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Yin S, Li Z, Yang F, Guo H, Zhao Q, Zhang Y, Yin Y, Wu X, He J. A Comprehensive Genomic Analysis of Chinese Indigenous Ningxiang Pigs: Genomic Breed Compositions, Runs of Homozygosity, and Beyond. Int J Mol Sci 2023; 24:14550. [PMID: 37833998 PMCID: PMC10572203 DOI: 10.3390/ijms241914550] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 09/20/2023] [Accepted: 09/22/2023] [Indexed: 10/15/2023] Open
Abstract
Ningxiang pigs are a renowned indigenous pig breed in China, known for their meat quality, disease resistance, and environmental adaptability. In recent decades, consumer demand for meats from indigenous breeds has grown significantly, fueling the selection and crossbreeding of Ningxiang pigs (NXP). The latter has raised concerns about the conservation and sustainable use of Ningxiang pigs as an important genetic resource. To address these concerns, we conducted a comprehensive genomic study using 2242 geographically identified Ningxiang pigs. The estimated genomic breed composition (GBC) suggested 2077 pigs as purebred Ningxiang pigs based on a ≥94% NXP-GBC cut-off. The remaining 165 pigs were claimed to be crosses, including those between Duroc and Ningxiang pigs and between Ningxiang and Shaziling pigs, and non-Ningxiang pigs. Runs of homozygosity (ROH) were identified in the 2077 purebred Ningxiang pigs. The number and length of ROH varied between individuals, with an average of 32.14 ROH per animal and an average total length of 202.4 Mb per animal. Short ROH (1-5 Mb) was the most abundant, representing 66.5% of all ROH and 32.6% of total ROH coverage. The genomic inbreeding estimate was low (0.089) in purebred Ningxiang pigs compared to imported western pig breeds. Nine ROH islands were identified, pinpointing candidate genes and QTLs associated with economic traits of interest, such as reproduction, carcass and growth traits, lipid metabolism, and fat deposition. Further investigation of these ROH islands and candidate genes is anticipated to better understand the genomics of Ningxiang pigs.
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Affiliation(s)
- Shishu Yin
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (S.Y.); (Z.L.); (F.Y.); (H.G.); (Q.Z.); (Y.Z.)
| | - Zhi Li
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (S.Y.); (Z.L.); (F.Y.); (H.G.); (Q.Z.); (Y.Z.)
| | - Fang Yang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (S.Y.); (Z.L.); (F.Y.); (H.G.); (Q.Z.); (Y.Z.)
| | - Haimin Guo
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (S.Y.); (Z.L.); (F.Y.); (H.G.); (Q.Z.); (Y.Z.)
| | - Qinghua Zhao
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (S.Y.); (Z.L.); (F.Y.); (H.G.); (Q.Z.); (Y.Z.)
| | - Yuebo Zhang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (S.Y.); (Z.L.); (F.Y.); (H.G.); (Q.Z.); (Y.Z.)
- Key Laboratory for Evaluation and Utilization of Livestock and Poultry Resources (Pigs) of the Ministry of Agriculture and Rural Affairs, Changsha 410128, China;
| | - Yulong Yin
- Key Laboratory for Evaluation and Utilization of Livestock and Poultry Resources (Pigs) of the Ministry of Agriculture and Rural Affairs, Changsha 410128, China;
- Animal Nutrition Genome and Germplasm Innovation Research Center, Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
- Laboratory of Animal Nutrition Physiology and Metabolism, The Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha 410125, China
| | - Xiaolin Wu
- Council on Dairy Cattle Breeding, Bowie, MD 20716, USA
- Department of Animal and Dairy Sciences, University of Wisconsin, Madison, WI 53706, USA
| | - Jun He
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (S.Y.); (Z.L.); (F.Y.); (H.G.); (Q.Z.); (Y.Z.)
- Key Laboratory for Evaluation and Utilization of Livestock and Poultry Resources (Pigs) of the Ministry of Agriculture and Rural Affairs, Changsha 410128, China;
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Rawat P, Sehar U, Bisht J, Reddy PH. Support Provided by Caregivers for Community-Dwelling Diabetic Hispanic Adults with Intellectual Disabilities and Comorbid Conditions. Int J Mol Sci 2023; 24:3848. [PMID: 36835260 PMCID: PMC9962604 DOI: 10.3390/ijms24043848] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 02/06/2023] [Accepted: 02/13/2023] [Indexed: 02/17/2023] Open
Abstract
Diabetes is an age-related chronic health condition and a major public health concern. Diabetes is one of the significant causes of morbidity and mortality and a major contributing factor to dementia. Recent research reveals that Hispanic Americans are at an increased risk of chronic conditions such as diabetes, dementia, and obesity. Recent research also revealed that diabetes develops at least ten years earlier in Hispanics and Latinos than in neighboring non-Hispanic whites. Furthermore, the management of diabetes and providing necessary/timely support is a challenging task for healthcare professionals. Caregiver support is an emerging area of research for people with diabetes, mainly family caregiver support work for Hispanic and Native Americans. Our article discusses several aspects of diabetes, factors associated with diabetes among Hispanics, its management, and how caregivers can support individuals with diabetes.
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Affiliation(s)
- Priyanka Rawat
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - Ujala Sehar
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - Jasbir Bisht
- Department of Pediatrics, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - P. Hemachandra Reddy
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
- Department of Speech, Language and Hearing Sciences, School Health Professions, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
- Department of Public Health, School of Population and Public Health, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
- Neurology Department, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
- Nutritional Sciences Department, College of Human Sciences, Texas Tech University, Lubbock, TX 79409, USA
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Demin KA, Krotova NA, Ilyin NP, Galstyan DS, Kolesnikova TO, Strekalova T, de Abreu MS, Petersen EV, Zabegalov KN, Kalueff AV. Evolutionarily conserved gene expression patterns for affective disorders revealed using cross-species brain transcriptomic analyses in humans, rats and zebrafish. Sci Rep 2022; 12:20836. [PMID: 36460699 PMCID: PMC9718822 DOI: 10.1038/s41598-022-22688-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 10/18/2022] [Indexed: 12/03/2022] Open
Abstract
Widespread, debilitating and often treatment-resistant, depression and other stress-related neuropsychiatric disorders represent an urgent unmet biomedical and societal problem. Although animal models of these disorders are commonly used to study stress pathogenesis, they are often difficult to translate across species into valuable and meaningful clinically relevant data. To address this problem, here we utilized several cross-species/cross-taxon approaches to identify potential evolutionarily conserved differentially expressed genes and their sets. We also assessed enrichment of these genes for transcription factors DNA-binding sites down- and up- stream from their genetic sequences. For this, we compared our own RNA-seq brain transcriptomic data obtained from chronically stressed rats and zebrafish with publicly available human transcriptomic data for patients with major depression and their respective healthy control groups. Utilizing these data from the three species, we next analyzed their differential gene expression, gene set enrichment and protein-protein interaction networks, combined with validated tools for data pooling. This approach allowed us to identify several key brain proteins (GRIA1, DLG1, CDH1, THRB, PLCG2, NGEF, IKZF1 and FEZF2) as promising, evolutionarily conserved and shared affective 'hub' protein targets, as well as to propose a novel gene set that may be used to further study affective pathogenesis. Overall, these approaches may advance cross-species brain transcriptomic analyses, and call for further cross-species studies into putative shared molecular mechanisms of affective pathogenesis.
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Affiliation(s)
- Konstantin A Demin
- Almazov National Medical Research Centre, Ministry of Healthcare of Russian Federation, St. Petersburg, Russia.
- Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia.
| | - Nataliya A Krotova
- Almazov National Medical Research Centre, Ministry of Healthcare of Russian Federation, St. Petersburg, Russia
- Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
| | - Nikita P Ilyin
- Almazov National Medical Research Centre, Ministry of Healthcare of Russian Federation, St. Petersburg, Russia
- Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
- Neurobiology Program, Sirius University of Science and Technology, Sochi, Russia
| | - David S Galstyan
- Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
- Laboratory of Preclinical Bioscreening, Granov Russian Research Center of Radiology and Surgical Technologies, Ministry of Healthcare of Russian Federation, Pesochny, Russia
| | | | | | | | | | | | - Allan V Kalueff
- Laboratory of Preclinical Bioscreening, Granov Russian Research Center of Radiology and Surgical Technologies, Ministry of Healthcare of Russian Federation, Pesochny, Russia.
- Institute of Neurosciences and Medicine, Novosibirsk, Russia.
- Ural Federal University, Ekaterinburg, Russia.
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Vagena E, Crneta J, Engström P, He L, Yulyaningsih E, Korpel NL, Cheang RT, Bachor TP, Huang A, Michel G, Attal K, Berrios DI, Valdearcos M, Koliwad SK, Olson DP, Yi CX, Xu AW. ASB4 modulates central melanocortinergic neurons and calcitonin signaling to control satiety and glucose homeostasis. Sci Signal 2022; 15:eabj8204. [PMID: 35536884 DOI: 10.1126/scisignal.abj8204] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Variants in the gene encoding ankyrin repeat and SOCS box-containing 4 (ASB4) are linked to human obesity. Here, we characterized the pathways underlying the metabolic functions of ASB4. Hypothalamic Asb4 expression was suppressed by fasting in wild-type mice but not in mice deficient in AgRP, which encodes Agouti-related protein (AgRP), an appetite-stimulating hormone, suggesting that ASB4 is a negative target of AgRP. Many ASB4 neurons in the brain were adjacent to AgRP terminals, and feeding induced by AgRP neuronal activation was disrupted in Asb4-deficient mice. Acute knockdown of Asb4 in the brain caused marked hyperphagia due to increased meal size, and Asb4 deficiency led to increased meal size and food intake at the onset of refeeding, when very large meals were consumed. Asb4-deficient mice were resistant to the meal-terminating effects of exogenously administered calcitonin and showed decreased neuronal expression of Calcr, which encodes the calcitonin receptor. Pro-opiomelanocortin (POMC) neurons in the arcuate nucleus in mice are involved in glucose homeostasis, and Asb4 deficiency specifically in POMC neurons resulted in glucose intolerance that was independent of obesity. Furthermore, individuals with type 2 diabetes showed reduced ASB4 abundance in the infundibular nuclei, the human equivalent of the arcuate nucleus. Together, our results indicate that ASB4 acts in the brain to improve glucose homeostasis and to induce satiety after substantial meals, particularly those after food deprivation.
