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Carrasco-Luna J, Navarro-Solera M, Gombert M, Martín-Carbonell V, Carrasco-García Á, Del Castillo-Villaescusa C, García-Pérez MÁ, Codoñer-Franch P. Association of the rs17782313, rs17773430 and rs34114122 Polymorphisms of/near MC4R Gene with Obesity-Related Biomarkers in a Spanish Pediatric Cohort. CHILDREN (BASEL, SWITZERLAND) 2023; 10:1221. [PMID: 37508717 PMCID: PMC10378299 DOI: 10.3390/children10071221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 06/28/2023] [Accepted: 07/12/2023] [Indexed: 07/30/2023]
Abstract
Obesity is a multifactorial disease whose onset and development are shaped by the individual genetic background. The melanocortin 4 receptor gene (MC4R) is involved in the regulation of food intake and energy expenditure. Some of the single nucleotide polymorphisms (SNPs) of this gene are related to obesity and metabolic risk factors. The present study was undertaken to assess the relationship between three polymorphism SNPs, namely, rs17782313, rs17773430 and rs34114122, and obesity and metabolic risk factors. One hundred seventy-eight children with obesity aged between 7 and 16 years were studied to determine anthropometric variables and biochemical and inflammatory parameters. Our results highlight that metabolic risk factors, especially alterations in carbohydrate metabolism, were related to rs17782313. The presence of the minor C allele in the three variants (C-C-C) was significantly associated with anthropometric measures indicative of obesity, such as the body mass and fat mass indexes, and increased the values of insulinemia to 21.91 µIU/mL with respect to the wild type values. Our study suggests that the C-C-C haplotype of the SNPs rs17782313, rs17773430 and rs34114122 of the MC4R gene potentiates metabolic risk factors at early ages in children with obesity.
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Affiliation(s)
- Joaquín Carrasco-Luna
- Department of Pediatrics, Obstetrics and Gynecology, University of Valencia, 46010 Valencia, Spain
- Department for Biotechnology, Faculty of Experimental Science, Catholic University of Valencia, 46001 Valencia, Spain
| | - María Navarro-Solera
- Department of Pediatrics, Obstetrics and Gynecology, University of Valencia, 46010 Valencia, Spain
| | - Marie Gombert
- Biosciences Division, Center for Health Sciences, SRI International, Menlo Park, CA 94025, USA
| | - Vanessa Martín-Carbonell
- Department of Pediatrics, Obstetrics and Gynecology, University of Valencia, 46010 Valencia, Spain
| | - Álvaro Carrasco-García
- Department of Pediatrics, Obstetrics and Gynecology, University of Valencia, 46010 Valencia, Spain
| | - Cristina Del Castillo-Villaescusa
- Department of Pediatrics, University Hospital Doctor Peset, Foundation of Promotion of Health, Biomedical Research in the Valencian Region (FISABIO), 46020 Valencia, Spain
| | - Miguel Ángel García-Pérez
- Department of Genetics, Faculty of Biological Sciences, University of Valencia, INCLIVA, 46100 Valencia, Spain
| | - Pilar Codoñer-Franch
- Department of Pediatrics, Obstetrics and Gynecology, University of Valencia, 46010 Valencia, Spain
- Department of Pediatrics, University Hospital Doctor Peset, Foundation of Promotion of Health, Biomedical Research in the Valencian Region (FISABIO), 46020 Valencia, Spain
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Moazzam-Jazi M, Sadat Zahedi A, Akbarzadeh M, Azizi F, Daneshpour MS. Diverse effect of MC4R risk alleles on obesity-related traits over a lifetime: Evidence from a well-designed cohort study. Gene 2022; 807:145950. [PMID: 34481003 DOI: 10.1016/j.gene.2021.145950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 08/26/2021] [Accepted: 08/30/2021] [Indexed: 11/30/2022]
Abstract
This population-based longitudinal study is the first investigation that assesses the association of common MC4R SNPs with the obesity-related parameters over time and determines the effect of risk alleles during the three adulthood life periods (early, middle, and late) in a large Iranian cohort, a population with a unique genetic make-up that has been understudied and relatively unexplored. We obtained the genotype of 5370 unrelated adults who participated in the ongoing Tehran Cardiometabolic Genetic Study (TCGS) cohort project for the common MC4R SNPs. Linear regression and linear mixed model analyses were performed to examine the effect of MC4R polymorphisms on maximum BMI and other obesity-related factors over time. We recognized that several SNPs associated with the maximum BMI and the increased BMI, waist circumference, and waist-hip ratio across Iranian adults over a lifetime. Interestingly, we found that rs9954571-A has a yet unreported protective role against obesity-related factors, including BMI, waist circumference, waist-hip ratio, and triglyceride level. Additionally, a survey of the impact of the MC4R risk score throughout the adulthood life periods indicated that the MC4R risk score is influenced both the elevated BMI and waist circumference only during the early adulthood period. Our findings can expand our knowledge about the MC4R genetic variant's contributions to adulthood obesity and highlight the importance of evaluating the genetic components affecting obesity over a lifetime, which could be considered for obesity clinical screening and treatment.
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Affiliation(s)
- Maryam Moazzam-Jazi
- Cellular, and Molecular Endocrine Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Asiyeh Sadat Zahedi
- Cellular, and Molecular Endocrine Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mahdi Akbarzadeh
- Cellular, and Molecular Endocrine Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Fereidoun Azizi
- Cellular, and Molecular Endocrine Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Maryam S Daneshpour
- Cellular, and Molecular Endocrine Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Asadi M, Amoli M, Ansari Y, Far I, Pashaie N, Noroozi N. Association study of Melanocortin-4 Receptor (rs17782313) and PKHD1 (rs2784243) variations and early incidence of obesity at the age of maturity. ADVANCES IN HUMAN BIOLOGY 2022. [DOI: 10.4103/aihb.aihb_160_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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Adamska-Patruno E, Bauer W, Bielska D, Fiedorczuk J, Moroz M, Krasowska U, Czajkowski P, Wielogorska M, Maliszewska K, Puckowska S, Szczerbinski L, Lipinska D, Gorska M, Kretowski A. An Association between Diet and MC4R Genetic Polymorphism, in Relation to Obesity and Metabolic Parameters-A Cross Sectional Population-Based Study. Int J Mol Sci 2021; 22:ijms222112044. [PMID: 34769477 PMCID: PMC8584592 DOI: 10.3390/ijms222112044] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 10/27/2021] [Accepted: 11/05/2021] [Indexed: 11/30/2022] Open
Abstract
The melanocortin-4 receptor (MC4R) gene harbours one of the strongest susceptibility loci for obesity and obesity-related metabolic consequences. We analysed whether dietary factors may attenuate the associations between MC4R genotypes and obesity and metabolic parameters. In 819 participants genotyped for common MC4R polymorphisms (rs17782313, rs12970134, rs633265, and rs135034), the anthropometric measurements, body fat content and distribution (visceral and subcutaneous adipose tissue, VAT and SAT, respectively), and blood glucose, insulin, total-, LDL-, HDL-cholesterol, triglycerides concentrations, and daily macronutrient intake were assessed. ANOVA or Kruskal–Wallis tests were used, and multivariate linear regression models were developed. We observed that the CC genotype carriers (rs17782313) presented higher VAT, VAT/SAT ratio, fasting blood glucose and triglyceride concentrations when they were stratified to the upper quantiles of protein intake. An increase in energy derived from proteins was associated with higher BMI (Est. 5.74, R2 = 0.12), body fat content (Est. 8.44, R2 = 0.82), VAT (Est. 32.59, R2 = 0.06), and VAT/SAT ratio (Est. 0.96, R2 = 0.05). The AA genotype carriers (rs12970134) presented higher BMI, body fat, SAT and VAT, fasting blood glucose, triglycerides and total cholesterol concentrations. An increase in energy derived from proteins by AA carriers was associated with higher VAT (Est.19.95, R2 = 0.06) and VAT/SAT ratio (Est. 0.64, R2 = 0.05). Our findings suggest that associations of the common MC4R SNPs with obesity and its metabolic complications may be dependent on the daily dietary intake, which may open new areas for developing personalised diets for preventing and treating obesity and obesity-related comorbidities.
