1
|
Synergistic effect of LEP and LEPR gene polymorphism on body mass index in a Chinese population. Obes Res Clin Pract 2015; 7:e445-9. [PMID: 24308887 DOI: 10.1016/j.orcp.2012.06.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2011] [Revised: 06/06/2012] [Accepted: 06/25/2012] [Indexed: 11/21/2022]
Abstract
Both leptin (LEP) and leptin receptor (LEPR) are important in the regulation of body weight. In this study, we evaluated the individual and combined effects of a polymorphic microsatellite marker in the LEP gene 3' flanking region and two polymorphisms (Lys109Arg and Lys656Asn) of the LEPR gene on metabolic markers for obesity in a Chinese population. The genotypes of polymorphisms in LEP and LEPR gene were determined by PCR and SSCP assay in 230 simple obese subjects and 202 control subjects of Chinese population. Logistic regression analysis showed that polymorphism in LEP gene 3' flanking region was associated with waist/hip ratio (WHR) (P = 0.042). Individually, Lys109Arg variant in LEPR gene was associated with systolic blood pressure (P = 0.031) in males, and Lys656Asn variant was associated with serum triglyceride level (P = 0.026). Interestingly, only subjects that simultaneously exhibit all three polymorphisms showed a significantly elevated BMI (29.30 ± 0.85 vs 26.91 ± 1.19, P = 0.037). Taken together, our data suggest that a combination of polymorphism in the LEP gene 3' flanking region, and Lys109Arg, Lys656Asn variants in LEPR gene is associated with obesity in Chinese Han population.
Collapse
|
2
|
Zhao H, Li K, Tang JY, Zhou JC, Wang KN, Xia XJ, Lei XG. Expression of Selenoprotein Genes Is Affected by Obesity of Pigs Fed a High-Fat Diet. J Nutr 2015; 145:1394-401. [PMID: 25972525 PMCID: PMC4478952 DOI: 10.3945/jn.115.211318] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 04/16/2015] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Relations of the 25 mammalian selenoprotein genes with obesity and the associated inflammation remain unclear. OBJECTIVE This study explored impacts of high-fat diet-induced obesity on inflammation and expressions of selenoprotein and obesity-related genes in 10 tissues of pigs. METHODS Plasma and 10 tissues were collected from pigs (n = 10) fed a corn-soy-based control diet or that diet containing 3-7% lard from weanling to finishing (180 d). Plasma concentrations (n = 8) of cytokines and thyroid hormones and tissue mRNA abundance (n = 4) of 25 selenoprotein genes and 16 obesity-related genes were compared between the pigs fed the control and high-fat diets. Stepwise regression was applied to analyze correlations among all these measures, including the previously reported body physical and plasma biochemical variables. RESULTS The high-fat diet elevated (P < 0.05) plasma concentrations of tumor necrosis factor α, interleukin-6, leptin, and leptin receptor by 29-42% and affected (P < 0.05-0.1) tissue mRNA levels of the selenoprotein and obesity-related genes in 3 patterns. Specifically, the high-fat diet up-regulated 12 selenoprotein genes in 6 tissues, down-regulated 13 selenoprotein genes in 7 tissues, and exerted no effect on 5 genes in any tissue. Body weights and plasma triglyceride concentrations of pigs showed the strongest regressions to tissue mRNA abundances of selenoprotein and obesity-related genes. Among the selenoprotein genes, selenoprotein V and I were ranked as the strongest independent variables for the regression of phenotypic and plasma measures. Meanwhile, agouti signaling protein, adiponectin, and resistin genes represented the strongest independent variables of the obesity-related genes for the regression of tissue selenoprotein mRNA. CONCLUSIONS The high-fat diet induced inflammation in pigs and affected their gene expression of selenoproteins associated with thioredoxin and oxidoreductase systems, local tissue thyroid hormone activity, endoplasmic reticulum protein degradation, and phosphorylation of lipids. This porcine model may be used to study interactive mechanisms between excess fat intake and selenoprotein function.
