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Analysis of the genetic basis of height in large Jewish nuclear families. PLoS Genet 2019; 15:e1008082. [PMID: 31283753 PMCID: PMC6638967 DOI: 10.1371/journal.pgen.1008082] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2018] [Revised: 07/18/2019] [Accepted: 03/11/2019] [Indexed: 12/26/2022] Open
Abstract
Despite intensive study, most of the specific genetic factors that contribute to variation in human height remain undiscovered. We conducted a family-based linkage study of height in a unique cohort of very large nuclear families from a founder (Jewish) population. This design allowed for increased power to detect linkage, compared to previous family-based studies. Loci we identified in discovery families could explain an estimated lower bound of 6% of the variance in height in validation families. We showed that these loci are not tagging known common variants associated with height. Rather, we suggest that the observed signals arise from variants with large effects that are rare globally but elevated in frequency in the Jewish population. Rare variants with large effects have been suggested to account for some of the missing heritability of height, but detection of such variants in genome-wide association studies (GWAS) requires very large sample sizes due to their low frequencies. Here, we designed a unique study of height, in which we sought to increase the effective frequency of rare variants in our sample. This was done by assembling a cohort of very large nuclear families, with an average of 12 and a maximum of 20 siblings per nuclear family. In this design, any variant segregating in our cohort has a minimum expected frequency of ~1%, regardless of its frequency in the general population. In addition, we recruited all participants from a founder (Jewish) population, in which some variants that are rare in a cosmopolitan population can rise to high frequencies. To further increase power, we developed methods to obtain highly accurate height measurements, genotype calls, and inheritance pattern reconstructions. These factors allowed us to detect many more QTLs than previous family-based studies of height, despite a modest sample size of only 397 participants. The approach described in this paper provides insights into the genetic basis of height and the roles of population-specific vs. cosmopolitan variants, and may serve as a complement to GWAS for genetic investigations of other complex traits.
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Zhang Y, Whaley-Connell AT, Sowers JR, Ren J. Autophagy as an emerging target in cardiorenal metabolic disease: From pathophysiology to management. Pharmacol Ther 2018; 191:1-22. [PMID: 29909238 PMCID: PMC6195437 DOI: 10.1016/j.pharmthera.2018.06.004] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 06/05/2018] [Indexed: 12/16/2022]
Abstract
Although advances in medical technology and health care have improved the early diagnosis and management for cardiorenal metabolic disorders, the prevalence of obesity, insulin resistance, diabetes, hypertension, dyslipidemia, and kidney disease remains high. Findings from numerous population-based studies, clinical trials, and experimental evidence have consolidated a number of theories for the pathogenesis of cardiorenal metabolic anomalies including resistance to the metabolic action of insulin, abnormal glucose and lipid metabolism, oxidative and nitrosative stress, endoplasmic reticulum (ER) stress, apoptosis, mitochondrial damage, and inflammation. Accumulating evidence has recently suggested a pivotal role for proteotoxicity, the unfavorable effects of poor protein quality control, in the pathophysiology of metabolic dysregulation and related cardiovascular complications. The ubiquitin-proteasome system (UPS) and autophagy-lysosomal pathways, two major although distinct cellular clearance machineries, govern protein quality control by degradation and clearance of long-lived or damaged proteins and organelles. Ample evidence has depicted an important role for protein quality control, particularly autophagy, in the maintenance of metabolic homeostasis. To this end, autophagy offers promising targets for novel strategies to prevent and treat cardiorenal metabolic diseases. Targeting autophagy using pharmacological or natural agents exhibits exciting new strategies for the growing problem of cardiorenal metabolic disorders.
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Affiliation(s)
- Yingmei Zhang
- Shanghai Institute of Cardiovascular Diseases, Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai 200032, China; Center for Cardiovascular Research and Alternative Medicine, University of Wyoming College of Health Sciences, Laramie, WY 82071, USA.
| | - Adam T Whaley-Connell
- Research Service, Harry S Truman Memorial Veterans' Hospital, University of Missouri-Columbia School of Medicine, Columbia, MO, USA; Diabetes and Cardiovascular Center, Department of Medicine, University of Missouri-Columbia School of Medicine, Columbia, MO, USA
| | - James R Sowers
- Research Service, Harry S Truman Memorial Veterans' Hospital, University of Missouri-Columbia School of Medicine, Columbia, MO, USA; Diabetes and Cardiovascular Center, Department of Medicine, University of Missouri-Columbia School of Medicine, Columbia, MO, USA
| | - Jun Ren
- Shanghai Institute of Cardiovascular Diseases, Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai 200032, China; Center for Cardiovascular Research and Alternative Medicine, University of Wyoming College of Health Sciences, Laramie, WY 82071, USA.
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Poltorak A, Apalko S, Sherbak S. Wild-derived mice: from genetic diversity to variation in immune responses. Mamm Genome 2018; 29:577-584. [PMID: 30056578 DOI: 10.1007/s00335-018-9766-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 07/23/2018] [Indexed: 10/28/2022]
Abstract
Classical inbred mouse strains have historically been instrumental in mapping immunological traits. However, most of the classical strains originate from a relatively limited number of founder animals, largely within the Mus musculus domesticus subspecies. Therefore, their genetic diversity is ultimately limited. For this reason, it is not feasible to use these mice for exhaustive interrogation of immune signaling pathways. In order to investigate networks through forward genetic analysis, larger genetic diversity is required than is introduced under laboratory conditions. Recently, inbred strains from other mouse subspecies were established such as Mus musculus castaneus and Mus musculus musculus, which diverged from a shared common ancestor with Mus musculus domesticus more than one million years ago. A direct genomic comparison clearly demonstrates the evolutionary divergence that has occurred between wild-derived mice and the classical inbred strains. When compared to classical inbred strains, wild-derived mice exhibit polymorphisms every 100-200 base pairs. Studying the molecular basis of these traits provides us with insight into how the immune system can evolve regulatory features to accommodate environment-specific constraints. Because most wild-derived strains are able to breed with classical inbred mice, they represent a rich source of evolutionarily significant diversity for forward genetic studies. These organisms are an emerging, though still largely unexplored, model for the identification and study of novel immunological genes.
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Affiliation(s)
- Alexander Poltorak
- Department of Immunology, Tufts University, Boston, MA, 02111, USA. .,Petrozavodsk State University, Karelia, Russian Federation.
| | | | - Sergei Sherbak
- City Hospital, 40, St. Petersburg, Russian Federation.,St. Petersburg State University, St. Petersburg, Russian Federation
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Jose PA, Welch W. Do You Want to Ditch Sodium? Meet Nitric Oxide Synthase 1β at the Macula Densa. J Am Soc Nephrol 2016; 27:2217-8. [PMID: 26903534 DOI: 10.1681/asn.2015121378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Affiliation(s)
- Pedro A Jose
- Department of Medicine, Division of Kidney Diseases and Hypertension and Department of Physiology, The George Washington University School of Medicine and Health Sciences, Washington, DC; and
| | - William Welch
- Department of Medicine, Division of Nephrology and Hypertension, Hypertension, Kidney and Vascular Research Center, Georgetown University, Washington, DC
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5
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Abstract
Adhesion G protein-coupled receptors (aGPCRs) have a long evolutionary history dating back to very basal unicellular eukaryotes. Almost every vertebrate is equipped with a set of different aGPCRs. Genomic sequence data of several hundred extinct and extant species allows for reconstruction of aGPCR phylogeny in vertebrates and non-vertebrates in general but also provides a detailed view into the recent evolutionary history of human aGPCRs. Mining these sequence sources with bioinformatic tools can unveil many facets of formerly unappreciated aGPCR functions. In this review, we extracted such information from the literature and open public sources and provide insights into the history of aGPCR in humans. This includes comprehensive analyses of signatures of selection, variability of human aGPCR genes, and quantitative traits at human aGPCR loci. As indicated by a large number of genome-wide genotype-phenotype association studies, variations in aGPCR contribute to specific human phenotypes. Our survey demonstrates that aGPCRs are significantly involved in adaptation processes, phenotype variations, and diseases in humans.
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Affiliation(s)
- Peter Kovacs
- Integrated Research and Treatment Center (IFB) AdiposityDiseases, Medical Faculty, University of Leipzig, Liebigstr. 21, Leipzig, 04103, Germany.
| | - Torsten Schöneberg
- Institute of Biochemistry, Medical Faculty, University of Leipzig, Johannisallee 30, Leipzig, 04103, Germany.
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6
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Tekola-Ayele F, Doumatey AP, Shriner D, Bentley AR, Chen G, Zhou J, Fasanmade O, Johnson T, Oli J, Okafor G, Eghan BA, Agyenim-Boateng K, Adebamowo C, Amoah A, Acheampong J, Adeyemo A, Rotimi CN. Genome-wide association study identifies African-ancestry specific variants for metabolic syndrome. Mol Genet Metab 2015; 116:305-13. [PMID: 26507551 PMCID: PMC5292212 DOI: 10.1016/j.ymgme.2015.10.008] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 10/21/2015] [Accepted: 10/21/2015] [Indexed: 12/21/2022]
Abstract
The metabolic syndrome (MetS) is a constellation of metabolic disorders that increase the risk of developing several diseases including type 2 diabetes and cardiovascular diseases. Although genome-wide association studies (GWAS) have successfully identified variants associated with individual traits comprising MetS, the genetic basis and pathophysiological mechanisms underlying the clustering of these traits remain unclear. We conducted GWAS of MetS in 1427 Africans from Ghana and Nigeria followed by replication testing and meta-analysis in another continental African sample from Kenya. Further replication testing was performed in an African American sample from the Atherosclerosis Risk in Communities (ARIC) study. We found two African-ancestry specific variants that were significantly associated with MetS: SNP rs73989312[A] near CA10 that conferred increased risk (P=3.86 × 10(-8), OR=6.80) and SNP rs77244975[C] in CTNNA3 that conferred protection against MetS (P=1.63 × 10(-8), OR=0.15). Given the exclusive expression of CA10 in the brain, our CA10 finding strengthens previously reported link between brain function and MetS. We also identified two variants that are not African specific: rs76822696[A] near RALYL associated with increased MetS risk (P=7.37 × 10(-9), OR=1.59) and rs7964157[T] near KSR2 associated with reduced MetS risk (P=4.52 × 10(-8), Pmeta=7.82 × 10(-9), OR=0.53). The KSR2 locus displayed pleiotropic associations with triglyceride and measures of blood pressure. Rare KSR2 mutations have been reported to be associated with early onset obesity and insulin resistance. Finally, we replicated the LPL and CETP loci previously found to be associated with MetS in Europeans. These findings provide novel insights into the genetics of MetS in Africans and demonstrate the utility of conducting trans-ethnic disease gene mapping studies for testing the cosmopolitan significance of GWAS signals of cardio-metabolic traits.