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Affiliation(s)
- Edyta Adamska-Patruno
- Clinical Research Centre, Medical University of Bialystok, Marii Sklodowskiej-Curie 24A, 15-276 Bialystok, Poland; (W.B.); (U.K.); (P.C.); (S.P.); (L.S.); (A.K.)
- Correspondence:
| | - Witold Bauer
- Clinical Research Centre, Medical University of Bialystok, Marii Sklodowskiej-Curie 24A, 15-276 Bialystok, Poland; (W.B.); (U.K.); (P.C.); (S.P.); (L.S.); (A.K.)
| | - Dorota Bielska
- Department of Family Medicine, Medical University of Bialystok, Mieszka I 4b, 15-054 Bialystok, Poland;
| | - Joanna Fiedorczuk
- Clinical Research Centre, Medical University of Bialystok Clinical Hospital, Marii Sklodowskiej-Curie 24A, 15-276 Bialystok, Poland; (J.F.); (M.M.)
| | - Monika Moroz
- Clinical Research Centre, Medical University of Bialystok Clinical Hospital, Marii Sklodowskiej-Curie 24A, 15-276 Bialystok, Poland; (J.F.); (M.M.)
| | - Urszula Krasowska
- Clinical Research Centre, Medical University of Bialystok, Marii Sklodowskiej-Curie 24A, 15-276 Bialystok, Poland; (W.B.); (U.K.); (P.C.); (S.P.); (L.S.); (A.K.)
| | - Przemyslaw Czajkowski
- Clinical Research Centre, Medical University of Bialystok, Marii Sklodowskiej-Curie 24A, 15-276 Bialystok, Poland; (W.B.); (U.K.); (P.C.); (S.P.); (L.S.); (A.K.)
| | - Marta Wielogorska
- Department of Endocrinology, Diabetology and Internal Medicine, Medical University of Bialystok, Marii Sklodowskiej-Curie 24A, 15-276 Bialystok, Poland; (M.W.); (K.M.); (D.L.); (M.G.)
| | - Katarzyna Maliszewska
- Department of Endocrinology, Diabetology and Internal Medicine, Medical University of Bialystok, Marii Sklodowskiej-Curie 24A, 15-276 Bialystok, Poland; (M.W.); (K.M.); (D.L.); (M.G.)
| | - Sylwia Puckowska
- Clinical Research Centre, Medical University of Bialystok, Marii Sklodowskiej-Curie 24A, 15-276 Bialystok, Poland; (W.B.); (U.K.); (P.C.); (S.P.); (L.S.); (A.K.)
| | - Lukasz Szczerbinski
- Clinical Research Centre, Medical University of Bialystok, Marii Sklodowskiej-Curie 24A, 15-276 Bialystok, Poland; (W.B.); (U.K.); (P.C.); (S.P.); (L.S.); (A.K.)
| | - Danuta Lipinska
- Department of Endocrinology, Diabetology and Internal Medicine, Medical University of Bialystok, Marii Sklodowskiej-Curie 24A, 15-276 Bialystok, Poland; (M.W.); (K.M.); (D.L.); (M.G.)
| | - Maria Gorska
- Department of Endocrinology, Diabetology and Internal Medicine, Medical University of Bialystok, Marii Sklodowskiej-Curie 24A, 15-276 Bialystok, Poland; (M.W.); (K.M.); (D.L.); (M.G.)
| | - Adam Kretowski
- Clinical Research Centre, Medical University of Bialystok, Marii Sklodowskiej-Curie 24A, 15-276 Bialystok, Poland; (W.B.); (U.K.); (P.C.); (S.P.); (L.S.); (A.K.)
- Clinical Research Centre, Medical University of Bialystok Clinical Hospital, Marii Sklodowskiej-Curie 24A, 15-276 Bialystok, Poland; (J.F.); (M.M.)
- Department of Endocrinology, Diabetology and Internal Medicine, Medical University of Bialystok, Marii Sklodowskiej-Curie 24A, 15-276 Bialystok, Poland; (M.W.); (K.M.); (D.L.); (M.G.)
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Warner ET, Jiang L, Adjei DN, Turman C, Gordon W, Wang L, Tamimi R, Kraft P, Lindström S. A Genome-Wide Association Study of Childhood Body Fatness. Obesity (Silver Spring) 2021; 29:446-453. [PMID: 33491310 PMCID: PMC7842657 DOI: 10.1002/oby.23070] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 10/18/2020] [Accepted: 10/20/2020] [Indexed: 11/05/2022]
Abstract
OBJECTIVE This study aimed to uncover genetic contributors to adiposity in early life. METHODS A genome-wide association study of childhood body fatness in 34,401 individuals within the Nurses' Health Studies and the Health Professionals Follow-up Study was conducted. Data were imputed to the 1000 Genomes Phase 3 version 5 reference panel. RESULTS A total of 1,354 single-nucleotide polymorphisms (P < 10-4 ) were selected for replication in a previously published genome-wide association study of childhood BMI. Nineteen significant genome-wide (P < 5 × 10-8 ) regions were observed, fourteen of which were previously associated with childhood obesity and five were novel: BNDF (P = 7.58 × 10-13 ), PRKD1 (P = 1.43 × 10-10 ), 20p13 (P = 2.05 × 10-10 ), FHIT (P = 1.77 × 10-8 ), and LOC101927575 (P = 3.22 × 10-8 ). The BNDF, FHIT, and PRKD1 regions were previously associated with adult BMI. LOC101927575 and 20p13 regions have not previously been associated with adiposity phenotypes. In a transcriptome-wide analysis, associations for POMC at 2p23.3 (P = 3.36 × 10-6 ) and with TMEM18 at 2p25.3 (P = 3.53 × 10-7 ) were observed. Childhood body fatness was genetically correlated with hip (rg = 0.42, P = 4.44 × 10-16 ) and waist circumference (rg = 0.39, P = 5.56 × 10-16 ), as well as age at menarche (rg = -0.37, P = 7.96 × 10-19 ). CONCLUSIONS Additional loci that contribute to childhood adiposity were identified, further explicating its genetic architecture.
