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Bustos-Aibar M, Aguilera CM, Alcalá-Fdez J, Ruiz-Ojeda FJ, Plaza-Díaz J, Plaza-Florido A, Tofe I, Gil-Campos M, Gacto MJ, Anguita-Ruiz A. Shared gene expression signatures between visceral adipose and skeletal muscle tissues are associated with cardiometabolic traits in children with obesity. Comput Biol Med 2023; 163:107085. [PMID: 37399741 DOI: 10.1016/j.compbiomed.2023.107085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 04/28/2023] [Accepted: 05/27/2023] [Indexed: 07/05/2023]
Abstract
Obesity in children is related to the development of cardiometabolic complications later in life, where molecular changes of visceral adipose tissue (VAT) and skeletal muscle tissue (SMT) have been proven to be fundamental. The aim of this study is to unveil the gene expression architecture of both tissues in a cohort of Spanish boys with obesity, using a clustering method known as weighted gene co-expression network analysis. For this purpose, we have followed a multi-objective analytic pipeline consisting of three main approaches; identification of gene co-expression clusters associated with childhood obesity, individually in VAT and SMT (intra-tissue, approach I); identification of gene co-expression clusters associated with obesity-metabolic alterations, individually in VAT and SMT (intra-tissue, approach II); and identification of gene co-expression clusters associated with obesity-metabolic alterations simultaneously in VAT and SMT (inter-tissue, approach III). In both tissues, we identified independent and inter-tissue gene co-expression signatures associated with obesity and cardiovascular risk, some of which exceeded multiple-test correction filters. In these signatures, we could identify some central hub genes (e.g., NDUFB8, GUCY1B1, KCNMA1, NPR2, PPP3CC) participating in relevant metabolic pathways exceeding multiple-testing correction filters. We identified the central hub genes PIK3R2, PPP3C and PTPN5 associated with MAPK signaling and insulin resistance terms. This is the first time that these genes have been associated with childhood obesity in both tissues. Therefore, they could be potential novel molecular targets for drugs and health interventions, opening new lines of research on the personalized care in this pathology. This work generates interesting hypotheses about the transcriptomics alterations underlying metabolic health alterations in obesity in the pediatric population.
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Affiliation(s)
- Mireia Bustos-Aibar
- Department of Biochemistry and Molecular Biology II, School of Pharmacy, University of Granada, 18071, Granada, Spain.
| | - Concepción M Aguilera
- Department of Biochemistry and Molecular Biology II, School of Pharmacy, University of Granada, 18071, Granada, Spain; Biomedical Research Networking Center for Physiopathology of Obesity and Nutrition, Carlos III Health Institute, 28029, Madrid, Spain.
| | - Jesús Alcalá-Fdez
- Department of Computer Science and Artificial Intelligence, Andalusian Research Institute in Data Science and Computational Intelligence (DaSCI), University of Granada, 18071, Granada, Spain.
| | - Francisco J Ruiz-Ojeda
- Department of Biochemistry and Molecular Biology II, School of Pharmacy, University of Granada, 18071, Granada, Spain; RG Adipocytes and Metabolism, Institute for Diabetes and Obesity, Helmholtz Diabetes Center at the Helmholtz Zentrum München, Neuherberg, 85764, Munich, Germany.
| | - Julio Plaza-Díaz
- Department of Biochemistry and Molecular Biology II, School of Pharmacy, University of Granada, 18071, Granada, Spain; Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON K1H 8L1, Ontario, Canada.
| | - Abel Plaza-Florido
- PROmoting FITness and Health through physical activity research group, Sport and Health University Research Institute, Department of Physical Education and Sports, University of Granada, 18071, Granada, Spain; Pediatric Exercise and Genomics Research Center, Department of Pediatrics, School of Medicine, University of California at Irvine, Irvine, 92617, CA, United States.
| | - Inés Tofe
- Biomedical Research Networking Center for Physiopathology of Obesity and Nutrition, Carlos III Health Institute, 28029, Madrid, Spain; University Clinical Hospital, Institute Maimónides of Biomedicine Investigation of Córdoba, University of Córdoba, 14004, Córdoba, Spain.
| | - Mercedes Gil-Campos
- Biomedical Research Networking Center for Physiopathology of Obesity and Nutrition, Carlos III Health Institute, 28029, Madrid, Spain; University Clinical Hospital, Institute Maimónides of Biomedicine Investigation of Córdoba, University of Córdoba, 14004, Córdoba, Spain.
| | - María J Gacto
- Department of Software Engineering, University of Granada, 18071, Granada, Spain.
| | - Augusto Anguita-Ruiz
- Department of Biochemistry and Molecular Biology II, School of Pharmacy, University of Granada, 18071, Granada, Spain; Barcelona Institute for Global Health, ISGlobal, 08003, Barcelona, Spain.
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2
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Vu JP, Luong L, Sanford D, Oh S, Kuc A, Pisegna R, Lewis M, Pisegna JR, Germano PM. PACAP and VIP Neuropeptides' and Receptors' Effects on Appetite, Satiety and Metabolism. BIOLOGY 2023; 12:1013. [PMID: 37508442 PMCID: PMC10376325 DOI: 10.3390/biology12071013] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 07/10/2023] [Accepted: 07/12/2023] [Indexed: 07/30/2023]
Abstract
The overwhelming increase in the prevalence of obesity and related disorders in recent years is one of the greatest threats to the global healthcare system since it generates immense healthcare costs. As the prevalence of obesity approaches epidemic proportions, the importance of elucidating the mechanisms regulating appetite, satiety, body metabolism, energy balance and adiposity has garnered significant attention. Currently, gastrointestinal (GI) bariatric surgery remains the only approach capable of achieving successful weight loss. Appetite, satiety, feeding behavior, energy intake and expenditure are regulated by central and peripheral neurohormonal mechanisms that have not been fully elucidated yet. Pituitary Adenylate Cyclase-Activating Polypeptide (PACAP) and Vasoactive Intestinal Polypeptide (VIP) are members of a family of regulatory peptides that are widely distributed in parallel with their specific receptors, VPAC1R, VPAC2R and PAC1R, in the central nervous system (CNS) and in the periphery, such as in the gastrointestinal tract and its associated organs and immune cells. PACAP and VIP have been reported to play an important role in the regulation of body phenotype, metabolism and homeostatic functions. The purpose of this review is to present recent data on the effects of PACAP, VIP, VPAC1R, VPAC2R and PAC1R on the modulation of appetite, satiety, metabolism, calorie intake and fat accumulation, to evaluate their potential use as therapeutic targets for the treatment of obesity and metabolic syndrome.
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Affiliation(s)
- John P Vu
- Research Service, Veterans Affairs Greater Los Angeles Healthcare System, Los Angeles, CA 90073, USA
- CURE/Digestive Diseases Research Center, Department of Medicine, University of California, Los Angeles, CA 90073, USA
| | - Leon Luong
- Research Service, Veterans Affairs Greater Los Angeles Healthcare System, Los Angeles, CA 90073, USA
- CURE/Digestive Diseases Research Center, Department of Medicine, University of California, Los Angeles, CA 90073, USA
| | - Daniel Sanford
- Research Service, Veterans Affairs Greater Los Angeles Healthcare System, Los Angeles, CA 90073, USA
- CURE/Digestive Diseases Research Center, Department of Medicine, University of California, Los Angeles, CA 90073, USA
| | - Suwan Oh
- Research Service, Veterans Affairs Greater Los Angeles Healthcare System, Los Angeles, CA 90073, USA
- CURE/Digestive Diseases Research Center, Department of Medicine, University of California, Los Angeles, CA 90073, USA
| | - Alma Kuc
- Research Service, Veterans Affairs Greater Los Angeles Healthcare System, Los Angeles, CA 90073, USA
| | - Rita Pisegna
- Research Service, Veterans Affairs Greater Los Angeles Healthcare System, Los Angeles, CA 90073, USA
| | - Michael Lewis
- Division of Hematology and Oncology, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90078, USA
- Department of Pathology, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Department of Pathology, Veterans Affairs Greater Los Angeles Health Care System, Los Angeles, CA 90073, USA
| | - Joseph R Pisegna
- Research Service, Veterans Affairs Greater Los Angeles Healthcare System, Los Angeles, CA 90073, USA
- CURE/Digestive Diseases Research Center, Department of Medicine, University of California, Los Angeles, CA 90073, USA
- Division of Gastroenterology, Hepatology and Parenteral Nutrition, VA Greater Los Angeles Healthcare System and Department of Medicine, Los Angeles, CA 90073, USA
- Division of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Patrizia M Germano
- Research Service, Veterans Affairs Greater Los Angeles Healthcare System, Los Angeles, CA 90073, USA
- CURE/Digestive Diseases Research Center, Department of Medicine, University of California, Los Angeles, CA 90073, USA
- Division of Pulmonary and Critical Care, Veterans Affairs Greater Los Angeles Healthcare System, Los Angeles, CA 90073, USA
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3
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Montégut L, Lopez-Otin C, Magnan C, Kroemer G. Old Paradoxes and New Opportunities for Appetite Control in Obesity. Trends Endocrinol Metab 2021; 32:264-294. [PMID: 33707095 DOI: 10.1016/j.tem.2021.02.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 02/09/2021] [Accepted: 02/11/2021] [Indexed: 12/13/2022]
Abstract
Human obesity is accompanied by alterations in the blood concentrations of multiple circulating appetite regulators. Paradoxically, most of the appetite-inhibitory hormones are elevated in nonsyndromic obesity, while most of the appetite stimulatory hormones are reduced, perhaps reflecting vain attempts of regulation by inefficient feedback circuitries. In this context, it is important to understand which appetite regulators exhibit a convergent rather than paradoxical behavior and hence are likely to contribute to the maintenance of the obese state. Pharmacological interventions in obesity should preferentially consist of the supplementation of deficient appetite inhibitors or the neutralization of excessive appetite stimulators. Here, we critically analyze the current literature on appetite-regulatory peptide hormones. We propose a short-list of appetite modulators that may constitute the best candidates for therapeutic interventions.
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Affiliation(s)
- Léa Montégut
- Centre de Recherche des Cordeliers, Equipe labellisée par la Ligue Contre le Cancer, Université de Paris, Sorbonne Université, INSERM U1138, Institut Universitaire de France, Paris, France; Metabolomics and Cell Biology Platforms, Institut Gustave Roussy, Villejuif, France
| | - Carlos Lopez-Otin
- Departamento de Bioquímica y Biología Molecular, Facultad de Medicina, Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, 33006, Oviedo, Spain
| | | | - Guido Kroemer
- Centre de Recherche des Cordeliers, Equipe labellisée par la Ligue Contre le Cancer, Université de Paris, Sorbonne Université, INSERM U1138, Institut Universitaire de France, Paris, France; Metabolomics and Cell Biology Platforms, Institut Gustave Roussy, Villejuif, France; Unité de Biologie Fonctionnelle et Adaptative, Sorbonne Paris Cité, CNRS UMR8251, Université Paris Diderot, Paris, France; Pôle de Biologie, Hôpital Européen Georges Pompidou, AP-, HP, Paris, France; Suzhou Institute for Systems Medicine, Chinese Academy of Medical Sciences, Suzhou, China; Karolinska Institute, Department of Women's and Children's Health, Karolinska University Hospital, Stockholm, Sweden.
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Genome-Wide Association Analysis Identified ANXA1 Associated with Shoulder Impingement Syndrome in UK Biobank Samples. G3-GENES GENOMES GENETICS 2020; 10:3279-3284. [PMID: 32690583 PMCID: PMC7466970 DOI: 10.1534/g3.120.401257] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Shoulder impingement syndrome (SIS) is a common shoulder disorder with unclear genetic mechanism. In this study, Genome-wide Association Study (GWAS) was conducted to identify the candidate loci associated with SIS by using the UK Biobank samples (including 3,626 SIS patients and 3,626 control subjects). Based on the GWAS results, gene set enrichment analysis was further performed to detect the candidate gene ontology and pathways associated with SIS. We identified multiple risk loci associated with SIS, such as rs750968 (P = 4.82 × 10−8), rs754832 (P = 4.83 × 10−8) and rs1873119 (P = 6.39 × 10−8) of ANXA1 gene. Some candidate pathways have been identified related to SIS, including those linked to infection response and hypoxia, “ZHOU_INFLAMMATORY_RESPONSE_FIMA_DN” (P = 0.012) and “MANALO_HYPOXIA_UP” (P = 5.00 × 10−5). Our results provide novel clues for understanding the genetic mechanism of SIS.
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5
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Tam V, Patel N, Turcotte M, Bossé Y, Paré G, Meyre D. Benefits and limitations of genome-wide association studies. Nat Rev Genet 2019; 20:467-484. [PMID: 31068683 DOI: 10.1038/s41576-019-0127-1] [Citation(s) in RCA: 920] [Impact Index Per Article: 184.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Genome-wide association studies (GWAS) involve testing genetic variants across the genomes of many individuals to identify genotype-phenotype associations. GWAS have revolutionized the field of complex disease genetics over the past decade, providing numerous compelling associations for human complex traits and diseases. Despite clear successes in identifying novel disease susceptibility genes and biological pathways and in translating these findings into clinical care, GWAS have not been without controversy. Prominent criticisms include concerns that GWAS will eventually implicate the entire genome in disease predisposition and that most association signals reflect variants and genes with no direct biological relevance to disease. In this Review, we comprehensively assess the benefits and limitations of GWAS in human populations and discuss the relevance of performing more GWAS.