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Affiliation(s)
- Fasil Tekola-Ayele
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Ayo P Doumatey
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Daniel Shriner
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Amy R Bentley
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Guanjie Chen
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jie Zhou
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | | | | | - Johnnie Oli
- University of Nigeria Teaching Hospital, Enugu, Nigeria
| | | | - Benjami A Eghan
- University of Science and Technology, Department of Medicine, Kumasi, Ghana
| | | | - Clement Adebamowo
- Department of Epidemiology and Public Health, School of Medicine, University of Maryland, Baltimore, MD, USA
| | - Albert Amoah
- University of Ghana Medical School, Department of Medicine, Accra, Ghana
| | - Joseph Acheampong
- University of Science and Technology, Department of Medicine, Kumasi, Ghana
| | - Adebowale Adeyemo
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Charles N Rotimi
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
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Arbour L, Asuri S, Whittome B, Polanco F, Hegele RA. The Genetics of Cardiovascular Disease in Canadian and International Aboriginal Populations. Can J Cardiol 2015; 31:1094-115. [DOI: 10.1016/j.cjca.2015.07.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Revised: 07/08/2015] [Accepted: 07/09/2015] [Indexed: 12/16/2022] Open
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Tozaki T, Hirota K, Sugita S, Ishida N, Miyake T, Oki H, Hasegawa T. A genome-wide scan for tying-up syndrome in Japanese Thoroughbreds. Anim Genet 2015; 41 Suppl 2:80-6. [PMID: 21070280 DOI: 10.1111/j.1365-2052.2010.02112.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Tying-up syndrome, also known as recurrent exertional rhabdomyolysis in Thoroughbreds, is a common muscle disorder for racehorses. In this study, we performed a multipoint linkage analysis using LOKI based on the Bayesian Markov chain Monte Carlo method using 5 half-sib families (51 affected and 277 nonaffected horses in total), and a genome-wide association study (GWAS) using microsatellites (144 affected and 144 nonaffected horses) to map candidate regions for tying-up syndrome in Japanese Thoroughbreds. The linkage analysis identified one strong L-score (82.45) between the loci UCDEQ411 and COR058 (24.9-27.9 Mb) on ECA12. The GWAS identified two suggestive genomic regions on ECA12 (24.9-27.8 Mb) and ECA20 (29.3-33.5 Mb). Based on both results, the genomic region between UCDEQ411 and TKY499 (24.9-27.8 Mb) on ECA12 was the most significant and was considered as a candidate region for tying-up syndrome in Japanese Thoroughbreds.
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Affiliation(s)
- T Tozaki
- Department of Molecular Genetics, Laboratory of Racing Chemistry, Utsunomiya, Tochigi, Japan.
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Winnier DA, Fourcaudot M, Norton L, Abdul-Ghani MA, Hu SL, Farook VS, Coletta DK, Kumar S, Puppala S, Chittoor G, Dyer TD, Arya R, Carless M, Lehman DM, Curran JE, Cromack DT, Tripathy D, Blangero J, Duggirala R, Göring HHH, DeFronzo RA, Jenkinson CP. Transcriptomic identification of ADH1B as a novel candidate gene for obesity and insulin resistance in human adipose tissue in Mexican Americans from the Veterans Administration Genetic Epidemiology Study (VAGES). PLoS One 2015; 10:e0119941. [PMID: 25830378 PMCID: PMC4382323 DOI: 10.1371/journal.pone.0119941] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Accepted: 02/04/2015] [Indexed: 01/01/2023] Open
Abstract
Type 2 diabetes (T2D) is a complex metabolic disease that is more prevalent in ethnic groups such as Mexican Americans, and is strongly associated with the risk factors obesity and insulin resistance. The goal of this study was to perform whole genome gene expression profiling in adipose tissue to detect common patterns of gene regulation associated with obesity and insulin resistance. We used phenotypic and genotypic data from 308 Mexican American participants from the Veterans Administration Genetic Epidemiology Study (VAGES). Basal fasting RNA was extracted from adipose tissue biopsies from a subset of 75 unrelated individuals, and gene expression data generated on the Illumina BeadArray platform. The number of gene probes with significant expression above baseline was approximately 31,000. We performed multiple regression analysis of all probes with 15 metabolic traits. Adipose tissue had 3,012 genes significantly associated with the traits of interest (false discovery rate, FDR ≤ 0.05). The significance of gene expression changes was used to select 52 genes with significant (FDR ≤ 10(-4)) gene expression changes across multiple traits. Gene sets/Pathways analysis identified one gene, alcohol dehydrogenase 1B (ADH1B) that was significantly enriched (P < 10(-60)) as a prime candidate for involvement in multiple relevant metabolic pathways. Illumina BeadChip derived ADH1B expression data was consistent with quantitative real time PCR data. We observed significant inverse correlations with waist circumference (2.8 x 10(-9)), BMI (5.4 x 10(-6)), and fasting plasma insulin (P < 0.001). These findings are consistent with a central role for ADH1B in obesity and insulin resistance and provide evidence for a novel genetic regulatory mechanism for human metabolic diseases related to these traits.
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Affiliation(s)
- Deidre A. Winnier
- Division of Diabetes, Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States of America
| | - Marcel Fourcaudot
- Division of Diabetes, Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States of America
| | - Luke Norton
- Division of Diabetes, Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States of America
| | - Muhammad A. Abdul-Ghani
- Division of Diabetes, Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States of America
| | - Shirley L. Hu
- Division of Nephrology, Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States of America
| | - Vidya S. Farook
- Texas Biomedical Research Institute, San Antonio, TX, United States of America
| | - Dawn K. Coletta
- School of Life Sciences, Arizona State University, Tempe, AZ, United States of America
| | - Satish Kumar
- Texas Biomedical Research Institute, San Antonio, TX, United States of America
| | - Sobha Puppala
- Texas Biomedical Research Institute, San Antonio, TX, United States of America
| | - Geetha Chittoor
- Texas Biomedical Research Institute, San Antonio, TX, United States of America
| | - Thomas D. Dyer
- Texas Biomedical Research Institute, San Antonio, TX, United States of America
| | - Rector Arya
- Division of Endocrinology and Diabetes, Department of Pediatrics, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States of America
| | - Melanie Carless
- Texas Biomedical Research Institute, San Antonio, TX, United States of America
| | - Donna M. Lehman
- Division of Clinical Epidemiology, Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States of America
| | - Joanne E. Curran
- Texas Biomedical Research Institute, San Antonio, TX, United States of America
| | - Douglas T. Cromack
- Division of Orthopedics, Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States of America
- South Texas Veterans Health Care System, San Antonio, TX, United States of America
| | - Devjit Tripathy
- Division of Diabetes, Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States of America
- South Texas Veterans Health Care System, San Antonio, TX, United States of America
| | - John Blangero
- Texas Biomedical Research Institute, San Antonio, TX, United States of America
| | | | - Harald H. H. Göring
- Texas Biomedical Research Institute, San Antonio, TX, United States of America
| | - Ralph A. DeFronzo
- Division of Diabetes, Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States of America
- South Texas Veterans Health Care System, San Antonio, TX, United States of America
| | - Christopher P. Jenkinson
- Division of Diabetes, Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States of America
- Texas Biomedical Research Institute, San Antonio, TX, United States of America
- South Texas Veterans Health Care System, San Antonio, TX, United States of America
- * E-mail:
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Hasstedt SJ, Xin Y, Mao R, Lewis T, Adams TD, Hunt SC. A Copy Number Variant on Chromosome 20q13.3 Implicated in Thinness and Severe Obesity. J Obes 2015; 2015:623431. [PMID: 26881067 PMCID: PMC4736014 DOI: 10.1155/2015/623431] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 12/20/2015] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND/OBJECTIVES To identify copy number variants (CNVs) which are associated with body mass index (BMI). SUBJECTS/METHODS CNVs were identified using array comparative genomic hybridization (aCGH) on members of pedigrees ascertained through severely obese (BMI ≥ 35 kg/m(2)) sib pairs (86 pedigrees) and thin (BMI ≤ 23 kg/m(2)) probands (3 pedigrees). Association was inferred through pleiotropy of BMI with CNV log2 intensity ratio. RESULTS A 77-kilobase CNV on chromosome 20q13.3, confirmed by real-time qPCR, exhibited deletions in the obese subjects and duplications in the thin subjects (P = 2.2 × 10(-6)). Further support for the presence of a deletion derived from inference by likelihood analysis of null alleles for SNPs residing in the region. CONCLUSIONS One or more of 7 genes residing in a chromosome 20q13.3 CNV region appears to influence BMI. The strongest candidate is ARFRP1, which affects glucose metabolism in mice.
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Affiliation(s)
- Sandra J. Hasstedt
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
- *Sandra J. Hasstedt:
| | - Yuanpei Xin
- Cardiovascular Genetics Division, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Rong Mao
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
- ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT, USA
| | - Tracey Lewis
- ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT, USA
| | - Ted D. Adams
- Cardiovascular Genetics Division, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Steven C. Hunt
- Cardiovascular Genetics Division, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
- Department of Genetic Medicine, Weill Cornell Medical College in Qatar, Doha, Qatar
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Abstract
Knowledge gained over the past 10 years about the mechanisms that underpin autophagy has provided a universal framework for studies of diverse physiological and pathological processes. Of particular interest is the emerging role of autophagy in the maintenance of energy homeostasis, both at the cellular level and within the organism as a whole. Dysregulation of autophagy might contribute to the development of metabolic disorders, including insulin resistance, diabetes mellitus, obesity, atherosclerosis and osteoporosis. The authors of this Review highlight research findings on the regulation of cellular autophagy by nutrients. They also describe the role of autophagy in various tissues in the regulation of energy metabolism and the development of diseases related to altered metabolism. Finally, the potential of pharmacological modulation of autophagy as a treatment for human metabolic disorders is discussed.