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Affiliation(s)
- Erica T. Warner
- Clinical Translational Epidemiology Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Lai Jiang
- Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, MA
| | - David Nana Adjei
- Department of Biostatistics, Harvard TH Chan School of Public Health, Boston, MA
| | - Constance Turman
- Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, MA
| | - William Gordon
- Department of Epidemiology, University of Washington, Seattle, WA
| | - Lu Wang
- Department of Environmental & Occupational Health Sciences, University of Washington, Seattle, WA
| | - Rulla Tamimi
- Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, MA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
| | - Peter Kraft
- Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, MA
- Department of Biostatistics, Harvard TH Chan School of Public Health, Boston, MA
| | - Sara Lindström
- Department of Epidemiology, University of Washington, Seattle, WA
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA
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Identification of Candidate Genes and Pathways Associated with Obesity-Related Traits in Canines via Gene-Set Enrichment and Pathway-Based GWAS Analysis. Animals (Basel) 2020; 10:ani10112071. [PMID: 33182249 PMCID: PMC7695335 DOI: 10.3390/ani10112071] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 11/06/2020] [Accepted: 11/06/2020] [Indexed: 02/06/2023] Open
Abstract
The present study aimed to identify causative loci and genes enriched in pathways associated with canine obesity using a genome-wide association study (GWAS). The GWAS was first performed to identify candidate single-nucleotide polymorphisms (SNPs) associated with obesity and obesity-related traits including body weight and blood sugar in 18 different breeds of 153 dogs. A total of 10 and 2 SNPs were found to be significantly (p < 3.74 × 10-7) associated with body weight and blood sugar, respectively. None of the SNPs were identified to be significantly associated with obesity trait. We subsequently followed up the GWAS analysis with gene-set enrichment and pathway analyses. A gene-set with 1057, 1409, and 1243 SNPs annotated to 449, 933 and 820 genes for obesity, body weight, and blood sugar, respectively was created by sub-setting the GWAS result at a threshold of p < 0.01 for the gene-set enrichment analysis. In total, 84 GO and 21 KEGG pathways for obesity, 114 GO and 44 KEGG pathways for blood sugar, 120 GO and 24 KEGG pathways for body weight were found to be enriched. Among the pathways and GO terms, we highlighted five enriched pathways (Wnt signaling pathway, adherens junction, pathways in cancer, axon guidance, and insulin secretion) and seven GO terms (fat cell differentiation, calcium ion binding, cytoplasm, nucleus, phospholipid transport, central nervous system development, and cell surface) that were found to be shared among all the traits. Our data provide insights into the genes and pathways associated with obesity and obesity-related traits.
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Bakhashab S, Filimban N, Altall RM, Nassir R, Qusti SY, Alqahtani MH, Abuzenadah AM, Dallol A. The Effect Sizes of PPARγ rs1801282 , FTO rs9939609, and MC4R rs2229616 Variants on Type 2 Diabetes Mellitus Risk among the Western Saudi Population: A Cross-Sectional Prospective Study. Genes (Basel) 2020; 11:genes11010098. [PMID: 31947684 PMCID: PMC7017045 DOI: 10.3390/genes11010098] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 01/05/2020] [Accepted: 01/09/2020] [Indexed: 12/20/2022] Open
Abstract
Type 2 diabetes mellitus (T2DM) is a common polygenic disease with associated comorbidities. Obesity is a major risk factor for the development of T2DM. The aim of this study is to determine the allele and genotype frequency of peroxisome proliferator-activated receptor-γ (PPARγ) rs1801282, fat mass and obesity-associated protein (FTO) rs9939609, and melanocortin 4 receptor (MC4R) rs2229616 polymorphisms and their association with risk of T2DM in the western Saudi population as mediators of adiposity phenotypes. In a cross-sectional prospective study, genomic DNA from control and T2DM patients were isolated and genotyped for these single-nucleotide polymorphisms. There was a significant association of the MC4R rs2229616 variant with T2DM, but no association with T2DM was detected with PPARγ rs1801282 or FTO rs9939609. The combination of C/C for PPARγ rs1801282, A/A for FTO rs9939609, and C/C for MC4R rs2229616 increased the risk of T2DM by 1.82. The A/T genotype for FTO rs9939609 was predicted to decrease the risk of T2DM when combined with C/C for PPARγ rs1801282 and C/C for MC4R rs2229616 or C/C for PPARγ rs1801282 and C/T MC4R rs2229616. In conclusion, our study showed the risk of the assessed variants for the development of T2DM in the Saudi population.
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Affiliation(s)
- Sherin Bakhashab
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, P.O Box 80218, Jeddah 21589, Saudi Arabia; (N.F.); (R.M.A.); (S.Y.Q.)
- Center of Innovation in Personalized Medicine, King Abdulaziz University, P.O Box 80216, Jeddah 21589, Saudi Arabia; (A.M.A.); (A.D.)
- Correspondence: ; Tel.: +966126400000
| | - Najlaa Filimban
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, P.O Box 80218, Jeddah 21589, Saudi Arabia; (N.F.); (R.M.A.); (S.Y.Q.)
- King Faisal Specialist Hospital and Research Center, Clinical Genomics, Department of Genetics, P.O. Box 3354, Riyadh 11211, Saudi Arabia
| | - Rana M. Altall
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, P.O Box 80218, Jeddah 21589, Saudi Arabia; (N.F.); (R.M.A.); (S.Y.Q.)
| | - Rami Nassir
- Department of Pathology, Faculty of Medicine, Umm Al-Qura University, P.O. Box 715, Makkah 21955, Saudi Arabia;
| | - Safaa Y. Qusti
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, P.O Box 80218, Jeddah 21589, Saudi Arabia; (N.F.); (R.M.A.); (S.Y.Q.)
| | - Mohammed H. Alqahtani
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, P.O Box 80216, Jeddah 21589, Saudi Arabia;
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, P.O Box 80216, Jeddah 21589, Saudi Arabia
| | - Adel M. Abuzenadah
- Center of Innovation in Personalized Medicine, King Abdulaziz University, P.O Box 80216, Jeddah 21589, Saudi Arabia; (A.M.A.); (A.D.)
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, P.O Box 80216, Jeddah 21589, Saudi Arabia;
| | - Ashraf Dallol
- Center of Innovation in Personalized Medicine, King Abdulaziz University, P.O Box 80216, Jeddah 21589, Saudi Arabia; (A.M.A.); (A.D.)