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Affiliation(s)
- Eirini Vagena
- Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jasmina Crneta
- Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Pauline Engström
- Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Li He
- Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Ernie Yulyaningsih
- Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Nikita L Korpel
- Department of Endocrinology and Metabolism, Laboratory of Endocrinology, Amsterdam University Medical Center, University of Amsterdam, Amsterdam Gastroenterology and Metabolism, Meibergdreef 9, Amsterdam 1105 AZ, Netherlands
| | - Rachel T Cheang
- Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Tomas P Bachor
- Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Alyssa Huang
- Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Guillermina Michel
- Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Kush Attal
- Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - David I Berrios
- Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Martin Valdearcos
- Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Suneil K Koliwad
- Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - David P Olson
- Department of Pediatrics, Michigan Medicine, Ann Arbor, MI 48109, USA
| | - Chun-Xia Yi
- Department of Endocrinology and Metabolism, Laboratory of Endocrinology, Amsterdam University Medical Center, University of Amsterdam, Amsterdam Gastroenterology and Metabolism, Meibergdreef 9, Amsterdam 1105 AZ, Netherlands
| | - Allison W Xu
- Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA.,Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA
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SAINI SIMMI, WALIA GAGANDEEPKAUR, SACHDEVA MOHINDERPAL, GUPTA VIPIN. Genomics of body fat distribution. J Genet 2021. [DOI: 10.1007/s12041-021-01281-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Michelini S, Chiurazzi P, Marino V, Dell’Orco D, Manara E, Baglivo M, Fiorentino A, Maltese PE, Pinelli M, Herbst KL, Dautaj A, Bertelli M. Aldo-Keto Reductase 1C1 ( AKR1C1) as the First Mutated Gene in a Family with Nonsyndromic Primary Lipedema. Int J Mol Sci 2020; 21:ijms21176264. [PMID: 32872468 PMCID: PMC7503355 DOI: 10.3390/ijms21176264] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 08/21/2020] [Accepted: 08/27/2020] [Indexed: 12/17/2022] Open
Abstract
Lipedema is an often underdiagnosed chronic disorder that affects subcutaneous adipose tissue almost exclusively in women, which leads to disproportionate fat accumulation in the lower and upper body extremities. Common comorbidities include anxiety, depression, and pain. The correlation between mood disorder and subcutaneous fat deposition suggests the involvement of steroids metabolism and neurohormones signaling, however no clear association has been established so far. In this study, we report on a family with three patients affected by sex-limited autosomal dominant nonsyndromic lipedema. They had been screened by whole exome sequencing (WES) which led to the discovery of a missense variant p.(Leu213Gln) in AKR1C1, the gene encoding for an aldo-keto reductase catalyzing the reduction of progesterone to its inactive form, 20-α-hydroxyprogesterone. Comparative molecular dynamics simulations of the wild-type vs. variant enzyme, corroborated by a thorough structural and functional bioinformatic analysis, suggest a partial loss-of-function of the variant. This would result in a slower and less efficient reduction of progesterone to hydroxyprogesterone and an increased subcutaneous fat deposition in variant carriers. Overall, our results suggest that AKR1C1 is the first candidate gene associated with nonsyndromic lipedema.
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Affiliation(s)
- Sandro Michelini
- Dipartimento di Riabilitazione, Ospedale San Giovanni Battista, A.C.I.S.M.O.M., 00148 Rome, Italy; (S.M.); (A.F.)
| | - Pietro Chiurazzi
- Istituto di Medicina Genomica, Università Cattolica del Sacro Cuore, 00168 Rome, Italy;
- Fondazione Policlinico Universitario “A.Gemelli” IRCCS, UOC Genetica Medica, 00168 Rome, Italy
| | - Valerio Marino
- Dipartimento di Neuroscienze, Biomedicina e Movimento, Sezione di Chimica Biologica, Università di Verona, 37134 Verona, Italy; (V.M.); (D.D.)
| | - Daniele Dell’Orco
- Dipartimento di Neuroscienze, Biomedicina e Movimento, Sezione di Chimica Biologica, Università di Verona, 37134 Verona, Italy; (V.M.); (D.D.)
| | - Elena Manara
- MAGI Euregio, 39100 Bolzano, Italy; (E.M.); (M.B.)
| | | | - Alessandro Fiorentino
- Dipartimento di Riabilitazione, Ospedale San Giovanni Battista, A.C.I.S.M.O.M., 00148 Rome, Italy; (S.M.); (A.F.)
| | | | - Michele Pinelli
- Dipartimento di Scienze Mediche Traslazionali, Sezione di Pediatria, Università di Napoli Federico II, 80131 Naples, Italy;
- Telethon Institute of Genetics and Medicine (TIGEM), 80078 Pozzuoli, Italy
| | - Karen Louise Herbst
- Departments of Medicine, Pharmacy, Medical Imaging, Division of Endocrinology, University of Arizona, Tucson, AZ 85721, USA;
| | | | - Matteo Bertelli
- MAGI Euregio, 39100 Bolzano, Italy; (E.M.); (M.B.)
- EBTNA-Lab, 38068 Rovereto, Italy;
- Correspondence:
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Carson C, Lawson HA. Genetic background and diet affect brown adipose gene coexpression networks associated with metabolic phenotypes. Physiol Genomics 2020; 52:223-233. [PMID: 32338175 PMCID: PMC7311675 DOI: 10.1152/physiolgenomics.00003.2020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 04/01/2020] [Accepted: 04/22/2020] [Indexed: 01/10/2023] Open
Abstract
Adipose is a dynamic endocrine organ that is critical for regulating metabolism and is highly responsive to nutritional environment. Brown adipose tissue is an exciting potential therapeutic target; however, there are no systematic studies of gene-by-environment interactions affecting function of this organ. We leveraged a weighted gene coexpression network analysis to identify transcriptional networks in brown adipose tissue from LG/J and SM/J inbred mice fed high- or low-fat diets and correlate these networks with metabolic phenotypes. We identified eight primary gene network modules associated with variation in obesity and diabetes-related traits. Four modules were enriched for metabolically relevant processes such as immune and cytokine response, cell division, peroxisome functions, and organic molecule metabolic processes. The relative expression of genes in these modules is highly dependent on both genetic background and dietary environment. Genes in the immune/cytokine response and cell division modules are particularly highly expressed in high fat-fed SM/J mice, which show unique brown adipose-dependent remission of diabetes. The interconnectivity of genes in these modules is also heavily dependent on diet and strain, with most genes showing both higher expression and coexpression under the same context. We highlight several genes of interest, Col28a1, Cyp26b1, Bmp8b, and Ngef, that have distinct expression patterns among strain-by-diet contexts and fall under metabolic quantitative trait loci previously mapped in an F16 generation of an advanced intercross between LG/J and SM/J. Each of these genes have some connection to obesity and diabetes-related traits, but have not been studied in brown adipose tissue. Our results provide important insights into the relationship between brown adipose and systemic metabolism by being the first gene-by-environment study of brown adipose transcriptional networks.
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Affiliation(s)
- Caryn Carson
- Department of Genetics, Washington University School of Medicine, Saint Louis, Missouri
| | - Heather A Lawson
- Department of Genetics, Washington University School of Medicine, Saint Louis, Missouri
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8
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Enriched developmental biology molecular pathways impact on antipsychotics-induced weight gain. Pharmacogenet Genomics 2019; 30:9-20. [PMID: 31651721 DOI: 10.1097/fpc.0000000000000390] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Psychotropic-induced weight gain (PIWG) may lead to increased risk for cardiovasculardiseases, metabolic disorders and treatment discontinuation. PIWG may be genetically driven. The analysis of complete molecular pathways may grant suffcient power to tackle the biologic variance of PIWG. Such identifcation would help to move a step forward in the direction of personalized treatment in psychiatry. A genetic sample from the CATIE trial (n = 765; M = 556, mean age = 40.93 ± 11.03) treated with diverse antipsychotic drugs was investigated. A molecular pathway analysis was conducted for the identifcation of the molecular pathways enriched in variations associated with PIWG. The developmental biology molecular pathway was signifcantly (P.adj = 0.018) enriched in genetic variations signifcantly (P < 0.01) associated with PIWG. A total of 18 genes were identifed and discussed. The developmental biology molecular pathway is involved in the regulation of β-cell development, and the transcriptional regulation of white adipocyte differentiation. Results from the current contribution correlate with previous evidence and it is consistent with our earlier result on the STAR*D sample. Furthermore, the involvement of the β-cell development and the transcriptional regulation of white adipocyte differentiation pathways stress the relevance of the peripheral tissue rearrangement, rather than increased food intake, in the biologic modifcations that follow psychotropic treatment and may lead to PIWG. Further research is warranted.
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Gene-Environment Interactions on Body Fat Distribution. Int J Mol Sci 2019; 20:ijms20153690. [PMID: 31357654 PMCID: PMC6696304 DOI: 10.3390/ijms20153690] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 07/18/2019] [Accepted: 07/19/2019] [Indexed: 02/08/2023] Open
Abstract
The prevalence of obesity has been increasing markedly in the U.S. and worldwide in the past decades; and notably, the obese populations are signified by not only the overall elevated adiposity but also particularly harmful accumulation of body fat in the central region of the body, namely, abdominal obesity. The profound shift from “traditional” to “obesogenic” environments, principally featured by the abundance of palatable, energy-dense diet, reduced physical activity, and prolonged sedentary time, promotes the obesity epidemics and detrimental body fat distribution. Recent advances in genomics studies shed light on the genetic basis of obesity and body fat distribution. In addition, growing evidence from investigations in large cohorts and clinical trials has lent support to interactions between genetic variations and environmental factors, e.g., diet and lifestyle factors, in relation to obesity and body fat distribution. This review summarizes the recent discoveries from observational studies and randomized clinical trials on the gene–environment interactions on obesity and body fat distribution.
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Aguayo-Mazzucato C, Diaque P, Hernandez S, Rosas S, Kostic A, Caballero AE. Understanding the growing epidemic of type 2 diabetes in the Hispanic population living in the United States. Diabetes Metab Res Rev 2019; 35:e3097. [PMID: 30445663 PMCID: PMC6953173 DOI: 10.1002/dmrr.3097] [Citation(s) in RCA: 116] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 11/12/2018] [Accepted: 11/13/2018] [Indexed: 12/15/2022]
Abstract
The prevalence and incidence of type 2 diabetes (T2D) among the Hispanic population in the United States are higher than the national average. This is partly due to sociocultural factors, such as lower income and decreased access to education and health care, as well as a genetic susceptibility to obesity and higher insulin resistance. This review focuses on understanding the Hispanic population living in the United States from a multidisciplinary approach and underlines the importance of cultural, social, and biological factors in determining the increased risk of T2D in this population. An overview of the acute and chronic complications of T2D upon this population is included, which is of paramount importance to understand the toll that diabetes has upon this population, the health system, and society as a whole. Specific interventions directed to the Hispanic populations are needed to prevent and alleviate some of the burdens of T2D. Different prevention strategies based on medications, lifestyle modifications, and educational programmes are discussed herein. Diabetes self-management education (DSME) is a critical element of care of all people with diabetes and is considered necessary to improve patient outcomes. To be more effective, programmes should take into consideration cultural factors that influence the development and progression of diabetes. These interventions aim to enhance long-term effects by reducing the incidence, morbidity, and mortality of T2D in the Hispanic population of the United States.