Collapse
Affiliation(s)
- Hua Zhao
- International Center of Future Agriculture for Human Health, Sichuan Agricultural University, Sichuan, China;
| | - Ke Li
- International Center of Future Agriculture for Human Health, Sichuan Agricultural University, Sichuan, China
| | - Jia-Yong Tang
- International Center of Future Agriculture for Human Health, Sichuan Agricultural University, Sichuan, China
| | - Ji-Chang Zhou
- Molecular Biology Laboratory, Shenzhen Center for Chronic Disease Control, Shenzhen, China
| | - Kang-Ning Wang
- International Center of Future Agriculture for Human Health, Sichuan Agricultural University, Sichuan, China
| | - Xin-Jie Xia
- International Center of Future Agriculture for Human Health, Sichuan Agricultural University, Sichuan, China;,Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China; and
| | - Xin Gen Lei
- International Center of Future Agriculture for Human Health, Sichuan Agricultural University, Sichuan, China; Department of Animal Science, Cornell University, Ithaca, NY
| |
Collapse
|
3
|
Alemany M. Do the interactions between glucocorticoids and sex hormones regulate the development of the metabolic syndrome? Front Endocrinol (Lausanne) 2012; 3:27. [PMID: 22649414 PMCID: PMC3355885 DOI: 10.3389/fendo.2012.00027] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/27/2011] [Accepted: 02/06/2012] [Indexed: 12/14/2022] Open
Abstract
The metabolic syndrome is basically a maturity-onset disease. Typically, its manifestations begin to flourish years after the initial dietary or environmental aggression began. Since most hormonal, metabolic, or defense responses are practically immediate, the procrastinated response do not seem justified. Only in childhood, the damages of the metabolic syndrome appear with minimal delay. Sex affects the incidence of the metabolic syndrome, but this is more an effect of timing than absolute gender differences, females holding better than males up to menopause, when the differences between sexes tend to disappear. The metabolic syndrome is related to an immune response, countered by a permanent increase in glucocorticoids, which keep the immune system at bay but also induce insulin resistance, alter the lipid metabolism, favor fat deposition, mobilize protein, and decrease androgen synthesis. Androgens limit the operation of glucocorticoids, which is also partly blocked by estrogens, since they decrease inflammation (which enhances glucocorticoid release). These facts suggest that the appearance of the metabolic syndrome symptoms depends on the strength (i.e., levels) of androgens and estrogens. The predominance of glucocorticoids and the full manifestation of the syndrome in men are favored by decreased androgen activity. Low androgens can be found in infancy, maturity, advanced age, or because of their inhibition by glucocorticoids (inflammation, stress, medical treatment). Estrogens decrease inflammation and reduce the glucocorticoid response. Low estrogen (infancy, menopause) again allow the predominance of glucocorticoids and the manifestation of the metabolic syndrome. It is postulated that the equilibrium between sex hormones and glucocorticoids may be a critical element in the timing of the manifestation of metabolic syndrome-related pathologies.
Collapse
Affiliation(s)
- Marià Alemany
- Faculty of Biology, Department of Nutrition and Food Science, University of Barcelona Barcelona, Spain.
| |
Collapse
|
4
|
Walter S, Atzmon G, Demerath EW, Garcia ME, Kaplan RC, Kumari M, Lunetta KL, Milaneschi Y, Tanaka T, Tranah GJ, Völker U, Yu L, Arnold A, Benjamin EJ, Biffar R, Buchman AS, Boerwinkle E, Couper D, De Jager PL, Evans DA, Harris TB, Hoffmann W, Hofman A, Karasik D, Kiel DP, Kocher T, Kuningas M, Launer LJ, Lohman KK, Lutsey PL, Mackenbach J, Marciante K, Psaty BM, Reiman EM, Rotter JI, Seshadri S, Shardell MD, Smith AV, van Duijn C, Walston J, Zillikens MC, Bandinelli S, Baumeister SE, Bennett DA, Ferrucci L, Gudnason V, Kivimaki M, Liu Y, Murabito JM, Newman AB, Tiemeier H, Franceschini N. A genome-wide association study of aging. Neurobiol Aging 2011; 32:2109.e15-28. [PMID: 21782286 PMCID: PMC3193030 DOI: 10.1016/j.neurobiolaging.2011.05.026] [Citation(s) in RCA: 111] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2011] [Revised: 04/14/2011] [Accepted: 05/30/2011] [Indexed: 12/22/2022]
Abstract
Human longevity and healthy aging show moderate heritability (20%-50%). We conducted a meta-analysis of genome-wide association studies from 9 studies from the Cohorts for Heart and Aging Research in Genomic Epidemiology Consortium for 2 outcomes: (1) all-cause mortality, and (2) survival free of major disease or death. No single nucleotide polymorphism (SNP) was a genome-wide significant predictor of either outcome (p < 5 × 10(-8)). We found 14 independent SNPs that predicted risk of death, and 8 SNPs that predicted event-free survival (p < 10(-5)). These SNPs are in or near genes that are highly expressed in the brain (HECW2, HIP1, BIN2, GRIA1), genes involved in neural development and function (KCNQ4, LMO4, GRIA1, NETO1) and autophagy (ATG4C), and genes that are associated with risk of various diseases including cancer and Alzheimer's disease. In addition to considerable overlap between the traits, pathway and network analysis corroborated these findings. These findings indicate that variation in genes involved in neurological processes may be an important factor in regulating aging free of major disease and achieving longevity.
Collapse
Affiliation(s)
- Stefan Walter
- Department of Public Health, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Gil Atzmon
- Institute for Aging Research and the Diabetes Research Center. Albert Einstein College of Medicine, Bronx, NY, United States of America
- Department of Medicine Albert Einstein College of Medicine, Bronx, NY, United States of America
- Department of Genetic Albert Einstein College of Medicine, Bronx, NY, United States of America
| | - Ellen W. Demerath
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Melissa E. Garcia
- Laboratory of Epidemiology, Demography, and Biometry, National Institute on Aging, National Institutes of Health, Bethesda, MD, United States of America
| | - Robert C. Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx NY, United States of America
| | - Meena Kumari
- Department of Epidemiology and Public Health, University College London, London, United Kingdom
| | - Kathryn L. Lunetta
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, United States of America
| | - Yuri Milaneschi
- Clinical Research Branch, National Institute on Aging, Baltimore, MD, United States of America
| | - Toshiko Tanaka
- Clinical Research Branch, National Institute on Aging, Baltimore, MD, United States of America
| | - Gregory J. Tranah
- California Pacific Medical Center, San Francisco, CA, United States of America
| | - Uwe Völker
- Interfaculty Institute for Genetics and Functional Genomics, Ernst-Moritz-Arndt-University Greifswald, Greifswald, Germany
| | - Lei Yu
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, IL, United States of America
| | - Alice Arnold
- Department of Biostatistics, Unversity of Washington, Seattle, WA, United States of America
| | - Emelia J. Benjamin
- Sections of General Internal Medicine, Preventive Medicine, Cardiology and Neurology, Department of Medicine, Boston University School of Medicine, Boston, MA, United States of America
- The National Heart Lung and Blood Institute’s Framingham Heart Study, Framingham, MA, United States of America
| | - Reiner Biffar
- Dental School, Ernst-Moritz-Arndt-University Greifswald, Greifswald, Germany
| | - Aron S. Buchman
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, IL, United States of America
| | - Eric Boerwinkle
- Human Genetics Center, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - David Couper
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, United States of America
| | - Philip L. De Jager
- Program in Translational NeuroPsychiatric Genomics, Department of Neurology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States of America
| | - Denis A. Evans
- Rush Institute for Healthy Aging, Rush University Medical Center, Chicago, IL, United States of America
| | - Tamara B. Harris
- Laboratory of Epidemiology, Demography, and Biometry, National Institute on Aging, National Institutes of Health, Bethesda, MD, United States of America
| | - Wolfgang Hoffmann
- Institute of Community Medicine, Ernst-Moritz-Arndt-University Greifswald, Greifswald, Germany
- Center for Integrated Dementia Care Research (CIDC), a scientific cooperation between the Universities and University Hospitals of Rostock and Greifswald and the German Center for Neurodegenerative Disease (DZNE), Bonn, Germany
| | - Albert Hofman
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - David Karasik
- Hebrew SeniorLife Institute for Aging Research and Harvard Medical School, Boston, MA, United States of America
| | - Douglas P. Kiel
- Hebrew SeniorLife Institute for Aging Research and Harvard Medical School, Boston, MA, United States of America
| | - Thomas Kocher
- Dental School, Ernst-Moritz-Arndt-University Greifswald, Greifswald, Germany
| | - Maris Kuningas
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Lenore J. Launer
- Laboratory of Epidemiology, Demography, and Biometry, National Institute on Aging, National Institutes of Health, Bethesda, MD, United States of America
| | - Kurt K. Lohman
- Center for Human Genomics, Department of Epidemiology and Prevention, Wake Forest University School of Medicine, Winston-Salem, NC, United States of America
| | - Pamela L. Lutsey
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Johan Mackenbach
- Department of Public Health, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Kristin Marciante
- Cardiovascular Health Research Unit, Departments of Medicine, Epidemiology, and Health Services, University of Washington, Seattle WA, United States of America
| | - Bruce M. Psaty
- Cardiovascular Health Research Unit, Departments of Medicine, Epidemiology, and Health Services, University of Washington, Seattle WA, United States of America
- Group Health Research Unit, Group Health Cooperative, Seattle, WA, United States of America
| | - Eric M. Reiman
- Neurogenomics Division, The Translational Genomics Research Institute, Banner Alzheimer’s Institute, Phoenix, AZ, United States of America
| | - Jerome I. Rotter
- Medical Genetics Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States of America
| | - Sudha Seshadri
- Sections of General Internal Medicine, Preventive Medicine, Cardiology and Neurology, Department of Medicine, Boston University School of Medicine, Boston, MA, United States of America
- The National Heart Lung and Blood Institute’s Framingham Heart Study, Framingham, MA, United States of America
| | - Michelle D. Shardell
- Epidemiology and Public Health, University of Maryland, MD, United States of America
| | | | - Cornelia van Duijn
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Jeremy Walston
- Johns Hopkins University School of Medicine Division of Geriatric Medicine and Gerontology, Baltimore, MD, United States of America
| | - M. Carola Zillikens
- Johns Hopkins University School of Medicine Division of Geriatric Medicine and Gerontology, Baltimore, MD, United States of America
| | | | - Sebastian E. Baumeister
- Institute of Community Medicine, Ernst-Moritz-Arndt-University Greifswald, Greifswald, Germany
| | - David A. Bennett
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, IL, United States of America
| | - Luigi Ferrucci
- Clinical Research Branch, National Institute on Aging, Baltimore, MD, United States of America
| | | | - Mika Kivimaki
- Department of Epidemiology and Public Health, University College London, London, United Kingdom
| | - Yongmei Liu
- Center for Human Genomics, Department of Epidemiology and Prevention, Wake Forest University School of Medicine, Winston-Salem, NC, United States of America
| | - Joanne M. Murabito
- Sections of General Internal Medicine, Preventive Medicine, Cardiology and Neurology, Department of Medicine, Boston University School of Medicine, Boston, MA, United States of America
- The National Heart Lung and Blood Institute’s Framingham Heart Study, Framingham, MA, United States of America
| | - Anne B. Newman
- Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, United States of America
| | - Henning Tiemeier
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Child and Adolescent Psychiatry, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Nora Franceschini
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, United States of America
| |
Collapse
|
5
|
Okada T, Ohzeki T, Nakagawa Y, Sugihara S, Arisaka O. Impact of leptin and leptin-receptor gene polymorphisms on serum lipids in Japanese obese children. Acta Paediatr 2010; 99:1213-7. [PMID: 20222875 DOI: 10.1111/j.1651-2227.2010.01778.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
AIM Leptin is one of the factors affecting serum lipid profile. We investigated the association between serum lipids and leptin/leptin receptor (LEPR) gene polymorphisms in obese Japanese children. METHODS One hundred and thirty-six obese children (99 males and 37 females, relative weight over than 20%) from 5 to 17 years of age were recruited from 10 institutes. Four known polymorphisms in leptin gene [(+19)A G, (-2548)G A, (-188)C A, (-633)C T] and four known polymorphisms in LEPR gene [Lys109Arg, Gln223Arg, Pro(G)1019Pro(A), Ser(T)343Ser(C)] were determined using polymerase chain reaction-restriction fragment length polymorphism-based analyses. RESULTS No associations were found between leptin gene polymorphisms and serum lipid profile. On the other hand, Lys109Arg and Ser343Ser polymorphism in LEPR gene, but not Gln223Arg or Pro1019Pro, had significant relationships with serum lipid profile; lower total and low-density lipoprotein cholesterol levels in Arg109Arg homozygotes, and lower TG levels in Ser343Ser(C/C) homozygotes. In addition, LEPR gene also associated with relative weight; Arg109Arg homozygotes had higher relative weight and Ser343Ser(C/C) homozygotes had lower one. CONCLUSION These results suggest that LEPR gene polymorphisms may partly contribute to serum lipid profile in obese children.
Collapse
Affiliation(s)
- T Okada
- Department of Pediatrics and Child Health, Nihon University School of Medicine, Tokyo, Japan.
| | | | | | | | | |
Collapse
|
6
|
Calton MA, Vaisse C. Narrowing down the role of common variants in the genetic predisposition to obesity. Genome Med 2009; 1:31. [PMID: 19341502 PMCID: PMC2664942 DOI: 10.1186/gm31] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
The extent to which common variants contribute to common phenotypes and disease in humans has important consequences for the future of medical genomics. Two reports have recently clarified this issue for one of the most pressing public health concerns, obesity. These large and comprehensive genome-wide association studies find that common variants within at least 11 genes are associated with obesity. Interestingly, most of these genes are highly expressed in the central nervous system, further highlighting its role in the pathogenesis of obesity. However, the individual and combined effects of these variants explain only a small fraction of the inherited variability in obesity, suggesting that rare variants may contribute significantly to the genetic predisposition for this condition.
Collapse
Affiliation(s)
- Melissa A Calton
- Diabetes Center, University of California San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA
| | | |
Collapse
|
7
|
Calton MA, Ersoy BA, Zhang S, Kane JP, Malloy MJ, Pullinger CR, Bromberg Y, Pennacchio LA, Dent R, McPherson R, Ahituv N, Vaisse C. Association of functionally significant Melanocortin-4 but not Melanocortin-3 receptor mutations with severe adult obesity in a large North American case-control study. Hum Mol Genet 2008; 18:1140-7. [PMID: 19091795 DOI: 10.1093/hmg/ddn431] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Functionally significant heterozygous mutations in the Melanocortin-4 receptor (MC4R) have been implicated in 2.5% of early onset obesity cases in European cohorts. The role of mutations in this gene in severely obese adults, particularly in smaller North American patient cohorts, has been less convincing. More recently, it has been proposed that mutations in a phylogenetically and physiologically related receptor, the Melanocortin-3 receptor (MC3R), could also be a cause of severe human obesity. The objectives of this study were to determine if mutations impairing the function of MC4R or MC3R were associated with severe obesity in North American adults. We studied MC4R and MC3R mutations detected in a total of 1821 adults (889 severely obese and 932 lean controls) from two cohorts. We systematically and comparatively evaluated the functional consequences of all mutations found in both MC4R and MC3R. The total prevalence of rare MC4R variants in severely obese North American adults was 2.25% (CI(95%): 1.44-3.47) compared with 0.64% (CI(95%): 0.26-1.43) in lean controls (P < 0.005). After classification of functional consequence, the prevalence of MC4R mutations with functional alterations was significantly greater when compared with controls (P < 0.005). In contrast, the prevalence of rare MC3R variants was not significantly increased in severely obese adults [0.67% (CI(95%): 0.27-1.50) versus 0.32% (CI(95%): 0.06-0.99)] (P = 0.332). Our results confirm that mutations in MC4R are a significant cause of severe obesity, extending this finding to North American adults. However, our data suggest that MC3R mutations are not associated with severe obesity in this population.
Collapse
Affiliation(s)
- Melissa A Calton
- Diabetes Center, University of California San Francisco, San Francisco, CA 94143, USA
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
8
|
Hansen JA, Petersdorf EW, Lin MT, Wang S, Chien JW, Storer B, Martin PJ. Genetics of allogeneic hematopoietic cell transplantation. Role of HLA matching, functional variation in immune response genes. Immunol Res 2008; 41:56-78. [PMID: 17989941 DOI: 10.1007/s12026-007-0043-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Successful outcome following hematopoietic stem cell transplantation (HSCT) is ultimately determined by the ability to achieve sustained engraftment and immune reconstitution, control of graft-versus-host disease (GVHD), and in patients with hematological malignancy the complete eradication of abnormal or malignant cells. GVHD, which can be a serious and fatal complication, is an immune reaction that is initiated by donor T cells in response to recipient alloantigens. Genetic variation in both patient and donor can significantly affect transplant outcome by causing disparity for transplant antigens, and by altering the function of immune response genes that control cellular activation and inflammation. Genetic variation can modulate the intensity of the alloimmune response, the risk of transplant-related organ toxicity and mortality, and may also affect the development of tolerance and the reconstitution of the immune system following HSCT.