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, P.O Box 80216, Jeddah 21589, Saudi Arabia;
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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: 955] [Impact Index Per Article: 191.0] [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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Batarfi AA, Filimban N, Bajouh OS, Dallol A, Chaudhary AG, Bakhashab S. MC4R variants rs12970134 and rs17782313 are associated with obese polycystic ovary syndrome patients in the Western region of Saudi Arabia. BMC MEDICAL GENETICS 2019; 20:144. [PMID: 31429705 PMCID: PMC6701028 DOI: 10.1186/s12881-019-0876-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 08/12/2019] [Indexed: 12/24/2022]
Abstract
BACKGROUND Polycystic ovary syndrome (PCOS) is a common endocrine disorder causing infertility in reproductive-age women. The cause of PCOS is not fully understood but it is thought to be influenced by environmental and genetic factors. Obesity is greatly related to PCOS and its reduction is one of the major aims in treating PCOS. Melanocortin 4 receptor (MC4R) gene polymorphisms were detected to be associated with different levels of obesity. Therefore, we aimed to determine the genotype and allele frequency of MC4R variants rs12970134 (A/G) and rs17782313 (C/T) in PCOS and investigate their association with PCOS and its clinical variables. METHODS A case-control study was conducted on 189 women, consisting of 95 PCOS cases and 94 controls. Genotyping was performed by real-time polymerase chain reaction (PCR) using TaqMan™ Genotyping assays. Quantitative data were presented as (median ± interquartile range (IQR) whereas qualitative data were presented as frequencies. The chi-squared test was used to observe the difference between SNPs within the study groups (PCOS and control subjects). Multinomial logistic regression was used to test the risk of obesity and development of PCOS considering p < 0.05 is statistically significant. RESULTS Rs12970134 and rs17782313 are significantly associated with body mass index (BMI, kg/m2, p < 0.0001) in PCOS women but not associated with PCOS itself. Risk alleles in our population are A in rs12970134 and C in rs17782313 that are associated with high BMI (> 30 kg/m2) in obese women with PCOS (OR = 1.348, p = 0.002 and OR = 1.364, p = 0.002 respectively) in the homozygous state. In addition, we found that the other genotypes for non-obese PCOS group, AG/GG for rs12970134 and CT/TT for rs17782313, are associated with hirsutism, loss of hair, hyperandrogenism and anti-Müllerian hormone in PCOS. CONCLUSIONS These findings demonstrate that MC4R single nucleotide polymorphisms, rs12970134 and rs17782313, are correlated with elevated BMI in PCOS but are not causative factors for PCOS among women in the western region of Saudi Arabia. Moreover, the reverse genotypes are associated with major clinical variants in non-obese (< 30 kg/m2) PCOS patients may demonstrate a poor prognosis for this group.
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Affiliation(s)
- Asma A Batarfi
- Biochemistry Department, King Abdulaziz University, P.O. Box 80218, Abdullah Sulayman St., Jeddah, 21589, Saudi Arabia
| | - Najlaa Filimban
- Centre of Innovation in Personalized Medicine, King Abdulaziz University, P.O. Box 80216, Jeddah, Saudi Arabia
| | - Osama S Bajouh
- Centre of Innovation in Personalized Medicine, King Abdulaziz University, P.O. Box 80216, Jeddah, Saudi Arabia.,Department of Obstetrics and Gynaecology, Faculty of Medicine, King Abdulaziz University, P.O. Box 80205, Jeddah, Saudi Arabia
| | - Ashraf Dallol
- Centre of Innovation in Personalized Medicine, King Abdulaziz University, P.O. Box 80216, Jeddah, Saudi Arabia
| | - Adeel G Chaudhary
- Centre of Innovation in Personalized Medicine, King Abdulaziz University, P.O. Box 80216, Jeddah, Saudi Arabia
| | - Sherin Bakhashab
- Biochemistry Department, King Abdulaziz University, P.O. Box 80218, Abdullah Sulayman St., Jeddah, 21589, Saudi Arabia. .,Centre of Innovation in Personalized Medicine, King Abdulaziz University, P.O. Box 80216, Jeddah, Saudi Arabia.
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10
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Epigenome-wide methylation differences in a group of lean and obese women - A HUNT Study. Sci Rep 2018; 8:16330. [PMID: 30397228 PMCID: PMC6218540 DOI: 10.1038/s41598-018-34003-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 10/07/2018] [Indexed: 01/04/2023] Open
Abstract
Knowledge of epigenetically regulated biomarkers linked to obesity development is still scarce. Improving molecular understanding of the involved factors and pathways would improve obesity phenotype characterization and reveal potentially relevant targets for obesity intervention. The Illumina Infinium HumanMethylation450 BeadChip was used in a leucocyte epigenome-wide association study (EWAS) to quantify differential DNA methylation in 60 lean compared with 60 obese young women. Replication was done in monozygotic twins discordant for obesity. At adolescence and adulthood, the two weight groups differed significantly in obesity-related traits and metabolic risk factors. Differential hypomethylation was overrepresented in obese compared to lean women. In the adjusted model, the EWAS revealed 10 differentially methylated CpG sites linked to 8 gene loci – COX6A1P2/FGD2, SBNO2, TEX41, RPS6KA2, IGHE/IGHG1/IGHD, DMAP1, SOCS3, and SETBP1– and an enhancer locus at chromosome 2 (2p25.1). The sites linked to TEX41, IGHE/IGHG1/IGHD, DMAP1, and SETBP1 were novel findings, while COX6A1P/FGD2, SBNO2, RPS6KA2, and SOCS3 had been identified previously with concordant direction of effects. RPS6KA2, DMAP1, and SETBP1 were replicated in the BMI-discordant monozygotic twin cohort using the FDR of 5%.
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11
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Mǎrginean CO, Mǎrginean C, Meliţ LE. New Insights Regarding Genetic Aspects of Childhood Obesity: A Minireview. Front Pediatr 2018; 6:271. [PMID: 30338250 PMCID: PMC6180186 DOI: 10.3389/fped.2018.00271] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 09/10/2018] [Indexed: 01/26/2023] Open
Abstract
Introduction: Childhood obesity is occurring at alarming rates in both developed and developing countries. "Obesogenic" environmental factors must be associated with variants of different risk alleles to determine polygenic or common obesity, and their impact depends on different developmental stages.The interaction between obesogenic environment and genetic susceptibility results in the so-called polygenic forms of obesity. In contrast, monogenic and syndromic obesity are not influenced by environmental events. Therefore, this review aimed to underline the roles of some of the most studied genes in the development of monogenic and polygenic obesity in children. Results: Among the most common obesity related genes, we chose the fat mass and obesity-associated (FTO) gene, leptin gene and its receptor, tumor necrosis factor alpha (TNF-α), the melanocortin 4 receptor gene (MC4R), Ectoenzyme nucleotide pyrophosphate phosphodiesterase 1 (ENPP1), and others, such as peroxisome proliferator-activated receptor gamma (PPARG), angiotensin-converting enzyme (ACE), glutathione S-transferase (GST), and interleukin-6 (IL-6) genes. The roles of these genes are complex and interdependent, being linked to different cornerstones in obesity development, such as appetite behavior, control of food intake and energy balance, insulin signaling, lipid and glucose metabolism, metabolic disorders, adipocyte differentiation, and so on. Conclusions: Genetic predisposition is mandatory, but not enough to trigger obesity.Dietary interventions and proper lifestyle changes can prevent obesity development in genetically predisposed children. Further studies are needed to identify the precise role of both genetic and obesogenic factors in the development of childhood obesity in order to design effective preventive methods.