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Affiliation(s)
- Kook Hwan Kim
- Department of Medicine and Samsung Advanced Institute for Health Sciences and Technology, Samsung Medical Centre, Sungkyunkwan University School of Medicine, 81 Irwon-ro Gangnam-gu, Seoul 135-710, Korea
| | - Myung-Shik Lee
- Department of Medicine and Samsung Advanced Institute for Health Sciences and Technology, Samsung Medical Centre, Sungkyunkwan University School of Medicine, 81 Irwon-ro Gangnam-gu, Seoul 135-710, Korea
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12
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Gragnoli C. Hypothesis of the neuroendocrine cortisol pathway gene role in the comorbidity of depression, type 2 diabetes, and metabolic syndrome. APPLICATION OF CLINICAL GENETICS 2014; 7:43-53. [PMID: 24817815 PMCID: PMC4012344 DOI: 10.2147/tacg.s39993] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Depression, type 2 diabetes (T2D), and metabolic syndrome (MetS) are often comorbid. Depression per se increases the risk for T2D by 60%. This risk is not accounted for by the use of antidepressant therapy. Stress causes hyperactivation of the hypothalamic–pituitary–adrenal (HPA) axis, by triggering the hypothalamic corticotropin-releasing hormone (CRH) secretion, which stimulates the anterior pituitary to release the adrenocorticotropin hormone (ACTH), which causes the adrenal secretion of cortisol. Depression is associated with an increased level of cortisol, and CRH and ACTH at inappropriately “normal” levels, that is too high compared to their expected lower levels due to cortisol negative feedback. T2D and MetS are also associated with hypercortisolism. High levels of cortisol can impair mood as well as cause hyperglycemia and insulin resistance and other traits typical of T2D and MetS. We hypothesize that HPA axis hyperactivation may be due to variants in the genes of the CRH receptors (CRHR1, CRHR2), corticotropin receptors (or melanocortin receptors, MC1R-MC5R), glucocorticoid receptor (NR3C1), mineralocorticoid receptor (NR3C2), and of the FK506 binding protein 51 (FKBP5), and that these variants may be partially responsible for the clinical association of depression, T2D and MetS. In this review, we will focus on the correlation of stress, HPA axis hyperactivation, and the possible genetic role of the CRHR1, CRHR2, MCR1–5, NR3C1, and NR3C2 receptors and FKBP5 in the susceptibility to the comorbidity of depression, T2D, and MetS. New studies are needed to confirm the hypothesized role of these genes in the clinical association of depression, T2D, and MetS.
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Affiliation(s)
- Claudia Gragnoli
- Center for Biotechnology and Department of Biology, College of Science and Technology, Temple University, Philadelphia, PA, USA ; Molecular Biology Laboratory, Bios Biotech Multi-Diagnostic Health Center, Rome, Italy
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13
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Zhang W, He C. WITHDRAWN: Regulation of plasma membrane receptors by a new autophagy-related BECN/Beclin family member. Autophagy 2014; 10:938-41. [PMID: 24569622 DOI: 10.4161/auto.28149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- Weiran Zhang
- Department of Cell and Molecular Biology; Feinberg School of Medicine; Northwestern University; Chicago, IL USA
| | - Congcong He
- Department of Cell and Molecular Biology; Feinberg School of Medicine; Northwestern University; Chicago, IL USA
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14
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He C, Wei Y, Sun K, Li B, Dong X, Zou Z, Liu Y, Kinch LN, Khan S, Sinha S, Xavier RJ, Grishin NV, Xiao G, Eskelinen EL, Scherer PE, Whistler JL, Levine B. Beclin 2 functions in autophagy, degradation of G protein-coupled receptors, and metabolism. Cell 2013; 154:1085-1099. [PMID: 23954414 PMCID: PMC4231430 DOI: 10.1016/j.cell.2013.07.035] [Citation(s) in RCA: 114] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Revised: 05/14/2013] [Accepted: 07/10/2013] [Indexed: 11/26/2022]
Abstract
The molecular mechanism of autophagy and its relationship to other lysosomal degradation pathways remain incompletely understood. Here, we identified a previously uncharacterized mammalian-specific protein, Beclin 2, which, like Beclin 1, functions in autophagy and interacts with class III PI3K complex components and Bcl-2. However, Beclin 2, but not Beclin 1, functions in an additional lysosomal degradation pathway. Beclin 2 is required for ligand-induced endolysosomal degradation of several G protein-coupled receptors (GPCRs) through its interaction with GASP1. Beclin 2 homozygous knockout mice have decreased embryonic viability, and heterozygous knockout mice have defective autophagy, increased levels of brain cannabinoid 1 receptor, elevated food intake, and obesity and insulin resistance. Our findings identify Beclin 2 as a converging regulator of autophagy and GPCR turnover and highlight the functional and mechanistic diversity of Beclin family members in autophagy, endolysosomal trafficking, and metabolism.
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Affiliation(s)
- Congcong He
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Center for Autophagy Research, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yongjie Wei
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Center for Autophagy Research, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Kai Sun
- Touchstone Diabetes Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Binghua Li
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xiaonan Dong
- Center for Autophagy Research, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Zhongju Zou
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Center for Autophagy Research, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yang Liu
- Center for Autophagy Research, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Lisa N Kinch
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Shaheen Khan
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Sangita Sinha
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND 58102, USA
| | - Ramnik J Xavier
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Gastrointestinal Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Nick V Grishin
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Guanghua Xiao
- Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Eeva-Liisa Eskelinen
- Department of Biosciences, Division of Biochemistry and Biotechnology, University of Helsinki, Helsinki, FI-00014 Finland
| | - Philipp E Scherer
- Touchstone Diabetes Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jennifer L Whistler
- Ernest Gallo Clinic and Research Center, University of California San Francisco, Emeryville, CA 94608, USA
| | - Beth Levine
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Center for Autophagy Research, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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15
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Shia WC, Ku TH, Tsao YM, Hsia CH, Chang YM, Huang CH, Chung YC, Hsu SL, Liang KW, Hsu FR. Genetic copy number variants in myocardial infarction patients with hyperlipidemia. BMC Genomics 2011; 12 Suppl 3:S23. [PMID: 22369086 PMCID: PMC3333183 DOI: 10.1186/1471-2164-12-s3-s23] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Cardiovascular disease is the chief cause of death in Taiwan and many countries, of which myocardial infarction (MI) is the most serious condition. Hyperlipidemia appears to be a significant cause of myocardial infarction, because it causes atherosclerosis directly. In recent years, copy number variation (CNV) has been analyzed in genomewide association studies of complex diseases. In this study, CNV was analyzed in blood samples and SNP arrays from 31 myocardial infarction patients with hyperlipidemia. RESULTS We identified seven CNV regions that were associated significantly with hyperlipidemia and myocardial infarction in our patients through multistage analysis (P<0.001), at 1p21.3, 1q31.2 (CDC73), 1q42.2 (DISC1), 3p21.31 (CDCP1), 10q11.21 (RET) 12p12.3 (PIK3C2G) and 16q23.3 (CDH13), respectively. In particular, the CNV region at 10q11.21 was examined by quantitative real-time PCR, the results of which were consistent with microarray findings. CONCLUSIONS Our preliminary results constitute an alternative method of evaluating the relationship between CNV regions and cardiovascular disease. These susceptibility CNV regions may be used as biomarkers for early-stage diagnosis of hyperlipidemia and myocardial infarction, rendering them valuable for further research and discussion.
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Affiliation(s)
- Wei-Chung Shia
- Department of Information Engineering and Computer Science, Feng Chia University, Taichung City, Taiwan
| | - Tien-Hsiung Ku
- Department of Anesthesia, Changhua Christian Hospital, Changhua County, Taiwan
| | - Yu-Ming Tsao
- Department of Computer Science, National Chiao Tung University, Hsinchu, Taiwan
| | - Chien-Hsun Hsia
- Department of Cardiovascular Medicine, Changhua Christian Hospital, Changhua County, Taiwan
| | - Yung-Ming Chang
- Department of Cardiovascular Medicine, Changhua Christian Hospital, Changhua County, Taiwan
| | - Ching-Hui Huang
- Department of Cardiovascular Medicine, Changhua Christian Hospital, Changhua County, Taiwan
| | - Yeh-Ching Chung
- Department of Computer Science, National Tsing Hua University, Hsinchu, Taiwan
| | - Shih-Lan Hsu
- Department of Medical Education and Research, Taichung Veterans General Hospital, Taichung City, Taiwan
| | - Kae-Woei Liang
- Department of Cardiovascular Medicine, Taichung Veterans General Hospital, Taichung City, Taiwan
| | - Fang-Rong Hsu
- Department of Information Engineering and Computer Science, Feng Chia University, Taichung City, Taiwan
- Master's Program in Biomedical Informatics and Biomedical Engineering, Feng Chia University, Taichung City, Taiwan
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16
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Low-pass genome-wide sequencing and variant inference using identity-by-descent in an isolated human population. Genetics 2011; 190:679-89. [PMID: 22135348 DOI: 10.1534/genetics.111.134874] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Whole-genome sequencing in an isolated population with few founders directly ascertains variants from the population bottleneck that may be rare elsewhere. In such populations, shared haplotypes allow imputation of variants in unsequenced samples without resorting to complex statistical methods as in studies of outbred cohorts. We focus on an isolated population cohort from the Pacific Island of Kosrae, Micronesia, where we previously collected SNP array and rich phenotype data for the majority of the population. We report identification of long regions with haplotypes co-inherited between pairs of individuals and methodology to leverage such shared genetic content for imputation. Our estimates show that sequencing as few as 40 personal genomes allows for inference in up to 60% of the 3000-person cohort at the average locus. We ascertained a pilot data set of whole-genome sequences from seven Kosraean individuals, with average 5× coverage. This assay identified 5,735,306 unique sites of which 1,212,831 were previously unknown. Additionally, these variants are unusually enriched for alleles that are rare in other populations when compared to geographic neighbors (published Korean genome SJK). We used the presence of shared haplotypes between the seven Kosraen individuals to estimate expected imputation accuracy of known and novel homozygous variants at 99.6% and 97.3%, respectively. This study presents whole-genome analysis of a homogenous isolate population with emphasis on optimal rare variant inference.