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Affiliation(s)
- Vivian Tam
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, Ontario, Canada
| | - Nikunj Patel
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, Ontario, Canada
| | - Michelle Turcotte
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, Ontario, Canada
| | - Yohan Bossé
- Institut Universitaire de Cardiologie et de Pneumologie de Québec-Université Laval, Québec City, Québec, Canada.,Department of Molecular Medicine, Laval University, Québec City, Quebec, Canada
| | - Guillaume Paré
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, Ontario, Canada.,Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | - David Meyre
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, Ontario, Canada. .,Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada. .,Inserm UMRS 954 N-GERE (Nutrition-Genetics-Environmental Risks), University of Lorraine, Faculty of Medicine, Nancy, France.
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6
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Bains M, Laney C, Wolfe AE, Orr M, Waschek JA, Ericsson AC, Dorsam GP. Vasoactive Intestinal Peptide Deficiency Is Associated With Altered Gut Microbiota Communities in Male and Female C57BL/6 Mice. Front Microbiol 2019; 10:2689. [PMID: 31849864 PMCID: PMC6900961 DOI: 10.3389/fmicb.2019.02689] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 11/06/2019] [Indexed: 12/13/2022] Open
Abstract
Vasoactive intestinal peptide (VIP) is crucial for gastrointestinal tract (GIT) health. VIP sustains GIT homeostasis through maintenance of the intestinal epithelial barrier and acts as a potent anti-inflammatory mediator that contributes to gut bacterial tolerance. Based on these biological functions by VIP, we hypothesized that its deficiency would alter gut microbial ecology. To this end, fecal samples from male and female VIP+/+, VIP+/-, and VIP-/- littermates (n = 47) were collected and 16S rRNA sequencing was conducted. Our data revealed significant changes in bacterial composition, biodiversity, and weight loss from VIP-/- mice compared to VIP+/+ and VIP+/- littermates, irrespective of sex. The gut bacteria compositional changes observed in VIP-/- mice was consistent with gut microbial structure changes reported for certain inflammatory and autoimmune disorders. Moreover, predicted functional changes by PICRUSt software suggested an energy surplus within the altered microbiota from VIP-/- mice. These data support that VIP plays an important role in maintaining microbiota balance, biodiversity, and GIT function, and its genetic removal results in significant gut microbiota restructuring and weight loss.
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Affiliation(s)
- Manpreet Bains
- Department of Microbiological Sciences, College of Agriculture, Food Systems and Natural Resources, North Dakota State University, Fargo, ND, United States
| | - Caleb Laney
- Department of Microbiological Sciences, College of Agriculture, Food Systems and Natural Resources, North Dakota State University, Fargo, ND, United States
| | - Annie E. Wolfe
- Metagenomics Center, Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO, United States
| | - Megan Orr
- Department of Statistics, College of Science and Math, North Dakota State University, Fargo, ND, United States
| | - James A. Waschek
- Intellectual and Developmental Disabilities Research Center, Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior/Neuropsychiatric Institute, University of California, Los Angeles, Los Angeles, CA, United States
| | - Aaron C. Ericsson
- Metagenomics Center, Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO, United States
| | - Glenn P. Dorsam
- Department of Microbiological Sciences, College of Agriculture, Food Systems and Natural Resources, North Dakota State University, Fargo, ND, United States
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7
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Shindler AE, Hill-Yardin EL, Petrovski S, Bishop N, Franks AE. Towards Identifying Genetic Biomarkers for Gastrointestinal Dysfunction in Autism. J Autism Dev Disord 2019; 50:76-86. [DOI: 10.1007/s10803-019-04231-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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8
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Jiao H, Zang Y, Zhang M, Zhang Y, Wang Y, Wang K, Price RA, Li WD. Genome-Wide Interaction and Pathway Association Studies for Body Mass Index. Front Genet 2019; 10:404. [PMID: 31118946 PMCID: PMC6504780 DOI: 10.3389/fgene.2019.00404] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Accepted: 04/12/2019] [Indexed: 11/24/2022] Open
Abstract
Objective: We investigated gene interactions (epistasis) for body mass index (BMI) in a European-American adult female cohort via genome-wide interaction analyses (GWIA) and pathway association analyses. Methods: Genome-wide pairwise interaction analyses were carried out for BMI in 493 extremely obese cases (BMI > 35 kg/m2) and 537 never-overweight controls (BMI < 25 kg/m2). To further validate the results, specific SNPs were selected based on the GWIA results for haplotype-based association studies. Pathway-based association analyses were performed using a modified Gene Set Enrichment Algorithm (GSEA) (GenGen program) to further explore BMI-related pathways using our genome wide association study (GWAS) data set, GIANT, ENGAGE, and DIAGRAM Consortia. Results: The EXOC4-1q23.1 interaction was associated with BMI, with the most significant epistasis between rs7800006 and rs10797020 (P = 2.63 × 10-11). In the pathway-based association analysis, Tob1 pathway showed the most significant association with BMI (empirical P < 0.001, FDR = 0.044, FWER = 0.040). These findings were further validated in different populations. Conclusion: Genome-wide pairwise SNP-SNP interaction and pathway analyses suggest that EXOC4 and TOB1-related pathways may contribute to the development of obesity.
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Affiliation(s)
- Hongxiao Jiao
- Research Center of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Yong Zang
- Department of Genetics, College of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Miaomiao Zhang
- Department of Genetics, College of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Yuan Zhang
- Department of Genetics, College of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Yaogang Wang
- College of Public Health, Tianjin Medical University, Tianjin, China
| | - Kai Wang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
- Laboratory Medicine, Department of Pathology, University of Pennsylvania, Philadelphia, PA, United States
| | - R. Arlen Price
- Department of Psychiatry, Center for Neurobiology and Behavior, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, United States
| | - Wei-Dong Li
- Department of Genetics, College of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
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9
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Su S, Li H, Du F, Zhang C, Li X, Jing X, Liu L, Li Z, Yang X, Xu P, Yuan X, Zhu J, Bouzoualegh R. Combined QTL and Genome Scan Analyses With the Help of 2b-RAD Identify Growth-Associated Genetic Markers in a New Fast-Growing Carp Strain. Front Genet 2018; 9:592. [PMID: 30581452 PMCID: PMC6293859 DOI: 10.3389/fgene.2018.00592] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Accepted: 11/15/2018] [Indexed: 11/17/2022] Open
Abstract
Common carp is one of the oldest and most popular cultured freshwater fish species both globally and in China. In a previous study, we used a carp strain with a long breeding tradition in China, named Huanghe, to create a new fast-growing strain by selection for fast growth for 6 years. The growth performance at 8 months of age has been improved by 20.84%. To achieve this, we combined the best linear unbiased prediction with marker-assisted selection techniques. Recent progress in genome-wide association studies and genomic selection in livestock breeding inspired common carp breeders to consider genome-based breeding approaches. In this study, we developed a 2b-RAD sequence assay as a means of investigating the quantitative trait loci in common carp. A total of 4,953,017,786 clean reads were generated for 250 specimens (average reads/specimen = 19,812,071) with BsaXI Restriction Enzyme. From these, 56,663 SNPs were identified, covering 50 chromosomes and 3,377 scaffolds. Principal component analysis indicated that selection and control groups are relatively clearly distinct. Top 1% of Fst values was selected as the threshold signature of artificial selection. Among the 244 identified loci, genes associated with sex-related factors and nutritional metabolism (especially fat metabolism) were annotated. Eighteen QTL were associated with growth parameters. Body length at 3 months of age and body weight (both at 3 and 8 months) were controlled by polygenic effects, but body size (length, depth, width) at 8 months of age was controlled mainly by several loci with major effects. Importantly, a single shared QTL (IGF2 gene) partially controlled the body length, depth, and width. By merging the above results, we concluded that mainly the genes related to neural pathways, sex and fatty acid metabolism contributed to the improved growth performance of the new Huanghe carp strain. These findings are one of the first investigations into the potential use of genomic selection in the breeding of common carp. Moreover, our results show that combining the Fst, QTL mapping and CRISPR–Cas9 methods can be an effective way to identify important novel candidate molecular markers in economic breeding programs.
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Affiliation(s)
- Shengyan Su
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China.,Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
| | - Hengde Li
- Ministry of Agriculture Key Laboratory of Aquatic Genomics, CAFS Key Laboratory of Aquatic Genomics and Beijing Key Laboratory of Fishery Biotechnology, Center for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, China
| | - Fukuan Du
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
| | - Chengfeng Zhang
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China.,Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
| | - Xinyuan Li
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
| | - Xiaojun Jing
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China.,Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
| | - Liyue Liu
- China Zebrafish Resource Center, Wuhan, China
| | - Zhixun Li
- Henan Academy of Fishery Sciences, Zhengzhou, China
| | - Xingli Yang
- Henan Academy of Fishery Sciences, Zhengzhou, China
| | - Pao Xu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China.,Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
| | - Xinhua Yuan
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China.,Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
| | - Jian Zhu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China.,Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
| | - Raouf Bouzoualegh
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
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10
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Ma M, Liang X, Cheng S, Zhang L, Cheng B, Yang J, Ding M, Zhao Y, Li P, Du Y, Liu L, Wen Y, He A, Fan Q, Guo X, Zhang F. Integrating genome-wide association study, chromosomal enhancer maps and element-gene interaction networks detected brain regions related associations between elements and ADHD/IQ. Behav Brain Res 2018; 353:137-142. [DOI: 10.1016/j.bbr.2018.07.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 06/05/2018] [Accepted: 07/13/2018] [Indexed: 11/26/2022]
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11
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Scirocco A, Pallotta L, Rengo M, Ignazzi A, Carabotti M, Cicenia A, Vona R, Chirletti P, Maselli MA, Donghia R, Coluzzi M, Matarrese P, Silecchia G, Severi C. Myogenic oxidative imbalance interferes with antral motility in obese subjects. Dig Liver Dis 2018; 50:820-827. [PMID: 29625905 DOI: 10.1016/j.dld.2018.03.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 03/03/2018] [Accepted: 03/06/2018] [Indexed: 12/11/2022]
Abstract
BACKGROUND Obesity is characterized by a systemic low-grade chronic inflammatory oxidative condition that affects vascular and cardiac smooth muscle relaxation. In human antrum, relaxation is mediated by vasoactive intestinal peptide (VIP) through cAMP and cGMP signaling pathways. A genome-wide association study has demonstrated an association between VIP and obesity. AIM To evaluate smooth muscle activity in human obese antrum, both in in vitro preparations as well as in vivo. METHODS Antral muscle strips and cells were isolated from surgical gastric samples from obese and normal weight subjects. Muscle contraction and relaxation, myogenic oxidative stress and inflammatory status were analyzed in vitro. Distal antral motility was evaluated in vivo by magnetic resonance imaging. RESULTS Obese antral muscle cells showed an oxidative-inflammatory imbalance with overexpression of NLRP3 inflammasome, increased IL-1β secretion and caspase1-activation, and reduced antioxidant capacity associated with a myogenic motor impairment of VIP-induced relaxation. The intracellular alterations were characterized by a decreased activation of the cAMP-signaling pathway and a decreased expression of eNOS. These in vitro alterations coincided with the hindering of antral motor activity observed in vivo. Apocynin treatment, counteracting oxidative stress, reverted alterations observed in obese antral muscle. CONCLUSION Antral myogenic activity of obese subjects can be impaired by alterations of signaling pathways induced by oxidative stress.
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Affiliation(s)
- Annunziata Scirocco
- Experimental Pharmacology Laboratory, Scientific Institute of Gastroenterology "S. de Bellis", Castellana Grotte, BA, Italy
| | - Lucia Pallotta
- Department of Internal Medicine and Medical Specialties, University Sapienza, Rome, Italy
| | - Marco Rengo
- Department of Radiological Sciences, Oncology and Pathology, I.C.O.T., University Sapienza, Latina, Italy
| | - Antonia Ignazzi
- Experimental Pharmacology Laboratory, Scientific Institute of Gastroenterology "S. de Bellis", Castellana Grotte, BA, Italy
| | - Marilia Carabotti
- Department of Internal Medicine and Medical Specialties, University Sapienza, Rome, Italy
| | - Alessia Cicenia
- Department of Internal Medicine and Medical Specialties, University Sapienza, Rome, Italy
| | - Rosa Vona
- Center for Gender-Specific Medicine, Istituto Superiore di Sanità, Rome Italy
| | - Piero Chirletti
- Department of General Surgery Francesco Durante, University Sapienza, Rome, Italy
| | - Maria Antonietta Maselli
- Experimental Pharmacology Laboratory, Scientific Institute of Gastroenterology "S. de Bellis", Castellana Grotte, BA, Italy
| | - Rossella Donghia
- Experimental Pharmacology Laboratory, Scientific Institute of Gastroenterology "S. de Bellis", Castellana Grotte, BA, Italy
| | - Mariagrazia Coluzzi
- Department of Medical Surgical Sciences and Biotechnology, University Sapienza, Latina, Italy
| | - Paola Matarrese
- Center for Gender-Specific Medicine, Istituto Superiore di Sanità, Rome Italy
| | - Gianfranco Silecchia
- Department of Medical Surgical Sciences and Biotechnology, University Sapienza, Latina, Italy
| | - Carola Severi
- Department of Internal Medicine and Medical Specialties, University Sapienza, Rome, Italy.