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Affiliation(s)
- Cristina Oana Mǎrginean
- Department of Pediatrics, University of Medicine and Pharmacy Târgu Mureş, Târgu Mureş, Romania
| | - Claudiu Mǎrginean
- Department of Obstetrics and Gynecology, University of Medicine and Pharmacy Târgu Mureş, Târgu Mureş, Romania
| | - Lorena Elena Meliţ
- Department of Pediatrics, University of Medicine and Pharmacy Târgu Mureş, Târgu Mureş, Romania
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12
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Leońska-Duniec A, Jastrzębski Z, Zarębska A, Smółka W, Cięszczyk P. Impact of the Polymorphism Near MC4R (rs17782313) on Obesity- and Metabolic-Related Traits in Women Participating in an Aerobic Training Program. J Hum Kinet 2017; 58:111-119. [PMID: 28828082 PMCID: PMC5548159 DOI: 10.1515/hukin-2017-0073] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The C/T polymorphism (rs17782313) mapped 188 kb downstream of the melanocortin-4 receptor gene (MC4R) shows a strong relationship with an increased body mass index (BMI) and the risk of type 2 diabetes. However, the information on polymorphism’s potential modifying effect on obesity- and metabolic-related traits achieved through training is still unknown. Therefore, we decided to check if selected body measurements observed in physically active participants would be modulated by the genotype. The genotype distribution was examined in a group of 201 Polish women measured for chosen traits before and after the completion of a 12 week moderate-intensive aerobic training program. A statistically significant relationship between the glucose level and the genotype was identified (p = 0.046). Participants with CC and CT genotypes had a higher glucose level during the entire study period compared with the TT genotype. However, our results did not confirm the relationship between the C allele and an increased BMI or other obesity-related traits. Additionally, we did not observe a near MC4R C/T polymorphism x physical activity interaction. However, our results revealed that majority of obesity-related variables changed significantly during the 12 week training program. The effect sizes (d) of these changes ranged from small to medium (d = 0.11-0.80), whereas the largest effect (d = 0.80; i.e. medium) was reported for the fat mass content (FM). We found a relationship between the near MC4R C/T polymorphism and an increased glucose level, and it is thus a candidate to influence type 2 diabetes. Interestingly, after the 12 week training program, participants with the C (risk) allele with fasting hyperglycemia had a normal glucose level. Although, this change was not statistically significant, it shows an important trend which needs further investigation.
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Affiliation(s)
- Agata Leońska-Duniec
- Faculty of Physical Culture and Health Promotion, University of Szczecin, Szczecin, Poland
| | - Zbigniew Jastrzębski
- Faculty of Tourism and Recreation, Gdansk University of Physical Education and Sport, Gdansk, Poland
| | - Aleksandra Zarębska
- Faculty of Tourism and Recreation, Gdansk University of Physical Education and Sport, Gdansk, Poland
| | - Wojciech Smółka
- Clinical Department of Laryngology, School of Medicine in Katowice, Medical University of Silesia, Katowice, Poland
| | - Paweł Cięszczyk
- Faculty of Physical Education, Gdansk University of Physical Education and Sport, Gdansk, Poland
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13
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Recent progress in genetics, epigenetics and metagenomics unveils the pathophysiology of human obesity. Clin Sci (Lond) 2017; 130:943-86. [PMID: 27154742 DOI: 10.1042/cs20160136] [Citation(s) in RCA: 227] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 02/24/2016] [Indexed: 12/19/2022]
Abstract
In high-, middle- and low-income countries, the rising prevalence of obesity is the underlying cause of numerous health complications and increased mortality. Being a complex and heritable disorder, obesity results from the interplay between genetic susceptibility, epigenetics, metagenomics and the environment. Attempts at understanding the genetic basis of obesity have identified numerous genes associated with syndromic monogenic, non-syndromic monogenic, oligogenic and polygenic obesity. The genetics of leanness are also considered relevant as it mirrors some of obesity's aetiologies. In this report, we summarize ten genetically elucidated obesity syndromes, some of which are involved in ciliary functioning. We comprehensively review 11 monogenic obesity genes identified to date and their role in energy maintenance as part of the leptin-melanocortin pathway. With the emergence of genome-wide association studies over the last decade, 227 genetic variants involved in different biological pathways (central nervous system, food sensing and digestion, adipocyte differentiation, insulin signalling, lipid metabolism, muscle and liver biology, gut microbiota) have been associated with polygenic obesity. Advances in obligatory and facilitated epigenetic variation, and gene-environment interaction studies have partly accounted for the missing heritability of obesity and provided additional insight into its aetiology. The role of gut microbiota in obesity pathophysiology, as well as the 12 genes associated with lipodystrophies is discussed. Furthermore, in an attempt to improve future studies and merge the gap between research and clinical practice, we provide suggestions on how high-throughput '-omic' data can be integrated in order to get closer to the new age of personalized medicine.
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14
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Bradnová O, Vejražková D, Vaňková M, Lukášová P, Včelák J, Stanická S, Dvořáková K, Bendlová B. Metabolic and hormonal consequencies of the "obesity risk" MC4R variant (rs12970134) in Czech women. Physiol Res 2016; 64:S187-95. [PMID: 26680479 DOI: 10.33549/physiolres.933119] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Although the mutations in MC4R gene became known as the most common genetic cause of human obesity, the effect of rs12970134 A/G near MC4R gene on insulin resistance has been described. The aim of this study was to determine the effect of rs12970134 on obesity, hormone levels, and glucose metabolism in a cohort of women varying in glucose tolerance: 850 normoglycemic women, 423 diagnosed with polycystic ovary syndrome (PCOS), 402 gestational diabetics (GDM), and 250 type 2 diabetic (T2D) women. We did not confirm the explicit effect of rs12970134 on obesity. However, the influence of the A-allele on body adiposity index was observed in a cohort of women diagnosed with PCOS. In normoglycemic women, the A-allele carriership was associated with lower fasting levels of glucose, insulin, C-peptide, and index of insulin resistance. Furthermore, higher levels of growth hormone, leptin and SHBG, and lower levels of fT3, testosterone, and androstenedione were recorded in normoglycemic A-allele carriers. In conclusion, the study presents the evidence of the impact of rs12970134 on complex hypothalamic regulations.
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Affiliation(s)
- O Bradnová
- Department of Molecular Endocrinology, Institute of Endocrinology, Prague, Czech Republic.
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15
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Kirac D, Kasimay Cakir O, Avcilar T, Deyneli O, Kurtel H, Yazici D, Kaspar EC, Celik N, Guney AI. Effects of MC4R, FTO, and NMB gene variants to obesity, physical activity, and eating behavior phenotypes. IUBMB Life 2016; 68:806-16. [PMID: 27634552 DOI: 10.1002/iub.1558] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 08/23/2016] [Indexed: 02/01/2023]
Abstract
Obesity is a major contributory factor of morbidity and mortality. It has been suggested that biological systems may be involved in the tendency to be and to remain physically inactive also behaviors such as food and beverage preferences and nutrient intake may at least partially genetically determined. Consequently, besides environment, genetic factors may also contribute to the level of physical activity and eating behaviors thus effect obesity. Therefore the aim of this study is to investigate the effect of various gene mutations on obesity, physical activity levels and eating behavior phenotypes. One hundred patients and 100 controls were enrolled to the study. Physical activity levels were measured with an actical acceloremeter device. Eating behaviors were evaluated using Three-Factor Eating questionnaire (TFEQ). Associations between eating behavior scores and physical characteristics were also evaluated. The information about other obesity risk factors were also collected. Mutations were investigated with PCR, direct sequencing and Real-Time PCR. rs1051168, rs8050146 -2778C > T mutations were found statistically significant in patients, rs1121980 was found statistically significant in controls. 21 mutations were found in MC4R and near MC4R of which 18 of them are novel and 8 of them cause amino acid change. In addition, it was found that, some obesity related factors and questions of TFEQ are associated with various investigated gene mutations. Any relation between gene mutations and physical activity levels were not detected. It is thought that, due to the genotype data and eating behaviors, it may be possible to recommend patients for proper eating patterns to prevent obesity. © 2016 IUBMB Life, 68(10):806-816, 2016.
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Affiliation(s)
- Deniz Kirac
- Department of Medical Biology, Yeditepe University, Istanbul, Turkey.
| | | | - Tuba Avcilar
- Department of Medical Genetics, Marmara University, Istanbul, Turkey
| | - Oguzhan Deyneli
- Department of Endocrinology and Metabolism, Marmara University, Istanbul, Turkey
| | - Hizir Kurtel
- Department of Physiology, Marmara University, Istanbul, Turkey
| | - Dilek Yazici
- Department of Endocrinology and Metabolism, Marmara University, Istanbul, Turkey
| | | | - Nurgul Celik
- Department of Medical Genetics, Marmara University, Istanbul, Turkey
| | - Ahmet Ilter Guney
- Department of Medical Genetics, Marmara University, Istanbul, Turkey
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16
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Lacour A, Ellinghaus D, Schreiber S, Franke A, Becker T. Haplotype synthesis analysis reveals functional variants underlying known genome-wide associated susceptibility loci. Bioinformatics 2016; 32:2136-42. [PMID: 27153721 DOI: 10.1093/bioinformatics/btw125] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 03/01/2016] [Indexed: 12/11/2022] Open
Abstract
MOTIVATION The functional mechanisms underlying disease association remain unknown for Genome-wide Association Studies (GWAS) susceptibility variants located outside coding regions. Synthesis of effects from multiple surrounding functional variants has been suggested as an explanation of hard-to-interpret findings. We define filter criteria based on linkage disequilibrium measures and allele frequencies which reflect expected properties of synthesizing variant sets. For eligible candidate sets, we search for haplotype markers that are highly correlated with associated variants. RESULTS Via simulations we assess the performance of our approach and suggest parameter settings which guarantee 95% sensitivity at 20-fold reduced computational cost. We apply our method to 1000 Genomes data and confirmed Crohn's Disease (CD) and Type 2 Diabetes (T2D) variants. A proportion of 36.9% allowed explanation by three-variant-haplotypes carrying at least two functional variants, as compared to 16.4% for random variants ([Formula: see text]). Association could be explained by missense variants for MUC19, PER3 (CD) and HMG20A (T2D). In a CD GWAS-imputed using haplotype reference consortium data (64 976 haplotypes)-we could confirm the syntheses of MUC19 and PER3 and identified synthesis by missense variants for 6 further genes (ZGPAZ, GPR65, CLN3/NPIPB8, LOC102723878, rs2872507, GCKR). In all instances, the odds ratios of the synthesizing haplotypes were virtually identical to that of the index SNP. In summary, we demonstrate the potential of synthesis analysis to guide functional follow-up of GWAS findings. AVAILABILITY AND IMPLEMENTATION All methods are implemented in the C/C ++ toolkit GetSynth, available at http://sourceforge.net/projects/getsynth/ CONTACT tim.becker@uni-greifswald.de SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- André Lacour
- German Center for Neurodegenerative Diseases (DZNE), Bonn 53127, Germany
| | - David Ellinghaus
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel 24105, Germany
| | - Stefan Schreiber
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel 24105, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel 24105, Germany
| | - Tim Becker
- Institute for Community Medicine, Ernst Moritz Arndt University Greifswald, Greifswald 17475, Germany
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17
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Obesity-Related Diseases and Syndromes: Insulin Resistance, Type 2 Diabetes Mellitus, Non-alcoholic Fatty Liver Disease, Cardiovascular Disease, and Metabolic Syndrome. Obesity (Silver Spring) 2016. [DOI: 10.1007/978-3-319-39409-1_5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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18
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Gervasini G, Gamero-Villarroel C. Discussing the putative role of obesity-associated genes in the etiopathogenesis of eating disorders. Pharmacogenomics 2015; 16:1287-1305. [DOI: 10.2217/pgs.15.77] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
In addition to the identification of mutations clearly related to Mendelian forms of obesity; genome-wide association studies and follow-up studies have in the last years pinpointed several loci associated with BMI. These genetic alterations are located in or near genes expressed in the hypothalamus that are involved in the regulation of eating behavior. Accordingly, it seems plausible that these SNPs, or others located in related genes, could also help develop aberrant conduct patterns that favor the establishment of eating disorders should other susceptibility factors or personality dimensions be present. However, and somewhat surprisingly, with few exceptions such as BDNF, the great majority of the genes governing these pathways remain untested in patients with anorexia nervosa, bulimia nervosa or binge-eating disorder. In the present work, we review the few existing studies, but also indications and biological concepts that point to these genes in the CNS as good candidates for association studies with eating disorder patients.
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Affiliation(s)
- Guillermo Gervasini
- Department of Medical & Surgical Therapeutics, Division of Pharmacology, Medical School, University of Extremadura, Av. Elvas s/n, E-06005, Badajoz, Spain
| | - Carmen Gamero-Villarroel
- Department of Medical & Surgical Therapeutics, Division of Pharmacology, Medical School, University of Extremadura, Av. Elvas s/n, E-06005, Badajoz, Spain
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19
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Fine Mapping of a GWAS-Derived Obesity Candidate Region on Chromosome 16p11.2. PLoS One 2015; 10:e0125660. [PMID: 25955518 PMCID: PMC4425372 DOI: 10.1371/journal.pone.0125660] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 03/17/2015] [Indexed: 11/19/2022] Open
Abstract
INTRODUCTION Large-scale genome-wide association studies (GWASs) have identified 97 chromosomal loci associated with increased body mass index in population-based studies on adults. One of these SNPs, rs7359397, tags a large region (approx. 1MB) with high linkage disequilibrium (r2>0.7), which comprises five genes (SH2B1, APOBR, sulfotransferases: SULT1A1 and SULT1A2, TUFM). We had previously described a rare mutation in SH2B1 solely identified in extremely obese individuals but not in lean controls. METHODS The coding regions of the genes APOBR, SULT1A1, SULT1A2, and TUFM were screened for mutations (dHPLC, SSCP, Sanger re-sequencing) in 95 extremely obese children and adolescents. Detected non-synonymous variants were genotyped (TaqMan SNP Genotyping, MALDI TOF, PCR-RFLP) in independent large study groups (up to 3,210 extremely obese/overweight cases, 485 lean controls and 615 obesity trios). In silico tools were used for the prediction of potential functional effects of detected variants. RESULTS Except for TUFM we detected non-synonymous variants in all screened genes. Two polymorphisms rs180743 (APOBR p.Pro428Ala) and rs3833080 (APOBR p.Gly369_Asp370del9) showed nominal association to (extreme) obesity (uncorrected p = 0.003 and p = 0.002, respectively). In silico analyses predicted a functional implication for rs180743 (APOBR p.Pro428Ala). Both APOBR variants are located in the repetitive region with unknown function. CONCLUSION Variants in APOBR contributed as strongly as variants in SH2B1 to the association with extreme obesity in the chromosomal region chr16p11.2. In silico analyses implied no functional effect of several of the detected variants. Further in vitro or in vivo analyses on the functional implications of the obesity associated variants are warranted.
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20
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Jin P, Wu X, Xu S, Zhang H, Li Y, Cao Z, Li H, Wang S. Differential expression of six genes and correlation with fatness traits in a unique broiler population. Saudi J Biol Sci 2015; 24:945-949. [PMID: 28490969 PMCID: PMC5415145 DOI: 10.1016/j.sjbs.2015.04.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2015] [Revised: 04/16/2015] [Accepted: 04/22/2015] [Indexed: 11/20/2022] Open
Abstract
Previous results from genome wide association studies (GWASs) in chickens divergently selected for abdominal fat content of Northeast Agricultural University (NEAUHLF) showed that many single nucleotide polymorphism (SNP) variants were associated with abdominal fat content. Of them, six top significant SNPs at the genome level were located within SRD5A3, SGCZ, DLC1, GBE1, GALNT9 and DNAJB6 genes. Here, expression levels of these six candidate genes were investigated in abdominal fat and liver tissue between fat and lean broilers from the 14th generation population of NEAUHLF. The results showed that expression levels of SRD5A3, SGCZ and DNAJB6 in the abdominal fat and SRD5A3, DLC1, GALNT9, DNAJB6 and GBE1 in the liver tissue differed significantly between the fat and lean birds, and were correlated with abdominal fat traits. The findings will provide important references for further function investigation of the six candidate genes involved in abdominal fat deposition in chickens.
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Affiliation(s)
- Pengcheng Jin
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture, Harbin 150030, China
| | - Xianwen Wu
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture, Harbin 150030, China
| | - Songsong Xu
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture, Harbin 150030, China
| | - Hui Zhang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture, Harbin 150030, China
| | - Yumao Li
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture, Harbin 150030, China
| | - Zhiping Cao
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture, Harbin 150030, China
| | - Hui Li
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture, Harbin 150030, China
| | - Shouzhi Wang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture, Harbin 150030, China
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21
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Duan DM, Wu S, Hsu LA, Teng MS, Lin JF, Sun YC, Cheng CF, Ko YL. Associations between TRPV4 genotypes and body mass index in Taiwanese subjects. Mol Genet Genomics 2015; 290:1357-65. [DOI: 10.1007/s00438-015-0996-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Accepted: 01/17/2015] [Indexed: 08/22/2023]
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22
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Abstract
Heritability of obesity and body weight variation is high. Molecular genetic studies have led to the identification of mutations in a few genes, with a major effect on obesity (major genes and monogenic forms). Analyses of these genes have helped to unravel important pathways and have created a more profound understanding of body weight regulation. For most individuals, a polygenic basis is relevant for the genetic predisposition to obesity. Small effect sizes are conveyed by the polygenic variants. Hence, only if a number of these variants is harboured, a sizeable phenotypic effect is detectable. Most, if not all, of the genes relevant to weight regulation are expressed in the hypothalamus. This underscores the major role of this region of the brain in body weight regulation.
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Affiliation(s)
- Anke Hinney
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, Universitätsklinikum Essen, Essen, Germany.
| | - Anna-Lena Volckmar
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, Universitätsklinikum Essen, Essen, Germany.
| | - Jochen Antel
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, Universitätsklinikum Essen, Essen, Germany.
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23
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Gamero-Villarroel C, González LM, Gordillo I, Carrillo JA, García-Herráiz A, Flores I, Rodríguez-López R, Gervasini G. Impact of NEGR1 genetic variability on psychological traits of patients with eating disorders. THE PHARMACOGENOMICS JOURNAL 2014; 15:278-83. [PMID: 25245582 DOI: 10.1038/tpj.2014.53] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Revised: 07/04/2014] [Accepted: 08/13/2014] [Indexed: 01/24/2023]
Abstract
Genetics variants in the NEGR1 gene, strongly expressed in the brain, have been reported to affect the neuronal control of food intake therefore inducing obesity. With the same rationale, we hypothesized that this genetic variability may be associated with psychological traits commonly displayed by eating disorder (ED) patients and/or with the risk for the disorder. We analyzed 21 tag-single-nucleotide polymorphisms (SNPs) in the coding sequence and adjacent regions of the NEGR1 gene. A total of 169 ED patients (106 with anorexia nervosa (AN) and 63 with bulimia nervosa (BN)) and 312 healthy subjects were genotyped. Personality traits and general psychopathological symptoms were assessed by the Eating Disorders Inventory Test-2 (EDI-2) and Symptom Checklist 90 Revised inventories. None of the SNPs or haplotypes analyzed were associated with a greater risk of ED or correlated with anthropometric parameters. However, in patients with BN, four SNPs (rs12740031, rs10789322, rs6659202 and rs591540) correlated with the scores in Drive for Thinness (DT), Ineffectiveness (I) and Interoceptive Awareness (IA) (Bonferroni-P<0.05 in all instances). The first two SNPs along with rs954299 and rs2422021 formed a haplotype block, which showed a consistent association with the EDI-2 score in BN patients (Bonferroni-P=0.01). A subsequent three-SNP sliding-window approach identified a central area, encompassing both the haplotype block and the individually relevant SNPs that strongly correlated with the scores of BN patients in DT, I, IA and Bulimia. No associations were identified in the AN group. These preliminary results indicate that NEGR1 could be an important locus influencing certain personality dimensions in BN patients.
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Affiliation(s)
- C Gamero-Villarroel
- Department of Medical & Surgical Therapeutics, Division of Pharmacology, Medical School, University of Extremadura, Badajoz, Spain
| | - L María González
- Department of Medical & Surgical Therapeutics, Division of Pharmacology, Medical School, University of Extremadura, Badajoz, Spain
| | - I Gordillo
- Department of Medical & Surgical Therapeutics, Division of Pharmacology, Medical School, University of Extremadura, Badajoz, Spain
| | - J Antonio Carrillo
- Department of Medical & Surgical Therapeutics, Division of Pharmacology, Medical School, University of Extremadura, Badajoz, Spain
| | - A García-Herráiz
- Eating Disorders Unit, Institute of Mental Disorders, Health Service of Extremadura, Badajoz, Spain
| | - I Flores
- Eating Disorders Unit, Institute of Mental Disorders, Health Service of Extremadura, Badajoz, Spain
| | - R Rodríguez-López
- Service of Clinical Analyses, General University Hospital, Valencia, Spain
| | - G Gervasini
- Department of Medical & Surgical Therapeutics, Division of Pharmacology, Medical School, University of Extremadura, Badajoz, Spain
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24
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Evans DS, Calton MA, Kim MJ, Kwok PY, Miljkovic I, Harris T, Koster A, Liu Y, Tranah GJ, Ahituv N, Hsueh WC, Vaisse C. Genetic association study of adiposity and melanocortin-4 receptor (MC4R) common variants: replication and functional characterization of non-coding regions. PLoS One 2014; 9:e96805. [PMID: 24820477 PMCID: PMC4018404 DOI: 10.1371/journal.pone.0096805] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2013] [Accepted: 04/11/2014] [Indexed: 11/29/2022] Open
Abstract
Common genetic variants 3' of MC4R within two large linkage disequilibrium (LD) blocks spanning 288 kb have been associated with common and rare forms of obesity. This large association region has not been refined and the relevant DNA segments within the association region have not been identified. In this study, we investigated whether common variants in the MC4R gene region were associated with adiposity-related traits in a biracial population-based study. Single nucleotide polymorphisms (SNPs) in the MC4R region were genotyped with a custom array and a genome-wide array and associations between SNPs and five adiposity-related traits were determined using race-stratified linear regression. Previously reported associations between lower BMI and the minor alleles of rs2229616/Val103Ile and rs52820871/Ile251Leu were replicated in white female participants. Among white participants, rs11152221 in a proximal 3' LD block (closer to MC4R) was significantly associated with multiple adiposity traits, but SNPs in a distal 3' LD block (farther from MC4R) were not. In a case-control study of severe obesity, rs11152221 was significantly associated. The association results directed our follow-up studies to the proximal LD block downstream of MC4R. By considering nucleotide conservation, the significance of association, and proximity to the MC4R gene, we identified a candidate MC4R regulatory region. This candidate region was sequenced in 20 individuals from a study of severe obesity in an attempt to identify additional variants, and the candidate region was tested for enhancer activity using in vivo enhancer assays in zebrafish and mice. Novel variants were not identified by sequencing and the candidate region did not drive reporter gene expression in zebrafish or mice. The identification of a putative insulator in this region could help to explain the challenges faced in this study and others to link SNPs associated with adiposity to altered MC4R expression.
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Affiliation(s)
- Daniel S. Evans
- California Pacific Medical Center Research Institute, San Francisco, California, United States of America
| | - Melissa A. Calton
- Diabetes Center and Department of Medicine, University of California, San Francisco, California, United States of America
| | - Mee J. Kim
- Department of Bioengineering and Therapeutic Sciences and Institute for Human Genetics, University of California, San Francisco, California, United States of America
| | - Pui-Yan Kwok
- Cardiovascular Research Institute, Institute for Human Genetics, and Department of Dermatology, University of California, San Francisco, California, United States of America
| | - Iva Miljkovic
- Department of Epidemiology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Tamara Harris
- National Institute on Aging, Bethesda, Maryland, United States of America
| | - Annemarie Koster
- National Institute on Aging, Bethesda, Maryland, United States of America
| | - Yongmei Liu
- Department of Epidemiology and Prevention, Division of Public Health Sciences, Wake Forest University, Winston-Salem, North Carolina, United States of America
| | - Gregory J. Tranah
- California Pacific Medical Center Research Institute, San Francisco, California, United States of America
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences and Institute for Human Genetics, University of California, San Francisco, California, United States of America
| | - Wen-Chi Hsueh
- Diabetes Center and Department of Medicine, University of California, San Francisco, California, United States of America
| | - Christian Vaisse
- Diabetes Center and Department of Medicine, University of California, San Francisco, California, United States of America
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Albuquerque D, Nóbrega C, Rodríguez-López R, Manco L. Association study of common polymorphisms in MSRA, TFAP2B, MC4R, NRXN3, PPARGC1A, TMEM18, SEC16B, HOXB5 and OLFM4 genes with obesity-related traits among Portuguese children. J Hum Genet 2014; 59:307-13. [PMID: 24670271 DOI: 10.1038/jhg.2014.23] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Revised: 02/06/2014] [Accepted: 03/03/2014] [Indexed: 02/01/2023]
Abstract
At least 52 genetic loci were associated with obesity-related traits. However, little is known about the genetic basis of obesity among children. This study aims to test whether 10 polymorphisms in obesity-related genes methionine sulfoxide reductase A (MSRA), transcription factor AP-2 beta (TFAP2B), melanocortin 4 receptor (MC4R), neurexin 3 (NRXN3), peroxisome proliferator-activated receptor gamma coactivator 1 alpha (PPARGC1A), transmembrane protein 18 (TMEM18), homolog of S. cerevisiae Sec16 (SEC16B), homeobox B5 (HOXB5) and olfactomedin 4 (OLFM4) are associated with the risk of obesity in Portuguese children. A total of 730 children aging from 6 to 12 years old, recruited randomly from public schools in Portugal, were analysed. Anthropometric measurements were obtained and children were classified into three phenotypic groups, normal weight (n=256), overweight (n=320) and obese (n=154), according to the International Obesity Task Force cutoffs. Polymorphisms were genotyped by allelic discrimination TaqMan assays. The MC4R rs12970134 polymorphism was nominally associated with body mass index (BMI) (P=0.035), BMI Z-score (P=0.043) and waist circumference (P=0.020), and borderline associated with weight (P=0.053). Near nominal associations were also found for the PPARGC1A rs8192678 polymorphism with weight (P=0.061), and for the MSRA rs545854 polymorphism with BMI (P=0.055) and BMI Z-score (P=0.056). Furthermore, logistic regression showed that MC4R rs12970134 and TFAP2B rs987237 were nominally, respectively, associated (P=0.029) and borderline associated (P=0.056) with the obese phenotype. This study highlighted the possible association of MC4R, PPARGC1A, MSRA and TFAP2B polymorphisms with several obesity-related traits in a sample of Portuguese children. The two significant associated TFAP2B rs987237 and MC4R rs12970134 polymorphisms showed an opposite direction of effect to that in the original reports.
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Affiliation(s)
- David Albuquerque
- Department of Life Sciences, Research Centre for Anthropology and Health (CIAS), University of Coimbra, Coimbra, Portugal
| | - Clévio Nóbrega
- Center for Neurosciences and Cell Biology, University of Coimbra, Coimbra, Portugal
| | | | - Licínio Manco
- Department of Life Sciences, Research Centre for Anthropology and Health (CIAS), University of Coimbra, Coimbra, Portugal
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26
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Albuquerque D, Estévez MN, Víbora PB, Giralt PS, Balsera AM, Cortés PG, López MJ, Luego LM, Gervasini G, