize pre-haptoglobin2, rather structural (and possibly functional) analog proteins belonging to the mannose-associated serine protease family, with properdin being the most likely possible candidate.
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Affiliation(s)
- Lucas Scheffler
- Leipzig University Medical Center, IFB Adiposity Diseases, Leipzig, Germany
| | - Alyce Crane
- Leipzig University Medical Center, IFB Adiposity Diseases, Leipzig, Germany
| | - Henrike Heyne
- Leipzig University Medical Center, IFB Adiposity Diseases, Leipzig, Germany
| | - Anke Tönjes
- Divisions of Endocrinology and Nephrology, University of Leipzig, Leipzig, Germany
| | - Dorit Schleinitz
- Leipzig University Medical Center, IFB Adiposity Diseases, Leipzig, Germany
| | - Christian H. Ihling
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin-Luther-University Halle-Wittenberg, Halle, Germany
| | - Michael Stumvoll
- Divisions of Endocrinology and Nephrology, University of Leipzig, Leipzig, Germany
| | - Rachel Freire
- Mucosal Immunology And Biology Research Center, Massachusetts General Hospital––Harvard Medical School, Boston, MA, United States
| | - Maria Fiorentino
- Mucosal Immunology And Biology Research Center, Massachusetts General Hospital––Harvard Medical School, Boston, MA, United States
| | - Alessio Fasano
- Mucosal Immunology And Biology Research Center, Massachusetts General Hospital––Harvard Medical School, Boston, MA, United States
| | - Peter Kovacs
- Leipzig University Medical Center, IFB Adiposity Diseases, Leipzig, Germany
- *Correspondence: John T. Heiker, ; Peter Kovacs,
| | - John T. Heiker
- Faculty of Biosciences, Pharmacy and Psychology, Institute of Biochemistry, University of Leipzig, Leipzig, Germany
- *Correspondence: John T. Heiker, ; Peter Kovacs,
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17
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Gross A, Tönjes A, Scholz M. On the impact of relatedness on SNP association analysis. BMC Genet 2017; 18:104. [PMID: 29212447 PMCID: PMC5719591 DOI: 10.1186/s12863-017-0571-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 11/23/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND When testing for SNP (single nucleotide polymorphism) associations in related individuals, observations are not independent. Simple linear regression assuming independent normally distributed residuals results in an increased type I error and the power of the test is also affected in a more complicate manner. Inflation of type I error is often successfully corrected by genomic control. However, this reduces the power of the test when relatedness is of concern. In the present paper, we derive explicit formulae to investigate how heritability and strength of relatedness contribute to variance inflation of the effect estimate of the linear model. Further, we study the consequences of variance inflation on hypothesis testing and compare the results with those of genomic control correction. We apply the developed theory to the publicly available HapMap trio data (N=129), the Sorbs (a self-contained population with N=977 characterised by a cryptic relatedness structure) and synthetic family studies with different sample sizes (ranging from N=129 to N=999) and different degrees of relatedness. RESULTS We derive explicit and easily to apply approximation formulae to estimate the impact of relatedness on the variance of the effect estimate of the linear regression model. Variance inflation increases with increasing heritability. Relatedness structure also impacts the degree of variance inflation as shown for example family structures. Variance inflation is smallest for HapMap trios, followed by a synthetic family study corresponding to the trio data but with larger sample size than HapMap. Next strongest inflation is observed for the Sorbs, and finally, for a synthetic family study with a more extreme relatedness structure but with similar sample size as the Sorbs. Type I error increases rapidly with increasing inflation. However, for smaller significance levels, power increases with increasing inflation while the opposite holds for larger significance levels. When genomic control is applied, type I error is preserved while power decreases rapidly with increasing variance inflation. CONCLUSIONS Stronger relatedness as well as higher heritability result in increased variance of the effect estimate of simple linear regression analysis. While type I error rates are generally inflated, the behaviour of power is more complex since power can be increased or reduced in dependence on relatedness and the heritability of the phenotype. Genomic control cannot be recommended to deal with inflation due to relatedness. Although it preserves type I error, the loss in power can be considerable. We provide a simple formula for estimating variance inflation given the relatedness structure and the heritability of a trait of interest. As a rule of thumb, variance inflation below 1.05 does not require correction and simple linear regression analysis is still appropriate.
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Affiliation(s)
- Arnd Gross
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Haertelstrasse 16-18, Leipzig, 04107, Germany. .,LIFE - Leipzig Research Center for Civilization Diseases, University of Leipzig, Philipp-Rosenthal-Strasse 27, Leipzig, 04103, Germany.
| | - Anke Tönjes
- Department of Medicine, University of Leipzig, Liebigstrasse 18, Leipzig, 04103, Germany
| | - Markus Scholz
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Haertelstrasse 16-18, Leipzig, 04107, Germany.,LIFE - Leipzig Research Center for Civilization Diseases, University of Leipzig, Philipp-Rosenthal-Strasse 27, Leipzig, 04103, Germany
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18
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Das R, Wexler P, Pirooznia M, Elhaik E. The Origins of Ashkenaz, Ashkenazic Jews, and Yiddish. Front Genet 2017; 8:87. [PMID: 28680441 PMCID: PMC5478715 DOI: 10.3389/fgene.2017.00087] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2016] [Accepted: 06/07/2017] [Indexed: 12/11/2022] Open
Abstract
Recently, the geographical origins of Ashkenazic Jews (AJs) and their native language Yiddish were investigated by applying the Geographic Population Structure (GPS) to a cohort of exclusively Yiddish-speaking and multilingual AJs. GPS localized most AJs along major ancient trade routes in northeastern Turkey adjacent to primeval villages with names that resemble the word "Ashkenaz." These findings were compatible with the hypothesis of an Irano-Turko-Slavic origin for AJs and a Slavic origin for Yiddish and at odds with the Rhineland hypothesis advocating a Levantine origin for AJs and German origins for Yiddish. We discuss how these findings advance three ongoing debates concerning (1) the historical meaning of the term "Ashkenaz;" (2) the genetic structure of AJs and their geographical origins as inferred from multiple studies employing both modern and ancient DNA and original ancient DNA analyses; and (3) the development of Yiddish. We provide additional validation to the non-Levantine origin of AJs using ancient DNA from the Near East and the Levant. Due to the rising popularity of geo-localization tools to address questions of origin, we briefly discuss the advantages and limitations of popular tools with focus on the GPS approach. Our results reinforce the non-Levantine origins of AJs.
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Affiliation(s)
- Ranajit Das
- Manipal Centre for Natural Sciences, Manipal UniversityManipal, India
| | - Paul Wexler
- Department of Linguistics, Tel Aviv UniversityTel-Aviv, Israel
| | - Mehdi Pirooznia
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins UniversityBaltimore, MD, United States
| | - Eran Elhaik
- Department of Animal and Plant Sciences, University of SheffieldSheffield, United Kingdom
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Ehler E, Vanek D. Forensic genetic analyses in isolated populations with examples of central European Valachs and Roma. J Forensic Leg Med 2017; 48:46-52. [PMID: 28454050 DOI: 10.1016/j.jflm.2017.04.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 03/22/2017] [Accepted: 04/09/2017] [Indexed: 01/27/2023]
Abstract
Isolated populations present a constant threat to the correctness of forensic genetic casework. In this review article we present several examples of how analyzing samples from isolated populations can bias the results of the forensic statistics and analyses. We select our examples from isolated populations from central and southeastern Europe, namely the Valachs and the European Roma. We also provide the reader with general strategies and principles to improve the laboratory practice (best practice) and reporting of samples from supposedly isolated populations. These include reporting the precise population data used for computing the forensic statistics, using the appropriate θ correction factor for calculating allele frequencies, typing ancestry informative markers in samples of unknown or uncertain ethnicity and establishing ethnic-specific forensic databases.
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Affiliation(s)
- Edvard Ehler
- Department of Biology and Environmental Studies, Charles University in Prague, Faculty of Education, Magdaleny Rettigove 4, Prague, 116 39, Czech Republic; Institute of Anthropology, Faculty of Biology, Adam Mickiewicz University, ul. Umultowska 89, 61-614, Poznan, Poland.
| | - Daniel Vanek
- Forensic DNA Service, Janovskeho 18, Prague 7, 170 00, Czech Republic; Charles University in Prague, 2nd Faculty of Medicine, V Uvalu 84, Prague, 150 06, Czech Republic; Nemocnice Na Bulovce, Institute of Legal Medicine, Budinova 2, Prague, 180 81, Czech Republic.