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12
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A Genomewide Integrative Analysis of GWAS and eQTLs Data Identifies Multiple Genes and Gene Sets Associated with Obesity. BIOMED RESEARCH INTERNATIONAL 2018; 2018:3848560. [PMID: 29854750 PMCID: PMC5964558 DOI: 10.1155/2018/3848560] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 03/20/2018] [Accepted: 04/03/2018] [Indexed: 12/02/2022]
Abstract
To identify novel susceptibility genes and gene sets for obesity, we conducted a genomewide expression association analysis of obesity via integrating genomewide association study (GWAS) and expression quantitative trait loci (eQTLs) data. GWAS summary data of body mass index (BMI) and waist-to-hip ratio (WHR) was driven from a published study, totally involving 339,224 individuals. The eQTLs dataset (containing 927,753 eQTLs) was obtained from eQTLs meta-analysis of 5,311 subjects. Integrative analysis of GWAS and eQTLs data was conducted by SMR software. The SMR single gene analysis results were further subjected to gene set enrichment analysis (GSEA) for identifying obesity associated gene sets. A total of 13,311 annotated gene sets were analyzed in this study. SMR single gene analysis identified 20 BMI associated genes (TUFM, SPI1, APOB48R, etc.). Also 3 WHR associated genes were detected (CPEB4, WARS2, and L3MBTL3). The significant association between Chr16p11 and BMI was observed by GSEA (FDR adjusted p value = 0.040). The TGCTGCT, MIR-15A, MIR-16, MIR-15B, MIR-195, MIR-424, and MIR-497 (FDR adjusted p value = 0.049) gene set appeared to be linked with WHR. Our results provide novel clues for the genetic mechanism studies of obesity. This study also illustrated the good performance of SMR for susceptibility gene mapping.
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13
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Franco-Tormo MJ, Salas-Crisostomo M, Rocha NB, Budde H, Machado S, Murillo-Rodríguez E. CRISPR/Cas9, the Powerful New Genome-Editing Tool for Putative Therapeutics in Obesity. J Mol Neurosci 2018; 65:10-16. [PMID: 29732484 DOI: 10.1007/s12031-018-1076-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 04/20/2018] [Indexed: 12/12/2022]
Abstract
The molecular technology known as clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) is revolutionizing the field of medical research and deepening our understanding of numerous biological processes. The attraction of CRISPR/Cas9 lies in its ability to efficiently edit DNA or modulate gene expression in living eukaryotic cells and organisms, a technology that was once considered either too expensive or scientifically risky. CRISPR/Cas9 has been successfully applied in agriculture to develop the next generation of disease-resistant plants. Now, the capability of gene editing has been translated to the biomedical area, focusing on the future of medicine faced with drug-resistant microbes by selectively targeting genes involved in antibiotic resistance, for example, or finding the ultimate strategy for cancer or HIV. In this regard, it was recently demonstrated that an injection of cancer-fighting CRISPR-modified white blood cells in a patient suffering from metastatic lung cancer could lead to promising results. Researchers and bioethicists are debating questions about the regulation of CRISPR/Cas9 that must be addressed. While legal challenges surround the use of this technique for genetically modifying cell lines in humans, we review the basic understanding of CRISPR/Cas9 and discuss how this technology could represent a candidate for treatment of non-communicable diseases in nutrition, such as obesity.
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Affiliation(s)
- María José Franco-Tormo
- Laboratorio de Neurociencias Moleculares e Integrativas, Escuela de Medicina División Ciencias de la Salud, Universidad Anáhuac Mayab, A.P. 96 Cordemex C.P, 97310, Mérida, Yucatán, Mexico.,Intercontinental Neuroscience Research Group, Mérida, Yucatán, Mexico
| | - Mireille Salas-Crisostomo
- Laboratorio de Neurociencias Moleculares e Integrativas, Escuela de Medicina División Ciencias de la Salud, Universidad Anáhuac Mayab, A.P. 96 Cordemex C.P, 97310, Mérida, Yucatán, Mexico.,Intercontinental Neuroscience Research Group, Mérida, Yucatán, Mexico
| | - Nuno Barbosa Rocha
- Intercontinental Neuroscience Research Group, Mérida, Yucatán, Mexico.,Health School, Polytechnic Institute of Porto, Porto, Portugal
| | - Henning Budde
- Intercontinental Neuroscience Research Group, Mérida, Yucatán, Mexico.,Faculty of Human Sciences, Medical School Hamburg, Hamburg, Germany.,Physical Activity, Physical Education, Health and Sport Research Centre (PAPESH), Sports Science Department, School of Science and Engineering, Reykjavik University, Reykjavik, Iceland.,Lithuanian Sports University, Kaunas, Lithuania
| | - Sérgio Machado
- Intercontinental Neuroscience Research Group, Mérida, Yucatán, Mexico.,Laboratory of Panic and Respiration, Institute of Psychiatry of Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.,Physical Activity Neuroscience Laboratory, Physical Activity Sciences Postgraduate Program of Salgado de Oliveira University, Niterói, Brazil
| | - Eric Murillo-Rodríguez
- Laboratorio de Neurociencias Moleculares e Integrativas, Escuela de Medicina División Ciencias de la Salud, Universidad Anáhuac Mayab, A.P. 96 Cordemex C.P, 97310, Mérida, Yucatán, Mexico. .,Intercontinental Neuroscience Research Group, Mérida, Yucatán, Mexico.
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14
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Integrating genome-wide association study and expression quantitative trait locus study identifies multiple genes and gene sets associated with schizophrenia. Prog Neuropsychopharmacol Biol Psychiatry 2018; 81:50-54. [PMID: 29024729 DOI: 10.1016/j.pnpbp.2017.10.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 09/25/2017] [Accepted: 10/04/2017] [Indexed: 02/02/2023]
Abstract
Schizophrenia is a serious mental disease with high heritability. To better understand the genetic basis of schizophrenia, we conducted a large scale integrative analysis of genome-wide association study (GWAS) and expression quantitative trait loci (eQTLs) data. GWAS summary data was derived from a published GWAS of schizophrenia, containing 9394 schizophrenia patients and 12,462 healthy controls. The eQTLs dataset was obtained from an eQTLs meta-analysis of 5311 subjects, containing 923,021 cis-eQTLs for 14,329 genes and 4732 trans-eQTLs for 2612 genes. Genome-wide single gene expression association analysis was conducted by SMR software. The SMR analysis results were further subjected to gene set enrichment analysis (GSEA) to identify schizophrenia associated gene sets. SMR detected 49 genes significantly associated with schizophrenia. The top five significant genes were CRELD2 (p value=1.65×10-11), DIP2B (p value=3.94×10-11), ZDHHC18 (p value=1.52×10-10) and ZDHHC5 (p value=7.45×10-10), C11ORF75 (p value=3.70×10-9). GSEA identified 80 gene sets with p values <0.01. The top five significant gene sets were COWLING_MYCN_TARGETS (p value <0.001) and CHR16P11 (p value <0.001), ACTACCT_MIR196A_MIR196B (p value=0.002), CELLULAR_COMPONENT_DISASSEMBLY (p value=0.002) and GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN (p value=0.002). Our results provide useful information for revealing the genetic basis of schizophrenia.
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15
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Sharp GC, Salas LA, Monnereau C, Allard C, Yousefi P, Everson TM, Bohlin J, Xu Z, Huang RC, Reese SE, Xu CJ, Baïz N, Hoyo C, Agha G, Roy R, Holloway JW, Ghantous A, Merid SK, Bakulski KM, Küpers LK, Zhang H, Richmond RC, Page CM, Duijts L, Lie RT, Melton PE, Vonk JM, Nohr EA, Williams-DeVane C, Huen K, Rifas-Shiman SL, Ruiz-Arenas C, Gonseth S, Rezwan FI, Herceg Z, Ekström S, Croen L, Falahi F, Perron P, Karagas MR, Quraishi BM, Suderman M, Magnus MC, Jaddoe VWV, Taylor JA, Anderson D, Zhao S, Smit HA, Josey MJ, Bradman A, Baccarelli AA, Bustamante M, Håberg SE, Pershagen G, Hertz-Picciotto I, Newschaffer C, Corpeleijn E, Bouchard L, Lawlor DA, Maguire RL, Barcellos LF, Davey Smith G, Eskenazi B, Karmaus W, Marsit CJ, Hivert MF, Snieder H, Fallin MD, Melén E, Munthe-Kaas MC, Arshad H, Wiemels JL, Annesi-Maesano I, Vrijheid M, Oken E, Holland N, Murphy SK, Sørensen TIA, Koppelman GH, Newnham JP, Wilcox AJ, Nystad W, London SJ, Felix JF, Relton CL. Maternal BMI at the start of pregnancy and offspring epigenome-wide DNA methylation: findings from the pregnancy and childhood epigenetics (PACE) consortium. Hum Mol Genet 2017; 26:4067-4085. [PMID: 29016858 PMCID: PMC5656174 DOI: 10.1093/hmg/ddx290] [Citation(s) in RCA: 150] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 06/23/2017] [Accepted: 07/17/2017] [Indexed: 12/16/2022] Open
Abstract
Pre-pregnancy maternal obesity is associated with adverse offspring outcomes at birth and later in life. Individual studies have shown that epigenetic modifications such as DNA methylation could contribute. Within the Pregnancy and Childhood Epigenetics (PACE) Consortium, we meta-analysed the association between pre-pregnancy maternal BMI and methylation at over 450,000 sites in newborn blood DNA, across 19 cohorts (9,340 mother-newborn pairs). We attempted to infer causality by comparing the effects of maternal versus paternal BMI and incorporating genetic variation. In four additional cohorts (1,817 mother-child pairs), we meta-analysed the association between maternal BMI at the start of pregnancy and blood methylation in adolescents. In newborns, maternal BMI was associated with small (<0.2% per BMI unit (1 kg/m2), P < 1.06 × 10-7) methylation variation at 9,044 sites throughout the genome. Adjustment for estimated cell proportions greatly attenuated the number of significant CpGs to 104, including 86 sites common to the unadjusted model. At 72/86 sites, the direction of the association was the same in newborns and adolescents, suggesting persistence of signals. However, we found evidence for acausal intrauterine effect of maternal BMI on newborn methylation at just 8/86 sites. In conclusion, this well-powered analysis identified robust associations between maternal adiposity and variations in newborn blood DNA methylation, but these small effects may be better explained by genetic or lifestyle factors than a causal intrauterine mechanism. This highlights the need for large-scale collaborative approaches and the application of causal inference techniques in epigenetic epidemiology.