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17
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Gragnoli C. Hypercholesterolemia and a candidate gene within the 12q24 locus. Cardiovasc Diabetol 2011; 10:38. [PMID: 21554682 PMCID: PMC3116465 DOI: 10.1186/1475-2840-10-38] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2011] [Accepted: 05/09/2011] [Indexed: 11/24/2022] Open
Abstract
Background The 12q24 locus entails at least one gene responsible for hypercholesterolemia. Within the 12q24 locus lies the gene of proteasome modulator 9 (PSMD9). PSMD9 is in linkage with type 2 diabetes (T2D), T2D-nephropathy and macrovascular pathology in Italian families and PSMD9 rare mutations contribute to T2D. Aims In the present study, we aimed at determining whether the PSMD9 T2D risk single nucleotide polymorphisms (SNPs) IVS3 + nt460 A > G, IVS3 + nt437 T > C and E197G A > G are linked to hypercholesterolemia in 200 T2D Italian families. Methods We characterized 200 Italian families for presence and/or absence of hypercholesterolemia characterized by LDL levels ≥ 100 mg/dl in drug-naïve patients and/or presence of a diagnosis of hypercholesterolemia in a patient treated with statin medication. The phenotypes were described as unknown in all cases in which the diagnosis was either unclear or the data were missing. We tested in the 200 Italians families for evidence of linkage of the PSMD9 SNPs with hypercholesterolemia. The non-parametric linkage analysis was performed for the qualitative phenotype by using the Merlin software; the Lod score and correspondent P-value were calculated. For the significant linkage score, 1000 replicates were performed to calculate the empirical P-value. Results The PSMD9 gene SNPs studied show linkage to hypercholesterolemia. The results are not due to random chance. Conclusions PSMD9 should be tested in all populations reporting linkage to hypercholesterolemia within the chromosome 12q24 locus. The impact of this gene on hypercholesterolemia and contribution to cardio- and cerebrovascular events may be high.
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Affiliation(s)
- Claudia Gragnoli
- Laboratory of Molecular Genetics of Complex and Monogenic Disorders, Department of Medicine and Cellular & Molecular Physiology and Biostatistics, Penn State University and M.S. Hershey Medical Center, Hershey, PA, USA.
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18
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Revelli JP, Smith D, Allen J, Jeter-Jones S, Shadoan MK, Desai U, Schneider M, van Sligtenhorst I, Kirkpatrick L, Platt KA, Suwanichkul A, Savelieva K, Gerhardt B, Mitchell J, Syrewicz J, Zambrowicz B, Hamman BD, Vogel P, Powell DR. Profound obesity secondary to hyperphagia in mice lacking kinase suppressor of ras 2. Obesity (Silver Spring) 2011; 19:1010-8. [PMID: 21127480 DOI: 10.1038/oby.2010.282] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The kinase suppressor of ras 2 (KSR2) gene resides at human chromosome 12q24, a region linked to obesity and type 2 diabetes (T2D). While knocking out and phenotypically screening mouse orthologs of thousands of druggable human genes, we found KSR2 knockout (KSR2(-/-)) mice to be more obese and glucose intolerant than melanocortin 4 receptor(-/-) (MC4R(-/-)) mice. The obesity and T2D of KSR2(-/-) mice resulted from hyperphagia which was unresponsive to leptin and did not originate downstream of MC4R. The kinases AMP-activated protein kinase (AMPK) and mammalian target of rapamycin (mTOR) are each linked to food intake regulation, but only mTOR had increased activity in KSR2(-/-) mouse brain, and the ability of rapamycin to inhibit food intake in KSR2(-/-) mice further implicated mTOR in this process. The metabolic phenotype of KSR2 heterozygous (KSR2(+/minus;)) and KSR2(-/-) mice suggests that human KSR2 variants may contribute to a similar phenotype linked to human chromosome 12q24.
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Cummings N, Shields KA, Curran JE, Bozaoglu K, Trevaskis J, Gluschenko K, Cai G, Comuzzie AG, Dyer TD, Walder KR, Zimmet P, Collier GR, Blangero J, Jowett JBM. Genetic variation in SH3-domain GRB2-like (endophilin)-interacting protein 1 has a major impact on fat mass. Int J Obes (Lond) 2011; 36:201-6. [PMID: 21407171 DOI: 10.1038/ijo.2011.67] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
OBJECTIVE The SH3-domain GRB2-like (endophilin)-interacting protein 1 (SGIP1) gene has been shown to be differentially expressed in the hypothalamus of lean versus obese Israeli sand rats (Psammomys obesus), and is suspected of having a role in regulating food intake. The purpose of this study was to assess the role of genetic variation in SGIP1 in human disease. SUBJECTS We performed single-nucleotide polymorphism (SNP) genotyping in a large family pedigree cohort from the island of Mauritius. The Mauritius Family Study (MFS) consists of 400 individuals from 24 Indo-Mauritian families recruited from the genetically homogeneous population of Mauritius. We measured markers of the metabolic syndrome, including diabetes and obesity-related phenotypes such as fasting plasma glucose, waist:hip ratio, body mass index and fat mass. RESULTS Statistical genetic analysis revealed associations between SGIP1 polymorphisms and fat mass (in kilograms) as measured by bioimpedance. SNP genotyping identified associations between several genetic variants and fat mass, with the strongest association for rs2146905 (P=4.7 × 10(-5)). A strong allelic effect was noted for several SNPs where fat mass was reduced by up to 9.4% for individuals homozygous for the minor allele. CONCLUSIONS Our results show association between genetic variants in SGIP1 and fat mass. We provide evidence that variation in SGIP1 is a potentially important determinant of obesity-related traits in humans.
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Affiliation(s)
- N Cummings
- Genomics and Systems Biology, Baker IDI Heart and Diabetes Institute, Melbourne, Victoria, Australia
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20
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Modifier locus of the skeletal muscle involvement in Emery-Dreifuss muscular dystrophy. Hum Genet 2010; 129:149-59. [PMID: 21063730 DOI: 10.1007/s00439-010-0909-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2010] [Accepted: 10/28/2010] [Indexed: 02/02/2023]
Abstract
Autosomal dominant Emery-Dreifuss muscular dystrophy is caused by mutations in LMNA gene encoding lamins A and C. The disease is characterized by early onset joint contractures during childhood associated with humero-peroneal muscular wasting and weakness, and by the development of a cardiac disease in adulthood. Important intra-familial variability characterized by a wide range of age at onset of myopathic symptoms (AOMS) has been recurrently reported, suggesting the contribution of a modifier gene. Our objective was to identify a modifier locus of AOMS in relation with the LMNA mutation. To map the modifier locus, we genotyped 291 microsatellite markers in 59 individuals of a large French family, where 19 patients carrying the same LMNA mutation, exhibited wide range of AOMS. We performed Bayesian Markov Chain Monte Carlo-based joint segregation and linkage methods implemented in the Loki software, and detected a strong linkage signal on chromosome 2 between markers D2S143 and D2S2244 (211 cM) with a Bayes factor of 28.7 (empirical p value = 0.0032). The linked region harbours two main candidate genes, DES and MYL1 encoding desmin and light chain of myosin. Importantly, the impact of the genotype on the phenotype for this locus showed an overdominant effect with AOMS 2 years earlier for the homozygotes of the rare allele and 37 years earlier for the heterozygotes than the homozygotes for the common allele. These results provide important highlights for the natural history and for the physiopathology of Emery-Dreifuss muscular dystrophy.
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Systematic haplotype analysis resolves a complex plasma plant sterol locus on the Micronesian Island of Kosrae. Proc Natl Acad Sci U S A 2009; 106:13886-91. [PMID: 19667188 DOI: 10.1073/pnas.0907336106] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Pinpointing culprit causal variants along signal peaks of genome-wide association studies (GWAS) is challenging. To overcome confounding effects of multiple independent variants at such a locus and narrow the interval for causal allele capture, we developed an approach that maps local shared haplotypes harboring a putative causal variant. We demonstrate our method in an extreme isolate founder population, the pacific Island of Kosrae. We analyzed plasma plant sterol (PPS) levels, a surrogate measure of cholesterol absorption from the intestine, where previous studies have implicated 2p21 mutations in the ATP binding cassette subfamily G members 5 or 8 (ABCG5 or ABCG8) genes. We have previously reported that 11.1% of the islanders are carriers of a frameshift ABCG8 mutation increasing PPS levels in carriers by 50%. GWAS adjusted for this mutation revealed genomewide significant signals along 11 Mb around it. To fine-map this signal, we detected pairwise identity-by-descent haplotypes using our tool GERMLINE and implemented a clustering algorithm to identify haplotypes shared across multiple samples with their unique shared boundaries. A single 526-kb haplotype mapped strongly to PPS levels, dramatically refining the mapped interval. This haplotype spans the ABCG5/ABCG8 genes, is carried by 1.8% of the islanders, and results in a striking 100% increase of PPS in carriers. Resequencing of ABCG5 in these carriers found a D450H missense mutation along the associated haplotype. These findings exemplify the power of haplotype analysis for mapping mutations in isolated populations and specifically for dissecting effects of multiple variants of the same locus.
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22
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Vistoropsky Y, Trofimov S, Malkin I, Kobyliansky E, Livshits G. Genetic and environmental determinants of hepatocyte growth factor levels and their association with obesity and blood pressure. Ann Hum Biol 2009; 35:93-103. [DOI: 10.1080/03014460701822003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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23
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Linkage analysis of adult height in a large pedigree from a Dutch genetically isolated population. Hum Genet 2009; 126:457-71. [PMID: 19466457 DOI: 10.1007/s00439-009-0686-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2009] [Accepted: 05/13/2009] [Indexed: 01/05/2023]
Abstract
Despite extensive research of genetic determinants of human adult height, the genes identified up until now allow to predict only a small proportion of the trait's variance. To identify new genes we analyzed 2,486 genotyped and phenotyped individuals in a large pedigree including 23,612 members in 18 generations. The pedigree was derived from a young genetically isolated Dutch population, where genetic heterogeneity is expected to be low and linkage disequilibrium has been shown to be increased. Complex segregation analysis confirmed high heritability of adult height, and suggested mixed model of height inheritance in this population. The estimates of the model parameters obtained from complex segregation analysis were used in parametric linkage analysis, which highlighted three genome-wide significant and additionally at least four suggestive loci involved in height. Significant peaks were located at the chromosomal regions 1p32 (LOD score = 3.35), 2p16 (LOD score = 3.29) and 16q24 (LOD score = 3.94). For the latter region, a strong association signal (FDR q < 0.05) was obtained for 19 SNPs, 17 of them were located in the CDH13 (cadherin 13) gene of which one (rs1035569) explained 1.5% of the total height variance.
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Cox HC, Bellis C, Lea RA, Quinlan S, Hughes R, Dyer T, Charlesworth J, Blangero J, Griffiths LR. Principal component and linkage analysis of cardiovascular risk traits in the Norfolk isolate. Hum Hered 2009; 68:55-64. [PMID: 19339786 DOI: 10.1159/000210449] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2008] [Accepted: 10/27/2008] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVE(S) An individual's risk of developing cardiovascular disease (CVD) is influenced by genetic factors. This study focussed on mapping genetic loci for CVD-risk traits in a unique population isolate derived from Norfolk Island. METHODS This investigation focussed on 377 individuals descended from the population founders. Principal component analysis was used to extract orthogonal components from 11 cardiovascular risk traits. Multipoint variance component methods were used to assess genome-wide linkage using SOLAR to the derived factors. A total of 285 of the 377 related individuals were informative for linkage analysis. RESULTS A total of 4 principal components accounting for 83% of the total variance were derived. Principal component 1 was loaded with body size indicators; principal component 2 with body size, cholesterol and triglyceride levels; principal component 3 with the blood pressures; and principal component 4 with LDL-cholesterol and total cholesterol levels. Suggestive evidence of linkage for principal component 2 (h(2) = 0.35) was observed on chromosome 5q35 (LOD = 1.85; p = 0.0008). While peak regions on chromosome 10p11.2 (LOD = 1.27; p = 0.005) and 12q13 (LOD = 1.63; p = 0.003) were observed to segregate with principal components 1 (h(2) = 0.33) and 4 (h(2) = 0.42), respectively. CONCLUSION(S) This study investigated a number of CVD risk traits in a unique isolated population. Findings support the clustering of CVD risk traits and provide interesting evidence of a region on chromosome 5q35 segregating with weight, waist circumference, HDL-c and total triglyceride levels.
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Affiliation(s)
- Hannah C Cox
- Genomics Research Centre, Griffith Institute for Health and Medical Research, Griffith University, Gold Coast, Qld., Australia
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25
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Ma D, Feitosa MF, Wilk JB, Laramie JM, Yu K, Leiendecker-Foster C, Myers RH, Province MA, Borecki IB. Leptin is associated with blood pressure and hypertension in women from the National Heart, Lung, and Blood Institute Family Heart Study. Hypertension 2009; 53:473-9. [PMID: 19204185 DOI: 10.1161/hypertensionaha.108.118133] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Leptin is a key neuroendocrine hormone regulating food intake, metabolism, and fat accumulation, and it may also affect blood pressure and contribute to hypertension through sympathetic activation in the vasculature or at the renal level. Although previous studies have shown that the distribution of leptin is significantly different between males and females, as is the risk of hypertension between males and females, results regarding the role of leptin in the gender-specific regulation of blood pressure are controversial. Thus, we performed family-based association analyses in the National Heart, Lung, and Blood Institute Family Heart Study to test the hypothesis that LEPTIN gene variants and the plasma leptin level influence variability in blood pressure and the risk of hypertension differently by gender. We identified significant associations between LEPTIN single nucleotide polymorphisms with blood pressure and hypertension, but in postmenopausal women only. We also identified significant associations between plasma leptin levels and both blood pressure and hypertension in women. The current study supports a role for LEPTIN and plasma leptin levels in blood pressure regulation in women. It also provides insight into the gender differences in hypertension, as well as the differential distribution and activity of leptin in men and women.
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Affiliation(s)
- Duanduan Ma
- Division of Statistical Genomics, Washington University School of Medicine, St. Louis, MO 63108, USA
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26
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Genome-wide association studies in an isolated founder population from the Pacific Island of Kosrae. PLoS Genet 2009; 5:e1000365. [PMID: 19197348 PMCID: PMC2628735 DOI: 10.1371/journal.pgen.1000365] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2008] [Accepted: 01/05/2009] [Indexed: 12/15/2022] Open
Abstract
It has been argued that the limited genetic diversity and reduced allelic heterogeneity observed in isolated founder populations facilitates discovery of loci contributing to both Mendelian and complex disease. A strong founder effect, severe isolation, and substantial inbreeding have dramatically reduced genetic diversity in natives from the island of Kosrae, Federated States of Micronesia, who exhibit a high prevalence of obesity and other metabolic disorders. We hypothesized that genetic drift and possibly natural selection on Kosrae might have increased the frequency of previously rare genetic variants with relatively large effects, making these alleles readily detectable in genome-wide association analysis. However, mapping in large, inbred cohorts introduces analytic challenges, as extensive relatedness between subjects violates the assumptions of independence upon which traditional association test statistics are based. We performed genome-wide association analysis for 15 quantitative traits in 2,906 members of the Kosrae population, using novel approaches to manage the extreme relatedness in the sample. As positive controls, we observe association to known loci for plasma cholesterol, triglycerides, and C-reactive protein and to a compelling candidate loci for thyroid stimulating hormone and fasting plasma glucose. We show that our study is well powered to detect common alleles explaining >/=5% phenotypic variance. However, no such large effects were observed with genome-wide significance, arguing that even in such a severely inbred population, common alleles typically have modest effects. Finally, we show that a majority of common variants discovered in Caucasians have indistinguishable effect sizes on Kosrae, despite the major differences in population genetics and environment.
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Yokoyama H, Kawai K, Ohishi M, Sone H. Familial predisposition to cardiovascular risk and disease contributes to cardiovascular risk and disease interacting with other cardiovascular risk factors in diabetes—Implication for common soil (JDDM 14). Atherosclerosis 2008; 201:332-8. [DOI: 10.1016/j.atherosclerosis.2008.02.025] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/11/2007] [Revised: 02/11/2008] [Accepted: 02/16/2008] [Indexed: 10/22/2022]
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August GP, Caprio S, Fennoy I, Freemark M, Kaufman FR, Lustig RH, Silverstein JH, Speiser PW, Styne DM, Montori VM. Prevention and treatment of pediatric obesity: an endocrine society clinical practice guideline based on expert opinion. J Clin Endocrinol Metab 2008; 93:4576-99. [PMID: 18782869 PMCID: PMC6048599 DOI: 10.1210/jc.2007-2458] [Citation(s) in RCA: 354] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2007] [Accepted: 08/29/2008] [Indexed: 02/06/2023]
Abstract
OBJECTIVE Our objective was to formulate practice guidelines for the treatment and prevention of pediatric obesity. CONCLUSIONS We recommend defining overweight as body mass index (BMI) in at least the 85th percentile but < the 95th percentile and obesity as BMI in at least the 95th percentile against routine endocrine studies unless the height velocity is attenuated or inappropriate for the family background or stage of puberty; referring patients to a geneticist if there is evidence of a genetic syndrome; evaluating for obesity-associated comorbidities in children with BMI in at least the 85th percentile; and prescribing and supporting intensive lifestyle (dietary, physical activity, and behavioral) modification as the prerequisite for any treatment. We suggest that pharmacotherapy (in combination with lifestyle modification) be considered in: 1) obese children only after failure of a formal program of intensive lifestyle modification; and 2) overweight children only if severe comorbidities persist despite intensive lifestyle modification, particularly in children with a strong family history of type 2 diabetes or premature cardiovascular disease. Pharmacotherapy should be provided only by clinicians who are experienced in the use of antiobesity agents and aware of the potential for adverse reactions. We suggest bariatric surgery for adolescents with BMI above 50 kg/m(2), or BMI above 40 kg/m(2) with severe comorbidities in whom lifestyle modifications and/or pharmacotherapy have failed. Candidates for surgery and their families must be psychologically stable and capable of adhering to lifestyle modifications. Access to experienced surgeons and sophisticated multidisciplinary teams who assess the benefits and risks of surgery is obligatory. We emphasize the prevention of obesity by recommending breast-feeding of infants for at least 6 months and advocating that schools provide for 60 min of moderate to vigorous daily exercise in all grades. We suggest that clinicians educate children and parents through anticipatory guidance about healthy dietary and activity habits, and we advocate for restricting the availability of unhealthy food choices in schools, policies to ban advertising unhealthy food choices to children, and community redesign to maximize opportunities for safe walking and bike riding to school, athletic activities, and neighborhood shopping.
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Affiliation(s)
- Gilbert P. August
- Professor Emeritus of Pediatrics, George Washington University School of Medicine (G.P.A.), Washington, D.C. 20037
| | - Sonia Caprio
- Yale University School of Medicine (S.C.), New Haven, Connecticut 06510
| | - Ilene Fennoy
- Columbia University (I.F.), New York, New York 10027
| | - Michael Freemark
- Duke University Medical Center (M.F.), Durham, North Carolina 27710
| | | | - Robert H. Lustig
- University of California San Francisco (R.H.L.), San Francisco, California 94143
| | | | | | - Dennis M. Styne
- University of California–Davis Medical Center (D.M.S.), Sacramento, California 95817
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Gusev A, Lowe JK, Stoffel M, Daly MJ, Altshuler D, Breslow JL, Friedman JM, Pe'er I. Whole population, genome-wide mapping of hidden relatedness. Genome Res 2008; 19:318-26. [PMID: 18971310 DOI: 10.1101/gr.081398.108] [Citation(s) in RCA: 308] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
We present GERMLINE, a robust algorithm for identifying segmental sharing indicative of recent common ancestry between pairs of individuals. Unlike methods with comparable objectives, GERMLINE scales linearly with the number of samples, enabling analysis of whole-genome data in large cohorts. Our approach is based on a dictionary of haplotypes that is used to efficiently discover short exact matches between individuals. We then expand these matches using dynamic programming to identify long, nearly identical segmental sharing that is indicative of relatedness. We use GERMLINE to comprehensively survey hidden relatedness both in the HapMap as well as in a densely typed island population of 3000 individuals. We verify that GERMLINE is in concordance with other methods when they can process the data, and also facilitates analysis of larger scale studies. We bolster these results by demonstrating novel applications of precise analysis of hidden relatedness for (1) identification and resolution of phasing errors and (2) exposing polymorphic deletions that are otherwise challenging to detect. This finding is supported by concordance of detected deletions with other evidence from independent databases and statistical analyses of fluorescence intensity not used by GERMLINE.
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Affiliation(s)
- Alexander Gusev
- Department of Computer Science, Columbia University, New York, New York 10027, USA.
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Burkhardt R, Kenny EE, Lowe JK, Birkeland A, Josowitz R, Noel M, Salit J, Maller JB, Pe'er I, Daly MJ, Altshuler D, Stoffel M, Friedman JM, Breslow JL. Common SNPs in HMGCR in micronesians and whites associated with LDL-cholesterol levels affect alternative splicing of exon13. Arterioscler Thromb Vasc Biol 2008; 28:2078-84. [PMID: 18802019 DOI: 10.1161/atvbaha.108.172288] [Citation(s) in RCA: 107] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
UNLABELLED Background- Variation in LDL-cholesterol (LDL-C) among individuals is a complex genetic trait involving multiple genes and gene-environment interactions. METHODS AND RESULTS In a genome-wide association study (GWAS) to identify genetic variants influencing LDL-C in an isolated population from Kosrae, we observed associations for SNPs in the gene encoding 3hydroxy-3-methylglutaryl (HMG)-coenzyme A (CoA) reductase (HMGCR). Three of these SNPs (rs7703051, rs12654264, and rs3846663) met the statistical threshold of genome-wide significance when combined with data from the Diabetes Genetics Initiative GWAS. We followed up the association results and identified a functional SNP in intron13 (rs3846662), which was in linkage disequilibrium with the SNPs of genome-wide significance and affected alternative splicing of HMGCR mRNA. In vitro studies in human lymphoblastoid cells demonstrated that homozygosity for the rs3846662 minor allele was associated with up to 2.2-fold lower expression of alternatively spliced HMGCR mRNA lacking exon13, and minigene transfection assays confirmed that allele status at rs3846662 directly modulated alternative splicing of HMGCR exon13 (42.9+/-3.9 versus 63.7+/-1.0%Deltaexon13/total HMGCR mRNA, P=0.02). Further, the alternative splice variant could not restore HMGCR activity when expressed in HMGCR deficient UT-2 cells. CONCLUSIONS We identified variants in HMGCR that are associated with LDL-C across populations and affect alternative splicing of HMGCR exon13.
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Affiliation(s)
- Ralph Burkhardt
- Laboratory of Biochemical Genetics and Metabolism, The Rockefeller University, New York, NY 10065, USA
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Barsalani R, Pighon A, Rabasa-Lhoret R, Yasari S, Lavoie JM. Liver of ovariectomized rats is resistant to resorption of lipids. Physiol Behav 2008; 95:216-21. [DOI: 10.1016/j.physbeh.2008.05.024] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2008] [Revised: 05/06/2008] [Accepted: 05/29/2008] [Indexed: 10/22/2022]
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Igo RP, Wijsman EM. Empirical significance values for linkage analysis: trait simulation using posterior model distributions from MCMC oligogenic segregation analysis. Genet Epidemiol 2008; 32:119-31. [PMID: 17849492 DOI: 10.1002/gepi.20267] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Variance-components (VC) linkage analysis is a powerful model-free method for assessing linkage, but the distribution of VC logarithm of the odds ratio (LOD) scores may deviate substantially from the assumed asymptotic distribution. Typically, the null distribution of the VC-LOD score and other linkage statistics has been estimated by generating new genotype data independently of the trait data, and computing a linkage statistic for many such marker-simulated data sets. However, marker simulation is susceptible to errors in the assumed marker and map model and is computationally intensive. Here, we describe a method for generating posterior distributions of linkage statistics through simulation of trait data based on the original sample and on results from an initial scan using a Bayesian Markov-chain Monte Carlo (MCMC) approach for oligogenic segregation analysis. We use samples of oligogenic trait models taken from the posterior distribution to generate new samples of trait data, which were paired with the original marker data for analysis. Empirical P-values obtained from trait and marker simulation were similar when derived for several strong linkage signals from published linkage scans, and for analysis of data with a known, simulated, trait model. Furthermore, trait simulation produces the expected null distribution of VC-LOD scores and is computationally fast when marker identity-by-descent estimates from the original data could be reused. These results suggest that trait simulation gives valid estimates of statistical significance of linkage signals. Finally, these results also demonstrate the feasibility of obtaining empirical significance levels for evaluating Bayesian oligogenic linkage signals with either marker or trait simulation.
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Affiliation(s)
- Robert P Igo
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, USA
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Ray A, Weeks DE. Relationship uncertainty linkage statistics (RULS): affected relative pair statistics that model relationship uncertainty. Genet Epidemiol 2008; 32:313-24. [DOI: 10.1002/gepi.20306] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Wong J, Nock NL, Xu Z, Kyle C, Daniels A, White M, Yue DK, Elston RC, Mountjoy KG. A polymorphism (D20S32e) close to the human melanocortin receptor 3 is associated with insulin resistance but not the metabolic syndrome. Diabetes Res Clin Pract 2008; 80:203-7. [PMID: 18180070 DOI: 10.1016/j.diabres.2007.11.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/19/2007] [Accepted: 11/06/2007] [Indexed: 11/17/2022]
Abstract
Insulin resistance (IR) is postulated to underlie diabetes, the metabolic syndrome (MS) and cardiovascular disease (CVD). The D20S32e marker close to the melanocortin receptor-3 (hMC3-R) has been shown to be associated with IR in a large New Zealand Māori kindred, a population at high risk for MS and CVD. Here we examine the potential association of the D20S32e marker with the MS in this 60 member Māori kindred. There was a significant association between the D20S32e "B" allele and the fasting insulin component under both polygenic (beta=-5.3077; p=0.008) and common sibship effect (beta=-4.2161; p=0.03) models. No significant association between the same allele of D20S32e and the MS was observed after adjusting for age under a polygenic (p=0.103) or sibling (p=0.09) correlation model. We conclude that in this Māori kindred, the D20S32e polymorphism is significantly associated with insulin resistance but not with MS. Our data supports the hypothesis that multiple gene variants are necessary for the development of the MS.
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Affiliation(s)
- Jencia Wong
- Diabetes Centre, Royal Prince Alfred Hospital, Sydney, Australia; Discipline of Medicine, University of Sydney, Sydney, Australia
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de Oliveira CM, Pereira AC, de Andrade M, Soler JM, Krieger JE. Heritability of cardiovascular risk factors in a Brazilian population: Baependi Heart Study. BMC MEDICAL GENETICS 2008; 9:32. [PMID: 18430212 PMCID: PMC2386446 DOI: 10.1186/1471-2350-9-32] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/29/2007] [Accepted: 04/22/2008] [Indexed: 12/22/2022]
Abstract
Background The heritability of cardiovascular risk factors is expected to differ between populations because of the different distribution of environmental risk factors, as well as the genetic make-up of different human populations. Methods The purpose of this analysis was to evaluate genetic and environmental influences on cardiovascular risk factor traits, using a variance component approach, by estimating the heritability of these traits in a sample of 1,666 individuals in 81 families ascertained randomly from a highly admixed population of a city in a rural area in Brazil. Results Before adjustment for sex, age, age2, and age × sex interaction, polygenic heritability of systolic (SBP) and diastolic (DBP) blood pressure were 15.0% and 16.4%, waist circumference 26.1%, triglycerides 25.7%, fasting glucose 32.8%, HDL-c 31.2%, total cholesterol 28.6%, LDL-c 26.3%, BMI 39.1%. Adjustment for covariates increased polygenic heritability estimates for all traits mainly systolic and diastolic blood pressure (25.9 and 26.2%, respectively), waist circumference (40.1%), and BMI (51.0%). Conclusion Heritability estimates for cardiovascular traits in the Brazilian population are high and not significantly different from other studied worldwide populations. Mapping efforts to identify genetic loci associated with variability of these traits are warranted.
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Cai G, Cole SA, Butte NF, Voruganti VS, Comuzzie AG. Genome-wide scan revealed genetic loci for energy metabolism in Hispanic children and adolescents. Int J Obes (Lond) 2008; 32:579-85. [PMID: 18317473 DOI: 10.1038/ijo.2008.20] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
OBJECTIVE Genome-wide scans were conducted in search for genetic locations linked to energy expenditure and substrate oxidation in children. DESIGN Pedigreed data of 1030 Hispanic children and adolescents were from the Viva La Familia Study which was designed to investigate genetic and environmental risk factors for the development of obesity in Hispanic families. A respiratory calorimeter was used to measure 24-h total energy expenditure (TEE), basal metabolic rate (BMR), sleep metabolic rate (SMR), 24-h respiratory quotient (24RQ), basal metabolic respiratory quotient (BMRQ) and sleep respiratory quotient (SRQ). Protein, fat and carbohydrate oxidation (PROOX, FATOX and CHOOX, respectively) were also estimated. All participants were genotyped for 384 single tandem repeat markers spaced an average of 10 cM apart. Computer program SOLAR was used to perform the genetic linkage analyses. RESULTS Significant linkage for TEE was detected on chromosome 1 near marker D1S2841, with a logarithm of the odds (LOD) score of 4.0. SMR, BMRQ and PROOX were associated with loci on chromosome 18, 17 and 9, respectively, with LOD scores of 4.88, 3.17 and 4.55, respectively. A genome-wide scan of SMR per kg fat-free mass (SpFFM) peaked in the same region as SMR on chromosome 18 (LOD, 5.24). Suggestive linkage was observed for CHOOX and FATOX. Several candidate genes were found in the above chromosomal regions including leptin receptor (LEPR). CONCLUSION Regions on chromosomes 1, 9, 17 and 18 harbor genes affecting variation in energy expenditure and substrate oxidation in Hispanic children and adolescents.
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Affiliation(s)
- G Cai
- USDA/ARS Children's Nutrition Research Center, Baylor College of Medicine, Houston, TX 77030, USA
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Xiong DH, Liu JF, Guo YF, Guo Y, Yang TL, Jiang H, Chen Y, Yang F, Recker RR, Deng HW. Quantitative trait loci mapping. Methods Mol Biol 2008; 455:203-235. [PMID: 18463822 DOI: 10.1007/978-1-59745-104-8_16] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
This chapter presents current methods for mapping quantitative trait loci (QTLs) in natural populations especially in humans. We discussed the experimental designs for QTL mapping, traditional methods adopted such as linkage mapping approaches and methods for linkage disequilibrium (LD) mapping. Multiple traits and interaction analysis are also outlined. The application of modern genomic approaches, which mainly exploit the microarray technology, into QTL mapping was detailed. The latter are very recent protocols and are less developed than linkage and association methods at present. The main focus of this chapter is technical issues although statistical issues are also covered to certain extent. Finally, we summarize the limitations of the current QTL approaches and discuss the solutions to certain problems.
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Affiliation(s)
- Dong-Hai Xiong
- Osteoporosis Research Center, Creighton University, Omaha, NE, USA
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Visscher PM, Macgregor S, Benyamin B, Zhu G, Gordon S, Medland S, Hill WG, Hottenga JJ, Willemsen G, Boomsma DI, Liu YZ, Deng HW, Montgomery GW, Martin NG. Genome partitioning of genetic variation for height from 11,214 sibling pairs. Am J Hum Genet 2007; 81:1104-10. [PMID: 17924350 PMCID: PMC2265649 DOI: 10.1086/522934] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2007] [Accepted: 07/24/2007] [Indexed: 01/24/2023] Open
Abstract
Height has been used for more than a century as a model by which to understand quantitative genetic variation in humans. We report that the entire genome appears to contribute to its additive genetic variance. We used genotypes and phenotypes of 11,214 sibling pairs from three countries to partition additive genetic variance across the genome. Using genome scans to estimate the proportion of the genomes of each chromosome from siblings that were identical by descent, we estimated the heritability of height contributed by each of the 22 autosomes and the X chromosome. We show that additive genetic variance is spread across multiple chromosomes and that at least six chromosomes (i.e., 3, 4, 8, 15, 17, and 18) are responsible for the observed variation. Indeed, the data are not inconsistent with a uniform spread of trait loci throughout the genome. Our estimate of the variance explained by a chromosome is correlated with the number of times suggestive or significant linkage with height has been reported for that chromosome. Variance due to dominance was not significant but was difficult to assess because of the high sampling correlation between additive and dominance components. Results were consistent with the absence of any large between-chromosome epistatic effects. Notwithstanding the proposed architecture of complex traits that involves widespread gene-gene and gene-environment interactions, our results suggest that variation in height in humans can be explained by many loci distributed over all autosomes, with an additive mode of gene action.
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Affiliation(s)
- Peter M Visscher
- Genetic Epidemiology, Queensland Institute of Medical Research, Brisbane, Australia.
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Daw EW, Chen SN, Czernuszewicz G, Lombardi R, Lu Y, Ma J, Roberts R, Shete S, Marian AJ. Genome-wide mapping of modifier chromosomal loci for human hypertrophic cardiomyopathy. Hum Mol Genet 2007; 16:2463-71. [PMID: 17652099 PMCID: PMC2772866 DOI: 10.1093/hmg/ddm202] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Hypertrophic cardiomyopathy (HCM) is a disease of mutant sarcomeric proteins (except for phenocopy). Cardiac hypertrophy is the clinical diagnostic hallmark of HCM and a major determinant of morbidity and mortality in various cardiovascular diseases. However, there is remarkable variability in expression of hypertrophy, even among HCM patients with identical causal mutations. We hypothesized modifier genes are partly responsible for the variation in hypertrophic expressivity. To map the modifier loci, we typed 811 short-tandem repeat markers ( approximately 5 cMdense) in 100 members of an HCM family including 36 with the InsG791 mutation in MYBPC3. We performed oligogenic simultaneous segregation and linkage analyses using Markov Chain Monte Carlo methods and detected linkage on 3q26.2 (180 cM), 10p13 (41 cM), 17q24 (108 cM) with log of the posterior placement probability ratio (LOP) of 3.51, 4.86 and 4.17, respectively, and suggestive linkage (LOP of 2.40) on 16q12.2 (73 cM). The effect sizes varied according to the modifier locus, age and sex. It ranged from approximately 8 g shift in left ventricular mass for 10p13 locus heterozygosity for the common allele to approximately 90 g shift for 3q26.2 locus homozygosity for the uncommon allele. Refining the 10p13 locus restricted the candidate modifier genes to ITGA8, C10orf97 (CARP) and PTER. ITGA8 and CARP are biologically plausible candidates as they are implicated in cardiac fibrosis and apoptosis, respectively. Since cardiac hypertrophy is a major determinant of total and cardiovascular mortality and morbidity, regardless of the etiology, identification of the specific modifier genes could have significant prognostic and therapeutic implications for various cardiovascular diseases.
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Affiliation(s)
- E. Warwick Daw
- Department of Epidemiology, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Suet Nee Chen
- Center for Cardiovascular Genetic Research, The Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center, Houston, TX 77030, USA
| | - Grazyna Czernuszewicz
- Center for Cardiovascular Genetic Research, The Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center, Houston, TX 77030, USA
| | - Raffaella Lombardi
- Center for Cardiovascular Genetic Research, The Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center, Houston, TX 77030, USA
| | - Yue Lu
- Department of Epidemiology, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jianzhong Ma
- Department of Epidemiology, MD Anderson Cancer Center, Houston, TX 77030, USA
| | | | - Sanjay Shete
- Department of Epidemiology, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ali J. Marian
- Center for Cardiovascular Genetic Research, The Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center, Houston, TX 77030, USA
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Kaun KR, Riedl CAL, Chakaborty-Chatterjee M, Belay AT, Douglas SJ, Gibbs AG, Sokolowski MB. Natural variation in food acquisition mediatedviaaDrosophilacGMP-dependent protein kinase. J Exp Biol 2007; 210:3547-58. [DOI: 10.1242/jeb.006924] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
SUMMARYIn natural environments where food abundance and quality can change drastically over time, animals must continuously alter their food acquisition strategies. Although genetic variation contributes to this plasticity, the specific genes involved and their interactions with the environment are poorly understood. Here we report that natural variation in the Drosophilagene, foraging (for), which encodes a cGMP-dependent protein kinase (PKG), affects larval food acquisition in an environmentally dependent fashion. When food is plentiful, the wild-type rover(forR) allele confers lower food intake and higher glucose absorption than both the wild-type sitter (fors) allele and the mutant fors2 allele. When food is scarce, forR, fors and fors2 larvae increase food intake to a common maximal level, but forRlarvae retain their increased absorption efficiency. Changes in forexpression can induce corrective behavioral modifications in response to food deprivation. When reared in environments with low food levels, forR larvae have higher survivorship and faster development than fors and fors2larvae. Together, these results show that natural variation in forhas far reaching implications affecting a suite of phenotypes involved in the regulation of food acquisition.
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Affiliation(s)
- Karla R. Kaun
- Department of Biology, University of Toronto, 3359 Mississauga Road,Mississauga, Ontario, L5L 1C6, Canada
| | - Craig A. L. Riedl
- Department of Biology, University of Toronto, 3359 Mississauga Road,Mississauga, Ontario, L5L 1C6, Canada
| | | | - Amsale T. Belay
- Department of Biology, University of Toronto, 3359 Mississauga Road,Mississauga, Ontario, L5L 1C6, Canada
| | - Scott J. Douglas
- Department of Biology, University of Toronto, 3359 Mississauga Road,Mississauga, Ontario, L5L 1C6, Canada
| | - Allen G. Gibbs
- School of Life Sciences, University of Nevada, 4505 Maryland Parkway, Las Vegas, NV 89154-4004, USA
| | - Marla B. Sokolowski
- Department of Biology, University of Toronto, 3359 Mississauga Road,Mississauga, Ontario, L5L 1C6, Canada
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Terruzzi I, Senesi P, Fermo I, Lattuada G, Luzi L. Are genetic variants of the methyl group metabolism enzymes risk factors predisposing to obesity? J Endocrinol Invest 2007; 30:747-53. [PMID: 17993766 DOI: 10.1007/bf03350812] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Obesity, due to the combination of inherited genes and environmental factors, is continually increasing. We evaluated the relationship between polymorphisms of methylene-tetrahydrofolate reductase (MTHFR C677T and A1298C), methionine synthase (MTR A2756G), methionine synthase reductase (MTRR A66G), betaine:homocysteine methyltransferase (BHMT G742A) and cystathionine beta-synthase (CBS 68-bp ins) genes and the risk of obesity. We studied these polymorphic variants in 54 normal and 82 obese subjects [body mass index (BMI)=22.4+/-1.8, 34.1+/-7.1; ages 35.2+/-10.7, 43.3+/-10.6 respectively]. Levels of total plasma homocysteine (t-Hcy), folates, and vitamins B6 and B12 were not significantly different, while leptin concentration was significantly higher (p=0.005) in the obese patients compared to the lean controls. The frequency of only (a) MTHFR (AC), (b) MTR (AG), and (c) MTRR (AG) heterozygous genotypes was statistically different in the obese compared to the control group (p=0.03, p=0.007, and p=0.01). Single (a), (b), and (c) heterozygous genotypes had a significant risk of developing obesity [p=0.02, 0.01, and 0.03; odds ratio (OR)=2.5, 3.0, and 2.4; 95% confidence interval (CI)=1.2-5.3, 1.3-7.1, and 1.2-5.1 respectively] and the risk remarkably increased for combined genotypes a+b, a+c, b+c, and a+b+c (p=0.002, 0.002, 0.016, 0.006; OR=7.7, 5.4, 5.8, 15.4; 95% CI=1.9-30.4, 1.7-16.8, 1.4-23.2, 1.6- 152.3). These findings suggest that in obese subjects, Hcy cycle efficiency is impaired by MTHFR, MTR, and MTRR inability to supply methyl-group donors, providing evidence that MTHFR, MTR, and MTRR gene polymorphisms are genetic risk factors for obesity.
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Affiliation(s)
- I Terruzzi
- Division of Internal Medicine, Section of Nutrition/Metabolism, San Raffaele Scientific Institute, 20132 Milano, Italy.
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Bibliography. Current world literature. Diabetes and the endocrine pancreas II. Curr Opin Endocrinol Diabetes Obes 2007; 14:329-57. [PMID: 17940461 DOI: 10.1097/med.0b013e3282c3a898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Suckling K. Drug discovery in the metabolic syndrome: context and some recent developments. Expert Opin Ther Targets 2007; 11:801-8. [PMID: 17504017 DOI: 10.1517/14728222.11.6.801] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The metabolic syndrome, encompassing the clinically distinct but related areas of dyslipidaemia, insulin resistance, obesity and vascular disease, offers a wide arena for drug discovery. There is substantial and growing unmet medical need, particularly as the worldwide epidemic of obesity continues to develop. There are also many targets and biological mechanisms that can be exploited. However, the context for clinical development is challenging because of the many ways in which the syndrome can be approached. As with most therapeutic areas, preclinical data provide only limited confidence in the potential of a novel target in humans. In this review, the author outlines the context for drug discovery in the metabolic syndrome, the clinical and biological scope and recent developments in preclinical models. Finally, existing examples of drug targets for a range of biological mechanisms are considered, outlining their biology and points relevant to lead identification and optimisation and clinical development.
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Perola M, Sammalisto S, Hiekkalinna T, Martin NG, Visscher PM, Montgomery GW, Benyamin B, Harris JR, Boomsma D, Willemsen G, Hottenga JJ, Christensen K, Kyvik KO, Sørensen TIA, Pedersen NL, Magnusson PKE, Spector TD, Widen E, Silventoinen K, Kaprio J, Palotie A, Peltonen L. Combined genome scans for body stature in 6,602 European twins: evidence for common Caucasian loci. PLoS Genet 2007; 3:e97. [PMID: 17559308 PMCID: PMC1892350 DOI: 10.1371/journal.pgen.0030097] [Citation(s) in RCA: 132] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2007] [Accepted: 05/02/2007] [Indexed: 01/06/2023] Open
Abstract
Twin cohorts provide a unique advantage for investigations of the role of genetics and environment in the etiology of variation in common complex traits by reducing the variance due to environment, age, and cohort differences. The GenomEUtwin (http://www.genomeutwin.org) consortium consists of eight twin cohorts (Australian, Danish, Dutch, Finnish, Italian, Norwegian, Swedish, and United Kingdom) with the total resource of hundreds of thousands of twin pairs. We performed quantitative trait locus (QTL) analysis of one of the most heritable human complex traits, adult stature (body height) using genome-wide scans performed for 3,817 families (8,450 individuals) derived from twin cohorts from Australia, Denmark, Finland, Netherlands, Sweden, and United Kingdom with an approximate ten-centimorgan microsatellite marker map. The marker maps for different studies differed and they were combined and related to the sequence positions using software developed by us, which is publicly available (https://apps.bioinfo.helsinki.fi/software/cartographer.aspx). Variance component linkage analysis was performed with age, sex, and country of origin as covariates. The covariate adjusted heritability was 81% for stature in the pooled dataset. We found evidence for a major QTL for human stature on 8q21.3 (multipoint logarithm of the odds 3.28), and suggestive evidence for loci on Chromosomes X, 7, and 20. Some evidence of sex heterogeneity was found, however, no obvious female-specific QTLs emerged. Several cohorts contributed to the identified loci, suggesting an evolutionarily old genetic variant having effects on stature in European-based populations. To facilitate the genetic studies of stature we have also set up a website that lists all stature genome scans published and their most significant loci (http://www.genomeutwin.org/stature_gene_map.htm). Twin cohorts provide a unique advantage for research of the role of genetics and environment behind common complex traits by reducing the variance due to environment, age, and cohort differences. The GenomEUtwin consortium consists of eight twin cohorts with the total resource of hundreds of thousands of twin pairs (http://www.genomeutwin.org). We performed quantitative family-based genetic linkage analysis for one of the most heritable human complex traits, adult stature (body height), using genome-wide scans derived from twin cohorts from Australia, Denmark, Finland, Netherlands, Sweden, and United Kingdom. Age, sex, and country were adjusted for in the data analyses. Human stature was found to be very heritable across all the cohorts and in the combined dataset. We found evidence for a shared genetic locus accounting for human stature on Chromosome 8, and suggestive evidence for loci on Chromosomes X, 7, and 20. Since twins from several countries contributed to the identified loci, an evolutionarily old genetic variant must influence stature in European-based populations. To facilitate the research in the field we have also set up a website that lists all stature genome scans published and their most significant loci (http://www.genomeutwin.org/stature_gene_map.htm).
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Affiliation(s)
- Markus Perola
- Department of Molecular Medicine, National Public Health Institute, Helsinki, Finland
- Faculty of Medicine, Department of Medical Genetics, University of Helsinki, Helsinki, Finland
| | - Sampo Sammalisto
- Department of Molecular Medicine, National Public Health Institute, Helsinki, Finland
| | - Tero Hiekkalinna
- Department of Molecular Medicine, National Public Health Institute, Helsinki, Finland
| | - Nick G Martin
- Queensland Institute of Medical Research, Brisbane, Australia
| | | | | | - Beben Benyamin
- Queensland Institute of Medical Research, Brisbane, Australia
| | | | | | | | | | - Kaare Christensen
- Department of Epidemiology, Institute of Public Health, University of Southern Denmark, Odense, Denmark
| | - Kirsten Ohm Kyvik
- Department of Epidemiology, Institute of Public Health, University of Southern Denmark, Odense, Denmark
| | | | | | | | | | - Elisabeth Widen
- Finnish Genome Center, University of Helsinki, Helsinki, Finland
| | - Karri Silventoinen
- Faculty of Medicine, Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Jaakko Kaprio
- Faculty of Medicine, Department of Public Health, University of Helsinki, Helsinki, Finland
- Department of Mental Health and Alcohol Research, National Public Health Institute, Helsinki, Finland
| | - Aarno Palotie
- Finnish Genome Center, University of Helsinki, Helsinki, Finland
| | - Leena Peltonen
- Department of Molecular Medicine, National Public Health Institute, Helsinki, Finland
- Faculty of Medicine, Department of Medical Genetics, University of Helsinki, Helsinki, Finland
- The Broad Institute, Massachusetts Institute of Technology, Boston, Massachusetts, United States of America
- * To whom correspondence should be addressed. E-mail:
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45
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Abstract
According to the Centers for Disease Control and Prevention, the prevalence of obesity among adolescents ages 12 to 19 has soared in recent decades, from 5% in 1980 to 16% in 2002. Recent neuroendocrinologic research may help to explain the complexity of obesity and help providers develop more effective weight-loss strategies. Combining medical intervention with an individualized cognitive-behavioral program is the best approach for adolescents. Accompanying sidebars examine several such programs and provide additional resources for clinicians.
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Affiliation(s)
- Laura D Hoeman
- Behavioral Health Resources Acute Psychiatric Services, Olympia, WA, USA.
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46
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Abstract
This chapter presents the current state of knowledge in the field of the genetics of human obesity. The molecular approach has proved to be powerful in defining new syndromes associated with obesity. The pivotal role of leptin and melanocortin pathways has been recognized, but only in rare cases of obesity. In the more common form of obesity a multitude of polymorphisms located in genes and candidate regions throughout the genome regulate an individual's susceptibility to weight gain in a permissive environment. The effects are often uncertain and the results not always confirmed. Combining these single nucleotide polymorphisms and defining the associated risks for obesity will be a real challenge in the future. It is now necessary to integrate data of various origins (environment, genotype, expression) to clarify this field.
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47
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Zhao LJ, Guo YF, Xiong DH, Xiao P, Recker RR, Deng HW. Is a gene important for bone resorption a candidate for obesity? An association and linkage study on the RANK (receptor activator of nuclear factor-kappaB) gene in a large Caucasian sample. Hum Genet 2006; 120:561-70. [PMID: 16960694 PMCID: PMC1829481 DOI: 10.1007/s00439-006-0243-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2006] [Accepted: 07/31/2006] [Indexed: 11/26/2022]
Abstract
In light of findings that osteoporosis and obesity may share some common genetic determination and previous reports that RANK (receptor activator of nuclear factor-kappaB) is expressed in skeletal muscles which are important for energy metabolism, we hypothesize that RANK, a gene essential for osteoclastogenesis, is also important for obesity. In order to test the hypothesis with solid data we first performed a linkage analysis around the RANK gene in 4,102 Caucasian subjects from 434 pedigrees, then we genotyped 19 SNPs in or around the RANK gene. A family-based association test (FBAT) was performed with both a quantitative measure of obesity [fat mass, lean mass, body mass index (BMI), and percentage fat mass (PFM)] and a dichotomously defined obesity phenotype-OB (OB if BMI > or = 30 kg/m(2)). In the linkage analysis, an empirical P = 0.004 was achieved at the location of the RANK gene for BMI. Family-based association analysis revealed significant associations of eight SNPs with at least one obesity-related phenotype (P < 0.05). Evidence of association was obtained at SNP10 (P = 0.002) and SNP16 (P = 0.001) with OB; SNP1 with fat mass (P = 0.003); SNP1 (P = 0.003) and SNP7 (P = 0.003) with lean mass; SNP1 (P = 0.002) and SNP7 (P = 0.002) with BMI; SNP1 (P = 0.003), SNP4 (P = 0.007), and SNP7 (P = 0.002) with PFM. In order to deal with the complex multiple testing issues, we performed FBAT multi-marker test (FBAT-MM) to evaluate the association between all the 18 SNPs and each obesity phenotype. The P value is 0.126 for OB, 0.033 for fat mass, 0.021 for lean mass, 0.016 for BMI, and 0.006 for PFM. The haplotype data analyses provide further association evidence. In conclusion, for the first time, our results suggest that RANK is a novel candidate for determination of obesity.
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Affiliation(s)
- Lan-Juan Zhao
- Osteoporosis Research Center and Department of Biomedical Sciences, Creighton University, Omaha, NE 68131, USA
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48
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Cassels S. Overweight in the Pacific: links between foreign dependence, global food trade, and obesity in the Federated States of Micronesia. Global Health 2006; 2:10. [PMID: 16834782 PMCID: PMC1533815 DOI: 10.1186/1744-8603-2-10] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2006] [Accepted: 07/11/2006] [Indexed: 11/10/2022] Open
Abstract
The Federated States of Micronesia (FSM) has received considerable attention for their alarming rates of overweight and obesity. On Kosrae, one of the four districts in the FSM, 88% of adults aged 20 or older are overweight (BMI > 25), 59% are obese (BMI > 30), and 24% are extremely obese (BMI > 35). Recent genetic studies in Kosrae have shown that obesity is a highly heritable trait, and more work is underway to identify obesity genes in humans. However, less attention has been given to potential social and developmental causes of obesity in the FSM. This paper outlines the long history of foreign rule and social change over the last 100 years, and suggests that a combination of dietary change influenced by foreigners, dependence on foreign aid, and the ease of global food trade contributed to poor diet and increased rates of obesity in Micronesia. The last section of the paper highlights the Pacific tuna trade as an example of how foreign dependence and global food trade exacerbates their obesity epidemic.
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Affiliation(s)
- Susan Cassels
- Center for Studies in Demography and Ecology, University of Washington, Box 353412, Seattle, WA 98195, USA.
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