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Overcoming the dichotomy between open and isolated populations using genomic data from a large European dataset. Sci Rep 2017; 7:41614. [PMID: 28145502 PMCID: PMC5286425 DOI: 10.1038/srep41614] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 12/22/2016] [Indexed: 01/01/2023] Open
Abstract
Human populations are often dichotomized into “isolated” and “open” categories using cultural and/or geographical barriers to gene flow as differential criteria. Although widespread, the use of these alternative categories could obscure further heterogeneity due to inter-population differences in effective size, growth rate, and timing or amount of gene flow. We compared intra and inter-population variation measures combining novel and literature data relative to 87,818 autosomal SNPs in 14 open populations and 10 geographic and/or linguistic European isolates. Patterns of intra-population diversity were found to vary considerably more among isolates, probably due to differential levels of drift and inbreeding. The relatively large effective size estimated for some population isolates challenges the generalized view that they originate from small founding groups. Principal component scores based on measures of intra-population variation of isolated and open populations were found to be distributed along a continuum, with an area of intersection between the two groups. Patterns of inter-population diversity were even closer, as we were able to detect some differences between population groups only for a few multidimensional scaling dimensions. Therefore, different lines of evidence suggest that dichotomizing human populations into open and isolated groups fails to capture the actual relations among their genomic features.
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The Slavic NBN Founder Mutation: A Role for Reproductive Fitness? PLoS One 2016; 11:e0167984. [PMID: 27936167 PMCID: PMC5148078 DOI: 10.1371/journal.pone.0167984] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 11/23/2016] [Indexed: 01/21/2023] Open
Abstract
The vast majority of patients with Nijmegen Breakage Syndrome (NBS) are of Slavic origin and carry a deleterious deletion (c.657del5; rs587776650) in the NBN gene on chromosome 8q21. This mutation is essentially confined to Slavic populations and may thus be considered a Slavic founder mutation. Notably, not a single parenthood of a homozygous c.657del5 carrier has been reported to date, while heterozygous carriers do reproduce but have an increased cancer risk. These observations seem to conflict with the considerable carrier frequency of c.657del5 of 0.5% to 1% as observed in different Slavic populations because deleterious mutations would be eliminated quite rapidly by purifying selection. Therefore, we propose that heterozygous c.657del5 carriers have increased reproductive success, i.e., that the mutation confers heterozygote advantage. In fact, in our cohort study of the reproductive history of 24 NBS pedigrees from the Czech Republic, we observed that female carriers gave birth to more children on average than female non-carriers, while no such reproductive differences were observed for males. We also estimate that c.657del5 likely occurred less than 300 generations ago, thus supporting the view that the original mutation predated the historic split and subsequent spread of the ‘Slavic people’. We surmise that the higher fertility of female c.657del5 carriers reflects a lower miscarriage rate in these women, thereby reflecting the role of the NBN gene product, nibrin, in the repair of DNA double strand breaks and their processing in immune gene rearrangements, telomere maintenance, and meiotic recombination, akin to the previously described role of the DNA repair genes BRCA1 and BRCA2.
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Anagnostou P, Capocasa M, Dominici V, Montinaro F, Coia V, Destro-Bisol G. Evaluating mtDNA patterns of genetic isolation using a re-sampling procedure: A case study on Italian populations. Ann Hum Biol 2016; 44:140-148. [PMID: 27109644 DOI: 10.1080/03014460.2016.1181784] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
BACKGROUND A number of studies which have investigated isolation patterns in human populations rely on the analysis of intra- and inter-population genetic statistics of mtDNA polymorphisms. However, this approach makes it difficult to differentiate between the effects of long-term genetic isolation and the random fluctuations of statistics due to reduced sample size. AIM To overcome the confounding effect of sample size when detecting signatures of genetic isolation. SUBJECTS AND METHODS A re-sampling based procedure was employed to evaluate reduction in intra-population diversity, departure from surrounding genetic background and demographic stationarity in 34 Italian populations subject to isolation factors. RESULTS Signatures of genetic isolation were detected for all three statistics in seven populations: Pusteria valley, Sappada, Sauris, Timau settled in the eastern Italian Alps and Cappadocia, Filettino and Vallepietra settled in the Appenines. However, this study was unable to find signals for any of the statistics analysed in 19 populations. Finally, eight populations showing signals of isolation were found for one or two statistics. CONCLUSION The analysis revealed that the use of population genetic statistics combined with re-sampling procedure can help detect signatures of genetic isolation in human populations, even using a single, although highly informative, locus like mtDNA.
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Affiliation(s)
- Paolo Anagnostou
- a Dipartimento di Biologia Ambientale , Sapienza University of Rome , Rome , Italy.,b Istituto Italiano di Antropologia , Rome , Italy
| | - Marco Capocasa
- b Istituto Italiano di Antropologia , Rome , Italy.,c Dipartimento di Biologia e Biotecnologie 'Charles Darwin' , Sapienza University of Rome , Rome , Italy
| | - Valentina Dominici
- a Dipartimento di Biologia Ambientale , Sapienza University of Rome , Rome , Italy
| | | | - Valentina Coia
- e Istituto per le Mummie e l'Iceman, Accademia Europea di Bolzano (EURAC-Research) , Bolzano , Italy
| | - Giovanni Destro-Bisol
- a Dipartimento di Biologia Ambientale , Sapienza University of Rome , Rome , Italy.,b Istituto Italiano di Antropologia , Rome , Italy
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Coevolution of genes and languages and high levels of population structure among the highland populations of Daghestan. J Hum Genet 2015; 61:181-91. [PMID: 26607180 DOI: 10.1038/jhg.2015.132] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Revised: 08/11/2015] [Accepted: 10/08/2015] [Indexed: 01/29/2023]
Abstract
As a result of the combination of great linguistic and cultural diversity, the highland populations of Daghestan present an excellent opportunity to test the hypothesis of language-gene coevolution at a fine geographic scale. However, previous genetic studies generally have been restricted to uniparental markers and have not included many of the key populations of the region. To improve our understanding of the genetic structure of Daghestani populations and to investigate possible correlations between genetic and linguistic variation, we analyzed ~550,000 autosomal single nucleotide polymorphisms, phylogenetically informative Y chromosome markers and mtDNA haplotypes in 21 ethnic Daghestani groups. We found high levels of population structure in Daghestan consistent with the hypothesis of long-term isolation among populations of the highland Caucasus. Highland Daghestani populations exhibit extremely high levels of between-population diversity for all genetic systems tested, leading to some of the highest FST values observed for any region of the world. In addition, we find a significant positive correlation between gene and language diversity, suggesting that these two aspects of human diversity have coevolved as a result of historical patterns of social interaction among highland farmers at the community level. Finally, our data are consistent with the hypothesis that most Daghestanian-speaking groups descend from a common ancestral population (~6000-6500 years ago) that spread to the Caucasus by demic diffusion followed by population fragmentation and low levels of gene flow.
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Burkhardt R, Kirsten H, Beutner F, Holdt LM, Gross A, Teren A, Tönjes A, Becker S, Krohn K, Kovacs P, Stumvoll M, Teupser D, Thiery J, Ceglarek U, Scholz M. Integration of Genome-Wide SNP Data and Gene-Expression Profiles Reveals Six Novel Loci and Regulatory Mechanisms for Amino Acids and Acylcarnitines in Whole Blood. PLoS Genet 2015; 11:e1005510. [PMID: 26401656 PMCID: PMC4581711 DOI: 10.1371/journal.pgen.1005510] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 08/17/2015] [Indexed: 01/23/2023] Open
Abstract
Profiling amino acids and acylcarnitines in whole blood spots is a powerful tool in the laboratory diagnosis of several inborn errors of metabolism. Emerging data suggests that altered blood levels of amino acids and acylcarnitines are also associated with common metabolic diseases in adults. Thus, the identification of common genetic determinants for blood metabolites might shed light on pathways contributing to human physiology and common diseases. We applied a targeted mass-spectrometry-based method to analyze whole blood concentrations of 96 amino acids, acylcarnitines and pathway associated metabolite ratios in a Central European cohort of 2,107 adults and performed genome-wide association (GWA) to identify genetic modifiers of metabolite concentrations. We discovered and replicated six novel loci associated with blood levels of total acylcarnitine, arginine (both on chromosome 6; rs12210538, rs17657775), propionylcarnitine (chromosome 10; rs12779637), 2-hydroxyisovalerylcarnitine (chromosome 21; rs1571700), stearoylcarnitine (chromosome 1; rs3811444), and aspartic acid traits (chromosome 8; rs750472). Based on an integrative analysis of expression quantitative trait loci in blood mononuclear cells and correlations between gene expressions and metabolite levels, we provide evidence for putative causative genes: SLC22A16 for total acylcarnitines, ARG1 for arginine, HLCS for 2-hydroxyisovalerylcarnitine, JAM3 for stearoylcarnitine via a trans-effect at chromosome 1, and PPP1R16A for aspartic acid traits. Further, we report replication and provide additional functional evidence for ten loci that have previously been published for metabolites measured in plasma, serum or urine. In conclusion, our integrative analysis of SNP, gene-expression and metabolite data points to novel genetic factors that may be involved in the regulation of human metabolism. At several loci, we provide evidence for metabolite regulation via gene-expression and observed overlaps with GWAS loci for common diseases. These results form a strong rationale for subsequent functional and disease-related studies.