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Affiliation(s)
- Gemma C Sharp
- MRC Integrative Epidemiology Unit
- School of Social and Community Medicine
- School of Oral and Dental Sciences, University of Bristol, Bristol, UK
| | - Lucas A Salas
- ISGlobal, Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Claire Monnereau
- The Generation R Study Group
- Department of Epidemiology
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Catherine Allard
- Centre de Recherche du Centre Hospitalier, Université de Sherbrooke, QC, Canada
| | - Paul Yousefi
- Center for Environmental Research and Children's Health (CERCH), School of Public Health, University of California Berkeley
| | - Todd M Everson
- Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Jon Bohlin
- Department of Infection Epidemiology and Modeling, Norwegian Institute of Public Health, Oslo, Norway
| | - Zongli Xu
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, USA
| | - Rae-Chi Huang
- Telethon Kids Institute, University of Western Australia, Crawley, WA 6009, Australia
| | - Sarah E Reese
- National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, USA
| | - Cheng-Jian Xu
- Department of Pulmonology, GRIAC Research Institute
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Nour Baïz
- Epidemiology of Allergic and Respiratory Diseases Department (EPAR), Sorbonne Université, UPMC Univ Paris 06, INSERM, Pierre Louis Institute of Epidemiology and Public Health, Saint-Antoine Medical School, Paris, France
| | - Cathrine Hoyo
- Department of Biological Sciences
- Center for Human Health and the Environment, North Carolina State University, NC, USA
| | - Golareh Agha
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Ritu Roy
- University of California San Francisco, CA, USA
- HDF Comprehensive Cancer Center, University of California, San Francisco, CA, USA
- Computational Biology Core
| | - John W Holloway
- Human Development & Health, Faculty of Medicine, University of Southampton, UK
| | - Akram Ghantous
- Epigenetics Group, International Agency for Research on Cancer, Lyon, France
| | - Simon K Merid
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Kelly M Bakulski
- Department of Epidemiology, School of Public Health, University of Michigan, MI, USA
| | - Leanne K Küpers
- MRC Integrative Epidemiology Unit
- School of Social and Community Medicine
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Hongmei Zhang
- Division of Epidemiology, Biostatistics, and Environmental Health Sciences, School of Public Health, University of Memphis, Memphis, TN, USA
| | - Rebecca C Richmond
- MRC Integrative Epidemiology Unit
- School of Social and Community Medicine
| | - Christian M Page
- Department of Non-Communicable Disease, Norwegian Institute of Public Health, Oslo, Norway
| | - Liesbeth Duijts
- The Generation R Study Group
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Rolv T Lie
- Department of Global Public Health and Primary Care, University of Bergen, Norway
- Medical Birth Registry of Norway, Norwegian Institute of Public Health, Bergen, Norway
| | - Phillip E Melton
- The Curtin UWA Centre for Genetic Origins of Health and Disease, Faculty of Health Sciences, Curtin University Health Sciences, Curtin University and Faculty of Medicine Dentistry & Health Sciences, The University of Western Australia, Perth, Australia
- Faculty of Medicine Dentistry & Health Sciences, The University of Western Australia, Perth, Australia
| | - Judith M Vonk
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, GRIAC Research Institute Groningen, The Netherlands
| | - Ellen A Nohr
- Research Unit for Gynaecology and Obstetrics, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | | | - Karen Huen
- Center for Environmental Research and Children's Health (CERCH), School of Public Health, University of California Berkeley
| | - Sheryl L Rifas-Shiman
- Obesity Prevention Program, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, USA
| | - Carlos Ruiz-Arenas
- ISGlobal, Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - Semira Gonseth
- Department of Epidemiology and Biostatistics, University of California San Francisco, CA, USA
- School of Public Health, University of California Berkeley, CA, USA
| | - Faisal I Rezwan
- Human Development & Health, Faculty of Medicine, University of Southampton, UK
| | - Zdenko Herceg
- Epigenetics Group, International Agency for Research on Cancer, Lyon, France
| | - Sandra Ekström
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Lisa Croen
- Division of Research, Kaiser Permanente Northern California, CA, UDA
| | - Fahimeh Falahi
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Patrice Perron
- Centre de Recherche du Centre Hospitalier, Université de Sherbrooke, QC, Canada
- Department of Medicine, Université de Sherbrooke, QC, Canada
| | - Margaret R Karagas
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
- Children's Environmental Health & Disease Prevention Research Center at Dartmouth, Hanover, NH, USA
| | - Bilal M Quraishi
- Division of Epidemiology, Biostatistics, and Environmental Health Sciences, School of Public Health, University of Memphis, Memphis, TN, USA
| | - Matthew Suderman
- MRC Integrative Epidemiology Unit
- School of Social and Community Medicine
| | - Maria C Magnus
- MRC Integrative Epidemiology Unit
- School of Social and Community Medicine
- Department of Non-Communicable Disease, Norwegian Institute of Public Health, Oslo, Norway
| | - Vincent W V Jaddoe
- The Generation R Study Group
- Department of Epidemiology
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Jack A Taylor
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, USA
- Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
| | - Denise Anderson
- Telethon Kids Institute, University of Western Australia, Crawley, WA 6009, Australia
| | - Shanshan Zhao
- National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, USA
| | - Henriette A Smit
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, The Netherlands
| | - Michele J Josey
- Department of Biological & Biomedical Sciences, North Carolina Central University, Durham, NC, USA
- Epidemiology and Biostatistics Department, University of South Carolina (Columbia), SC, USA
| | - Asa Bradman
- Center for Environmental Research and Children's Health (CERCH), School of Public Health, University of California Berkeley
| | - Andrea A Baccarelli
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Mariona Bustamante
- ISGlobal, Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Siri E Håberg
- Domain of Mental and Physical Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Göran Pershagen
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Center for Occupational and Environmental Medicine, Stockholm County Council, Stockholm, Sweden
| | - Irva Hertz-Picciotto
- Department of Public Health, School of Medicine, University of California, Davis, CA, USA
| | - Craig Newschaffer
- AJ Drexel Autism Institute, Drexel University, Philadelphia, PA, USA
| | - Eva Corpeleijn
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Luigi Bouchard
- Department of Biochemistry, Université de Sherbrooke, QC, Canada
- ECOGENE-21 and Lipid Clinic, Chicoutimi Hospital, Saguenay, QC, Canada
| | - Debbie A Lawlor
- MRC Integrative Epidemiology Unit
- School of Social and Community Medicine
| | - Rachel L Maguire
- Department of Biological Sciences
- Department of Community and Family Medicine, Duke University Medical Center, Durham, NC, USA
| | - Lisa F Barcellos
- Center for Environmental Research and Children's Health (CERCH), School of Public Health, University of California Berkeley
| | - George Davey Smith
- MRC Integrative Epidemiology Unit
- School of Social and Community Medicine
| | - Brenda Eskenazi
- Center for Environmental Research and Children's Health (CERCH), School of Public Health, University of California Berkeley
| | - Wilfried Karmaus
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Carmen J Marsit
- Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Marie-France Hivert
- Obesity Prevention Program, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, USA
- Department of Medicine, Université de Sherbrooke, QC, Canada
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Harold Snieder
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - M Daniele Fallin
- Department of Mental Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Erik Melén
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Center for Occupational and Environmental Medicine, Stockholm County Council, Stockholm, Sweden
- Sachs’ Children’s Hospital, South General Hospital, Stockholm, Sweden
| | - Monica C Munthe-Kaas
- Department of Pediatric and Adolescent Medicine, Oslo University Hospital, Norway
- Norwegian Institute of Public Health, Oslo Norway
| | - Hasan Arshad
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
- NIHR Respiratory Biomedical Research Unit, University Hospital Southampton, Southampton, UK
- The David Hide Asthma and Allergy Research Centre, Isle of Wight, UK
| | - Joseph L Wiemels
- Department of Epidemiology and Biostatistics, University of California San Francisco, CA, USA
| | - Isabella Annesi-Maesano
- Epidemiology of Allergic and Respiratory Diseases Department (EPAR), Sorbonne Université, UPMC Univ Paris 06, INSERM, Pierre Louis Institute of Epidemiology and Public Health, Saint-Antoine Medical School, Paris, France
| | - Martine Vrijheid
- ISGlobal, Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - Emily Oken
- Obesity Prevention Program, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, USA
| | - Nina Holland
- Center for Environmental Research and Children's Health (CERCH), School of Public Health, University of California Berkeley
| | - Susan K Murphy
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC, USA
| | - Thorkild I A Sørensen
- MRC Integrative Epidemiology Unit
- Novo Nordisk Foundation Center for Basic Metabolic Research, Section on Metabolic Genetics, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Epidemiology, Bispebjerg and Frederiksberg Hospital, The Capital Region, Copenhagen, Denmark
| | - Gerard H Koppelman
- Department of Paediatric Pulmonology and Paediatric Allergy, University of Groningen, University Medical Center Groningen, Beatrix Children’s Hospital, GRIAC Research Institute, Groningen, the Netherlands
| | - John P Newnham
- School of Women's and Infants' Health, The University of Western Australia, Crawley, WA 6009, Australia
| | - Allen J Wilcox
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, USA
| | - Wenche Nystad
- Department of Non-Communicable Disease, Norwegian Institute of Public Health, Oslo, Norway
| | - Stephanie J London
- National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, USA
| | - Janine F Felix
- The Generation R Study Group
- Department of Epidemiology
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Caroline L Relton
- MRC Integrative Epidemiology Unit
- School of Social and Community Medicine
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16
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Integrating genome-wide association study and expression quantitative trait loci data identifies multiple genes and gene set associated with neuroticism. Prog Neuropsychopharmacol Biol Psychiatry 2017; 78:149-152. [PMID: 28552732 DOI: 10.1016/j.pnpbp.2017.05.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Revised: 05/17/2017] [Accepted: 05/19/2017] [Indexed: 11/23/2022]
Abstract
Neuroticism is a fundamental personality trait with significant genetic determinant. To identify novel susceptibility genes for neuroticism, we conducted an integrative analysis of genomic and transcriptomic data of genome wide association study (GWAS) and expression quantitative trait locus (eQTL) study. GWAS summary data was driven from published studies of neuroticism, totally involving 170,906 subjects. eQTL dataset containing 927,753 eQTLs were obtained from an eQTL meta-analysis of 5311 samples. Integrative analysis of GWAS and eQTL data was conducted by summary data-based Mendelian randomization (SMR) analysis software. To identify neuroticism associated gene sets, the SMR analysis results were further subjected to gene set enrichment analysis (GSEA). The gene set annotation dataset (containing 13,311 annotated gene sets) of GSEA Molecular Signatures Database was used. SMR single gene analysis identified 6 significant genes for neuroticism, including MSRA (p value=2.27×10-10), MGC57346 (p value=6.92×10-7), BLK (p value=1.01×10-6), XKR6 (p value=1.11×10-6), C17ORF69 (p value=1.12×10-6) and KIAA1267 (p value=4.00×10-6). Gene set enrichment analysis observed significant association for Chr8p23 gene set (false discovery rate=0.033). Our results provide novel clues for the genetic mechanism studies of neuroticism.
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17
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Waide EH, Tuggle CK, Serão NVL, Schroyen M, Hess A, Rowland RRR, Lunney JK, Plastow G, Dekkers JCM. Genomewide association of piglet responses to infection with one of two porcine reproductive and respiratory syndrome virus isolates. J Anim Sci 2017; 95:16-38. [PMID: 28177360 DOI: 10.2527/jas.2016.0874] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Porcine reproductive and respiratory syndrome (PRRS) is a devastating disease in the swine industry. Identification of host genetic factors that enable selection for improved performance during PRRS virus (PRRSV) infection would reduce the impact of this disease on animal welfare and production efficiency. We conducted genomewide association study (GWAS) analyses of data from 13 trials of approximately 200 commercial crossbred nursery-age piglets that were experimentally infected with 1 of 2 type 2 isolates of PRRSV (NVSL 97-7985 [NVSL] and KS2006-72109 [KS06]). Phenotypes analyzed were viral load (VL) in blood during the first 21 d after infection (dpi) and weight gain (WG) from 0 to 42 dpi. We accounted for the previously identified QTL in the region on SSC4 in our models to increase power to identify additional regions. Many regions identified by single-SNP analyses were not identified using Bayes-B, but both analyses identified the same regions on SSC3 and SSC5 to be associated with VL in the KS06 trials and on SSC6 in the NVSL trials ( < 5 × 10); for WG, regions on SSC5 and SSC17 were associated in the NVSL trials ( < 3 × 10). No regions were identified with either method for WG in the KS06 trials. Except for the region on SSC4, which was associated with VL for both isolates (but only with WG for NVSL), identified regions did not overlap between the 2 PRRSV isolate data sets, despite high estimates of the genetic correlation between isolates for traits based on these data. We also identified genomic regions whose associations with VL or WG interacted with either PRRSV isolate or with genotype at the SSC4 QTL. Gene ontology (GO) annotation terms for genes located near moderately associated SNP ( < 0.003) were enriched for multiple immunologically (VL) and metabolism- (WG) related GO terms. The biological relevance of these regions suggests that, although it may increase the number of false positives, the use of single-SNP analyses and a relaxed threshold also increased the identification of true positives. In conclusion, although only the SSC4 QTL was associated with response to both PRRSV isolates, genes near associated SNP were enriched for the same GO terms across PRRSV isolates, suggesting that host responses to these 2 isolates are affected by the actions of many genes that function together in similar biological processes.
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Wu Y, Wang W, Jiang W, Yao J, Zhang D. An investigation of obesity susceptibility genes in Northern Han Chinese by targeted resequencing. Medicine (Baltimore) 2017; 96:e6117. [PMID: 28207535 PMCID: PMC5319524 DOI: 10.1097/md.0000000000006117] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Our earlier genome-wide linkage study of body mass index (BMI) showed strong signals from 7q36.3 and 8q21.13. This case-control study set to investigate 2 genomic regions which may harbor variants contributed to development of obesity.We employed targeted resequencing technology to detect single nucleotide polymorphisms (SNPs) in 7q36.3 and 8q21.13 from 16 individuals with obesity. These were compared with 504 East Asians in the 1000 Genomes Project as a reference panel. Linkage disequilibrium (LD) block analysis was performed for the significant SNPs located near the same gene. Genes involved in statistically significant loci were then subject to gene set enrichment analysis (GSEA).The 16 individuals aged between 30 and 60 years with BMI = 33.25 ± 2.22 kg/m. A total of 12,131 genetic variants across all of samples were found. After correcting for multiple testing, 65 SNPs from 25 nearest genes (INSIG1, FABP5, PTPRN2, VIPR2, WDR60, SHH, UBE3C, LMBR1, PAG1, IMPA1, CHMP4, SNX16, BLACE, EN2, CNPY1, LOC100506302, RBM33, LOC389602, LOC285889, LINC01006, NOM1, DNAJB6, LOC101927914, ESYT2, LINC00689) were associated with obesity at significant level q-value ≤ 0.05. LD block analysis showed there were 10 pairs of loci with D' ≥ 0.8 and r ≥ 0.8. GSEA further identified 2 major related gene sets, involving lipid raft and lipid metabolic process, with FDR values <0.12 and <0.4, respectively.Our data are the first documentation of genetic variants in 7q36.3 and 8q21.13 associated with obesity using target capture sequencing and Northern Han Chinese samples. Additional replication and functional studies are merited to validate our findings.