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Affiliation(s)
| | - Paula Diaque
- Joslin Diabetes Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Sonia Hernandez
- Joslin Diabetes Center, Harvard Medical School, Boston, Massachusetts, USA
- Surgery Department, University of Chicago, Chicago, Illinois, USA
| | - Silvia Rosas
- Joslin Diabetes Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Aleksandar Kostic
- Joslin Diabetes Center, Harvard Medical School, Boston, Massachusetts, USA
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AMPK activation negatively regulates GDAP1, which influences metabolic processes and circadian gene expression in skeletal muscle. Mol Metab 2018; 16:12-23. [PMID: 30093355 PMCID: PMC6157647 DOI: 10.1016/j.molmet.2018.07.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Revised: 06/26/2018] [Accepted: 07/01/2018] [Indexed: 12/31/2022] Open
Abstract
Objective We sought to identify AMPK-regulated genes via bioinformatic analysis of microarray data generated from skeletal muscle of animal models with genetically altered AMPK activity. We hypothesized that such genes would play a role in metabolism. Ganglioside-induced differentiation-associated protein 1 (GDAP1), a gene which plays a role in mitochondrial fission and peroxisomal function in neuronal cells but whose function in skeletal muscle is undescribed, was identified and further validated. AMPK activation reduced GDAP1 expression in skeletal muscle. GDAP1 expression was elevated in skeletal muscle from type 2 diabetic patients but decreased after acute exercise. Methods The metabolic impact of GDAP1 silencing was determined in primary skeletal muscle cells via siRNA-transfections. Confocal microscopy was used to visualize whether silencing GDAP1 impacted mitochondrial network morphology and membrane potential. Results GDAP1 silencing increased mitochondrial protein abundance, decreased palmitate oxidation, and decreased non-mitochondrial respiration. Mitochondrial morphology was unaltered by GDAP1 silencing. GDAP1 silencing and treatment of cells with AMPK agonists altered several genes in the core molecular clock machinery. Conclusion We describe a role for GDAP1 in regulating mitochondrial proteins, circadian genes, and metabolic flux in skeletal muscle. Collectively, our results implicate GDAP1 in the circadian control of metabolism. Transcriptomic studies reveal GDAP1 mRNA is inversely associated with AMPK activity. GDAP1 silencing increases mitochondrial protein abundance in skeletal muscle. GDAP1 silencing influences expression of core molecular clock machinery. GDAP1 is a AMPK target involved in metabolism and circadian gene expression.
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Lichawska-Cieslar A, Pietrzycka R, Ligeza J, Kulecka M, Paziewska A, Kalita A, Dolicka DD, Wilamowski M, Miekus K, Ostrowski J, Mikula M, Jura J. RNA sequencing reveals widespread transcriptome changes in a renal carcinoma cell line. Oncotarget 2018; 9:8597-8613. [PMID: 29492220 PMCID: PMC5823589 DOI: 10.18632/oncotarget.24269] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 12/30/2017] [Indexed: 12/12/2022] Open
Abstract
We used RNA sequencing (RNA-Seq) technology to investigate changes in the transcriptome profile in the Caki-1 clear cell renal cell carcinoma (ccRCC) cells, which overexpress monocyte chemoattractant protein-induced protein 1 (MCPIP1). RNA-Seq data showed changes in 11.6% and 41.8% of the global transcriptome of Caki-1 cells overexpressing wild-type MCPIP1 or its D141N mutant, respectively. Gene ontology and KEGG pathway functional analyses showed that these transcripts encoded proteins involved in cell cycle progression, protein folding in the endoplasmic reticulum, hypoxia response and cell signalling. We identified 219 downregulated transcripts in MCPIP1-expressing cells that were either unchanged or upregulated in D141N-expressing cells. We validated downregulation of 15 transcripts belonging to different functional pathways by qRT-PCR. The growth and viability of MCPIP1-expressing cells was reduced because of elevated p21Cip1 levels. MCPIP1-expressing cells also showed reduced levels of DDB1 transcript that encodes component of the E3 ubiquitin ligase that degrades p21Cip1. These results demonstrate that MCPIP1 influences the growth and viability of ccRCC cells by increasing or decreasing the transcript levels for proteins involved in cell cycle progression, protein folding, hypoxia response, and cell signaling.
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Affiliation(s)
- Agata Lichawska-Cieslar
- Department of General Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Roza Pietrzycka
- Department of General Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Janusz Ligeza
- Department of General Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Maria Kulecka
- Departments of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, Warsaw, Poland
| | - Agnieszka Paziewska
- Departments of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, Warsaw, Poland
| | - Agata Kalita
- Department of General Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Dobrochna D. Dolicka
- Department of General Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Mateusz Wilamowski
- Department of General Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Katarzyna Miekus
- Department of General Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Jerzy Ostrowski
- Departments of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, Warsaw, Poland
- Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Centre and Institute of Oncology, Warsaw, Poland
| | - Michal Mikula
- Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Centre and Institute of Oncology, Warsaw, Poland
| | - Jolanta Jura
- Department of General Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
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13
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Fernández-Sanlés A, Sayols-Baixeras S, Subirana I, Degano IR, Elosua R. Association between DNA methylation and coronary heart disease or other atherosclerotic events: A systematic review. Atherosclerosis 2017; 263:325-333. [PMID: 28577936 DOI: 10.1016/j.atherosclerosis.2017.05.022] [Citation(s) in RCA: 91] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Revised: 04/05/2017] [Accepted: 05/17/2017] [Indexed: 11/24/2022]
Abstract
BACKGROUND AND AIMS The aim of this study was to perform a systematic review of the association between DNA methylation and coronary heart disease (CHD) or related atherosclerotic traits. METHODS A systematic review was designed. The condition of interest was DNA methylation, and the outcome was CHD or other atherosclerosis-related traits. Three DNA methylation approaches were considered: global methylation, candidate-gene, and epigenome-wide association studies (EWAS). A functional analysis was undertaken using the Ingenuity Pathway Analysis software. RESULTS In total, 51 articles were included in the analysis: 12 global methylation, 34 candidate-gene and 11 EWAS, with six studies using more than one approach. The results of the global methylation studies were inconsistent. The candidate-gene results were consistent for some genes, suggesting that hypermethylation in ESRα, ABCG1 and FOXP3 and hypomethylation in IL-6 were associated with CHD. The EWAS identified 84 genes showing differential methylation associated with CHD in more than one study. The probability of these findings was <1.37·10-5. One third of these genes have been related to obesity in genome-wide association studies. The functional analysis identified several diseases and functions related to these set of genes: inflammatory, metabolic and cardiovascular disease. CONCLUSIONS Global DNA methylation seems to be not associated with CHD. The evidence from candidate-gene studies was limited. The EWAS identified a set of 84 genes highlighting the relevance of obesity, inflammation, lipid and carbohydrate metabolism in CHD. This set of genes could be prioritized in future studies assessing the role of DNA methylation in CHD.
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Affiliation(s)
- Alba Fernández-Sanlés
- Cardiovascular Epidemiology and Genetics Research Group, REGICOR Study Group, IMIM (Hospital Del Mar Medical Research Institute), Barcelona, Catalonia, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Catalonia, Spain
| | - Sergi Sayols-Baixeras
- Cardiovascular Epidemiology and Genetics Research Group, REGICOR Study Group, IMIM (Hospital Del Mar Medical Research Institute), Barcelona, Catalonia, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Catalonia, Spain; CIBER Cardiovascular Diseases (CIBERCV), Barcelona, Catalonia, Spain
| | - Isaac Subirana
- Cardiovascular Epidemiology and Genetics Research Group, REGICOR Study Group, IMIM (Hospital Del Mar Medical Research Institute), Barcelona, Catalonia, Spain; CIBER Epidemiology and Public Health (CIBERESP), Barcelona, Catalonia, Spain
| | - Irene R Degano
- Cardiovascular Epidemiology and Genetics Research Group, REGICOR Study Group, IMIM (Hospital Del Mar Medical Research Institute), Barcelona, Catalonia, Spain; CIBER Cardiovascular Diseases (CIBERCV), Barcelona, Catalonia, Spain
| | - Roberto Elosua
- Cardiovascular Epidemiology and Genetics Research Group, REGICOR Study Group, IMIM (Hospital Del Mar Medical Research Institute), Barcelona, Catalonia, Spain; CIBER Cardiovascular Diseases (CIBERCV), Barcelona, Catalonia, Spain.
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14
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Abstract
Obesity is a major risk factor for chronic diseases and arises from the interactions between environmental factors and multiple genes. Psychosocial stress may affect the risk for obesity, modifying food intake and choice. A recent study suggested regulator of G-protein signaling 6 (RGS6) as a novel candidate gene for obesity in terms of reward-related feeding under stress. In this study, we tried to verify the unidentified connection between RGS6 and human obesity with psychosocial stress in a Korean population. A total of 1,462 adult subjects, who participated in the Korean Association Resource cohort project, were included for this analysis. Obesity-related traits including waist circumference, body mass index, and visceral adipose tissue were recorded. A total of 4 intronic SNPs for the RGS6 gene were used for this study. We found that interactions between SNP rs2239219 and psychosocial stress are significantly associated with abdominal obesity (p = 0.007). As risk allele of this SNP increased, prevalence of abdominal obesity under high-stress conditions gradually increased (p = 0.013). However, we found no SNPs-by-stress interaction effect on other adiposity phenotypes. This study suggests that RGS6 is closely linked to stress-induced abdominal obesity in Korean adults.
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Affiliation(s)
- Hyun-Jin Kim
- Institute of Health and Environment, Seoul National University, Seoul 08826, Republic of Korea
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15
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Kim HJ, Min JY, Min KB. Replication of Early B-cell Factor 1 (EBF1) Gene-by-psychosocial Stress Interaction Effects on Central Adiposity in a Korean Population. J Prev Med Public Health 2016; 49:253-259. [PMID: 27744667 PMCID: PMC5066423 DOI: 10.3961/jpmph.16.028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 07/10/2016] [Indexed: 12/18/2022] Open
Abstract
Objectives Central obesity plays a major role in the development of many chronic diseases, including cardiovascular disease and cancer. Chronic stress may be involved in the pathophysiology of central obesity. Although several large-scale genome-wide association studies have reported susceptibility genes for central adiposity, the effects of interactions between genes and psychosocial stress on central adiposity have rarely been examined. A recent study focusing on Caucasians discovered the novel gene early B-cell factor 1 (EBF1), which was associated with central obesity-related traits via interactions with stress levels. We aimed to evaluate EBF1 gene-by-stress interaction effects on central adiposity traits, including visceral adipose tissue (VAT), in Korean adults. Methods A total of 1467 Korean adults were included in this study. We selected 22 single-nucleotide polymorphisms (SNPs) in the EBF1 gene and analyzed their interactions with stress on central adiposity using additive, dominant, and recessive genetic modeling. Results The four SNPs that had strong linkage disequilibrium relationships (rs10061900, rs10070743, rs4704967, and rs10056564) demonstrated significant interactions with the waist-hip ratio in the dominant model (pint<0.007). In addition, two other SNPs (rs6556377 and rs13180086) were associated with VAT by interactions with stress levels, especially in the recessive genetic model (pint<0.007). As stress levels increased, the mean values of central adiposity traits according to SNP genotypes exhibited gradual but significant changes (p<0.05). Conclusions These results suggest that the common genetic variants for EBF1 are associated with central adiposity through interactions with stress levels, emphasizing the importance of managing stress in the prevention of central obesity.