Collapse
Affiliation(s)
- John A Hansen
- Division of Clinical Research, Fred Hutchinson Cancer Research Center, University of Washington, 1100 Fairview Ave N, D2-100, P.O. Box 19024, Seattle, WA 98109-1024, USA.
| | | | | | | | | | | | | |
Collapse
|
9
|
Abstract
The use of modern molecular biology tools in deciphering the perturbed biochemistry and physiology underlying the obese state has proven invaluable. Identifying the hypothalamic leptin/melanocortin pathway as critical in many cases of monogenic obesity has permitted targeted, hypothesis-driven experiments to be performed, and has implicated new candidates as causative for previously uncharacterized clinical cases of obesity. Meanwhile, the effects of mutations in the melanocortin-4 receptor gene, for which the obese phenotype varies in the degree of severity among individuals, are now thought to be influenced by one's environmental surroundings. Molecular approaches have revealed that syndromes (Prader-Willi and Bardet-Biedl) previously assumed to be controlled by a single gene are, conversely, regulated by multiple elements. Finally, the application of comprehensive profiling technologies coupled with creative statistical analyses has revealed that interactions between genetic and environmental factors are responsible for the common obesity currently challenging many Westernized societies. As such, an improved understanding of the different “types” of obesity not only permits the development of potential therapies, but also proposes novel and often unexpected directions in deciphering the dysfunctional state of obesity.
Collapse
|
10
|
Tiffin N, Adie E, Turner F, Brunner HG, van Driel MA, Oti M, Lopez-Bigas N, Ouzounis C, Perez-Iratxeta C, Andrade-Navarro MA, Adeyemo A, Patti ME, Semple CAM, Hide W. Computational disease gene identification: a concert of methods prioritizes type 2 diabetes and obesity candidate genes. Nucleic Acids Res 2006; 34:3067-81. [PMID: 16757574 PMCID: PMC1475747 DOI: 10.1093/nar/gkl381] [Citation(s) in RCA: 101] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Genome-wide experimental methods to identify disease genes, such as linkage analysis and association studies, generate increasingly large candidate gene sets for which comprehensive empirical analysis is impractical. Computational methods employ data from a variety of sources to identify the most likely candidate disease genes from these gene sets. Here, we review seven independent computational disease gene prioritization methods, and then apply them in concert to the analysis of 9556 positional candidate genes for type 2 diabetes (T2D) and the related trait obesity. We generate and analyse a list of nine primary candidate genes for T2D genes and five for obesity. Two genes, LPL and BCKDHA, are common to these two sets. We also present a set of secondary candidates for T2D (94 genes) and for obesity (116 genes) with 58 genes in common to both diseases.
Collapse
Affiliation(s)
- Nicki Tiffin
- South African National Bioinformatics Institute, University of the Western Cape, Bellville, 7535, South Africa.
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
11
|
Taniguchi H, Lowe CE, Cooper JD, Smyth DJ, Bailey R, Nutland S, Healy BC, Lam AC, Burren O, Walker NM, Smink LJ, Wicker LS, Todd JA. Discovery, linkage disequilibrium and association analyses of polymorphisms of the immune complement inhibitor, decay-accelerating factor gene (DAF/CD55) in type 1 diabetes. BMC Genet 2006; 7:22. [PMID: 16626483 PMCID: PMC1479364 DOI: 10.1186/1471-2156-7-22] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2006] [Accepted: 04/20/2006] [Indexed: 12/01/2022] Open
Abstract
Background Type 1 diabetes (T1D) is a common autoimmune disease resulting from T-cell mediated destruction of pancreatic beta cells. Decay accelerating factor (DAF, CD55), a glycosylphosphatidylinositol-anchored membrane protein, is a candidate for autoimmune disease susceptibility based on its role in restricting complement activation and evidence that DAF expression modulates the phenotype of mice models for autoimmune disease. In this study, we adopt a linkage disequilibrium (LD) mapping approach to test for an association between the DAF gene and T1D. Results Initially, we used HapMap II genotype data to examine LD across the DAF region. Additional resequencing was required, identifying 16 novel polymorphisms. Combining both datasets, a LD mapping approach was adopted to test for association with T1D. Seven tag SNPs were selected and genotyped in case-control (3,523 cases and 3,817 controls) and family (725 families) collections. Conclusion We obtained no evidence of association between T1D and the DAF region in two independent collections. In addition, we assessed the impact of using only HapMap II genotypes for the selection of tag SNPs and, based on this study, found that HapMap II genotypes may require additional SNP discovery for comprehensive LD mapping of some genes in common disease.
Collapse
Affiliation(s)
- Hidenori Taniguchi
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge, CB2 2XY, UK
| | - Christopher E Lowe
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge, CB2 2XY, UK
| | - Jason D Cooper
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge, CB2 2XY, UK
| | - Deborah J Smyth
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge, CB2 2XY, UK
| | - Rebecca Bailey
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge, CB2 2XY, UK
| | - Sarah Nutland
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge, CB2 2XY, UK
| | - Barry C Healy
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge, CB2 2XY, UK
| | - Alex C Lam
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge, CB2 2XY, UK
| | - Oliver Burren
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge, CB2 2XY, UK
| | - Neil M Walker
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge, CB2 2XY, UK
| | - Luc J Smink
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge, CB2 2XY, UK
| | - Linda S Wicker
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge, CB2 2XY, UK
| | - John A Todd
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge, CB2 2XY, UK
| |
Collapse
|
12
|
Smith WP, Vu Q, Li SS, Hansen JA, Zhao LP, Geraghty DE. Toward understanding MHC disease associations: partial resequencing of 46 distinct HLA haplotypes. Genomics 2006; 87:561-71. [PMID: 16434165 DOI: 10.1016/j.ygeno.2005.11.020] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2005] [Revised: 11/28/2005] [Accepted: 11/29/2005] [Indexed: 11/23/2022]
Abstract
We carried out a resequencing project that examined 552 kb of sequence from each of 46 individual HLA haplotypes representing a diversity of HLA allele types, generating nearly 27 Mb of fully phased genomic sequence. Haplotype blocks were defined extending from telomeric of HLA-F to centromeric of HLA-DP including in total 5186 MHC SNPs. To investigate basic questions about the evolutionary origin of common HLA haplotypes, and to obtain an estimate of rare variation in the MHC, we similarly examined two additional sets of samples. In 19 independent HLA-A1, B8, DR3 chromosomes, the most common HLA haplotype in Northern European Caucasians, variation was found at 11 SNP positions in the 3600-kb region from HLA-A to DR. Partial resequencing of 282 individuals in the gene-dense class III region identified significant variability beyond what could have been detected by linkage to common SNPs.
Collapse
Affiliation(s)
- Wade P Smith
- Clinical Research Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109-1024, USA
| | | | | | | | | | | |
Collapse
|
13
|
Chien JW, Zhao LP, Hansen JA, Fan WH, Parimon T, Clark JG. Genetic variation in bactericidal/permeability-increasing protein influences the risk of developing rapid airflow decline after hematopoietic cell transplantation. Blood 2005; 107:2200-7. [PMID: 16304058 PMCID: PMC1895720 DOI: 10.1182/blood-2005-06-2338] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Innate immunity is involved in the biology of graft versus host disease and common airway diseases. We screened 15 genes in this pathway using a linkage disequilibrium-based approach to identify potential candidate genes that may be involved in the development of airflow obstruction after hematopoietic cell transplantation. Sixty-nine single-nucleotide polymorphisms were selected for assessment in a discovery cohort (n = 363). Significant associations were validated in a validation cohort (n = 209). Expression of the candidate gene was demonstrated by detecting gene transcript and protein in malignant and normal small airway epithelial cells. In the discovery cohort, 133 patients developed significant airflow decline. Four patient and donor bactericidal/permeability-increasing (BPI) haplotypes were associated with a 2-fold to 3-fold increased risk of developing significant airflow decline (P values, .004-.038). This association was confirmed in the validation cohort, which had 66 patients with significant airflow decline, with 9 significant haplotypes (P values, .013-.043). BPI gene transcript and protein were detected in airway epithelial cells. These results suggest mutations in the BPI gene significantly influence the risk of developing rapid airflow decline after hematopoietic cell transplantation and may represent a novel therapeutic target for this form of airway disease.
Collapse
Affiliation(s)
- Jason W Chien
- Pulmonary and Critical Care Section, Clinical Research Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave North, D5-280, Seattle, WA 98109-1024, USA.