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Jiao H, Wang K, Yang F, Grant SFA, Hakonarson H, Price RA, Li WD. Pathway-Based Genome-Wide Association Studies for Plasma Triglycerides in Obese Females and Normal-Weight Controls. PLoS One 2015; 10:e0134923. [PMID: 26308950 PMCID: PMC4550433 DOI: 10.1371/journal.pone.0134923] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 07/15/2015] [Indexed: 12/27/2022] Open
Abstract
Pathway-based analysis as an alternative approach can provide complementary information to single-marker genome-wide association studies (GWASs), which always ignore the epistasis and does not have sufficient power to find rare variants. In this study, using genotypes from a genome-wide association study (GWAS), pathway-based association studies were carried out by a modified Gene Set Enrichment Algorithm (GSEA) method (GenGen) for triglyceride in 1028 unrelated European-American extremely obese females (BMI≥35kg/m2) and normal-weight controls (BMI<25kg/m2), and another pathway association analysis (ICSNPathway) was also used to verify the GenGen result in the same data. The GO0009110 pathway (vitamin anabolism) was among the strongest associations with triglyceride (empirical P<0.001); the result remained significant after FDR correction (P = 0.022). MMAB, an obesity-related locus, included in this pathway. The ABCG1 and BCL6 gene was found in several triglyceride-related pathways (empirical P<0.05), which were also replicated by ICSNPathway (empirical P<0.05, FDR<0.05). We also performed single-marked GWAS using PLINK for TG levels (log-transformed). Significant associations were found between ASTN2 gene SNPs and plasma triglyceride levels (rs7035794, P = 2.24×10−10). Our study suggested that vitamin anabolism pathway, BCL6 gene pathways and ASTN2 gene may contribute to the genetic variation of plasma triglyceride concentrations.
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Affiliation(s)
- Hongxiao Jiao
- Research Center of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Kai Wang
- Zilkha Neurogenetic Institute and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, 90089, United States of America
| | - Fuhua Yang
- Research Center of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Struan F. A. Grant
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, United States of America
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, United States of America
| | - Hakon Hakonarson
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, United States of America
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, United States of America
| | - R. Arlen Price
- Center for Neurobiology and Behavior, Department of Psychiatry, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, United States of America
- * E-mail: (WDL); (RAP)
| | - Wei-Dong Li
- Research Center of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
- Center for Neurobiology and Behavior, Department of Psychiatry, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, United States of America
- * E-mail: (WDL); (RAP)
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Regulation of Appetite, Body Composition, and Metabolic Hormones by Vasoactive Intestinal Polypeptide (VIP). J Mol Neurosci 2015; 56:377-87. [PMID: 25904310 DOI: 10.1007/s12031-015-0556-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 03/25/2015] [Indexed: 12/12/2022]
Abstract
Vasoactive intestinal peptide (VIP) is a 28-amino acid neuropeptide that belongs to the secretin-glucagon superfamily of peptides and has 68 % homology with PACAP. VIP is abundantly expressed in the central and peripheral nervous system and in the gastrointestinal tract, where it exercises several physiological functions. Previously, it has been reported that VIP regulates feeding behavior centrally in different species of vertebrates such as goldfishes, chicken and rodents. Additional studies are necessary to analyze the role of endogenous VIP on the regulation of appetite/satiety, feeding behavior, metabolic hormones, body mass composition and energy balance. The aim of the study was to elucidate the physiological pathways by which VIP regulates appetite/satiety, feeding behavior, metabolic hormones, and body mass composition. VIP deficient (VIP -/-) and age-matched wild-type (WT) littermates were weekly monitored from 5 to 22 weeks of age using a whole body composition EchoMRI analyzer. Food intake and feeding behavior were analyzed using the BioDAQ automated monitoring system. Plasma levels of metabolic hormones including active-ghrelin, GLP-1, leptin, PYY, pancreatic polypeptide (PP), adiponectin, and insulin were measured in fasting as well as in postprandial conditions. The genetic lack of VIP led to a significant reduction of body weight and fat mass and to an increase of lean mass as the mice aged. Additionally, VIP-/- mice had a disrupted pattern of circadian feeding behavior resulting in an abolished regular nocturnal/diurnal feeding. These changes were associated with an altered secretion of adiponectin, GLP-1, leptin, PYY and insulin in VIP-/- mice. Our data demonstrates that endogenous VIP is involved in the control of appetite/satiety, feeding behavior, body mass composition and in the secretion of six different key regulatory metabolic hormones. VIP plays a key role in the regulation of body phenotype by significantly enhancing body weight and fat mass accumulation. Therefore, VIP signaling is critical for the modulation of appetite/satiety and body mass phenotype and is a potential target for future treatment of obesity.
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Zhang F, Xiao X, Hao J, Wang S, Wen Y, Guo X. CPAS: A trans-omics pathway analysis tool for jointly analyzing DNA copy number variations and mRNA expression profiles data. J Biomed Inform 2015; 53:363-6. [DOI: 10.1016/j.jbi.2014.12.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 12/16/2014] [Accepted: 12/22/2014] [Indexed: 02/06/2023]
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Zhang F, Wen Y, Guo X, Zhang Y, Wang S, Yang T, Shen H, Chen X, Tan L, Tian Q, Deng HW. Genome-wide pathway-based association study implicates complement system in the development of Kashin-Beck disease in Han Chinese. Bone 2015; 71:36-41. [PMID: 25305519 DOI: 10.1016/j.bone.2014.09.025] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Revised: 09/06/2014] [Accepted: 09/30/2014] [Indexed: 11/22/2022]
Abstract
Kashin-Beck disease (KBD) is a chronic osteochondropathy. The pathogenesis of KBD remains unknown. To identify relevant biological pathways for KBD, we conducted a genome-wide pathway-based association study (GWPAS) following by replication analysis, totally using 2743 Chinese Han adults. A modified gene set enrichment algorithm was used to detect association between KBD and 963 biological pathways. Cartilage gene expression analysis and serum complement measurement were performed to evaluate the functional relevance of identified pathway with KBD. We found that the Complement and Coagulation Cascades (CACC) pathway was significantly associated with KBD (P value=3.09×10(-5), false-discovery rate=0.042). Within the CACC pathway, the most significant association was observed at rs1656966 (P value=1.97×10(-4)) of KNG1 gene. Further replication study observed that rs1656966 (P value=0.037) was significantly associated with KBD in an independent validation sample of 1026 subjects. Gene expression analysis observed that CFD (ratio=3.39±2.68), A2M (ratio=3.67±5.63), C5 (ratio=2.65±2.52) and CD46 (ratio=2.29±137) genes of the CACC pathway were up-regulated in KBD articular cartilage compared to healthy articular cartilage. The serum level of complement C5 in KBD patients were significantly higher than that in healthy controls (P value=0.038). Our study is the first to suggest that complement system-related CACC pathway contributed to the development of KBD.
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Affiliation(s)
- Feng Zhang
- Key Laboratory of Environment and Gene Related Diseases of Ministry Education, Key Laboratory of Trace Elements and Endemic Diseases of Ministry of Health, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, P. R. China
| | - Yan Wen
- Key Laboratory of Environment and Gene Related Diseases of Ministry Education, Key Laboratory of Trace Elements and Endemic Diseases of Ministry of Health, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, P. R. China
| | - Xiong Guo
- Key Laboratory of Environment and Gene Related Diseases of Ministry Education, Key Laboratory of Trace Elements and Endemic Diseases of Ministry of Health, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, P. R. China.
| | - Yingang Zhang
- Department of Orthopedics, First Affiliated Hospital of Medical College of Xi'an Jiaotong University, Xi'an, Shaanxi, P.R. China
| | - Sen Wang
- Key Laboratory of Environment and Gene Related Diseases of Ministry Education, Key Laboratory of Trace Elements and Endemic Diseases of Ministry of Health, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, P. R. China
| | - Tielin Yang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Institute of Molecular Genetics, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, P.R. China
| | - Hui Shen
- Department of Biostatistics and Bioinformatics, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, USA; Center for Bioinformatics and Genomics, Tulane University, New Orleans, LA, USA
| | - Xiangding Chen
- Laboratory of Molecular and Statistical Genetics, College of Life Sciences, Hunan Normal University, Changsha, P. R. China
| | - Lijun Tan
- Laboratory of Molecular and Statistical Genetics, College of Life Sciences, Hunan Normal University, Changsha, P. R. China
| | - Qing Tian
- Department of Biostatistics and Bioinformatics, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, USA; Center for Bioinformatics and Genomics, Tulane University, New Orleans, LA, USA
| | - Hong-Wen Deng
- Department of Biostatistics and Bioinformatics, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, USA; Center for Bioinformatics and Genomics, Tulane University, New Orleans, LA, USA
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Rêgo JL, Oliveira JM, Santana NDL, Machado PRL, Castellucci LC. The role of ERBB2 gene polymorphisms in leprosy susceptibility. Braz J Infect Dis 2015; 19:206-8. [PMID: 25636184 PMCID: PMC9425388 DOI: 10.1016/j.bjid.2014.12.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 12/01/2014] [Indexed: 11/25/2022] Open
Abstract
Mycobacterium leprae infects skin and peripheral nerves causing deformities and disability. The M. leprae bacterium binds to ErbB2 on the Schwann cell surface causing demyelination and favoring spread of the bacilli and causing nerve injury. Polymorphisms at the ERBB2 gene were previously investigated as genetic risk factors for leprosy in two Brazilian populations but with inconsistent results. Herein we extend the analysis of ERBB2 variants to a third geographically distinct population in Brazil. Our results show that there is no association between the genotyped SNPs and the disease (p > 0.05) in this population. A gene set or pathway analysis under the genomic region of ERBB2 will be necessary to clarify its regulation under M. leprae stimulus.
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Affiliation(s)
| | | | | | - Paulo Roberto Lima Machado
- Instituto Nacional de Ciência e Tecnologia em Doenças Tropicais, Brazil; Universidade Federal da Bahia, Salvador, BA, Brazil
| | - Léa Cristina Castellucci
- Instituto Nacional de Ciência e Tecnologia em Doenças Tropicais, Brazil; Universidade Federal da Bahia, Salvador, BA, Brazil
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Trans-omics pathway analysis suggests that eQTLs contribute to chondrocyte apoptosis of Kashin–Beck disease through regulating apoptosis pathway expression. Gene 2014; 553:166-9. [DOI: 10.1016/j.gene.2014.10.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Revised: 08/18/2014] [Accepted: 10/08/2014] [Indexed: 12/16/2022]
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Jiang Y, Bai X, Zhu X, Li J. The effects of Fructus Aurantii extract on the 5-hydroxytryptamine and vasoactive intestinal peptide contents of the rat gastrointestinal tract. PHARMACEUTICAL BIOLOGY 2014; 52:581-585. [PMID: 24707973 DOI: 10.3109/13880209.2013.854396] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Accepted: 10/06/2013] [Indexed: 06/03/2023]
Abstract
CONTEXT Fructus Aurantii, the unripe fruit of Citrus aurantium Linn (Rutaceae), is a Qi-regulating drug used in traditional Chinese medicine to improve gastrointestinal (GI) function. Vasoactive intestinal peptide (VIP) and 5-hydroxytryptamine (5-HT) regulate GI motility and fluid secretion. OBJECTIVE We tested whether the Fructus Aurantii extract altered VIP and 5-HT expression levels in rats. MATERIALS AND METHODS Experimental rats were administered 0.3 g/ml Fructus Aurantii water decoction at 2.0 ml/100 g body weight per day for 10 days by gavage feeding, while control rats were gavage fed equal volumes of distilled water. Expression levels of 5-HT and VIP were measured by immunohistochemical staining and microscopic image analysis of the GI mucosa and myenteric nerve plexus. RESULTS Average 5-HT staining intensity scores in the stomach antrum, duodenal mucosa and jejunal mucosa were significantly higher in the Fructus Aurantii treatment group than in the control group (antrum: 213% of control; duodenum: 193%; jejunum: 256%; p < 0.05 for all). In contrast, the average VIP density scores in the stomach antrum, duodenal mucosa and jejunal mucosa were significantly lower in the Fructus Aurantii group (antrum: 14% of control; duodenum: 15%; jejunum: 38%; p < 0.01 for all). Tissues from Fructus Aurantii-treated rats exhibited significantly greater numbers of 5-HT- and VIP-immunopositive cells in the gastric antrum, duodenum and jejunum mucosal layer but fewer VIP-expressing cells in the myenteric nerve plexus (p < 0.05 for both). CONCLUSION Fructus Aurantii can enhance gastrointestinal motility by altering 5-HT and VIP expression levels in the rat GI tract.