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Affiliation(s)
- Ralph Burkhardt
- LIFE Leipzig Research Center for Civilization Diseases, University of Leipzig, Leipzig Germany
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig, Germany
| | - Holger Kirsten
- LIFE Leipzig Research Center for Civilization Diseases, University of Leipzig, Leipzig Germany
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
- Department for Cell Therapy, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Frank Beutner
- LIFE Leipzig Research Center for Civilization Diseases, University of Leipzig, Leipzig Germany
- Heart Center Leipzig, Leipzig, Germany
| | - Lesca M. Holdt
- LIFE Leipzig Research Center for Civilization Diseases, University of Leipzig, Leipzig Germany
- Institute for Laboratory Medicine, Ludwig-Maximilians University Munich, Munich, Germany
| | - Arnd Gross
- LIFE Leipzig Research Center for Civilization Diseases, University of Leipzig, Leipzig Germany
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
| | - Andrej Teren
- LIFE Leipzig Research Center for Civilization Diseases, University of Leipzig, Leipzig Germany
- Heart Center Leipzig, Leipzig, Germany
| | - Anke Tönjes
- Medical Department, Clinic for Endocrinology and Nephrology, University of Leipzig, Leipzig, Germany
| | - Susen Becker
- LIFE Leipzig Research Center for Civilization Diseases, University of Leipzig, Leipzig Germany
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig, Germany
| | - Knut Krohn
- LIFE Leipzig Research Center for Civilization Diseases, University of Leipzig, Leipzig Germany
- Interdisciplinary Centre for Clinical Research, University of Leipzig, Leipzig, Germany
| | - Peter Kovacs
- Integrated Research and Treatment Center Adiposity Diseases, University of Leipzig, Leipzig Germany
| | - Michael Stumvoll
- Medical Department, Clinic for Endocrinology and Nephrology, University of Leipzig, Leipzig, Germany
- Integrated Research and Treatment Center Adiposity Diseases, University of Leipzig, Leipzig Germany
| | - Daniel Teupser
- LIFE Leipzig Research Center for Civilization Diseases, University of Leipzig, Leipzig Germany
- Institute for Laboratory Medicine, Ludwig-Maximilians University Munich, Munich, Germany
| | - Joachim Thiery
- LIFE Leipzig Research Center for Civilization Diseases, University of Leipzig, Leipzig Germany
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig, Germany
| | - Uta Ceglarek
- LIFE Leipzig Research Center for Civilization Diseases, University of Leipzig, Leipzig Germany
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig, Germany
| | - Markus Scholz
- LIFE Leipzig Research Center for Civilization Diseases, University of Leipzig, Leipzig Germany
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
- * E-mail:
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Genetic Heritage of the Balto-Slavic Speaking Populations: A Synthesis of Autosomal, Mitochondrial and Y-Chromosomal Data. PLoS One 2015; 10:e0135820. [PMID: 26332464 PMCID: PMC4558026 DOI: 10.1371/journal.pone.0135820] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 07/27/2015] [Indexed: 11/20/2022] Open
Abstract
The Slavic branch of the Balto-Slavic sub-family of Indo-European languages underwent rapid divergence as a result of the spatial expansion of its speakers from Central-East Europe, in early medieval times. This expansion–mainly to East Europe and the northern Balkans–resulted in the incorporation of genetic components from numerous autochthonous populations into the Slavic gene pools. Here, we characterize genetic variation in all extant ethnic groups speaking Balto-Slavic languages by analyzing mitochondrial DNA (n = 6,876), Y-chromosomes (n = 6,079) and genome-wide SNP profiles (n = 296), within the context of other European populations. We also reassess the phylogeny of Slavic languages within the Balto-Slavic branch of Indo-European. We find that genetic distances among Balto-Slavic populations, based on autosomal and Y-chromosomal loci, show a high correlation (0.9) both with each other and with geography, but a slightly lower correlation (0.7) with mitochondrial DNA and linguistic affiliation. The data suggest that genetic diversity of the present-day Slavs was predominantly shaped in situ, and we detect two different substrata: ‘central-east European’ for West and East Slavs, and ‘south-east European’ for South Slavs. A pattern of distribution of segments identical by descent between groups of East-West and South Slavs suggests shared ancestry or a modest gene flow between those two groups, which might derive from the historic spread of Slavic people.
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Rohde K, Federbusch M, Horstmann A, Keller M, Villringer A, Stumvoll M, Tönjes A, Kovacs P, Böttcher Y. Genetic variants in AKR1B10 associate with human eating behavior. BMC Genet 2015; 16:31. [PMID: 25887478 PMCID: PMC4379593 DOI: 10.1186/s12863-015-0189-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Accepted: 03/11/2015] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND The human Aldoketoreductase 1B10 gene (AKR1B10) encodes one of the enzymes belonging to the family of aldoketoreductases and may be involved in detoxification of nutrients during digestion. Further, AKR1B10 mRNA (messenger ribonucleic acid) expression was diminished in brain regions potentially involved in the regulation of eating behavior in rats which are more sensitive to cocaine and alcohol. We hypothesized that the human AKR1B10 gene may also play a role in the regulation of human eating behavior. RESULTS We investigated the effects of 5 genetic variants of AKR1B10 on human eating behavior among 548 subjects from a German self-contained population, the Sorbs, and in 350 subjects from another independent German cohort. Among the Sorbs, we observed nominal associations with disinhibition at the 5' untranslated region (5' UTR) variant rs10232478 and the intragenic variants rs1834150 and rs782881 (all P ≤ 0.05). Further, we detected a relationship of rs1834150 and rs782881 with waist, smoking consumption (rs782881) and coffee consumption (rs1834150) (all P ≤ 0.05). Albeit non-significant, replication analyses revealed similar effect directions for disinhibition at rs1834150 (combined P = 0.0096). Moreover, in the replication cohort we found rs1834150 related to increased restraint scores with a similar direction as in the Sorbs (combined P = 0.0072). CONCLUSION Our data suggest that genetic variants in the AKR1B10 locus may influence human eating behavior.
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Affiliation(s)
- Kerstin Rohde
- IFB AdiposityDiseases, University of Leipzig, Leipzig, Germany.
| | - Martin Federbusch
- Max-Planck-Institute for Human Cognitive and Brain Sciences, Department of Neurology, Leipzig, Germany.
| | - Annette Horstmann
- IFB AdiposityDiseases, University of Leipzig, Leipzig, Germany. .,Max-Planck-Institute for Human Cognitive and Brain Sciences, Department of Neurology, Leipzig, Germany.
| | - Maria Keller
- IFB AdiposityDiseases, University of Leipzig, Leipzig, Germany.
| | - Arno Villringer
- IFB AdiposityDiseases, University of Leipzig, Leipzig, Germany. .,Max-Planck-Institute for Human Cognitive and Brain Sciences, Department of Neurology, Leipzig, Germany. .,Clinic of Cognitive Neurology, University of Leipzig, Leipzig, Germany.
| | - Michael Stumvoll
- IFB AdiposityDiseases, University of Leipzig, Leipzig, Germany. .,Department of Medicine, University of Leipzig, Leipzig, Germany.
| | - Anke Tönjes
- Department of Medicine, University of Leipzig, Leipzig, Germany.
| | - Peter Kovacs
- IFB AdiposityDiseases, University of Leipzig, Leipzig, Germany.
| | - Yvonne Böttcher
- IFB AdiposityDiseases, University of Leipzig, Leipzig, Germany.
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Liu X, Hinney A, Scholz M, Scherag A, Tönjes A, Stumvoll M, Stadler PF, Hebebrand J, Böttcher Y. Indications for potential parent-of-origin effects within the FTO gene. PLoS One 2015; 10:e0119206. [PMID: 25793382 PMCID: PMC4368796 DOI: 10.1371/journal.pone.0119206] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Accepted: 01/28/2015] [Indexed: 12/18/2022] Open
Abstract
Genome-Wide Association Studies (GWAS) were successfully applied to discover associations with obesity. However, the GWAS design is usually based on unrelated individuals and inheritance information on the parental origin of the alleles is missing. Taking into account parent-of-origin may provide further insights into the genetic mechanisms contributing to obesity. We hypothesized that there may be variants within the robustly replicated fat mass and obesity associated (FTO) gene that may confer different risk for obesity depending on transmission from mother or father. Genome-wide genotypes and pedigree information from the Sorbs population were used. Phased genotypes among 525 individuals were generated by AlphaImpute. Subsequently, 22 SNPs within FTO introns 1 to 3 were selected and parent-of-origin specific association analyses were performed using PLINK. Interestingly, we identified several SNPs conferring different genetic effects (P≤0.05) depending on parental origin—among them, rs1861868, rs1121980 and rs9939973 (all in intron 1). To confirm our findings, we investigated the selected variants in 705 German trios comprising an (extremely) obese child or adolescent and both parents. Again, we observed evidence for POE effects in intron 2 and 3 (P≤0.05) as indicated by the parental asymmetry test. Our results suggest that the obesity risk transmitted by several FTO variants may depend on the parental origin of the allele. Larger family-based studies are warranted to replicate our findings.
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Affiliation(s)
- Xuanshi Liu
- IFB Adiposity Diseases, University of Leipzig, Leipzig, Germany
- Bioinformatics Group, Department of Computer Science, University of Leipzig, Leipzig, Germany
| | - Anke Hinney
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy Universitätsklinikum Essen, University of Duisburg-Essen, Essen, Germany
| | - Markus Scholz
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
| | - André Scherag
- Clinical Epidemiology, Integrated Research and Treatment Center (IFB) Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany
| | - Anke Tönjes
- Department of Medicine, University of Leipzig, Leipzig, Germany
| | - Michael Stumvoll
- IFB Adiposity Diseases, University of Leipzig, Leipzig, Germany
- Department of Medicine, University of Leipzig, Leipzig, Germany
| | - Peter F. Stadler
- Fraunhofer Institute for Cell Therapy and Immunology, AG RNomics, Leipzig, Germany
- Interdisciplinary Center of Bioinformatics, University of Leipzig, Leipzig, Germany
- Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria
- Sante Fe Institute, Santa Fe, New Mexico, United States of America
| | - Johannes Hebebrand
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy Universitätsklinikum Essen, University of Duisburg-Essen, Essen, Germany
| | - Yvonne Böttcher
- IFB Adiposity Diseases, University of Leipzig, Leipzig, Germany
- * E-mail: (YB)
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Rothe J, Melisch C, Powers N, Geppert M, Zander J, Purps J, Spors B, Nagy M. Genetic research at a fivefold children's burial from medieval Berlin. Forensic Sci Int Genet 2015; 15:90-7. [DOI: 10.1016/j.fsigen.2014.10.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Revised: 10/20/2014] [Accepted: 10/24/2014] [Indexed: 10/24/2022]
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Karafet TM, Bulayeva KB, Bulayev OA, Gurgenova F, Omarova J, Yepiskoposyan L, Savina OV, Veeramah KR, Hammer MF. Extensive genome-wide autozygosity in the population isolates of Daghestan. Eur J Hum Genet 2015; 23:1405-12. [PMID: 25604856 DOI: 10.1038/ejhg.2014.299] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Revised: 12/09/2014] [Accepted: 12/19/2014] [Indexed: 01/01/2023] Open
Abstract
Isolated populations are valuable resources for mapping disease genes, as inbreeding increases genome-wide homozygosity and enhances the ability to map disease alleles on a genetically uniform background within a relatively homogenous environment. The populations of Daghestan are thought to have resided in the Caucasus Mountains for hundreds of generations and are characterized by a high prevalence of certain complex diseases. To explore the extent to which their unique population history led to increased levels of inbreeding, we genotyped >550 000 autosomal single-nucleotide polymorphisms (SNPs) in a set of 14 population isolates speaking Nakh-Daghestanian (ND) languages. The ND-speaking populations showed greatly elevated coefficients of inbreeding, very high numbers and long lengths of Runs of Homozygosity, and elevated linkage disequilibrium compared with surrounding groups from the Caucasus, the Near East, Europe, Central and South Asia. These results are consistent with the hypothesis that most ND-speaking groups descend from a common ancestral population that fragmented into a series of genetic isolates in the Daghestanian highlands. They have subsequently maintained a long-term small effective population size as a result of constant inbreeding and very low levels of gene flow. Given these findings, Daghestanian population isolates are likely to be useful for mapping genes associated with complex diseases.
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Affiliation(s)
- Tatiana M Karafet
- ARL Division of Biotechnology, University of Arizona, Tucson, AZ, USA
| | - Kazima B Bulayeva
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Oleg A Bulayev
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Farida Gurgenova
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Jamilia Omarova
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Levon Yepiskoposyan
- Institute of Molecular Biology, National Academy of Sciences, Yerevan, Armenia
| | - Olga V Savina
- ARL Division of Biotechnology, University of Arizona, Tucson, AZ, USA
| | | | - Michael F Hammer
- ARL Division of Biotechnology, University of Arizona, Tucson, AZ, USA
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Burkhardt S, Gesing J, Kapellen TM, Kovacs P, Kratzsch J, Schlicke M, Stobbe H, Tönjes A, Klammt J, Pfäffle R. Novel heterozygous IGF1R mutation in two brothers with developing impaired glucose tolerance. J Pediatr Endocrinol Metab 2015; 28:217-25. [PMID: 25153223 DOI: 10.1515/jpem-2014-0132] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2014] [Accepted: 06/27/2014] [Indexed: 11/15/2022]
Abstract
Infants born small for gestational age (SGA) are at risk to develop metabolic complications. Insulin-like growth factor 1 (IGF-1) resistance due to IGF-1 receptor (IGF1R) mutations is a rare genetic condition that causes proportionate growth retardation. The contribution of an impaired IGF1R function to the development of comorbidities such as disturbed glucose homeostasis is not well understood. Genetic analysis and detailed auxological, endocrine and psychological investigations in two male SGA siblings were performed. The two patients and their father bear a novel heterozygous mutation (p.Cys1248Tyr) in the IGF1R gene. Both brothers displayed very similar growth pattern before and during recombinant human growth hormone treatment, whereas oral glucose tolerance tests showed variable manifestations of progressive impaired glucose tolerance. The father had already developed type 2 diabetes mellitus. Growth retardation in our patients is likely caused by the IGF1R mutation that might predispose to disturbances of carbohydrate homeostasis. Therefore, a close metabolic monitoring of affected patients is indicated, particularly if growth hormone therapy is commenced.
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31
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Rohde K, Keller M, Horstmann A, Liu X, Eichelmann F, Stumvoll M, Villringer A, Kovacs P, Tönjes A, Böttcher Y. Role of genetic variants in ADIPOQ in human eating behavior. GENES AND NUTRITION 2014; 10:449. [PMID: 25542302 DOI: 10.1007/s12263-014-0449-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Accepted: 11/29/2014] [Indexed: 12/12/2022]
Abstract
The beneficial effects of adiponectin and its negative correlation with BMI are well described. Adiponectin serum levels are altered in eating disorders such as anorexia nervosa, bulimia nervosa or binge eating. Here, we tested the hypothesis that (1) adiponectin serum levels correlate with human eating behavior factors and (2) that genetic variants of the ADIPOQ locus influence both serum levels and eating behavior. We analyzed 11 SNPs within ADIPOQ and in the 5' UTR and measured serum adiponectin levels in 1,036 individuals from the German Sorbs population. The German version of the three-factor eating questionnaire (FEV) was completed by 548 Sorbs. For replication purposes, we included an independent replication cohort from Germany (N = 350). In the Sorbs, we observed positive correlations of restraint with adiponectin serum levels (P = 0.001; r = 0.148) which, however, did not withstand adjustment for covariates (P = 0.083; r = 0.077). In addition, four SNPs were nominally associated with serum adiponectin levels (all P < 0.05). Of these, two variants (rs3774261; rs1501229, all P < 0.05) were also related to disinhibition. Furthermore, three variants were exclusively associated with hunger (rs2036373, P = 0.049) and disinhibition (rs822396; rs864265, all P < 0.05). However, none of these associations withstood Bonferroni corrections for multiple testing (all P > 9.3 × 10(-4)). In our replication cohort, we observed similar effect directions at rs1501229 for disinhibition and hunger. A meta-analysis resulted in nominal statistical significance P = 0.036 (Z score 2.086) and P = 0.017 (Z score 2.366), respectively. Given the observed relationship of the SNPs with adiponectin levels and eating behavior, our data support a potential role of adiponectin in human eating behavior. Whether the relationship with eating behavior is mediated by the effects of circulating adiponectin warrants further investigations.
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Affiliation(s)
- Kerstin Rohde
- IFB Adiposity Diseases, University of Leipzig, Liebigstraße 21, 04103, Leipzig, Germany,
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Tönjes A, Scholz M, Breitfeld J, Marzi C, Grallert H, Gross A, Ladenvall C, Schleinitz D, Krause K, Kirsten H, Laurila E, Kriebel J, Thorand B, Rathmann W, Groop L, Prokopenko I, Isomaa B, Beutner F, Kratzsch J, Thiery J, Fasshauer M, Klöting N, Gieger C, Blüher M, Stumvoll M, Kovacs P. Genome wide meta-analysis highlights the role of genetic variation in RARRES2 in the regulation of circulating serum chemerin. PLoS Genet 2014; 10:e1004854. [PMID: 25521368 PMCID: PMC4270463 DOI: 10.1371/journal.pgen.1004854] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 10/27/2014] [Indexed: 11/18/2022] Open
Abstract
Chemerin is an adipokine proposed to link obesity and chronic inflammation of adipose tissue. Genetic factors determining chemerin release from adipose tissue are yet unknown. We conducted a meta-analysis of genome-wide association studies (GWAS) for serum chemerin in three independent cohorts from Europe: Sorbs and KORA from Germany and PPP-Botnia from Finland (total N = 2,791). In addition, we measured mRNA expression of genes within the associated loci in peripheral mononuclear cells by micro-arrays, and within adipose tissue by quantitative RT-PCR and performed mRNA expression quantitative trait and expression-chemerin association studies to functionally substantiate our loci. Heritability estimate of circulating chemerin levels was 16.2% in the Sorbs cohort. Thirty single nucleotide polymorphisms (SNPs) at chromosome 7 within the retinoic acid receptor responder 2 (RARRES2)/Leucine Rich Repeat Containing (LRRC61) locus reached genome-wide significance (p<5.0×10−8) in the meta-analysis (the strongest evidence for association at rs7806429 with p = 7.8×10−14, beta = −0.067, explained variance 2.0%). All other SNPs within the cluster were in linkage disequilibrium with rs7806429 (minimum r2 = 0.43 in the Sorbs cohort). The results of the subgroup analyses of males and females were consistent with the results found in the total cohort. No significant SNP-sex interaction was observed. rs7806429 was associated with mRNA expression of RARRES2 in visceral adipose tissue in women (p<0.05 after adjusting for age and body mass index). In conclusion, the present meta-GWAS combined with mRNA expression studies highlights the role of genetic variation in the RARRES2 locus in the regulation of circulating chemerin concentrations. Chemerin is an adipokine proposed to link obesity and chronic inflammation of adipose tissue. In the present study we show that circulating chemerin is a heritable trait. In a meta-analysis of genome-wide association studies (GWAS) of 2,791 individuals from Germany and Finland, we identified common genetic variants which associate with serum chemerin levels. The variants map within the retinoic acid receptor responder 2 (RARRES2)/Leucine Rich Repeat Containing (LRRC61) at chromosome 7. To better understand the potential functionality of the identified variants, we also provide insights into the mRNA expression of RARRES2 (encoding chemerin) in blood and adipose tissue. Our results highlight the role and function of genetic variation in the RARRES2 locus in the regulation of circulating chemerin concentrations.
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Affiliation(s)
- Anke Tönjes
- Department of Medicine, University of Leipzig, Leipzig, Germany
| | - Markus Scholz
- Institute of Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
- LIFE Research Center, University of Leipzig, Leipzig, Germany
| | - Jana Breitfeld
- IFB Adiposity Diseases, University of Leipzig, Leipzig, Germany
| | - Carola Marzi
- Research Unit of Molecular Epidemiology, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology II, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
| | - Harald Grallert
- Research Unit of Molecular Epidemiology, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology II, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
| | - Arnd Gross
- Institute of Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
- LIFE Research Center, University of Leipzig, Leipzig, Germany
| | - Claes Ladenvall
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University and Lund University Diabetes Centre, CRC at Skåne University Hospital, Malmö, Sweden
| | | | - Kerstin Krause
- Department of Medicine, University of Leipzig, Leipzig, Germany
| | - Holger Kirsten
- Institute of Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
- LIFE Research Center, University of Leipzig, Leipzig, Germany
- Department for Cell Therapy, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Esa Laurila
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University and Lund University Diabetes Centre, CRC at Skåne University Hospital, Malmö, Sweden
| | - Jennifer Kriebel
- Research Unit of Molecular Epidemiology, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology II, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Barbara Thorand
- Institute of Epidemiology II, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, München, Germany
| | - Wolfgang Rathmann
- Institute of Biometrics and Epidemiology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Leif Groop
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University and Lund University Diabetes Centre, CRC at Skåne University Hospital, Malmö, Sweden
| | - Inga Prokopenko
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, United Kingdom
- Department of Genomics of Common Diseases, Imperial College London, London, United Kingdom
| | - Bo Isomaa
- Department of Social Services and Health Care, Jakobstad, Finland
- Folkhälsan Research Centre, Helsinki, Finland
| | - Frank Beutner
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig, Germany
| | - Jürgen Kratzsch
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig, Germany
| | - Joachim Thiery
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig, Germany
| | - Mathias Fasshauer
- Department of Medicine, University of Leipzig, Leipzig, Germany
- IFB Adiposity Diseases, University of Leipzig, Leipzig, Germany
| | - Nora Klöting
- Department of Medicine, University of Leipzig, Leipzig, Germany
- IFB Adiposity Diseases, University of Leipzig, Leipzig, Germany
| | - Christian Gieger
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Matthias Blüher
- Department of Medicine, University of Leipzig, Leipzig, Germany
- IFB Adiposity Diseases, University of Leipzig, Leipzig, Germany
| | - Michael Stumvoll
- Department of Medicine, University of Leipzig, Leipzig, Germany
- IFB Adiposity Diseases, University of Leipzig, Leipzig, Germany
- * E-mail: (MSt); (PK)
| | - Peter Kovacs
- IFB Adiposity Diseases, University of Leipzig, Leipzig, Germany
- * E-mail: (MSt); (PK)
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Keller M, Kralisch S, Rohde K, Schleinitz D, Dietrich A, Schön MR, Gärtner D, Lohmann T, Dreßler M, Tönjes A, Stumvoll M, Kovacs P, Fasshauer M, Blüher M, Böttcher Y. Global DNA methylation levels in human adipose tissue are related to fat distribution and glucose homeostasis. Diabetologia 2014; 57:2374-83. [PMID: 25145546 DOI: 10.1007/s00125-014-3356-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Accepted: 07/23/2014] [Indexed: 12/31/2022]
Abstract
AIMS/HYPOTHESIS Epigenetic alterations may influence the metabolic pathways involved in human obesity. We hypothesised that global DNA methylation levels in adipose tissue might be associated with obesity and related phenotypes. METHODS We measured global DNA methylation levels in paired samples of subcutaneous adipose tissue (SAT) and omental visceral adipose tissue (OVAT) from 51 individuals, and in leucocytes from 559 Sorbs, a population from Germany, using LUminometric Methylation Assay (LUMA). To further investigate the underlying mechanisms of the observed associations, we measured global methylation levels in 3T3-L1 adipocytes exposed to glucose, insulin and lipids. RESULTS Global methylation levels (±SD) were significantly higher in OVAT (74.27% ± 2.2%) compared with SAT (71.97% ± 2.4%; paired t test, p < 1 × 10(-9)). Furthermore, global methylation levels in SAT were positive correlates of measures of fat distribution (waist measurement, WHR) and glucose homeostasis (HbA1c) (all p < 0.015 after accounting for multiple testing and covariates). Global methylation levels in the German Sorb cohort were associated with glucose homeostasis, but this association did not withstand adjustment for covariates. Exposure of 3T3-L1 adipocytes to insulin, palmitate and glucose decreased global methylation levels 1 h after treatment relative to controls. CONCLUSIONS/INTERPRETATION Our data suggest that the variability in global methylation in adipose tissue might be related to alterations in glucose metabolism.
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Affiliation(s)
- Maria Keller
- Medical Faculty, IFB Adiposity Diseases, University of Leipzig, Liebigstrasse 21, 04103, Leipzig, Germany
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Veeramah KR, Novembre J. Demographic events and evolutionary forces shaping European genetic diversity. Cold Spring Harb Perspect Biol 2014; 6:a008516. [PMID: 25059709 PMCID: PMC4142961 DOI: 10.1101/cshperspect.a008516] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Europeans have been the focus of some of the largest studies of genetic diversity in any species to date. Recent genome-wide data have reinforced the hypothesis that present-day European genetic diversity is strongly correlated with geography. The remaining challenge now is to understand more precisely how patterns of diversity in Europe reflect ancient demographic events such as postglacial expansions or the spread of farming. It is likely that recent advances in paleogenetics will give us some of these answers. There has also been progress in identifying specific segments of European genomes that reflect adaptations to selective pressures from the physical environment, disease, and dietary shifts. A growing understanding of how modern European genetic diversity has been shaped by demographic and evolutionary forces is not only of basic historical and anthropological interest but also aids genetic studies of disease.
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Affiliation(s)
- Krishna R Veeramah
- Arizona Research Laboratories Division of Biotechnology, University of Arizona, Tucson, Arizona 85721
| | - John Novembre
- Department of Human Genetics, University of Chicago, Chicago, Illinois 60637
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Veeramah KR, Hammer MF. The impact of whole-genome sequencing on the reconstruction of human population history. Nat Rev Genet 2014; 15:149-62. [PMID: 24492235 DOI: 10.1038/nrg3625] [Citation(s) in RCA: 127] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Examining patterns of molecular genetic variation in both modern-day and ancient humans has proved to be a powerful approach to learn about our origins. Rapid advances in DNA sequencing technology have allowed us to characterize increasing amounts of genomic information. Although this clearly provides unprecedented power for inference, it also introduces more complexity into the way we use and interpret such data. Here, we review ongoing debates that have been influenced by improvements in our ability to sequence DNA and discuss some of the analytical challenges that need to be overcome in order to fully exploit the rich historical information that is contained in the entirety of the human genome.
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Affiliation(s)
- Krishna R Veeramah
- 1] Arizona Research Laboratories Division of Biotechnology, Room 231, Life Sciences South, 1007 East Lowell Street, University of Arizona, Tucson, Arizona 85721, USA. [2] Stony Brook University, Stony Brook, New York 11794-5245, USA
| | - Michael F Hammer
- Arizona Research Laboratories Division of Biotechnology, Room 231, Life Sciences South, 1007 East Lowell Street, University of Arizona, Tucson, Arizona 85721, USA
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Keller M, Liu X, Wohland T, Rohde K, Gast MT, Stumvoll M, Kovacs P, Tönjes A, Böttcher Y. TAS2R38 and its influence on smoking behavior and glucose homeostasis in the German Sorbs. PLoS One 2013; 8:e80512. [PMID: 24312479 PMCID: PMC3846558 DOI: 10.1371/journal.pone.0080512] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Accepted: 10/04/2013] [Indexed: 11/23/2022] Open
Abstract
Background Genetic variants within the bitter taste receptor gene TAS2R38 are associated with sensitivity to bitter taste and are related to eating behavior in the Amish population. Sensitivity to bitter taste is further related to anthropometric traits in an genetically isolated Italian population. We tested whether the TAS2R38 variants (rs713598; rs1726866 and rs10246939) may be related to eating behavior, anthropometric parameters, metabolic traits and consumer goods intake in the German Sorbs. Materials and Methods The three SNPs were genotyped in a total cohort of 1007 individuals (male/female: 405/602). The German version of the three-factor eating questionnaire was completed by 548 individuals. Genetic association analyses for smoking behavior, alcohol and coffee intake, eating behavior factors (restraint, disinhibition and hunger) and other metabolic traits were analyzed. Further, by combining the three SNPs we applied comparative haplotype analyses categorizing PAV (proline-alanine-valine) carriers (tasters) vs. homozygous AVI (alanin-valine-isoleucine) carriers (non-tasters). Results Significant associations of genetic variants within TAS2R38 were identified with percentage of body fat, which were driven by associations in women. In men, we observed significant associations with 30 min plasma glucose, and area under the curve for plasma glucose (0–120 min) (all adjusted P≤0.05). Further, we found that carriers of at least one PAV allele show significantly lower cigarette smoking per day (P = 0.002) as well as, albeit non-significant, lower alcohol intake. We did not confirm previously reported associations between genetic variants of TAS2R38 and eating behavior. Conclusion Our data suggest that genetic variation in TAS2R38 is related to individual body composition measures and may further influence consumer goods intake in the Sorbs possibly via individual sensitivity to bitter taste.
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Affiliation(s)
- Maria Keller
- IFB AdiposityDiseases, University of Leipzig, Leipzig, Germany
| | - Xuanshi Liu
- IFB AdiposityDiseases, University of Leipzig, Leipzig, Germany
- Bioinformatics Group, Department of Computer Science, University of Leipzig, Leipzig, Germany
| | - Tobias Wohland
- IFB AdiposityDiseases, University of Leipzig, Leipzig, Germany
| | - Kerstin Rohde
- IFB AdiposityDiseases, University of Leipzig, Leipzig, Germany
| | | | - Michael Stumvoll
- IFB AdiposityDiseases, University of Leipzig, Leipzig, Germany
- Department of Medicine, University of Leipzig, Leipzig, Germany
| | - Peter Kovacs
- IFB AdiposityDiseases, University of Leipzig, Leipzig, Germany
| | - Anke Tönjes
- Department of Medicine, University of Leipzig, Leipzig, Germany
| | - Yvonne Böttcher
- IFB AdiposityDiseases, University of Leipzig, Leipzig, Germany
- * E-mail:
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Alsmadi O, Thareja G, Alkayal F, Rajagopalan R, John SE, Hebbar P, Behbehani K, Thanaraj TA. Genetic substructure of Kuwaiti population reveals migration history. PLoS One 2013; 8:e74913. [PMID: 24066156 PMCID: PMC3774671 DOI: 10.1371/journal.pone.0074913] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2013] [Accepted: 08/07/2013] [Indexed: 12/21/2022] Open
Abstract
The State of Kuwait is characterized by settlers from Saudi Arabia, Iran, and other regions of the Arabian Peninsula. The settlements and subsequent admixtures have shaped the genetics of Kuwait. High prevalence of recessive disorders and metabolic syndromes (that increase risk of diabetes) is seen in the peninsula. Understanding the genetic structure of its population will aid studies designed to decipher the underlying causes of these disorders. In this study, we analyzed 572,366 SNP markers from 273 Kuwaiti natives genotyped using the illumina HumanOmniExpress BeadChip. Model-based clustering identified three genetic subgroups with different levels of admixture. A high level of concordance (Mantel test, p=0.0001 for 9999 repeats) was observed between the derived genetic clusters and the surname-based ancestries. Use of Human Genome Diversity Project (HGDP) data to understand admixtures in each group reveals the following: the first group (Kuwait P) is largely of West Asian ancestry, representing Persians with European admixture; the second group (Kuwait S) is predominantly of city-dwelling Saudi Arabian tribe ancestry, and the third group (Kuwait B) includes most of the tent-dwelling Bedouin surnames and is characterized by the presence of 17% African ancestry. Identity by Descent and Homozygosity analyses find Kuwait's population to be heterogeneous (placed between populations that have large amount of ROH and the ones with low ROH) with Kuwait S as highly endogamous, and Kuwait B as diverse. Population differentiation FST estimates place Kuwait P near Asian populations, Kuwait S near Negev Bedouin tribes, and Kuwait B near the Mozabite population. FST distances between the groups are in the range of 0.005 to 0.008; distances of this magnitude are known to cause false positives in disease association studies. Results of analysis for genetic features such as linkage disequilibrium decay patterns conform to Kuwait's geographical location at the nexus of Africa, Europe, and Asia.
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Keller M, Schleinitz D, Förster J, Tönjes A, Böttcher Y, Fischer-Rosinsky A, Breitfeld J, Weidle K, Rayner NW, Burkhardt R, Enigk B, Müller I, Halbritter J, Koriath M, Pfeiffer A, Krohn K, Groop L, Spranger J, Stumvoll M, Kovacs P. THOC5: a novel gene involved in HDL-cholesterol metabolism. J Lipid Res 2013; 54:3170-6. [PMID: 24023261 DOI: 10.1194/jlr.m039420] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Although numerous genes are known to regulate serum lipid traits, identified variants explain only a small proportion of the expected heritability. We intended to identify further genetic variants associated with lipid phenotypes in a self-contained population of Sorbs in Germany. We performed a genome-wide association study (GWAS) on LDL-cholesterol, HDL-cholesterol (HDL-C), and triglyceride (TG) levels in 839 Sorbs. All single-nucleotide polymorphisms with a P value <0.01 were subjected to a meta-analysis, including an independent Swedish cohort (Diabetes Genetics Initiative; n = ∼3,100). Novel association signals with the strongest effects were subjected to replication studies in an additional German cohort (Berlin, n = 2,031). In the initial GWAS in the Sorbs, we identified 14 loci associated with lipid phenotypes reaching P values <10⁻⁵ and confirmed significant effects for 18 previously reported loci. The combined meta-analysis of the three study cohorts (n(HDL) = 6041; n(LDL) = 5,995; n(TG) = 6,087) revealed a novel association for a variant in THOC5 (rs8135828) with serum HDL-C levels (P = 1.78 × 10⁻⁷; Z-score = -5.221). Consistently, the variant was also associated with circulating APOA1 levels in Sorbs. The small interfering RNA-mediated mRNA silencing of THOC5 in HepG2 cells resulted in lower mRNA levels of APOA1, SCARB1, and ABCG8 (all P < 0.05). We propose THOC5 to be a novel gene involved in the regulation of serum HDL-C levels.
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Affiliation(s)
- Maria Keller
- IFB Adiposity Diseases, University of Leipzig, Leipzig, Germany
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Gast MT, Tönjes A, Keller M, Horstmann A, Steinle N, Scholz M, Müller I, Villringer A, Stumvoll M, Kovacs P, Böttcher Y. The role of rs2237781 within GRM8 in eating behavior. Brain Behav 2013; 3:495-502. [PMID: 24392270 PMCID: PMC3869977 DOI: 10.1002/brb3.151] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Revised: 05/21/2013] [Accepted: 05/25/2013] [Indexed: 11/07/2022] Open
Abstract
INTRODUCTION The glutamate receptor, metabotropic 8 gene (GRM8) encodes a G-protein-coupled glutamate receptor and has been associated with smoking behavior and liability to alcoholism implying a role in addiction vulnerability. Data from animal studies suggest that GRM8 may be involved in the regulation of the neuropeptide Y and melanocortin pathways and might influence food intake and metabolism. This study aimed to investigate the effects of the genetic variant rs2237781 within GRM8 on human eating behavior. METHODS The initial analysis included 548 Sorbs from Germany who have been extensively phenotyped for metabolic traits and who completed the German version of the three-factor eating questionnaire. In addition, we analyzed two independent sample sets comprising 293 subjects from another German cohort and 430 Old Order Amish individuals. Genetic associations with restraint, disinhibition, and hunger were assessed in an additive linear regression model. RESULTS Among the Sorbs the major G allele of rs2237781 was significantly associated with increased restraint scores in eating behavior (P = 1.9 × 10(-4); β = +1.936). The German cohort and the Old Order Amish population revealed a trend in the same direction for restraint (P = 0.242; β = +0.874; P = 0.908; β = +0.096; respectively). A meta-analysis resulted in a combined P = 3.1 × 10(-3) (Z-score 2.948). CONCLUSION Our data suggest that rs2237781 within GRM8 may influence human eating behavior factors probably via pathways involved in addictive behavior.
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Affiliation(s)
| | - Anke Tönjes
- Department of Medicine, University of Leipzig Leipzig, Germany
| | - Maria Keller
- IFB Adiposity Diseases, University of Leipzig Leipzig, Germany
| | - Annette Horstmann
- IFB Adiposity Diseases, University of Leipzig Leipzig, Germany ; Department for Neurology, Max-Planck-Institute for Human Cognitive and Brain Sciences Leipzig, Germany
| | - Nanette Steinle
- Division of Endocrinology, Diabetes and Nutrition, University of Maryland School of Medicine Baltimore, Maryland ; Diabetes and Endocrinology Section, Veterans Administration Medical Center Baltimore, Maryland
| | - Markus Scholz
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig Leipzig, Germany ; LIFE Research Center, University of Leipzig Leipzig, Germany
| | - Ines Müller
- IFB Adiposity Diseases, University of Leipzig Leipzig, Germany
| | - Arno Villringer
- Department for Neurology, Max-Planck-Institute for Human Cognitive and Brain Sciences Leipzig, Germany ; Clinic of Cognitive Neurology, University of Leipzig Leipzig, Germany
| | - Michael Stumvoll
- Department of Medicine, University of Leipzig Leipzig, Germany ; IFB Adiposity Diseases, University of Leipzig Leipzig, Germany
| | - Peter Kovacs
- IFB Adiposity Diseases, University of Leipzig Leipzig, Germany
| | - Yvonne Böttcher
- IFB Adiposity Diseases, University of Leipzig Leipzig, Germany
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Breitfeld J, Heiker JT, Böttcher Y, Schleinitz D, Tönjes A, Weidle K, Krause K, Kuettner EB, Scholz M, Kiess W, Sträter N, Beck-Sickinger AG, Stumvoll M, Körner A, Blüher M, Kovacs P. Analysis of a rare functional truncating mutation rs61757459 in vaspin (SERPINA12) on circulating vaspin levels. J Mol Med (Berl) 2013; 91:1285-92. [PMID: 23756768 DOI: 10.1007/s00109-013-1062-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Revised: 05/17/2013] [Accepted: 05/30/2013] [Indexed: 11/30/2022]
Abstract
UNLABELLED A recent genome-wide association study suggests that genetic variation within the vaspin gene might contribute to the variability in circulating serum visceral adipose tissue-derived serine protease inhibitor (vaspin) concentrations. Here, we analyzed the functional consequences of the rare variant rs61757459 predicting a premature stop codon and its impact on circulating serum vaspin concentrations. In order to identify genetic variation, we sequenced the vaspin gene in 48 nonrelated Caucasian subjects. Rs61757459 was subsequently genotyped in three metabolically well-characterized German cohorts (N = 4,019). We addressed the impact of rs61757459 on the crystal structure of vaspin and investigated its effects on vaspin expression in vivo as well as in vitro using various cell lines (Escherichia coli, HEK293). Along with previously reported common genetic variants, sequencing of vaspin revealed a rare variant (rs61757459; minor allele frequency: 1 %) which predicts a premature stop codon p.R211X. Heterozygous carriers of this mutation had lower circulating vaspin levels when compared with noncarriers. In silico structure analysis of the truncated vaspin, which was estimated to be 24.5 kDa, suggested misfolding and potential instability due to the absence of core structural domains. Indeed, the truncated protein was detected after recombinant expression in E. coli and in lysate, but not in supernatant of HEK293 cells. We conclude that rs61757459 is a functional mutation that results in a truncated protein whose instability likely results in reduced serum vaspin levels. KEY MESSAGE A rare variant (rs61757459) in vaspin coding for the stop codon p.R211X is related to lower circulating vaspin concentrations. Structure analysis suggests misfolding and instability due to the absence of core structural domains. The truncated protein is detectable after recombinant expression in E. coli and in lysate, but not in supernatant of HEK293 cells.
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Affiliation(s)
- Jana Breitfeld
- Department of Medicine, University of Leipzig, Leipzig, Germany
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Breitfeld J, Tönjes A, Gast MT, Schleinitz D, Blüher M, Stumvoll M, Kovacs P, Böttcher Y. Role of vaspin in human eating behaviour. PLoS One 2013; 8:e54140. [PMID: 23342091 PMCID: PMC3544656 DOI: 10.1371/journal.pone.0054140] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2012] [Accepted: 12/10/2012] [Indexed: 12/19/2022] Open
Abstract
Objective The adipokine vaspin (visceral adipose tissue derived serine protease inhibitor, serpinA12) follows a meal-related diurnal variation in humans and intracerebroventricular vaspin administration leads to acutely reduced food intake in db/db mice. We therefore hypothesized that vaspin may play a role in human eating behaviour. Materials and Methods We measured serum vaspin concentrations in 548 subjects from a self-contained population of Sorbs (Germany) who underwent detailed metabolic testing including eating behaviour assessments using the three-factor eating questionnaire. In addition, genetic variation within vaspin was assessed by genotyping 28 single nucleotide polymorphisms (SNPs) in all study subjects. Results Serum vaspin concentrations correlated positively with restraint, disinhibition and hunger (all P<0.05), although the correlations did not withstand further adjustments for age, gender and BMI (all P>0.05). Independent of observed correlations, genetic variants in vaspin were associated with serum vaspin levels but showed no significant association with any of the eating behaviour phenotypes after accounting for multiple testing (P≥0.05 after adjusting for age, gender and BMI). Conclusion Our data suggest that serum vaspin concentrations might modulate human eating behaviour, which does not seem to be affected by common genetic variation in vaspin.
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Affiliation(s)
- Jana Breitfeld
- Department of Medicine, University of Leipzig, Leipzig, Germany
| | - Anke Tönjes
- Department of Medicine, University of Leipzig, Leipzig, Germany
- IFB Adiposity Diseases, University of Leipzig, Leipzig, Germany
| | | | | | - Matthias Blüher
- Department of Medicine, University of Leipzig, Leipzig, Germany
| | | | - Peter Kovacs
- Department of Medicine, University of Leipzig, Leipzig, Germany
- * E-mail:
| | - Yvonne Böttcher
- IFB Adiposity Diseases, University of Leipzig, Leipzig, Germany
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Esko T, Mezzavilla M, Nelis M, Borel C, Debniak T, Jakkula E, Julia A, Karachanak S, Khrunin A, Kisfali P, Krulisova V, Aušrelé Kučinskiené Z, Rehnström K, Traglia M, Nikitina-Zake L, Zimprich F, Antonarakis SE, Estivill X, Glavač D, Gut I, Klovins J, Krawczak M, Kučinskas V, Lathrop M, Macek M, Marsal S, Meitinger T, Melegh B, Limborska S, Lubinski J, Paolotie A, Schreiber S, Toncheva D, Toniolo D, Wichmann HE, Zimprich A, Metspalu M, Gasparini P, Metspalu A, D'Adamo P. Genetic characterization of northeastern Italian population isolates in the context of broader European genetic diversity. Eur J Hum Genet 2012; 21:659-65. [PMID: 23249956 PMCID: PMC3658181 DOI: 10.1038/ejhg.2012.229] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Population genetic studies on European populations have highlighted Italy as one of genetically most diverse regions. This is possibly due to the country's complex demographic history and large variability in terrain throughout the territory. This is the reason why Italy is enriched for population isolates, Sardinia being the best-known example. As the population isolates have a great potential in disease-causing genetic variants identification, we aimed to genetically characterize a region from northeastern Italy, which is known for isolated communities. Total of 1310 samples, collected from six geographically isolated villages, were genotyped at >145 000 single-nucleotide polymorphism positions. Newly genotyped data were analyzed jointly with the available genome-wide data sets of individuals of European descent, including several population isolates. Despite the linguistic differences and geographical isolation the village populations still show the greatest genetic similarity to other Italian samples. The genetic isolation and small effective population size of the village populations is manifested by higher levels of genomic homozygosity and elevated linkage disequilibrium. These estimates become even more striking when the detected substructure is taken into account. The observed level of genetic isolation in Friuli-Venezia Giulia region is more extreme according to several measures of isolation compared with Sardinians, French Basques and northern Finns, thus proving the status of an isolate.
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Affiliation(s)
- Tõnu Esko
- Estonian Genome Center, University of Tartu, Tartu, Estonia
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Rębała K, Martínez-Cruz B, Tönjes A, Kovacs P, Stumvoll M, Lindner I, Büttner A, Wichmann HE, Siváková D, Soták M, Quintana-Murci L, Szczerkowska Z, Comas D. Contemporary paternal genetic landscape of Polish and German populations: from early medieval Slavic expansion to post-World War II resettlements. Eur J Hum Genet 2012; 21:415-22. [PMID: 22968131 DOI: 10.1038/ejhg.2012.190] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Homogeneous Proto-Slavic genetic substrate and/or extensive mixing after World War II were suggested to explain homogeneity of contemporary Polish paternal lineages. Alternatively, Polish local populations might have displayed pre-war genetic heterogeneity owing to genetic drift and/or gene flow with neighbouring populations. Although sharp genetic discontinuity along the political border between Poland and Germany indisputably results from war-mediated resettlements and homogenisation, it remained unknown whether Y-chromosomal diversity in ethnically/linguistically defined populations was clinal or discontinuous before the war. In order to answer these questions and elucidate early Slavic migrations, 1156 individuals from several Slavic and German populations were analysed, including Polish pre-war regional populations and an autochthonous Slavic population from Germany. Y chromosomes were assigned to 39 haplogroups and genotyped for 19 STRs. Genetic distances revealed similar degree of differentiation of Slavic-speaking pre-war populations from German populations irrespective of duration and intensity of contacts with German speakers. Admixture estimates showed minor Slavic paternal ancestry (~20%) in modern eastern Germans and hardly detectable German paternal ancestry in Slavs neighbouring German populations for centuries. BATWING analysis of isolated Slavic populations revealed that their divergence was preceded by rapid demographic growth, undermining theory that Slavic expansion was primarily linguistic rather than population spread. Polish pre-war regional populations showed within-group heterogeneity and lower STR variation within R-M17 subclades compared with modern populations, which might have been homogenised by war resettlements. Our results suggest that genetic studies on early human history in the Vistula and Oder basins should rely on reconstructed pre-war rather than modern populations.
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Affiliation(s)
- Krzysztof Rębała
- Institut de Biologia Evolutiva, CSIC-UPF, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
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Scliar MO, Soares-Souza GB, Chevitarese J, Lemos L, Magalhães WCS, Fagundes NJ, Bonatto SL, Yeager M, Chanock SJ, Tarazona-Santos E. The population genetics of Quechuas, the largest native South American group: autosomal sequences, SNPs, and microsatellites evidence high level of diversity. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2012; 147:443-51. [PMID: 22282032 DOI: 10.1002/ajpa.22013] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2011] [Accepted: 12/09/2011] [Indexed: 11/12/2022]
Abstract
Elucidating the pattern of genetic diversity for non-European populations is necessary to make the benefits of human genetics research available to individuals from these groups. In the era of large human genomic initiatives, Native American populations have been neglected, in particular, the Quechua, the largest South Amerindian group settled along the Andes. We characterized the genetic diversity of a Quechua population in a global setting, using autosomal noncoding sequences (nine unlinked loci for a total of 16 kb), 351 unlinked SNPs and 678 microsatellites and tested predictions of the model of the evolution of Native Americans proposed by (Tarazona-Santos et al.: Am J Hum Genet 68 (2001) 1485-1496). European admixture is <5% and African ancestry is barely detectable in the studied population. The largest genetic distances were between African versus Quechua or Melanesian populations, which is concordant with the African origin of modern humans and the fact that South America was the last part of the world to be peopled. The diversity in the Quechua population is comparable with that of Eurasian populations, and the allele frequency spectrum based on resequencing data does not reflect a reduction in the proportion of rare alleles. Thus, the Quechua population is a large reservoir of common and rare genetic variants of South Amerindians. These results are consistent with and complement our evolutionary model of South Amerindians (Tarazona-Santos et al.: Am J Hum Genet 68 (2001) 1485-1496), proposed based on Y-chromosome data, which predicts high genomic diversity due to the high level of gene flow between Andean populations and their long-term effective population size.
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Affiliation(s)
- Marilia O Scliar
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais. Av. Antonio Carlos 6627, Pampulha. Caixa Postal 486, Belo Horizonte, Minas Gerais, CEP 31270-910, Brazil
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Dietrich K, Birkmeier S, Schleinitz D, Breitfeld J, Enigk B, Müller I, Böttcher Y, Lindner T, Stumvoll M, Tönjes A, Kovacs P. Association and evolutionary studies of the melatonin receptor 1B gene (MTNR1B) in the self-contained population of Sorbs from Germany. Diabet Med 2011; 28:1373-80. [PMID: 21711391 DOI: 10.1111/j.1464-5491.2011.03374.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
AIMS Several polymorphisms of the melatonin receptor 1B gene (MTNR1B) have been shown to be associated with elevated fasting plasma glucose and impaired early insulin release. The aim of this study was to assess the effects of MTNR1B variants on traits related to the metabolic syndrome in the self-contained population of Sorbs from Germany. As comprehensive studies concerning the conservation of MTNR1B are lacking, we also evaluated natural selection in vertebrates and human populations at this locus. METHODS Five single nucleotide polymorphisms representing all blocks of linkage disequilibrium within and surrounding the MTNR1B locus were genotyped in 937 Sorbs for association analyses on metabolic traits related to Type 2 diabetes. The associations were assessed by regression analyses, the conservation between species was investigated with phylogenetic analysis by maximum likelihood (PAML). In addition, various tests of population genetic measures (e.g. fixation index, Tajima's D) were performed. RESULTS Previously reported association between MTNR1B variants (rs10830963, rs4753426) and oral glucose tolerance test-derived indices of β-cell function (homeostasis model assessment-B, P = 3.7 × 10⁻⁶ and P = 0.004, respectively), as well as insulin (fasting insulin: P=2×10⁻³ and P=0.02; 30-min insulin: P = 2.1 × 10⁻⁴ and P=0.03, respectively) and fasting glucose (rs10830963, P=1.2×10⁻⁶) parameters could be replicated in the present study. Phylogenetic analysis by maximum likelihood analyses showed that the gene was strongly conserved between species (ω=0.2583). Structures important for the receptor function are also conserved. On the lineage leading to human adaptive selection was present (ω=1.1030). Population genetic measures further indicated natural selection. CONCLUSIONS Our data support the physiologic importance of MTNR1B in the context of glucose homeostasis and suggest evidence of selection at this locus.
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Affiliation(s)
- K Dietrich
- Interdisciplinary Centre for Clinical Research, University of Leipzig, Leipzig, Germany
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Novembre J, Ramachandran S. Perspectives on human population structure at the cusp of the sequencing era. Annu Rev Genomics Hum Genet 2011; 12:245-74. [PMID: 21801023 DOI: 10.1146/annurev-genom-090810-183123] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Human groups show structured levels of genetic similarity as a consequence of factors such as geographical subdivision and genetic drift. Surveying this structure gives us a scientific perspective on human origins, sheds light on evolutionary processes that shape both human adaptation and disease, and is integral to effectively carrying out the mission of global medical genetics and personalized medicine. Surveys of population structure have been ongoing for decades, but in the past three years, single-nucleotide-polymorphism (SNP) array technology has provided unprecedented detail on human population structure at global and regional scales. These studies have confirmed well-known relationships between distantly related populations and uncovered previously unresolvable relationships among closely related human groups. SNPs represent the first dense genome-wide markers, and as such, their analysis has raised many challenges and insights relevant to the study of population genetics with whole-genome sequences. Here we draw on the lessons from these studies to anticipate the directions that will be most fruitful to pursue during the emerging whole-genome sequencing era.
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Affiliation(s)
- John Novembre
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California 90403, USA.
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Gross A, Tönjes A, Kovacs P, Veeramah KR, Ahnert P, Roshyara NR, Gieger C, Rueckert IM, Loeffler M, Stoneking M, Wichmann HE, Novembre J, Stumvoll M, Scholz M. Population-genetic comparison of the Sorbian isolate population in Germany with the German KORA population using genome-wide SNP arrays. BMC Genet 2011; 12:67. [PMID: 21798003 PMCID: PMC3199861 DOI: 10.1186/1471-2156-12-67] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2011] [Accepted: 07/28/2011] [Indexed: 11/11/2022] Open
Abstract
Background The Sorbs are an ethnic minority in Germany with putative genetic isolation, making the population interesting for disease mapping. A sample of N = 977 Sorbs is currently analysed in several genome-wide meta-analyses. Since genetic differences between populations are a major confounding factor in genetic meta-analyses, we compare the Sorbs with the German outbred population of the KORA F3 study (N = 1644) and other publically available European HapMap populations by population genetic means. We also aim to separate effects of over-sampling of families in the Sorbs sample from effects of genetic isolation and compare the power of genetic association studies between the samples. Results The degree of relatedness was significantly higher in the Sorbs. Principal components analysis revealed a west to east clustering of KORA individuals born in Germany, KORA individuals born in Poland or Czech Republic, Half-Sorbs (less than four Sorbian grandparents) and Full-Sorbs. The Sorbs cluster is nearest to the cluster of KORA individuals born in Poland. The number of rare SNPs is significantly higher in the Sorbs sample. FST between KORA and Sorbs is an order of magnitude higher than between different regions in Germany. Compared to the other populations, Sorbs show a higher proportion of individuals with runs of homozygosity between 2.5 Mb and 5 Mb. Linkage disequilibrium (LD) at longer range is also slightly increased but this has no effect on the power of association studies. Oversampling of families in the Sorbs sample causes detectable bias regarding higher FST values and higher LD but the effect is an order of magnitude smaller than the observed differences between KORA and Sorbs. Relatedness in the Sorbs also influenced the power of uncorrected association analyses. Conclusions Sorbs show signs of genetic isolation which cannot be explained by over-sampling of relatives, but the effects are moderate in size. The Slavonic origin of the Sorbs is still genetically detectable. Regarding LD structure, a clear advantage for genome-wide association studies cannot be deduced. The significant amount of cryptic relatedness in the Sorbs sample results in inflated variances of Beta-estimators which should be considered in genetic association analyses.
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Affiliation(s)
- Arnd Gross
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Haertelstrasse 16-18, 04107 Leipzig, Germany
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