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Affiliation(s)
- Hyun-Jin Kim
- Institute of Health and Environment, Seoul National University, Seoul, Korea
| | - Jin-Young Min
- Institute of Health and Environment, Seoul National University, Seoul, Korea
| | - Kyoung-Bok Min
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Korea
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16
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Kim JY, DeMenna JT, Puppala S, Chittoor G, Schneider J, Duggirala R, Mandarino LJ, Shaibi GQ, Coletta DK. Physical activity and FTO genotype by physical activity interactive influences on obesity. BMC Genet 2016; 17:47. [PMID: 26908368 PMCID: PMC4765034 DOI: 10.1186/s12863-016-0357-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 02/17/2016] [Indexed: 01/16/2023] Open
Abstract
Background Although the effect of the fat mass and obesity-associated (FTO) gene on adiposity is well established, there is a lack of evidence whether physical activity (PA) modifies the effect of FTO variants on obesity in Latino populations. Therefore, the purpose of this study was to examine PA influences and interactive effects between FTO variants and PA on measures of adiposity in Latinos. Results After controlling for age and sex, participants who did not engage in regular PA exhibited higher BMI, fat mass, HC, and WC with statistical significance (P < 0.001). Although significant associations between the three FTO genotypes and adiposity measures were found, none of the FTO genotype by PA interaction assessments revealed nominally significant associations. However, several of such interactive influences exhibited considerable trend towards association. Conclusions These data suggest that adiposity measures are associated with PA and FTO variants in Latinos, but the impact of their interactive influences on these obesity measures appear to be minimal. Future studies with large sample sizes may help to determine whether individuals with specific FTO variants exhibit differential responses to PA interventions. Electronic supplementary material The online version of this article (doi:10.1186/s12863-016-0357-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Joon Young Kim
- Kinesiology Program, School of Nutrition and Health Promotion, Arizona State University, Phoenix, AZ, USA.
| | - Jacob T DeMenna
- College of Health Solutions, School for the Science of Health Care Delivery, Arizona State University, 550N. 3rd Street, Phoenix, 85004, AZ, USA.
| | - Sobha Puppala
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX, USA.
| | - Geetha Chittoor
- Department of Nutrition and UNC Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, NC, USA.
| | - Jennifer Schneider
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX, USA.
| | - Ravindranath Duggirala
- South Texas Diabetes and Obesity Institute Edinburg Regional Academic Health Center University of Texas Health Science Center at San Antonio, San Antonio, TX, USA.
| | - Lawrence J Mandarino
- College of Health Solutions, School for the Science of Health Care Delivery, Arizona State University, 550N. 3rd Street, Phoenix, 85004, AZ, USA. .,Mayo/ASU Center for Metabolic and Vascular Biology, Phoenix, AZ, USA.
| | - Gabriel Q Shaibi
- Kinesiology Program, School of Nutrition and Health Promotion, Arizona State University, Phoenix, AZ, USA. .,Mayo/ASU Center for Metabolic and Vascular Biology, Phoenix, AZ, USA. .,College of Nursing & Health Innovation, Arizona State University, Phoenix, AZ, USA.
| | - Dawn K Coletta
- College of Health Solutions, School for the Science of Health Care Delivery, Arizona State University, 550N. 3rd Street, Phoenix, 85004, AZ, USA. .,Mayo/ASU Center for Metabolic and Vascular Biology, Phoenix, AZ, USA.
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17
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Genetic Diversity and Association Studies in US Hispanic/Latino Populations: Applications in the Hispanic Community Health Study/Study of Latinos. Am J Hum Genet 2016; 98:165-84. [PMID: 26748518 DOI: 10.1016/j.ajhg.2015.12.001] [Citation(s) in RCA: 217] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 12/02/2015] [Indexed: 12/20/2022] Open
Abstract
US Hispanic/Latino individuals are diverse in genetic ancestry, culture, and environmental exposures. Here, we characterized and controlled for this diversity in genome-wide association studies (GWASs) for the Hispanic Community Health Study/Study of Latinos (HCHS/SOL). We simultaneously estimated population-structure principal components (PCs) robust to familial relatedness and pairwise kinship coefficients (KCs) robust to population structure, admixture, and Hardy-Weinberg departures. The PCs revealed substantial genetic differentiation within and among six self-identified background groups (Cuban, Dominican, Puerto Rican, Mexican, and Central and South American). To control for variation among groups, we developed a multi-dimensional clustering method to define a "genetic-analysis group" variable that retains many properties of self-identified background while achieving substantially greater genetic homogeneity within groups and including participants with non-specific self-identification. In GWASs of 22 biomedical traits, we used a linear mixed model (LMM) including pairwise empirical KCs to account for familial relatedness, PCs for ancestry, and genetic-analysis groups for additional group-associated effects. Including the genetic-analysis group as a covariate accounted for significant trait variation in 8 of 22 traits, even after we fit 20 PCs. Additionally, genetic-analysis groups had significant heterogeneity of residual variance for 20 of 22 traits, and modeling this heteroscedasticity within the LMM reduced genomic inflation for 19 traits. Furthermore, fitting an LMM that utilized a genetic-analysis group rather than a self-identified background group achieved higher power to detect previously reported associations. We expect that the methods applied here will be useful in other studies with multiple ethnic groups, admixture, and relatedness.
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18
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Brune JE, Kern M, Kunath A, Flehmig G, Schön MR, Lohmann T, Dressler M, Dietrich A, Fasshauer M, Kovacs P, Stumvoll M, Blüher M, Klöting N. Fat depot-specific expression of HOXC9 and HOXC10 may contribute to adverse fat distribution and related metabolic traits. Obesity (Silver Spring) 2016; 24:51-9. [PMID: 26647900 DOI: 10.1002/oby.21317] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 07/08/2015] [Accepted: 07/24/2015] [Indexed: 01/05/2023]
Abstract
OBJECTIVE Independent previous studies in both rodents and humans suggest a role of developmental genes in the origin of obesity and body fat distribution. Here, the hypothesis that human adipose tissue (AT) expression of the developmental genes homeobox transcription factors C9 (HOXC9) and C10 (HOXC10) is fat depot-specific and related to obesity-related traits was tested. METHODS In 636 individuals, HOXC9 and HOXC10 mRNA expression was investigated in paired abdominal subcutaneous (SC) and omental AT samples in relation to a wide range of age, BMI, fat distribution, and metabolic parameters and in subfractions of isolated adipocytes and cells of the stromal vascular fraction (SVF). RESULTS HOXC9 and HOXC10 mRNA expression is significantly higher in SC compared to omental AT. HOXC9 and HOXC10 mRNA expression significantly correlates with body fat mass, even after adjustment for age and gender. In smaller subgroups (depending on the availability of data), fat depot-related significant gender- and BMI-independent associations between HOXC9 and HOXC10 gene expression and parameters of glucose metabolism and AT biology were found (e.g., adipocyte size). CONCLUSIONS Taken together, these data suggest that HOXC9 and HOXC10 may play an important role in the development of obesity, adverse fat distribution, and subsequent alterations in whole-body metabolism and AT function.
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Affiliation(s)
- Jakob E Brune
- IFB AdiposityDiseases, University of Leipzig, Leipzig, Germany
| | - Matthias Kern
- Department of Medicine, University of Leipzig, Leipzig, Germany
| | - Anne Kunath
- Department of Medicine, University of Leipzig, Leipzig, Germany
- German Center for Diabetes Research (DZD), Leipzig, Germany
| | - Gesine Flehmig
- Department of Medicine, University of Leipzig, Leipzig, Germany
- German Center for Diabetes Research (DZD), Leipzig, Germany
| | - Michael R Schön
- Städtisches Klinikum Karlsruhe, Clinic of Visceral Surgery, Karlsruhe, Germany
| | | | | | - Arne Dietrich
- IFB AdiposityDiseases, University of Leipzig, Leipzig, Germany
- Department of Surgery, University of Leipzig, Leipzig, Germany
| | | | - Peter Kovacs
- Department of Medicine, University of Leipzig, Leipzig, Germany
| | | | - Matthias Blüher
- Department of Medicine, University of Leipzig, Leipzig, Germany
| | - Nora Klöting
- IFB AdiposityDiseases, University of Leipzig, Leipzig, Germany
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Srivastava A, Srivastava N, Mittal B. Genetics of Obesity. Indian J Clin Biochem 2015; 31:361-71. [PMID: 27605733 DOI: 10.1007/s12291-015-0541-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 12/08/2015] [Indexed: 12/29/2022]
Abstract
Numerous classical genetic studies have proved that genes are contributory factors for obesity. Genes are directly responsible for obesity associated disorders such as Bardet-Biedl and Prader-Willi syndromes. However, both genes as well as environment are associated with obesity in the general population. Genetic epidemiological approaches, particularly genome-wide association studies, have unraveled many genes which play important roles in human obesity. Elucidation of their biological functions can be very useful for understanding pathobiology of obesity. In the near future, further exploration of obesity genetics may help to develop useful diagnostic and predictive tests for obesity treatment.
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Affiliation(s)
- Apurva Srivastava
- Department of Medical Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Rae Bareli Road, Lucknow, Uttar Pradesh 226014 India ; Department of Physiology, King George's Medical University, Chowk, Lucknow, Uttar Pradesh 226003 India
| | - Neena Srivastava
- Department of Physiology, King George's Medical University, Chowk, Lucknow, Uttar Pradesh 226003 India
| | - Balraj Mittal
- Department of Medical Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Rae Bareli Road, Lucknow, Uttar Pradesh 226014 India
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20
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Kim HJ, Park JH, Lee S, Son HY, Hwang J, Chae J, Yun JM, Kwon H, Kim JI, Cho B. A Common Variant of NGEF Is Associated with Abdominal Visceral Fat in Korean Men. PLoS One 2015; 10:e0137564. [PMID: 26340433 PMCID: PMC4560439 DOI: 10.1371/journal.pone.0137564] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 08/17/2015] [Indexed: 12/28/2022] Open
Abstract
Central adiposity, rather than body mass index (BMI), is a key pathophysiological feature of the development of obesity-related diseases. Although genetic studies by anthropometric measures such as waist circumference have been widely conducted, genetic studies for abdominal fat deposition measured by computed tomography (CT) have been rarely performed. A total of 1,243 participants who were recruited from two health check-up centers were included in this study. We selected four and three single-nucleotide polymorphisms (SNPs) in NGEF and RGS6, respectively, and analyzed the associations between the seven SNPs and central adiposity measured by CT using an additive, dominant, or recessive model. The participants were generally healthy middle-aged men (50.7 ± 5.3 years). In the additive model, the rs11678490 A allele of NGEF was significantly associated with total adipose tissue, visceral adipose tissue (VAT), and subcutaneous adipose tissue (all P < 0.05). The AA genotype of this SNP in the recessive model showed a more significant association with all adiposity traits, and its association with VAT remained significant even after adjustment for BMI (P = 0.005). In the overall or visceral obesity group analysis, the AA genotype of rs11678490 showed no association with overall obesity (P = 0.148), whereas it was significantly associated with visceral obesity both before (P = 0.010) and after (P = 0.029) adjustment for BMI. In particular, an AA genotype effect was conspicuous between lower and upper groups with 5% extreme VAT phenotypes (OR = 9.59, 95% CI = 1.50-61.31). However, we found no significant association between SNPs of RGS6 and central adiposity. We identified a visceral-fat-associated SNP, rs11678490 of NGEF, in Korean men. This study suggests that the genetic background of central adiposity and BMI is different, and that additional efforts should be made to find the unique genetic architecture of intra-abdominal fat accumulation.