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Affiliation(s)
- Yihao Jiang
- College of Environmental and Chemical Engineering of Nanchang University , Nanchang, Jiangxi , P.R. China
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Simonson MA, McQueen MB, Keller MC. Whole-genome pathway analysis on 132,497 individuals identifies novel gene-sets associated with body mass index. PLoS One 2014; 9:e78546. [PMID: 24497910 PMCID: PMC3908858 DOI: 10.1371/journal.pone.0078546] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Accepted: 09/14/2013] [Indexed: 01/28/2023] Open
Abstract
Whole genome pathway analysis is a powerful tool for the exploration of the combined effects of gene-sets within biological pathways. This study applied Interval Based Enrichment Analysis (INRICH) to perform whole-genome pathway analysis of body-mass index (BMI). We used a discovery set composed of summary statistics from a meta-analysis of 123,865 subjects performed by the GIANT Consortium, and an independent sample of 8,632 subjects to assess replication of significant pathways. We examined SNPs within nominally significant pathways using linear mixed models to estimate their contribution to overall BMI heritability. Six pathways replicated as having significant enrichment for association after correcting for multiple testing, including the previously unknown relationships between BMI and the Reactome regulation of ornithine decarboxylase pathway, the KEGG lysosome pathway, and the Reactome stabilization of P53 pathway. Two non-overlapping sets of genes emerged from the six significant pathways. The clustering of shared genes based on previously identified protein-protein interactions listed in PubMed and OMIM supported the relatively independent biological effects of these two gene-sets. We estimate that the SNPs located in examined pathways explain ∼20% of the heritability for BMI that is tagged by common SNPs (3.35% of the 16.93% total).
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Affiliation(s)
- Matthew A. Simonson
- Department of Psychology and Neuroscience, Institute for Behavioral Genetics, University of Colorado, Boulder, Colorado, United States of America
- Mayo Clinic, Department of Health Sciences, Division of Biomedical Statistics and Informatics, Rochester, Minnesota, United States of America
- * E-mail:
| | - Matthew B. McQueen
- Department of Integrative Physiology, Institute for Behavioral Genetics, University of Colorado, Boulder, Colorado, United States of America
| | - Matthew C. Keller
- Department of Psychology and Neuroscience, Institute for Behavioral Genetics, University of Colorado, Boulder, Colorado, United States of America
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Báez-Ruiz A, Luna-Moreno D, Carmona-Castro A, Cárdenas-Vázquez R, Díaz-Muñoz M, Carmona-Alcocer V, Fuentes-Granados C, Manuel MA. Hypothalamic expression of anorexigenic and orexigenic hormone receptors in obese femalesNeotomodon alstoni:Effect of fasting. Nutr Neurosci 2013; 17:31-6. [DOI: 10.1179/1476830513y.0000000063] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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Evangelou M, Dudbridge F, Wernisch L. Two novel pathway analysis methods based on a hierarchical model. ACTA ACUST UNITED AC 2013; 30:690-7. [PMID: 24123673 PMCID: PMC3933872 DOI: 10.1093/bioinformatics/btt583] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Motivation: Over the past few years several pathway analysis methods have been proposed for exploring and enhancing the analysis of genome-wide association data. Hierarchical models have been advocated as a way to integrate SNP and pathway effects in the same model, but their computational complexity has prevented them being applied on a genome-wide scale to date. Methods: We present two novel methods for identifying associated pathways. In the proposed hierarchical model, the SNP effects are analytically integrated out of the analysis, allowing computationally tractable model fitting to genome-wide data. The first method uses Bayes factors for calculating the effect of the pathways, whereas the second method uses a machine learning algorithm and adaptive lasso for finding a sparse solution of associated pathways. Results: The performance of the proposed methods was explored on both simulated and real data. The results of the simulation study showed that the methods outperformed some well-established association methods: the commonly used Fisher’s method for combining P-values and also the recently published BGSA. The methods were applied to two genome-wide association study datasets that aimed to find the genetic structure of platelet function and body mass index, respectively. The results of the analyses replicated the results of previously published pathway analysis of these phenotypes but also identified novel pathways that are potentially involved. Availability: An R package is under preparation. In the meantime, the scripts of the methods are available on request from the authors. Contact: marina.evangelou@cimr.cam.ac.uk Supplementary Information: Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Marina Evangelou
- Medical Research Council Biostatistics Unit, Institute of Public Health, Cambridge, CB2 0SR, UK, JDRF/Wellcome Trust Diabetes and Inflammation Laboratory, NIHR Cambridge Biomedical Research Centre, Cambridge Institute for Medical Research, University of Cambridge, Addenbrooke's Hospital, Cambridge, CB2 0XY, UK and Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
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Ye Q, Zhao X, Xu K, Li Q, Cheng J, Gao Y, Du J, Shi H, Zhou L. Polymorphisms in lipid metabolism related miRNA binding sites and risk of metabolic syndrome. Gene 2013; 528:132-8. [DOI: 10.1016/j.gene.2013.07.036] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2013] [Revised: 04/15/2013] [Accepted: 07/18/2013] [Indexed: 01/28/2023]
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Knoll N, Jarick I, Volckmar AL, Klingenspor M, Illig T, Grallert H, Gieger C, Wichmann HE, Peters A, Hebebrand J, Scherag A, Hinney A. Gene set of nuclear-encoded mitochondrial regulators is enriched for common inherited variation in obesity. PLoS One 2013; 8:e55884. [PMID: 23409076 PMCID: PMC3568071 DOI: 10.1371/journal.pone.0055884] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Accepted: 01/03/2013] [Indexed: 01/13/2023] Open
Abstract
There are hints of an altered mitochondrial function in obesity. Nuclear-encoded genes are relevant for mitochondrial function (3 gene sets of known relevant pathways: (1) 16 nuclear regulators of mitochondrial genes, (2) 91 genes for oxidative phosphorylation and (3) 966 nuclear-encoded mitochondrial genes). Gene set enrichment analysis (GSEA) showed no association with type 2 diabetes mellitus in these gene sets. Here we performed a GSEA for the same gene sets for obesity. Genome wide association study (GWAS) data from a case-control approach on 453 extremely obese children and adolescents and 435 lean adult controls were used for GSEA. For independent confirmation, we analyzed 705 obesity GWAS trios (extremely obese child and both biological parents) and a population-based GWAS sample (KORA F4, n = 1,743). A meta-analysis was performed on all three samples. In each sample, the distribution of significance levels between the respective gene set and those of all genes was compared using the leading-edge-fraction-comparison test (cut-offs between the 50th and 95th percentile of the set of all gene-wise corrected p-values) as implemented in the MAGENTA software. In the case-control sample, significant enrichment of associations with obesity was observed above the 50th percentile for the set of the 16 nuclear regulators of mitochondrial genes (pGSEA,50 = 0.0103). This finding was not confirmed in the trios (pGSEA,50 = 0.5991), but in KORA (pGSEA,50 = 0.0398). The meta-analysis again indicated a trend for enrichment (pMAGENTA,50 = 0.1052, pMAGENTA,75 = 0.0251). The GSEA revealed that weak association signals for obesity might be enriched in the gene set of 16 nuclear regulators of mitochondrial genes.
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Affiliation(s)
- Nadja Knoll
- Department of Child and Adolescent Psychiatry, University of Duisburg-Essen, Essen, Germany
| | - Ivonne Jarick
- Institute of Medical Biometry and Epidemiology, Philipps-University of Marburg, Marburg, Germany
| | - Anna-Lena Volckmar
- Department of Child and Adolescent Psychiatry, University of Duisburg-Essen, Essen, Germany
| | - Martin Klingenspor
- Molecular Nutritional Medicine, Technical University of Munich, Else Kröner-Fresenius Center, Freising-Weihenstephan, Germany
| | - Thomas Illig
- Research Unit of Molecular Epidemiology, Helmholtz Center Munich – German Research Center for Environmental Health, Neuherberg, Germany
- Hannover Unified Biobank, Hannover Medical School, Hannover, Germany
| | - Harald Grallert
- Research Unit of Molecular Epidemiology, Helmholtz Center Munich – German Research Center for Environmental Health, Neuherberg, Germany
| | - Christian Gieger
- Institute of Genetic Epidemiology, Helmholtz Center Munich – German Research Center for Environmental Health, Neuherberg, Germany
| | - Heinz-Erich Wichmann
- Institute of Epidemiology I, Helmholtz Center Munich – German Research Center for Environmental Health, Neuherberg, Germany, Neuherberg, Germany
- Institute of Medical Informatics, Biometry, and Epidemiology, Chair of Epidemiology, Ludwig-Maximilians-Universität, Munich, Germany
- Munich University Hospital, Campus Grosshadern, Munich, Germany
| | - Annette Peters
- Institute of Epidemiology II, Helmholtz Center Munich – German Research Center for Environmental Health, Neuherberg, Germany
| | - Johannes Hebebrand
- Department of Child and Adolescent Psychiatry, University of Duisburg-Essen, Essen, Germany
| | - André Scherag
- Institute for Medical Informatics, Biometry and Epidemiology, University of Duisburg-Essen, Essen, Germany
| | - Anke Hinney
- Department of Child and Adolescent Psychiatry, University of Duisburg-Essen, Essen, Germany
- * E-mail:
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Lee S, Kwon MS, Park T. Network graph analysis of gene-gene interactions in genome-wide association study data. Genomics Inform 2012; 10:256-62. [PMID: 23346039 PMCID: PMC3543927 DOI: 10.5808/gi.2012.10.4.256] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Revised: 11/14/2012] [Accepted: 11/16/2012] [Indexed: 12/18/2022] Open
Abstract
Most common complex traits, such as obesity, hypertension, diabetes, and cancers, are known to be associated with multiple genes, environmental factors, and their epistasis. Recently, the development of advanced genotyping technologies has allowed us to perform genome-wide association studies (GWASs). For detecting the effects of multiple genes on complex traits, many approaches have been proposed for GWASs. Multifactor dimensionality reduction (MDR) is one of the powerful and efficient methods for detecting high-order gene-gene (GxG) interactions. However, the biological interpretation of GxG interactions identified by MDR analysis is not easy. In order to aid the interpretation of MDR results, we propose a network graph analysis to elucidate the meaning of identified GxG interactions. The proposed network graph analysis consists of three steps. The first step is for performing GxG interaction analysis using MDR analysis. The second step is to draw the network graph using the MDR result. The third step is to provide biological evidence of the identified GxG interaction using external biological databases. The proposed method was applied to Korean Association Resource (KARE) data, containing 8838 individuals with 327,632 single-nucleotide polymorphisms, in order to perform GxG interaction analysis of body mass index (BMI). Our network graph analysis successfully showed that many identified GxG interactions have known biological evidence related to BMI. We expect that our network graph analysis will be helpful to interpret the biological meaning of GxG interactions.
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Affiliation(s)
- Sungyoung Lee
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 151-747, Korea
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Zhang F, Guo X, Wu S, Han J, Liu Y, Shen H, Deng HW. Genome-wide pathway association studies of multiple correlated quantitative phenotypes using principle component analyses. PLoS One 2012; 7:e53320. [PMID: 23285279 PMCID: PMC3532454 DOI: 10.1371/journal.pone.0053320] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Accepted: 11/27/2012] [Indexed: 02/07/2023] Open
Abstract
Genome-wide pathway association studies provide novel insight into the biological mechanism underlying complex diseases. Current pathway association studies primarily focus on single important disease phenotype, which is sometimes insufficient to characterize the clinical manifestations of complex diseases. We present a multi-phenotypes pathway association study(MPPAS) approach using principle component analysis(PCA). In our approach, PCA is first applied to multiple correlated quantitative phenotypes for extracting a set of orthogonal phenotypic components. The extracted phenotypic components are then used for pathway association analysis instead of original quantitative phenotypes. Four statistics were proposed for PCA-based MPPAS in this study. Simulations using the real data from the HapMap project were conducted to evaluate the power and type I error rates of PCA-based MPPAS under various scenarios considering sample sizes, additive and interactive genetic effects. A real genome-wide association study data set of bone mineral density (BMD) at hip and spine were also analyzed by PCA-based MPPAS. Simulation studies illustrated the performance of PCA-based MPPAS for identifying the causal pathways underlying complex diseases. Genome-wide MPPAS of BMD detected associations between BMD and KENNY_CTNNB1_TARGETS_UP as well as LONGEVITYPATHWAY pathways in this study. We aim to provide a applicable MPPAS approach, which may help to gain deep understanding the potential biological mechanism of association results for complex diseases.
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Affiliation(s)
- Feng Zhang
- Key Laboratory of Environment and Gene Related Diseases of Ministry Education, Faculty of Public Health, College of Medicine, Xi'an Jiaotong University, Xi'an, Shaanxi, China
- * E-mail:
| | - Xiong Guo
- Key Laboratory of Environment and Gene Related Diseases of Ministry Education, Faculty of Public Health, College of Medicine, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Shixun Wu
- Key Laboratory of Environment and Gene Related Diseases of Ministry Education, Faculty of Public Health, College of Medicine, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Jing Han
- Key Laboratory of Environment and Gene Related Diseases of Ministry Education, Faculty of Public Health, College of Medicine, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Yongjun Liu
- Department of Biostatistics, School of Public Health and Tropical Medicine, Tulane University, New Orleans, Louisiana, United States of America
| | - Hui Shen
- Department of Biostatistics, School of Public Health and Tropical Medicine, Tulane University, New Orleans, Louisiana, United States of America
| | - Hong-Wen Deng
- Department of Biostatistics, School of Public Health and Tropical Medicine, Tulane University, New Orleans, Louisiana, United States of America
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Sanlioglu AD, Karacay B, Balci MK, Griffith TS, Sanlioglu S. Therapeutic potential of VIP vs PACAP in diabetes. J Mol Endocrinol 2012; 49:R157-67. [PMID: 22991228 DOI: 10.1530/jme-12-0156] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Type 2 diabetes (T2D) is characterized by chronic insulin resistance and a progressive decline in beta-cell function. Although rigorous glucose control can reduce morbidity and mortality associated with diabetes, achieving optimal long-term glycemic control remains to be accomplished in many diabetic patients. As beta-cell mass and function inevitably decline in T2D, exogenous insulin administration is almost unavoidable as a final outcome despite the use of oral antihyperglycemic agents in many diabetic patients. Pancreatic islet cell death, but not the defect in new islet formation or beta-cell replication, has been blamed for the decrease in beta-cell mass observed in T2D patients. Thus, therapeutic approaches designed to protect islet cells from apoptosis could significantly improve the management of T2D, because of its potential to reverse diabetes not just ameliorate glycemia. Therefore, an ideal beta-cell-preserving agent is expected to protect beta cells from apoptosis and stimulate postprandial insulin secretion along with increasing beta-cell replication and/or islet neogenesis. One such potential agent, the islet endocrine neuropeptide vasoactive intestinal peptide (VIP) strongly stimulates postprandial insulin secretion. Because of its broad spectrum of biological functions such as acting as a potent anti-inflammatory factor through suppression of Th1 immune response, and induction of immune tolerance via regulatory T cells, VIP has emerged as a promising therapeutic agent for the treatment of many autoimmune diseases including diabetes.
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Affiliation(s)
- Ahter D Sanlioglu
- Human Gene and Cell Therapy Center, Akdeniz University Hospitals and Clinics, B Block, 1st floor, Campus, Antalya 07058, Turkey
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Evangelou M, Rendon A, Ouwehand WH, Wernisch L, Dudbridge F. Comparison of methods for competitive tests of pathway analysis. PLoS One 2012; 7:e41018. [PMID: 22859961 PMCID: PMC3409204 DOI: 10.1371/journal.pone.0041018] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2012] [Accepted: 06/15/2012] [Indexed: 01/16/2023] Open
Abstract
It has been suggested that pathway analysis can complement single-SNP analysis in exploring genomewide association data. Pathway analysis incorporates the available biological knowledge of genes and SNPs and is expected to improve the chances of revealing the underlying genetic architecture of complex traits. Methods for pathway analysis can be classified as competitive (enrichment) or self-contained (association) according to the hypothesis tested. Although association tests are statistically more powerful than enrichment tests they can be difficult to calibrate because biases in analysis accumulate across multiple SNPs or genes. Furthermore, enrichment tests can be more scientifically relevant than association tests, as they detect pathways with relatively more evidence for association than the remaining genes. Here we show how some well known association tests can be simply adapted to test for enrichment, and compare their performance to some established enrichment tests. We propose versions of the Adaptive Rank Truncated Product (ARTP), Tail Strength Measure and Fisher's combination of p-values for testing the enrichment null hypothesis. We compare the behaviour of these proposed methods with the established Hypergeometric Test and Gene-Set Enrichment Analysis (GSEA). The results of the simulation study show that the modified version of the ARTP method has generally the best performance across the situations considered. The methods were also applied for finding enriched pathways for body mass index (BMI) and platelet function phenotypes. The pathway analysis of BMI identified the Vasoactive Intestinal Peptide pathway as significantly associated with BMI. This pathway has been previously reported as associated with BMI and the risk of obesity. The ARTP method was the method that identified the largest number of enriched pathways across all tested pathway databases and phenotypes. The simulation and data application results are in agreement with previous work on association tests and suggests that the ARTP should be preferred for both enrichment and association testing.
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Affiliation(s)
- Marina Evangelou
- Medical Research Council Biostatistics Unit, Institute of Public Health, Cambridge, United Kingdom
| | - Augusto Rendon
- Medical Research Council Biostatistics Unit, Institute of Public Health, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
- National Health Service Blood and Transplant, Cambridge, United Kingdom
| | - Willem H. Ouwehand
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
- National Health Service Blood and Transplant, Cambridge, United Kingdom
- Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Lorenz Wernisch
- Medical Research Council Biostatistics Unit, Institute of Public Health, Cambridge, United Kingdom
| | - Frank Dudbridge
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
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Hooton H, Angquist L, Holst C, Hager J, Rousseau F, Hansen RD, Tjønneland A, Roswall N, van der A DL, Overvad K, Jakobsen MU, Boeing H, Meidtner K, Palli D, Masala G, Bouatia-Naji N, Saris WHM, Feskens EJM, Wareham NJ, Vimaleswaran KS, Langin D, Loos RJF, Sørensen TIA, Clément K. Dietary factors impact on the association between CTSS variants and obesity related traits. PLoS One 2012; 7:e40394. [PMID: 22844403 PMCID: PMC3402491 DOI: 10.1371/journal.pone.0040394] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Accepted: 06/06/2012] [Indexed: 01/12/2023] Open
Abstract
Background/Aims Cathepsin S, a protein coded by the CTSS gene, is implicated in adipose tissue biology–this protein enhances adipose tissue development. Our hypothesis is that common variants in CTSS play a role in body weight regulation and in the development of obesity and that these effects are influenced by dietary factors–increased by high protein, glycemic index and energy diets. Methods Four tag SNPs (rs7511673, rs11576175, rs10888390 and rs1136774) were selected to capture all common variation in the CTSS region. Association between these four SNPs and several adiposity measurements (BMI, waist circumference, waist for given BMI and being a weight gainer–experiencing the greatest degree of unexplained annual weight gain during follow-up or not) given, where applicable, both as baseline values and gain during the study period (6–8 years) were tested in 11,091 European individuals (linear or logistic regression models). We also examined the interaction between the CTSS variants and dietary factors–energy density, protein content (in grams or in % of total energy intake) and glycemic index–on these four adiposity phenotypes. Results We found several associations between CTSS polymorphisms and anthropometric traits including baseline BMI (rs11576175 (SNP N°2), p = 0.02, β = −0.2446), and waist change over time (rs7511673 (SNP N°1), p = 0.01, β = −0.0433 and rs10888390 (SNP N°3), p = 0.04, β = −0.0342). In interaction with the percentage of proteins contained in the diet, rs11576175 (SNP N°2) was also associated with the risk of being a weight gainer (pinteraction = 0.01, OR = 1.0526)–the risk of being a weight gainer increased with the percentage of proteins contained in the diet. Conclusion CTSS variants seem to be nominally associated to obesity related traits and this association may be modified by dietary protein intake.
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Affiliation(s)
- Henri Hooton
- Institut national de la santé et de la recherché médicale (INSERM), U872, Nutriomique, Paris, France.
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Li A, Meyre D. Challenges in reproducibility of genetic association studies: lessons learned from the obesity field. Int J Obes (Lond) 2012; 37:559-67. [DOI: 10.1038/ijo.2012.82] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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Zhao Y, Yu H, Zhu Y, Ter-Minassian M, Peng Z, Shen H, Diao N, Chen F. Genetic association analysis using sibship data: a multilevel model approach. PLoS One 2012; 7:e31134. [PMID: 22312441 PMCID: PMC3270036 DOI: 10.1371/journal.pone.0031134] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2011] [Accepted: 01/03/2012] [Indexed: 11/29/2022] Open
Abstract
Family based association study (FBAS) has the advantages of controlling for population stratification and testing for linkage and association simultaneously. We propose a retrospective multilevel model (rMLM) approach to analyze sibship data by using genotypic information as the dependent variable. Simulated data sets were generated using the simulation of linkage and association (SIMLA) program. We compared rMLM to sib transmission/disequilibrium test (S-TDT), sibling disequilibrium test (SDT), conditional logistic regression (CLR) and generalized estimation equations (GEE) on the measures of power, type I error, estimation bias and standard error. The results indicated that rMLM was a valid test of association in the presence of linkage using sibship data. The advantages of rMLM became more evident when the data contained concordant sibships. Compared to GEE, rMLM had less underestimated odds ratio (OR). Our results support the application of rMLM to detect gene-disease associations using sibship data. However, the risk of increasing type I error rate should be cautioned when there is association without linkage between the disease locus and the genotyped marker.
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Affiliation(s)
- Yang Zhao
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
- Environmental and Occupational Medicine and Epidemiology Program, Department of Environmental Health, Harvard School of Public Health, Harvard University, Boston, Massachusetts, United States of America
| | - Hao Yu
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Ying Zhu
- Imperial College Business School, Imperial College London, London, United Kingdom
| | - Monica Ter-Minassian
- Environmental and Occupational Medicine and Epidemiology Program, Department of Environmental Health, Harvard School of Public Health, Harvard University, Boston, Massachusetts, United States of America
| | - Zhihang Peng
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Hongbing Shen
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Nancy Diao
- Environmental and Occupational Medicine and Epidemiology Program, Department of Environmental Health, Harvard School of Public Health, Harvard University, Boston, Massachusetts, United States of America
| | - Feng Chen
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
- * E-mail:
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Xiong Q, Ancona N, Hauser ER, Mukherjee S, Furey TS. Integrating genetic and gene expression evidence into genome-wide association analysis of gene sets. Genome Res 2012; 22:386-97. [PMID: 21940837 PMCID: PMC3266045 DOI: 10.1101/gr.124370.111] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2011] [Accepted: 09/19/2011] [Indexed: 12/11/2022]
Abstract
Single variant or single gene analyses generally account for only a small proportion of the phenotypic variation in complex traits. Alternatively, gene set or pathway association analyses are playing an increasingly important role in uncovering genetic architectures of complex traits through the identification of systematic genetic interactions. Two dominant paradigms for gene set analyses are association analyses based on SNP genotypes and those based on gene expression profiles. However, gene-disease association can manifest in many ways, such as alterations of gene expression, genotype, and copy number; thus, an integrative approach combining multiple forms of evidence can more accurately and comprehensively capture pathway associations. We have developed a single statistical framework, Gene Set Association Analysis (GSAA), that simultaneously measures genome-wide patterns of genetic variation and gene expression variation to identify sets of genes enriched for differential expression and/or trait-associated genetic markers. Simulation studies illustrate that joint analyses of genomic data increase the power to detect real associations when compared with gene set methods that use only one genomic data type. The analysis of two human diseases, glioblastoma and Crohn's disease, detected abnormalities in previously identified disease-associated pathways, such as pathways related to PI3K signaling, DNA damage response, and the activation of NFKB. In addition, GSAA predicted novel pathway associations, for example, differential genetic and expression characteristics in genes from the ABC transporter family in glioblastoma and from the HLA system in Crohn's disease. These demonstrate that GSAA can help uncover biological pathways underlying human diseases and complex traits.
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Affiliation(s)
- Qing Xiong
- Department of Genetics, Department of Biology, Lineberger Comprehensive Cancer Center, and Carolina Center for Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Nicola Ancona
- Institute of Intelligent Systems for Automation National Research Council, Bari IT 70126, Italy
| | - Elizabeth R. Hauser
- Center for Human Genetics and Section of Medical Genetics, Department of Medicine, Duke University, Durham, North Carolina 27710, USA
| | - Sayan Mukherjee
- Departments of Statistical Science, Computer Science, and Mathematics, Institute for Genome Sciences & Policy, Duke University, Durham, North Carolina 27708, USA
| | - Terrence S. Furey
- Department of Genetics, Department of Biology, Lineberger Comprehensive Cancer Center, and Carolina Center for Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
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Yu Z, Han S, Cao X, Zhu C, Wang X, Guo X. Genetic polymorphisms in adipokine genes and the risk of obesity: a systematic review and meta-analysis. Obesity (Silver Spring) 2012; 20:396-406. [PMID: 21660081 DOI: 10.1038/oby.2011.148] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Polymorphisms in adipokine genes, such as leptin (LEP), leptin receptor (LEPR), resistin (RETN), adiponectin (ADIPOQ), interleukin-1β (IL-1β), IL-6 (IL-6), and tumor necrosis factor-α (TNF-α) may be involved in the development of obesity. We conducted a systematic review of published evidence on the association between different adipokine genes and the risk of obesity. Librarian-designed searches of PubMed and HuGeNet, review of reference lists from published reviews and content expert advice identified potentially eligible studies. The genotyping information and polymorphisms of different adipokine genes, numbers of genotyped cases and controls and frequencies of genotypes were extracted from 48 eligible studies included in this review. Twenty-one polymorphisms each associated with obesity in at least one study were identified. Polymorphisms in the adipokine genes, LEP, LEPR, and RETN were not associated with obesity susceptibility, whereas ADIPOQ G276T (T vs. G: odds ratio (OR), 1.59; 95% confidence interval (CI), 1.39-1.81), IL-1β C3953T (CC vs. CT+TT: OR, 1.61; 95% CI, 1.18-2.20), and TNF-α G308A (GG vs. GA+AA: OR, 1.19; 95% CI, 1.02-1.39) polymorphisms were associated with an increased risk of obesity. The IL-6 G174C polymorphism was also associated obesity when using allelic comparisons, the recessive genetic model and the dominant genetic model with OR (95% CI) of 1.95 (1.37-2.77), 1.44 (1.15-1.80), and 1.36 (1.16-1.59), respectively. No significant evidence of publication bias was present. However, these "null" results were underpowered due to a small pooled sample size, and analysis of additional case-control studies with larger sample sizes should provide further clarifications.