| | | | | | | | | | | |
Collapse
|
14
|
Swarbrick MM, Waldenmaier B, Pennacchio LA, Lind DL, Cavazos MM, Geller F, Merriman R, Ustaszewska A, Malloy M, Scherag A, Hsueh WC, Rief W, Mauvais-Jarvis F, Pullinger CR, Kane JP, Dent R, McPherson R, Kwok PY, Hinney A, Hebebrand J, Vaisse C. Lack of support for the association between GAD2 polymorphisms and severe human obesity. PLoS Biol 2005; 3:e315. [PMID: 16122350 PMCID: PMC1193520 DOI: 10.1371/journal.pbio.0030315] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2004] [Accepted: 07/11/2005] [Indexed: 12/28/2022] Open
Abstract
The demonstration of association between common genetic variants and chronic human diseases such as obesity could have profound implications for the prediction, prevention, and treatment of these conditions. Unequivocal proof of such an association, however, requires independent replication of initial positive findings. Recently, three (−243 A>G, +61450 C>A, and +83897 T>A) single nucleotide polymorphisms (SNPs) within glutamate decarboxylase 2 (GAD2) were found to be associated with class III obesity (body mass index > 40 kg/m2). The association was observed among 188 families (612 individuals) segregating the condition, and a case-control study of 575 cases and 646 lean controls. Functional data supporting a pathophysiological role for one of the SNPs (−243 A>G) were also presented. The gene GAD2 encodes the 65-kDa subunit of glutamic acid decarboxylase—GAD65. In the present study, we attempted to replicate this association in larger groups of individuals, and to extend the functional studies of the −243 A>G SNP. Among 2,359 individuals comprising 693 German nuclear families with severe, early-onset obesity, we found no evidence for a relationship between the three GAD2 SNPs and obesity, whether SNPs were studied individually or as haplotypes. In two independent case-control studies (a total of 680 class III obesity cases and 1,186 lean controls), there was no significant relationship between the −243 A>G SNP and obesity (OR = 0.99, 95% CI 0.83–1.18, p = 0.89) in the pooled sample. These negative findings were recapitulated in a meta-analysis, incorporating all published data for the association between the −243G allele and class III obesity, which yielded an OR of 1.11 (95% CI 0.90–1.36, p = 0.28) in a total sample of 1,252 class III obese cases and 1,800 lean controls. Moreover, analysis of common haplotypes encompassing the GAD2 locus revealed no association with severe obesity in families with the condition. We also obtained functional data for the −243 A>G SNP that does not support a pathophysiological role for this variant in obesity. Potential confounding variables in association studies involving common variants and complex diseases (low power to detect modest genetic effects, overinterpretation of marginal data, population stratification, and biological plausibility) are also discussed in the context of GAD2 and severe obesity. A large genetic study involving multiple populations is not able to replicate previous findings linking variation in the GAD2 gene to susceptibility to obesity.
Collapse
Affiliation(s)
- Michael M Swarbrick
- 1Diabetes Center, University of California, San Francisco, California, United States of America
| | - Björn Waldenmaier
- 2Department of Child and Adolescent Psychiatry, University of Duisburg-Essen, Essen, Germany
| | - Len A Pennacchio
- 3Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Denise L Lind
- 4Cardiovascular Research Institute, University of California, San Francisco, California, United States of America
| | - Martha M Cavazos
- 1Diabetes Center, University of California, San Francisco, California, United States of America
| | - Frank Geller
- 5Institute of Medical Biometry and Epidemiology, Phillips-University of Marburg, Marburg, Germany
| | - Raphael Merriman
- 6Department of Medicine, University of California, San Francisco, California, United States of America
| | - Anna Ustaszewska
- 3Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Mary Malloy
- 4Cardiovascular Research Institute, University of California, San Francisco, California, United States of America
| | - André Scherag
- 5Institute of Medical Biometry and Epidemiology, Phillips-University of Marburg, Marburg, Germany
| | - Wen-Chi Hsueh
- 1Diabetes Center, University of California, San Francisco, California, United States of America
| | - Winfried Rief
- 7Department of Psychology, University of Marburg, Marburg, Germany
| | - Franck Mauvais-Jarvis
- 8Division of Diabetes, Endocrinology and Metabolism, Baylor College of Medicine, Houston, Texas, United States of America
| | - Clive R Pullinger
- 4Cardiovascular Research Institute, University of California, San Francisco, California, United States of America
| | - John P Kane
- 4Cardiovascular Research Institute, University of California, San Francisco, California, United States of America
| | - Robert Dent
- 9Ottawa Health Research Institute, Ottawa, Ontario, Canada
| | - Ruth McPherson
- 10University of Ottawa Heart Institute, Ottawa, Ontario, Canada
| | - Pui-Yan Kwok
- 4Cardiovascular Research Institute, University of California, San Francisco, California, United States of America
| | - Anke Hinney
- 2Department of Child and Adolescent Psychiatry, University of Duisburg-Essen, Essen, Germany
| | - Johannes Hebebrand
- 2Department of Child and Adolescent Psychiatry, University of Duisburg-Essen, Essen, Germany
| | - Christian Vaisse
- 1Diabetes Center, University of California, San Francisco, California, United States of America
| |
Collapse
|