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Affiliation(s)
- Hyun-Jin Kim
- Institute of Health and Environment, School of Public Health, Seoul National University, Seoul, South Korea
| | - Jin-Ho Park
- Department of Family Medicine, Seoul National University Hospital, Seoul, South Korea
| | - Seungbok Lee
- Genomic Medicine Institute (GMI), Medical Research Center, Seoul National University, Seoul, South Korea
| | - Ho-Young Son
- Department of Biochemistry, Seoul National University College of Medicine, Seoul, South Korea
| | - Jinha Hwang
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, South Korea
| | - Jeesoo Chae
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, South Korea
| | - Jae Moon Yun
- Department of Family Medicine, Seoul National University Hospital, Seoul, South Korea
| | - Hyuktae Kwon
- Department of Family Medicine, Healthcare Research Institute, Seoul National University Hospital Healthcare System Gangnam Center, Seoul, South Korea
| | - Jong-Il Kim
- Genomic Medicine Institute (GMI), Medical Research Center, Seoul National University, Seoul, South Korea
- Department of Biochemistry, Seoul National University College of Medicine, Seoul, South Korea
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, South Korea
- * E-mail: (JK); (BC)
| | - Belong Cho
- Department of Family Medicine, Seoul National University Hospital, Seoul, South Korea
- * E-mail: (JK); (BC)
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21
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Stewart A, Maity B, Fisher RA. Two for the Price of One: G Protein-Dependent and -Independent Functions of RGS6 In Vivo. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2015; 133:123-51. [PMID: 26123305 DOI: 10.1016/bs.pmbts.2015.03.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Regulator of G protein signaling 6 (RGS6) is unique among the members of the RGS protein family as it remains the only protein with the demonstrated capacity to control G protein-dependent and -independent signaling cascades in vivo. RGS6 inhibits signaling mediated by γ-aminobutyric acid B receptors, serotonin 1A receptors, μ opioid receptors, and muscarinic acetylcholine 2 receptors. RGS6 deletion triggers distinct behavioral phenotypes resulting from potentiated signaling by these G protein-coupled receptors namely ataxia, a reduction in anxiety and depression, enhanced analgesia, and increased parasympathetic tone, respectively. In addition, RGS6 possesses potent proapoptotic and growth suppressive actions. In heart, RGS6-dependent reactive oxygen species (ROS) production promotes doxorubicin (Dox)-induced cardiomyopathy, while in cancer cells RGS6/ROS signaling is necessary for activation of the ataxia telangiectasia mutated/p53/apoptosis pathway required for the chemotherapeutic efficacy of Dox. Further, by facilitating Tip60 (trans-acting regulator protein of HIV type 1-interacting protein 60 kDa)-dependent DNA methyltransferase 1 degradation, RGS6 suppresses cellular transformation in response to oncogenic Ras. The culmination of these G protein-independent actions results in potent tumor suppressor actions of RGS6 in the murine mammary epithelium. This work summarizes evidence from human genetic studies and model animals implicating RGS6 in normal physiology, disease, and the pharmacological actions of multiple drugs. Though efforts by multiple laboratories have contributed to the ever-growing RGS6 oeuvre, the pleiotropic nature of this gene will likely lead to additional work detailing the importance of RGS6 in neuropsychiatric disorders, cardiovascular disease, and cancer.
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Affiliation(s)
- Adele Stewart
- Department of Pharmacology, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Biswanath Maity
- Department of Pharmacology, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Rory A Fisher
- Department of Pharmacology, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA.
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Valera B, Sohani Z, Rana A, Poirier P, Anand SS. The ethnoepidemiology of obesity. Can J Cardiol 2014; 31:131-41. [PMID: 25661548 DOI: 10.1016/j.cjca.2014.10.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Revised: 10/02/2014] [Accepted: 10/06/2014] [Indexed: 12/25/2022] Open
Abstract
The prevalence of overweight and obesity varies significantly across ethnic groups and among aboriginal people in Canada and appears to be increasing overall in children and youth, which will have significant health consequences in the future. Individual health behaviours, genetic predisposition, and community-level factors all contribute to the high burden of overweight and obesity across communities in Canada. Preliminary studies indicate that individuals who live in neighbourhoods in Canada with increased walkability, fewer fast food outlets, and higher socioeconomic status have lower rates of overweight/obesity when compared with other neighbourhoods. However, more research is required to understand the impact of community level factors on overweight/obesity trends in Canadian ethnic groups, including children and youth, and aboriginal people.
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Affiliation(s)
- Beatriz Valera
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Québec, Québec, Canada
| | - Zahra Sohani
- Population Genomics Program, Department of Clinical Epidemiology & Biostatistics, Hamilton, Ontario, Canada; Chanchlani Research Centre, McMaster University, Hamilton, Ontario, Canada
| | - Ayesha Rana
- Population Genomics Program, Department of Clinical Epidemiology & Biostatistics, Hamilton, Ontario, Canada; Chanchlani Research Centre, McMaster University, Hamilton, Ontario, Canada
| | - Paul Poirier
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Québec, Québec, Canada; Faculté de pharmacie de l'Université Laval, Québec, Québec, Canada
| | - Sonia S Anand
- Population Genomics Program, Department of Clinical Epidemiology & Biostatistics, Hamilton, Ontario, Canada; Chanchlani Research Centre, McMaster University, Hamilton, Ontario, Canada; Department of Medicine, McMaster University, Hamilton, Ontario, Canada.
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Goni L, Milagro FI, Cuervo M, Martínez JA. Single-nucleotide polymorphisms and DNA methylation markers associated with central obesity and regulation of body weight. Nutr Rev 2014; 72:673-90. [DOI: 10.1111/nure.12143] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Affiliation(s)
- Leticia Goni
- Department of Nutrition, Food Science and Physiology; Centre for Nutrition Research; University of Navarra; Pamplona Spain
| | - Fermín I Milagro
- Department of Nutrition, Food Science and Physiology; Centre for Nutrition Research; University of Navarra; Pamplona Spain
- Instituto de Salud Carlos III; CIBER Fisiología Obesidad y Nutrición (CIBERobn); Madrid Spain
| | - Marta Cuervo
- Department of Nutrition, Food Science and Physiology; Centre for Nutrition Research; University of Navarra; Pamplona Spain
- Instituto de Salud Carlos III; CIBER Fisiología Obesidad y Nutrición (CIBERobn); Madrid Spain
| | - J Alfredo Martínez
- Department of Nutrition, Food Science and Physiology; Centre for Nutrition Research; University of Navarra; Pamplona Spain
- Instituto de Salud Carlos III; CIBER Fisiología Obesidad y Nutrición (CIBERobn); Madrid Spain
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24
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Crowther NJ, Ferris WF. The impact of insulin resistance, gender, genes, glucocorticoids and ethnicity on body fat distribution. JOURNAL OF ENDOCRINOLOGY, METABOLISM AND DIABETES OF SOUTH AFRICA 2014. [DOI: 10.1080/22201009.2010.10872241] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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Ma J, Sloan M, Fox CS, Hoffmann U, Smith CE, Saltzman E, Rogers GT, Jacques PF, McKeown NM. Sugar-sweetened beverage consumption is associated with abdominal fat partitioning in healthy adults. J Nutr 2014; 144:1283-90. [PMID: 24944282 PMCID: PMC4093984 DOI: 10.3945/jn.113.188599] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Abdominal adiposity, particularly visceral adipose tissue (VAT), is independently linked to the pathogenesis of diabetes and cardiovascular diseases. Emerging evidence suggests that greater intake of sugar-sweetened beverages (SSBs) may be associated with abnormal fat accumulation in VAT. We examined whether habitual SSB consumption and diet soda intakes are differentially associated with deposition of body fat. We conducted a cross-sectional analysis using previously collected data in 2596 middle-aged adults (1306 men and 1290 women) from the Framingham Heart Study Offspring and Third Generation cohorts. VAT and abdominal subcutaneous adipose tissue (SAT) were measured using multidetector computed tomography. Habitual intake of SSBs and diet soda was assessed by a validated food frequency questionnaire. We observed that SSB consumption was positively associated with VAT after adjustment for SAT and other potential confounders (P-trend < 0.001). We observed an inverse association between SSB consumption and SAT (P-trend = 0.04) that persisted after additional adjustment for VAT (P-trend < 0.001). Higher SSB consumption was positively associated with the VAT-to-SAT ratio (P-trend < 0.001). No significant association was found between diet soda consumption and either VAT or the VAT-to-SAT ratio, but diet soda was positively associated with SAT (P-trend < 0.001). Daily consumers of SSBs had a 10% higher absolute VAT volume and a 15% greater VAT-to-SAT ratio compared with nonconsumers, whereas consumption of diet soda was not associated with either volume or distribution of VAT.
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Affiliation(s)
| | - Matthew Sloan
- University of Massachusetts Medical School, Worcester, MA
| | - Caroline S. Fox
- National Heart, Lung, and Blood Institute Framingham Heart Study, Framingham, MA,Division of Endocrinology and Metabolism, Department of Medicine, Brigham and Women’s Hospital, Boston, MA,Harvard Medical School, Boston, MA; and
| | - Udo Hoffmann
- Harvard Medical School, Boston, MA; and,Radiology Department, Massachusetts General Hospital, Boston, MA
| | | | - Edward Saltzman
- Energy Metabolism Laboratory, Jean Mayer USDA Human Nutrition Research Center on Aging at Tufts University, Boston, MA
| | | | | | - Nicola M. McKeown
- Nutrition Epidemiology Program,,To whom correspondence should be addressed. E-mail:
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26
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Schleinitz D, Böttcher Y, Blüher M, Kovacs P. The genetics of fat distribution. Diabetologia 2014; 57:1276-86. [PMID: 24632736 DOI: 10.1007/s00125-014-3214-z] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Accepted: 02/18/2014] [Indexed: 12/22/2022]
Abstract
Fat stored in visceral depots makes obese individuals more prone to complications than subcutaneous fat. There is good evidence that body fat distribution (FD) is controlled by genetic factors. WHR, a surrogate measure of FD, shows significant heritability of up to ∼60%, even after adjusting for BMI. Genetic variants have been linked to various forms of altered FD such as lipodystrophies; however, the polygenic background of visceral obesity has only been sparsely investigated in the past. Recent genome-wide association studies (GWAS) for measures of FD revealed numerous loci harbouring genes potentially regulating FD. In addition, genes with fat depot-specific expression patterns (in particular subcutaneous vs visceral adipose tissue) provide plausible candidate genes involved in the regulation of FD. Many of these genes are differentially expressed in various fat compartments and correlate with obesity-related traits, thus further supporting their role as potential mediators of metabolic alterations associated with a distinct FD. Finally, developmental genes may at a very early stage determine specific FD in later life. Indeed, genes such as TBX15 not only manifest differential expression in various fat depots, but also correlate with obesity and related traits. Moreover, recent GWAS identified several polymorphisms in developmental genes (including TBX15, HOXC13, RSPO3 and CPEB4) strongly associated with FD. More accurate methods, including cardiometabolic imaging, for assessment of FD are needed to promote our understanding in this field, where the main focus is now to unravel the yet unknown biological function of these novel 'fat distribution genes'.
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Affiliation(s)
- Dorit Schleinitz
- Integrated Research and Treatment Center (IFB) AdiposityDiseases, University of Leipzig, Liebigstr. 21, 04103, Leipzig, Germany
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27
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Charles BA, Shriner D, Rotimi CN. Accounting for linkage disequilibrium in association analysis of diverse populations. Genet Epidemiol 2014; 38:265-73. [PMID: 24464495 DOI: 10.1002/gepi.21788] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Revised: 11/14/2013] [Accepted: 12/03/2013] [Indexed: 12/25/2022]
Abstract
The National Human Genome Research Institute's catalog of published genome-wide association studies (GWAS) lists over 10,000 genetic variants collectively associated with over 800 human diseases or traits. Most of these GWAS have been conducted in European-ancestry populations. Findings gleaned from these studies have led to identification of disease-associated loci and biologic pathways involved in disease etiology. In multiple instances, these genomic findings have led to the development of novel medical therapies or evidence for prescribing a given drug as the appropriate treatment for a given individual beyond phenotypic appearances or socially defined constructs of race or ethnicity. Such findings have implications for populations throughout the globe and GWAS are increasingly being conducted in more diverse populations. A major challenge for investigators seeking to follow up genomic findings between diverse populations is discordant patterns of linkage disequilibrium (LD). We provide an overview of common measures of LD and opportunities for their use in novel methods designed to address challenges associated with following up GWAS conducted in European-ancestry populations in African-ancestry populations or, more generally, between populations with discordant LD patterns. We detail the strengths and weaknesses associated with different approaches. We also describe application of these strategies in follow-up studies of populations with concordant LD patterns (replication) or discordant LD patterns (transferability) as well as fine-mapping studies. We review application of these methods to a variety of traits and diseases.
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Affiliation(s)
- Bashira A Charles
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, Maryland, United States of America
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28
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Fall T, Ingelsson E. Genome-wide association studies of obesity and metabolic syndrome. Mol Cell Endocrinol 2014; 382:740-757. [PMID: 22963884 DOI: 10.1016/j.mce.2012.08.018] [Citation(s) in RCA: 200] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Revised: 05/04/2012] [Accepted: 08/27/2012] [Indexed: 11/29/2022]
Abstract
Until just a few years ago, the genetic determinants of obesity and metabolic syndrome were largely unknown, with the exception of a few forms of monogenic extreme obesity. Since genome-wide association studies (GWAS) became available, large advances have been made. The first single nucleotide polymorphism robustly associated with increased body mass index (BMI) was in 2007 mapped to a gene with for the time unknown function. This gene, now known as fat mass and obesity associated (FTO) has been repeatedly replicated in several ethnicities and is affecting obesity by regulating appetite. Since the first report from a GWAS of obesity, an increasing number of markers have been shown to be associated with BMI, other measures of obesity or fat distribution and metabolic syndrome. This systematic review of obesity GWAS will summarize genome-wide significant findings for obesity and metabolic syndrome and briefly give a few suggestions of what is to be expected in the next few years.
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Affiliation(s)
- Tove Fall
- Dept. of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Erik Ingelsson
- Dept. of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 77 Stockholm, Sweden.
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29
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Pei YF, Zhang L, Liu Y, Li J, Shen H, Liu YZ, Tian Q, He H, Wu S, Ran S, Han Y, Hai R, Lin Y, Zhu J, Zhu XZ, Papasian CJ, Deng HW. Meta-analysis of genome-wide association data identifies novel susceptibility loci for obesity. Hum Mol Genet 2013; 23:820-30. [PMID: 24064335 DOI: 10.1093/hmg/ddt464] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Obesity is a major public health problem with strong genetic determination. Multiple genetic variants have been implicated for obesity by conducting genome-wide association (GWA) studies, primarily focused on body mass index (BMI). Fat body mass (FBM) is phenotypically more homogeneous than BMI and is more appropriate for obesity research; however, relatively few studies have been conducted on FBM. Aiming to identify variants associated with obesity, we carried out meta-analyses of seven GWA studies for BMI-related traits including FBM, and followed these analyses by de novo replication. The discovery cohorts consisted of 21 969 individuals from diverse ethnic populations and a total of over 4 million genotyped or imputed SNPs. The de novo replication cohorts consisted of 6663 subjects from two independent samples. To complement individual SNP-based association analyses, we also carried out gene-based GWA analyses in which all variations within a gene were considered jointly. Individual SNP-based association analyses identified a novel locus 1q21 [rs2230061, CTSS (Cathepsin S)] that was associated with FBM after the adjustment of lean body mass (LBM) (P = 3.57 × 10(-8)) at the genome-wide significance level. Gene-based association analyses identified a novel gene NLK (nemo-like kinase) in 17q11 that was significantly associated with FBM adjusted by LBM. In addition, we confirmed three previously reported obesity susceptibility loci: 16q12 [rs62033400, P = 1.97 × 10(-14), FTO (fat mass and obesity associated)], 18q22 [rs6567160, P = 8.09 × 10(-19), MC4R (melanocortin 4 receptor)] and 2p25 [rs939583, P = 1.07 × 10(-7), TMEM18 (transmembrane protein 18)]. We also found that rs6567160 may exert pleiotropic effects to both FBM and LBM. Our results provide additional insights into the molecular genetic basis of obesity and may provide future targets for effective prevention and therapeutic intervention.
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Affiliation(s)
- Yu-Fang Pei
- Center of System Biomedical Sciences, University of Shanghai for Science and Technology, Shanghai 200093, P R China
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A multi-platform draft de novo genome assembly and comparative analysis for the Scarlet Macaw (Ara macao). PLoS One 2013; 8:e62415. [PMID: 23667475 PMCID: PMC3648530 DOI: 10.1371/journal.pone.0062415] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Accepted: 03/21/2013] [Indexed: 12/31/2022] Open
Abstract
Data deposition to NCBI Genomes: This Whole Genome Shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession AMXX00000000 (SMACv1.0, unscaffolded genome assembly). The version described in this paper is the first version (AMXX01000000). The scaffolded assembly (SMACv1.1) has been deposited at DDBJ/EMBL/GenBank under the accession AOUJ00000000, and is also the first version (AOUJ01000000). Strong biological interest in traits such as the acquisition and utilization of speech, cognitive abilities, and longevity catalyzed the utilization of two next-generation sequencing platforms to provide the first-draft de novo genome assembly for the large, new world parrot Ara macao (Scarlet Macaw). Despite the challenges associated with genome assembly for an outbred avian species, including 951,507 high-quality putative single nucleotide polymorphisms, the final genome assembly (>1.035 Gb) includes more than 997 Mb of unambiguous sequence data (excluding N's). Cytogenetic analyses including ZooFISH revealed complex rearrangements associated with two scarlet macaw macrochromosomes (AMA6, AMA7), which supports the hypothesis that translocations, fusions, and intragenomic rearrangements are key factors associated with karyotype evolution among parrots. In silico annotation of the scarlet macaw genome provided robust evidence for 14,405 nuclear gene annotation models, their predicted transcripts and proteins, and a complete mitochondrial genome. Comparative analyses involving the scarlet macaw, chicken, and zebra finch genomes revealed high levels of nucleotide-based conservation as well as evidence for overall genome stability among the three highly divergent species. Application of a new whole-genome analysis of divergence involving all three species yielded prioritized candidate genes and noncoding regions for parrot traits of interest (i.e., speech, intelligence, longevity) which were independently supported by the results of previous human GWAS studies. We also observed evidence for genes and noncoding loci that displayed extreme conservation across the three avian lineages, thereby reflecting their likely biological and developmental importance among birds.
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Abstract
Excess intra-abdominal adipose tissue accumulation, often termed visceral obesity, is part of a phenotype including dysfunctional subcutaneous adipose tissue expansion and ectopic triglyceride storage closely related to clustering cardiometabolic risk factors. Hypertriglyceridemia; increased free fatty acid availability; adipose tissue release of proinflammatory cytokines; liver insulin resistance and inflammation; increased liver VLDL synthesis and secretion; reduced clearance of triglyceride-rich lipoproteins; presence of small, dense LDL particles; and reduced HDL cholesterol levels are among the many metabolic alterations closely related to this condition. Age, gender, genetics, and ethnicity are broad etiological factors contributing to variation in visceral adipose tissue accumulation. Specific mechanisms responsible for proportionally increased visceral fat storage when facing positive energy balance and weight gain may involve sex hormones, local cortisol production in abdominal adipose tissues, endocannabinoids, growth hormone, and dietary fructose. Physiological characteristics of abdominal adipose tissues such as adipocyte size and number, lipolytic responsiveness, lipid storage capacity, and inflammatory cytokine production are significant correlates and even possible determinants of the increased cardiometabolic risk associated with visceral obesity. Thiazolidinediones, estrogen replacement in postmenopausal women, and testosterone replacement in androgen-deficient men have been shown to favorably modulate body fat distribution and cardiometabolic risk to various degrees. However, some of these therapies must now be considered in the context of their serious side effects. Lifestyle interventions leading to weight loss generally induce preferential mobilization of visceral fat. In clinical practice, measuring waist circumference in addition to the body mass index could be helpful for the identification and management of a subgroup of overweight or obese patients at high cardiometabolic risk.
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Affiliation(s)
- André Tchernof
- Endocrinology and Genomics Axis, Centre Hospitalier Universitaire de Québec, Québec, Canada
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32
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Liu J, Lewinger JP, Gilliland FD, Gauderman WJ, Conti DV. Confounding and heterogeneity in genetic association studies with admixed populations. Am J Epidemiol 2013; 177:351-60. [PMID: 23334005 DOI: 10.1093/aje/kws234] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Association studies among admixed populations pose many challenges including confounding of genetic effects due to population substructure and heterogeneity due to different patterns of linkage disequilibrium (LD). We use simulations to investigate controlling for confounding by indicators of global ancestry and the impact of including a covariate for local ancestry. In addition, we investigate the use of an interaction term between a single-nucleotide polymorphism (SNP) and local ancestry to capture heterogeneity in SNP effects. Although adjustment for global ancestry can control for confounding, additional adjustment for local ancestry may increase power when the induced admixture LD is in the opposite direction as the LD in the ancestral population. However, if the induced LD is in the same direction, there is the potential for reduced power because of overadjustment. Furthermore, the inclusion of a SNP by local ancestry interaction term can increase power when there is substantial differential LD between ancestry populations. We examine these approaches in genome-wide data using the University of Southern California's Children's Health Study investigating asthma risk. The analysis highlights rs10519951 (P = 8.5 × 10(-7)), a SNP lacking any evidence of association from a conventional analysis (P = 0.5).
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Affiliation(s)
- Jinghua Liu
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA
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Belsky DW, Moffitt TE, Sugden K, Williams B, Houts R, McCarthy J, Caspi A. Development and evaluation of a genetic risk score for obesity. BIODEMOGRAPHY AND SOCIAL BIOLOGY 2013; 59:85-100. [PMID: 23701538 PMCID: PMC3671353 DOI: 10.1080/19485565.2013.774628] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Multi-locus profiles of genetic risk, so-called "genetic risk scores," can be used to translate discoveries from genome-wide association studies into tools for population health research. We developed a genetic risk score for obesity from results of 16 published genome-wide association studies of obesity phenotypes in European-descent samples. We then evaluated this genetic risk score using data from the Atherosclerosis Risk in Communities (ARIC) cohort GWAS sample (N = 10,745, 55% female, 77% white, 23% African American). Our 32-locus GRS was a statistically significant predictor of body mass index (BMI) and obesity among ARIC whites [for BMI, r = 0.13, p<1 × 10(-30); for obesity, area under the receiver operating characteristic curve (AUC) = 0.57 (95% CI 0.55-0.58)]. The GRS predicted differences in obesity risk net of demographic, geographic, and socioeconomic information. The GRS performed less well among African Americans. The genetic risk score we derived from GWAS provides a molecular measurement of genetic predisposition to elevated BMI and obesity.[Supplemental materials are available for this article. Go to the publisher's online edition of Biodemography and Social Biology for the following resource: Supplement to Development & Evaluation of a Genetic Risk Score for Obesity.].
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Affiliation(s)
- Daniel W Belsky
- Department of Health Policy & Management , University of North Carolina , Chapel Hill , NC, USA.
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Positive natural selection of TRIB2, a novel gene that influences visceral fat accumulation, in East Asia. Hum Genet 2012; 132:201-17. [PMID: 23108367 DOI: 10.1007/s00439-012-1240-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Accepted: 10/16/2012] [Indexed: 10/27/2022]
Abstract
Accumulation of visceral fat increases cardiovascular mortality in industrialized societies. However, during the evolution of the modern human, visceral fat may have acted as energy storage facility to survive in times of famine. Therefore, past natural selection might contribute to shaping the variation of visceral fat accumulation in present populations. Here, we report that the gene encoding tribbles homolog 2 (TRIB2) influenced visceral fat accumulation and was operated by recent positive natural selection in East Asians. Our candidate gene association analysis on 11 metabolic traits of 5,810 East Asians revealed that rs1057001, a T/A transversion polymorphism in 3'untranslated region (UTR) of TRIB2, was strongly associated with visceral fat area (VFA) and waist circumference adjusted for body mass index (P = 2.7 × 10(-6) and P = 9.0 × 10(-6), respectively). rs1057001 was in absolute linkage disequilibrium with a conserved insertion-deletion polymorphism in the 3'UTR and was associated with allelic imbalance of TRIB2 transcript levels in adipose tissues. rs1057001 showed high degree of interpopulation variation of the allele frequency; the low-VFA-associated A allele was found with high frequencies in East Asians. Haplotypes containing the rs1057001 A allele exhibited a signature of a selective sweep, which may have occurred 16,546-27,827 years ago in East Asians. Given the predominance of the thrifty gene hypothesis, it is surprising that the apparently non-thrifty allele was selectively favored in the evolution of modern humans. Environmental/physiological factors other than famine would be needed to explain the non-neutral evolution of TRIB2 in East Asians.
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Pereira RI, Wang CCL, Hosokawa P, Dickinson LM, Chonchol M, Krantz MJ, Steiner JF, Bessesen DH, Havranek EP, Long CS. Circulating adiponectin levels are lower in Latino versus non-Latino white patients at risk for cardiovascular disease, independent of adiposity measures. BMC Endocr Disord 2011; 11:13. [PMID: 21736747 PMCID: PMC3141565 DOI: 10.1186/1472-6823-11-13] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/27/2010] [Accepted: 07/07/2011] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Latinos in the United States have a higher prevalence of type 2 diabetes than non-Latino whites, even after controlling for adiposity. Decreased adiponectin is associated with insulin resistance and predicts T2DM, and therefore may mediate this ethnic difference. We compared total and high-molecular-weight (HMW) adiponectin in Latino versus white individuals, identified factors associated with adiponectin in each ethnic group, and measured the contribution of adiponectin to ethnic differences in insulin resistance. METHODS We utilized cross-sectional data from subjects in the Latinos Using Cardio Health Actions to reduce Risk study. Participants were Latino (n = 119) and non-Latino white (n = 60) men and women with hypertension and at least one other risk factor for CVD (age 61 ± 10 yrs, 49% with T2DM), seen at an integrated community health and hospital system in Denver, Colorado. Total and HMW adiponectin was measured by RIA and ELISA respectively. Fasting glucose and insulin were used to calculate the homeostasis model insulin resistance index (HOMA-IR). Variables independently associated with adiponectin levels were identified by linear regression analyses. Adiponectin's contribution to ethnic differences in insulin resistance was assessed in multivariate linear regression models of Latino ethnicity, with logHOMA-IR as a dependent variable, adjusting for possible confounders including age, gender, adiposity, and renal function. RESULTS Mean adiponectin levels were lower in Latino than white patients (beta estimates: -4.5 (-6.4, -2.5), p < 0.001 and -1.6 (-2.7, -0.5), p < 0.005 for total and HMW adiponectin), independent of age, gender, BMI/waist circumference, thiazolidinedione use, diabetes status, and renal function. An expected negative association between adiponectin and waist circumference was seen among women and non-Latino white men, but no relationship between these two variables was observed among Latino men. Ethnic differences in logHOMA-IR were no longer observed after controlling for adiponectin levels. CONCLUSIONS Among patients with CVD risk, total and HMW adiponectin is lower in Latinos, independent of adiposity and other known regulators of adiponectin. Ethnic differences in adiponectin regulation may exist and future research in this area is warranted. Adiponectin levels accounted for the observed variability in insulin resistance, suggesting a contribution of decreased adiponectin to insulin resistance in Latino populations.
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Affiliation(s)
- Rocio I Pereira
- Denver Health Medical Center, 660 Bannock Street, Denver, CO 80204, USA
- University of Colorado Denver, Anschutz Medical Campus, P.O. Box 6511, MS8106, Aurora, CO 80045, USA
| | - Cecilia CL Wang
- University of Colorado Denver, Anschutz Medical Campus, P.O. Box 6511, MS8106, Aurora, CO 80045, USA
- Denver Veterans Affairs Medical Center, 1055 Clermont Street, Denver, CO 80220, USA
| | - Patrick Hosokawa
- University of Colorado Denver, Anschutz Medical Campus, P.O. Box 6511, MS8106, Aurora, CO 80045, USA
| | - L Miriam Dickinson
- University of Colorado Denver, Anschutz Medical Campus, P.O. Box 6511, MS8106, Aurora, CO 80045, USA
| | - Michel Chonchol
- University of Colorado Denver, Anschutz Medical Campus, P.O. Box 6511, MS8106, Aurora, CO 80045, USA
| | - Mori J Krantz
- Denver Health Medical Center, 660 Bannock Street, Denver, CO 80204, USA
| | - John F Steiner
- Institute for Health Research, Kaiser Permanente, P.O. Box 378066, Denver, CO 80237, USA
| | - Daniel H Bessesen
- Denver Health Medical Center, 660 Bannock Street, Denver, CO 80204, USA
- University of Colorado Denver, Anschutz Medical Campus, P.O. Box 6511, MS8106, Aurora, CO 80045, USA
| | - Edward P Havranek
- Denver Health Medical Center, 660 Bannock Street, Denver, CO 80204, USA
| | - Carlin S Long
- Denver Health Medical Center, 660 Bannock Street, Denver, CO 80204, USA
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Sibbel SP, Talbert ME, Bowden DW, Haffner SM, Taylor KD, Chen YDI, Wagenknecht LE, Langefeld CD, Norris JM. RGS6 variants are associated with dietary fat intake in Hispanics: the IRAS Family Study. Obesity (Silver Spring) 2011; 19:1433-8. [PMID: 21233807 PMCID: PMC3683650 DOI: 10.1038/oby.2010.333] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Recently, a genome-wide association scan was completed in the IRAS (Insulin Resistance Atherosclerosis Study) Family Study (IRASFS) Hispanic-American cohort. Multiple single-nucleotide polymorphisms (SNPs) in the G-protein signaling 6 (RGS6) gene were found to be associated with adiposity phenotypes. RGS6 has shown downstream antagonistic interplay with opioid receptors, targets of fatty/sugary food agonists. The possibility that RGS6 promotes tolerance and tachyphylaxis among the opioid receptor is a plausible pathway for overconsuming fat/sugar-laden food. Therefore, we hypothesized that RGS6 variants are associated with intake of fatty/sugary foods. In 932 Hispanics from San Antonio and San Luis Valley, CO, the following dietary intake variables were assessed using the Block Brief 2000 food frequency questionnaire: total calories, total fat, % calories from fat, % calories from saturated fat, protein, % calories from protein, carbohydrates, % calories from carbohydrates, and daily frequency of servings of fats/oils/sweets. We tested for association between 23 SNPs in RGS6 and dietary intake using a variance components measured genotype approach. All models were adjusted for gender, recruitment site, admixture, BMI, and age. Using an additive genetic model, rs1402064 was associated with higher intake of fats/oils/sweets, total calories, total fat and saturated fat (P = 0.0007, 0.026, 0.023, and 0.024). SNPs rs847330 and rs847354 were associated with higher intake of fats/oils/sweets (P = 0.002 and 0.018), total fat (P = 0.040 and 0.048) and saturated fat (P = 0.044 and 0.041). Finally, rs769148 was associated with higher intake of fats/oils/sweets (P = 0.002). RGS6 is a new candidate gene for adiposity traits that may be associated with a behavioral tendency toward fat-laden food intake.
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Affiliation(s)
- Scott P. Sibbel
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Denver, Aurora, Colorado, USA
| | - Matthew E. Talbert
- Department of Biochemistry, Wake Forest University, Winston-Salem, North Carolina, USA
| | - Donald W. Bowden
- Department of Biochemistry, Wake Forest University, Winston-Salem, North Carolina, USA
| | - Steve M. Haffner
- Department of Medicine, Baylor College of Medicine, Houston, Texas, USA
| | - Kent D. Taylor
- Medical Genetics Institute, Burns and Allen Cedars-Sinai Research Institute, Los Angeles, California, USA
| | - Yii-Der I. Chen
- Medical Genetics Institute, Burns and Allen Cedars-Sinai Research Institute, Los Angeles, California, USA
| | - Lynne E. Wagenknecht
- Department of Epidemiology, Division of Public Health Sciences, Wake Forest University, Winston-Salem, North Carolina, USA
| | - Carl D. Langefeld
- Department of Biostatistical Sciences, Division of Public Health Sciences, Wake Forest University, Winston-Salem, North Carolina, USA.
| | - Jill M. Norris
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Denver, Aurora, Colorado, USA
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Dumitrescu L, Carty CL, Taylor K, Schumacher FR, Hindorff LA, Ambite JL, Anderson G, Best LG, Brown-Gentry K, Bůžková P, Carlson CS, Cochran B, Cole SA, Devereux RB, Duggan D, Eaton CB, Fornage M, Franceschini N, Haessler J, Howard BV, Johnson KC, Laston S, Kolonel LN, Lee ET, MacCluer JW, Manolio TA, Pendergrass SA, Quibrera M, Shohet RV, Wilkens LR, Haiman CA, Le Marchand L, Buyske S, Kooperberg C, North KE, Crawford DC. Genetic determinants of lipid traits in diverse populations from the population architecture using genomics and epidemiology (PAGE) study. PLoS Genet 2011; 7:e1002138. [PMID: 21738485 PMCID: PMC3128106 DOI: 10.1371/journal.pgen.1002138] [Citation(s) in RCA: 127] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2010] [Accepted: 04/30/2011] [Indexed: 01/06/2023] Open
Abstract
For the past five years, genome-wide association studies (GWAS) have identified hundreds of common variants associated with human diseases and traits, including high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C), and triglyceride (TG) levels. Approximately 95 loci associated with lipid levels have been identified primarily among populations of European ancestry. The Population Architecture using Genomics and Epidemiology (PAGE) study was established in 2008 to characterize GWAS-identified variants in diverse population-based studies. We genotyped 49 GWAS-identified SNPs associated with one or more lipid traits in at least two PAGE studies and across six racial/ethnic groups. We performed a meta-analysis testing for SNP associations with fasting HDL-C, LDL-C, and ln(TG) levels in self-identified European American (~20,000), African American (~9,000), American Indian (~6,000), Mexican American/Hispanic (~2,500), Japanese/East Asian (~690), and Pacific Islander/Native Hawaiian (~175) adults, regardless of lipid-lowering medication use. We replicated 55 of 60 (92%) SNP associations tested in European Americans at p<0.05. Despite sufficient power, we were unable to replicate ABCA1 rs4149268 and rs1883025, CETP rs1864163, and TTC39B rs471364 previously associated with HDL-C and MAFB rs6102059 previously associated with LDL-C. Based on significance (p<0.05) and consistent direction of effect, a majority of replicated genotype-phentoype associations for HDL-C, LDL-C, and ln(TG) in European Americans generalized to African Americans (48%, 61%, and 57%), American Indians (45%, 64%, and 77%), and Mexican Americans/Hispanics (57%, 56%, and 86%). Overall, 16 associations generalized across all three populations. For the associations that did not generalize, differences in effect sizes, allele frequencies, and linkage disequilibrium offer clues to the next generation of association studies for these traits.
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Affiliation(s)
- Logan Dumitrescu
- Center for Human Genetics Research, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Cara L. Carty
- Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Kira Taylor
- Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Fredrick R. Schumacher
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Lucia A. Hindorff
- Office of Population Genomics, National Human Genome Research Institute, Bethesda, Maryland, United States of America
| | - José L. Ambite
- Information Sciences Institute, University of Southern California, Los Angeles, California, United States of America
| | - Garnet Anderson
- Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Lyle G. Best
- Missouri Breaks Industries Research, Timber Lake, South Dakota, United States of America
| | - Kristin Brown-Gentry
- Center for Human Genetics Research, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Petra Bůžková
- Department of Biostatistics, University of Washington, Seattle, Washington, United States of America
| | - Christopher S. Carlson
- Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Barbara Cochran
- Sponsored Programs, Baylor College of Medicine, Houston, Texas, United States of America
| | - Shelley A. Cole
- Department of Genetics, Southwest Foundation for Biomedical Research, San Antonio, Texas, United States of America
| | - Richard B. Devereux
- Department of Medicine, Weill Cornell Medical College, New York, New York, United States of America
| | - Dave Duggan
- The Translational Genomics Research Institute, Phoenix, Arizona, United States of America
| | - Charles B. Eaton
- Department of Family Medicine and Community Health, Alpert Medical School of Brown University School of Medicine, Providence, Rhode Island, United States of America
| | - Myriam Fornage
- Institute of Molecular Medicine, University of Texas Health Sciences Center at Houston, Texas, United States of America
- Division of Epidemiology, School of Public Health, University of Texas Health Sciences Center, Houston, Texas, United States of America
| | - Nora Franceschini
- Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Jeff Haessler
- Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Barbara V. Howard
- Medstar Research Institute, Washington, D.C., United States of America
| | - Karen C. Johnson
- Department of Preventive Medicine, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
| | - Sandra Laston
- Department of Genetics, Southwest Foundation for Biomedical Research, San Antonio, Texas, United States of America
| | - Laurence N. Kolonel
- Epidemiology Program, University of Hawaii Cancer Center, Department of Medicine, John A. Burns School of Medicine, University of Hawaii, Honolulu, Hawaii, United States of America
| | - Elisa T. Lee
- University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
| | - Jean W. MacCluer
- Department of Genetics, Southwest Foundation for Biomedical Research, San Antonio, Texas, United States of America
| | - Teri A. Manolio
- Office of Population Genomics, National Human Genome Research Institute, Bethesda, Maryland, United States of America
| | - Sarah A. Pendergrass
- Center for Human Genetics Research, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Miguel Quibrera
- School of Public Health, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Ralph V. Shohet
- Center of Cardiovascular Research, Department of Medicine, John A. Burns School of Medicine, University of Hawaii, Honolulu, Hawaii, United States of America
| | - Lynne R. Wilkens
- Epidemiology Program, University of Hawaii Cancer Center, Department of Medicine, John A. Burns School of Medicine, University of Hawaii, Honolulu, Hawaii, United States of America
| | - Christopher A. Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Loïc Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Department of Medicine, John A. Burns School of Medicine, University of Hawaii, Honolulu, Hawaii, United States of America
| | - Steven Buyske
- Department of Statistics and Biostatistics, Rutgers University, Piscataway, New Jersey, United States of America
| | - Charles Kooperberg
- Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Kari E. North
- Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Carolina Center for Genome Sciences, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Dana C. Crawford
- Center for Human Genetics Research, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, United States of America
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Chen Y, Liu YJ, Pei YF, Yang TL, Deng FY, Liu XG, Li DY, Deng HW. Copy number variations at the Prader-Willi syndrome region on chromosome 15 and associations with obesity in whites. Obesity (Silver Spring) 2011; 19:1229-34. [PMID: 21233802 PMCID: PMC4512297 DOI: 10.1038/oby.2010.323] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Obesity is a serious health problem with strong genetic determination. Copy number variation (CNV) is a common type of genomic variant associated with some complex human diseases. However, it is not clear how CNVs contribute to the etiology of obesity. In this study, we examined 1,000 unrelated US whites to search for CNVs that may predispose to obesity. We focused our analyses on the Prader-Willi syndrome (PWS) critical region (chromosome 15q11-q13), because the PWS region is a hotspot for CNV generation and obesity is one of the major clinical manifestations for chromosome abnormalities at this region. We constructed a map containing 39 CNVs at the PWS critical region with CNV occurrence rates higher than 1%. Among them, three CNVs were significantly associated with body fat mass (P < 0.05), with a higher copy number (CN) associated with an increase of 5.08-9.77 kg in body fat mass. These three CNVs are close to two known PWS genes, NDN (necdin homolog) and C15orf2 (chromosome 15 open reading frame 2), and partially overlap with another obesity gene PWRN1 (Prader-Willi region nonprotein-coding RNA 1). Interestingly, our recently published whole genome association scan study using the same sample by examining single-nucleotide polymorphisms (SNPs) did not find any significant associations at these CNV regions, suggesting the importance of examining both CNVs and SNPs for better understanding of genetic basis of obesity. Further studies are warranted to validate these CNVs and their importance to obesity.
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Affiliation(s)
- Yuan Chen
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education and Institute of Molecular Genetics, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, Shaanxi, The People’s Republic of China
| | - Yong-Jun Liu
- School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri, USA
| | - Yu-Fang Pei
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education and Institute of Molecular Genetics, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, Shaanxi, The People’s Republic of China
- School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri, USA
| | - Tie-Lin Yang
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education and Institute of Molecular Genetics, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, Shaanxi, The People’s Republic of China
- School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri, USA
| | - Fei-Yan Deng
- School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri, USA
| | - Xiao-Gang Liu
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education and Institute of Molecular Genetics, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, Shaanxi, The People’s Republic of China
| | - Ding-You Li
- Department of Pediatrics, Children’s Mercy Hospital, Kansas City, Missouri, USA
| | - Hong-Wen Deng
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education and Institute of Molecular Genetics, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, Shaanxi, The People’s Republic of China
- School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri, USA
- Center of System Biomedical Sciences, Shanghai University of Science and Technology, Shanghai, The People’s Republic of China
- College of Life Sciences and Engineering, Beijing Jiao Tong University, Beijing, The People’s Republic of China
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Abstract
Despite years of investigation, very little is known about the genetic predisposition for gestational diabetes mellitus (GDM). However, the advent of genome-wide association and identification of loci contributing to susceptibility to type 2 diabetes mellitus has opened a small window into the genetics of GDM. More importantly, the study of the genetics of GDM has not only illuminated potential new biology underlying diabetes in pregnancy, but has also provided insights into fetal outcomes. Here, I review some of the insights into GDM and fetal outcomes gained through the study of both rare and common genetic variation. I also discuss whether recent testing of type 2 diabetes mellitus susceptibility loci in GDM case-control samples changes views of whether GDM is a distinct form of diabetes. Finally, I examine how the study of susceptibility loci can be used to influence clinical care, one of the great promises of the new era of human genome analysis.
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Affiliation(s)
- Richard M Watanabe
- Department of Preventive Medicine, Keck School of Medicine of USC, 1540 Alcazar St, CHP-220, Los Angeles, CA 90089-9011, USA.
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Palmer ND, Langefeld CD, Ziegler JT, Hsu F, Haffner SM, Fingerlin T, Norris JM, Chen YI, Rich SS, Haritunians T, Taylor KD, Bergman RN, Rotter JI, Bowden DW. Candidate loci for insulin sensitivity and disposition index from a genome-wide association analysis of Hispanic participants in the Insulin Resistance Atherosclerosis (IRAS) Family Study. Diabetologia 2010; 53:281-9. [PMID: 19902172 PMCID: PMC2809812 DOI: 10.1007/s00125-009-1586-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2009] [Accepted: 10/05/2009] [Indexed: 01/11/2023]
Abstract
AIMS/HYPOTHESIS The majority of type 2 diabetes genome-wide association studies (GWAS) to date have been performed in European-derived populations and have identified few variants that mediate their effect through insulin resistance. The aim of this study was to evaluate two quantitative, directly assessed measures of insulin resistance, namely insulin sensitivity index (S(I)) and insulin disposition index (DI), in Hispanic-American participants using an agnostic, high-density single nucleotide polymorphism (SNP) scan, and to validate these findings in additional samples. METHODS A two-stage GWAS was performed in Hispanic-American samples from the Insulin Resistance Atherosclerosis Family Study. In Stage 1, 317,000 SNPs were assessed using 229 DNA samples. SNPs with evidence of association with glucose homeostasis and adiposity traits were then genotyped on the entire set of Hispanic-American samples (n = 1,190). This report focuses on the glucose homeostasis traits: S(I) and DI. RESULTS Although evidence of association did not reach genome-wide significance (p = 5 x 10(-7)), in the combined analysis SNPs had admixture-adjusted p values of p (ADD) = 0.00010-0.0020 with 8 to 41% differences in genotypic means for S(I) and DI. CONCLUSIONS/INTERPRETATION Several candidate loci were identified that are nominally associated with S(I) and/or DI in Hispanic-American participants. Replication of these findings in independent cohorts and additional focused analysis of these loci is warranted.
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Affiliation(s)
- N D Palmer
- Department of Biochemistry, Centers for Human Genomics & Diabetes Research, Wake Forest University School of Medicine, 1 Medical Center Blvd, Winston-Salem, NC 27157, USA
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41
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Comuzzie AG, Higgins PB, Voruganti S, Cole S. Cutting the Fat. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2010. [DOI: 10.1016/b978-0-12-375003-7.00007-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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Wu S, Mar-Heyming R, Dugum EZ, Kolaitis NA, Qi H, Pajukanta P, Castellani LW, Lusis AJ, Drake TA. Upstream transcription factor 1 influences plasma lipid and metabolic traits in mice. Hum Mol Genet 2009; 19:597-608. [PMID: 19995791 DOI: 10.1093/hmg/ddp526] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Upstream transcription factor 1 (USF1) has been associated with familial combined hyperlipidemia, the metabolic syndrome, and related conditions, but the mechanisms involved are unknown. In this study, we report validation of Usf1 as a causal gene of cholesterol homeostasis, insulin sensitivity and body composition in mouse models using several complementary approaches and identify associated pathways and gene expression network modules. Over-expression of human USF1 in both transgenic mice and mice with transient liver-specific over-expression influenced metabolic trait phenotypes, including obesity, total cholesterol level, LDL/VLDL cholesterol and glucose/insulin ratio. Additional analyses of trait and hepatic gene expression data from an F2 population derived from C57BL/6J and C3H/HeJ strains in which there is a naturally occurring variation in Usf1 expression supported a causal role for Usf1 for relevant metabolic traits. Gene network and pathway analyses of the liver gene expression signatures in the F2 population and the hepatic over-expression model suggested the involvement of Usf1 in immune responses and metabolism, including an Igfbp2-centered module. In all three mouse model settings, notable sex specificity was observed, consistent with human studies showing differences in association with USF1 gene polymorphisms between sexes.
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Affiliation(s)
- Sulin Wu
- Department of Human Genetics, David Geffen School of Medicine at University of California, Los Angeles, CA 90095, USA
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