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Affiliation(s)
- Zhangbin Yu
- Department of Pediatrics, Nanjing Maternal and Child Health Hospital, Nanjing Medical University, Nanjing, PR China
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Paladini F, Adinolfi V, Cocco E, Ciociola E, Tamburrano G, Cascino I, Lucantoni F, Morano S, Sorrentino R. Gender-dependent association of type 2 diabetes with the vasoactive intestinal peptide receptor 1. Gene 2011; 493:278-81. [PMID: 22166542 DOI: 10.1016/j.gene.2011.11.055] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2011] [Revised: 11/21/2011] [Accepted: 11/22/2011] [Indexed: 12/14/2022]
Abstract
Type 2 diabetes is characterized by an inadequate pancreatic beta-cell response to the progressive insulin resistance. Its pathogenesis is complex and has been connected with a state of preclinical chronic inflammation. Vasoactive intestinal peptide (VIP) and its receptors play a relevant role in the homeostasis of insulin secretion as well as in the control of inflammation. In particular, VIP receptor 1 (VPAC1) has been found to be down-modulated during inflammation, and to be associated with several diseases. The objective of this study was to compare the distribution of SNPs mapping in the VIP receptor 1 gene in cases with type 2 diabetes and matched controls. Seven hundred cases with type 2 diabetes (423 males and 277 females) and 830 random controls (419 males and 411 females) were analyzed for the distribution of three common SNPs mapping in the VPAC1 gene. The results show a significantly different genotype distribution of the SNP rs9677 in the 3'-UTR of VPAC1 in female cases with type 2 diabetes compared to gender-matched controls (ptrend=6×10(-4)). The rs9677 CC genotype confers the highest risk (OR: 2.1) and correlates with worse clinical parameters such as higher level of total cholesterol, higher LDL/HDL ratio and a higher HbA1c concentration. The genetic association reported here indicates that VIP/VPAC1 signaling can be a relevant pathway in the pathogenesis of type 2 diabetes in females suggesting that at least some aspects of the genetic predisposition to this disease can be gender-specific.
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Affiliation(s)
- Fabiana Paladini
- Department of Biology and Biotechnology Charles Darwin, Sapienza, University of Rome, Italy
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41
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Day FR, Loos RJF. Developments in obesity genetics in the era of genome-wide association studies. JOURNAL OF NUTRIGENETICS AND NUTRIGENOMICS 2011; 4:222-38. [PMID: 22056736 DOI: 10.1159/000332158] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Obesity is an important factor contributing to the global burden of morbidity and mortality. By identifying obesity susceptibility genes, scientists aim to elucidate some of its aetiology. Early studies used candidate gene and genome-wide linkage approaches to search for such genes with limited success. However, the advent of genome-wide association studies (GWAS) has dramatically increased the pace of gene discovery. So far, GWAS have identified at least 50 loci robustly associated with body mass index (BMI), waist-to-hip ratio, body fat percentage and extreme obesity. Some of these have been shown to replicate in non-white populations and in children and adolescents. Furthermore, for some loci interaction studies have shown that the BMI-increasing effect is attenuated in physically active individuals. Despite many successful discoveries, the effect sizes of the established loci are small, and combined they explain only a fraction of the inter-individual variation in BMI. The low predictive value means that their value in mainstream health care is limited. However, as most of these newly established loci were not previously linked to obesity, they may provide new insights into body weight regulation. Continued efforts in gene discovery, using a range of approaches, will be needed to increase our understanding of obesity.
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Affiliation(s)
- Felix R Day
- MRC Epidemiology Unit, Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, UK
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Jensen MK, Pers TH, Dworzynski P, Girman CJ, Brunak S, Rimm EB. Protein interaction-based genome-wide analysis of incident coronary heart disease. CIRCULATION. CARDIOVASCULAR GENETICS 2011; 4:549-56. [PMID: 21880673 PMCID: PMC3197770 DOI: 10.1161/circgenetics.111.960393] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
BACKGROUND Network-based approaches may leverage genome-wide association (GWA) analysis by testing for the aggregate association across several pathway members. We aimed to examine if networks of genes that represent experimentally determined protein-protein interactions (PPIs) are enriched in genes associated with risk of coronary heart disease (CHD). METHODS AND RESULTS Genome-wide association analyses of approximately ≈700,000 single-nucleotide polymorphisms in 899 incident CHD cases and 1823 age- and sex-matched controls within the Nurses' Health and the Health Professionals Follow-up Studies were used to assign genewise P values. A large database of PPIs was used to assemble 8351 unbiased protein complexes and corresponding gene sets. Superimposed genewise P values were used to rank gene sets based on their enrichment in genes associated with CHD. After correcting for the number of complexes tested, 1 gene set was overrepresented in CHD-associated genes (P=0.002). Centered on the β1-adrenergic receptor gene (ADRB1), this complex included 18 protein interaction partners that have not been identified as candidate loci for CHD. Of the 19 genes in the top complex, 5 are involved in abnormal cardiovascular system physiological features based on knockout mice (4-fold enrichment; Fisher exact test, P=0.006). Ingenuity pathway analysis revealed that canonical pathways, especially related to blood pressure regulation, were significantly enriched in the genes from the top complex. CONCLUSIONS The integration of a GWA study with PPI data successfully identifies a set of candidate susceptibility genes for incident CHD that would have been missed in single-marker GWA analysis.
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Affiliation(s)
- Majken K. Jensen
- Department of Nutrition, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
| | - Tune H. Pers
- Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark
- Institute of Preventive Medicine, Copenhagen University Hospital, Centre for Health and Society
| | - Piotr Dworzynski
- Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark
| | | | - Søren Brunak
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Eric B. Rimm
- Department of Nutrition, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
- Department of Epidemiology, Harvard School of Public Health; Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
- Channing Laboratory, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
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Zhang F, Guo X, Deng HW. Multilocus association testing of quantitative traits based on partial least-squares analysis. PLoS One 2011; 6:e16739. [PMID: 21304821 PMCID: PMC3033421 DOI: 10.1371/journal.pone.0016739] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2010] [Accepted: 01/05/2011] [Indexed: 01/28/2023] Open
Abstract
Because of combining the genetic information of multiple loci, multilocus association studies (MLAS) are expected to be more powerful than single locus association studies (SLAS) in disease genes mapping. However, some researchers found that MLAS had similar or reduced power relative to SLAS, which was partly attributed to the increased degrees of freedom (dfs) in MLAS. Based on partial least-squares (PLS) analysis, we develop a MLAS approach, while avoiding large dfs in MLAS. In this approach, genotypes are first decomposed into the PLS components that not only capture majority of the genetic information of multiple loci, but also are relevant for target traits. The extracted PLS components are then regressed on target traits to detect association under multilinear regression. Simulation study based on real data from the HapMap project were used to assess the performance of our PLS-based MLAS as well as other popular multilinear regression-based MLAS approaches under various scenarios, considering genetic effects and linkage disequilibrium structure of candidate genetic regions. Using PLS-based MLAS approach, we conducted a genome-wide MLAS of lean body mass, and compared it with our previous genome-wide SLAS of lean body mass. Simulations and real data analyses results support the improved power of our PLS-based MLAS in disease genes mapping relative to other three MLAS approaches investigated in this study. We aim to provide an effective and powerful MLAS approach, which may help to overcome the limitations of SLAS in disease genes mapping.
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Affiliation(s)
- Feng Zhang
- Key Laboratory of Environment and Gene Related Diseases of Ministry Education, Faculty of Public Health, College of Medicine, Xi'an Jiaotong University, Xi'an, Shaanxi, People's Republic of China
- * E-mail: (FZ); (HWD)
| | - Xiong Guo
- Key Laboratory of Environment and Gene Related Diseases of Ministry Education, Faculty of Public Health, College of Medicine, Xi'an Jiaotong University, Xi'an, Shaanxi, People's Republic of China
| | - Hong-Wen Deng
- Center of System Biomedical Sciences, Shanghai University of Science and Technology, Shanghai, People's Republic of China
- Departments of Orthopedic Surgery and Basic Medical Science, School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri, United States of America
- * E-mail: (FZ); (HWD)
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Ritchie MD. Using biological knowledge to uncover the mystery in the search for epistasis in genome-wide association studies. Ann Hum Genet 2011; 75:172-82. [PMID: 21158748 DOI: 10.1111/j.1469-1809.2010.00630.x] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The search for the missing heritability in genome-wide association studies (GWAS) has become an important focus for the human genetics community. One suspected location of these genetic effects is in gene-gene interactions, or epistasis. The computational burden of exploring gene-gene interactions in the wealth of data generated in GWAS, along with small to moderate sample sizes, have led to epistasis being an afterthought, rather than a primary focus of GWAS analyses. In this review, I discuss some potential approaches to filter a GWAS dataset to a smaller, more manageable dataset where searching for epistasis is considerably more feasible. I describe a number of alternative approaches, but primarily focus on the use of prior biological knowledge from databases in the public domain to guide the search for epistasis. The manner in which prior knowledge is incorporated into a GWA study can be many and these data can be extracted from a variety of database sources. I discuss a number of these approaches and propose that a comprehensive approach will likely be most fruitful for searching for epistasis in large-scale genomic studies of the current state-of-the-art and into the future.
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Affiliation(s)
- Marylyn D Ritchie
- Department of Molecular Physiology, Center for Human Genetics Research, Vanderbilt University, Nashville, TN 37232-0700, USA.
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Moody TW, Ito T, Osefo N, Jensen RT. VIP and PACAP: recent insights into their functions/roles in physiology and disease from molecular and genetic studies. Curr Opin Endocrinol Diabetes Obes 2011; 18:61-7. [PMID: 21157320 PMCID: PMC3075877 DOI: 10.1097/med.0b013e328342568a] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
PURPOSE OF REVIEW Vasoactive intestinal peptide (VIP) and pituitary adenylate cyclase-activating polypeptide (PACAP) as well as the three classes of G-protein-coupled receptors mediating their effects, are widely distributed in the central nervous system (CNS) and peripheral tissues. These peptides are reported to have many effects in different tissues, which are physiological or pharmacological, and which receptor mediates which effect, has been difficult to determine, primarily due to lack of potent, stable, selective agonists/antagonists. Recently the use of animals with targeted knockout of the peptide or a specific receptor has provided important insights into their role in normal physiology and disease states. RECENT FINDINGS During the review period, considerable progress and insights has occurred in the understanding of the role of VIP/PACAP as well as their receptors in a number of different disorders/areas. Particularly, insights into their roles in energy metabolism, glucose regulation, various gastrointestinal processes including gastrointestinal inflammatory conditions and motility and their role in the CNS as well as CNS diseases has greatly expanded. SUMMARY PACAP/VIP as well as their three classes of receptors are important in many physiological/pathophysiological processes, some of which are identified in these studies using knockout animals. These studies may lead to new novel treatment approaches. Particularly important are their roles in glucose metabolism and on islets leading to possible novel approaches in diabetes; their novel anti-inflammatory, cytoprotective effects, their CNS neuroprotective effects, and their possible roles in diseases such as schizophrenia and chronic depression.
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Affiliation(s)
- Terry W. Moody
- Department of Health and Human Services, National Cancer Institute Office of the Director, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Tetsuhide Ito
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Science, Kyushu University, Fukuoka, Japan
| | - Nuramy Osefo
- Department of Health and Human Services, National Cancer Institute Office of the Director, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Robert T. Jensen
- Digestive Diseases Branch, National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892
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Hooton H, Dubern B, Henegar C, Paternoster L, Nohr EA, Alili R, Rousseau F, Pelloux V, Galan P, Hercberg S, Arner P, Sørensen TIA, Clément K. Association between CST3 rs2424577 polymorphism and corpulence related phenotypes during lifetime in populations of European ancestry. Obes Facts 2011; 4:131-44. [PMID: 21577020 PMCID: PMC6444514 DOI: 10.1159/000327797] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
OBJECTIVE Cystatin C, a protein coded by CST3 gene, is implicated in adipose tissue biology. Our hypothesis is that common variants in CST3 gene could play a role in the development of corpulence during lifetime. METHODS Two tag SNPs were selected to capture all SNPs in the CST3 region. We first investigated the association of the two tag SNPs individually and combined into haplotypes with corpulence related phenotypes in 4,288 French subjects (BMI = 24.31 ( 3.74 kg/m²). Significant findings were replicated in five independent populations--790 Danish lean men (BMI = 24.63 ( 2.30 kg/m²), 672 Danish obese men (BMI = 33.23 ( 2.34 kg/m²), 763 Swedish women (BMI = 21.73 ( 2.87 kg/m²), 1,848 Danish lean women (BMI = 22.66 ( 2.85 kg/m²) and 2,061 Danish obese women (BMI = 37.01 ( 3.59 kg/m²). RESULTS Rs2424577 was associated with BMI in three independent populations--G/G carriers were less corpulent than A/A carriers in the French individuals (p = 0.045) and in the Danish lean men (p = 0.021), and they were more corpulent in the group of Swedish women (p = 0.004). This phenomenon has been described as a flip-flop phenomenon, probably caused by a multilocus effect. CONCLUSION CST3 rs2424577 is associated with BMI in a complex fashion. This association is probably caused by the interaction between several functional variants.
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Affiliation(s)
- Henri Hooton
- INSERM U872 Equipe 7, Centre de Recherche des Cordeliers 15 Rue de l’Ecole de Medecine, 75006 Paris, France.
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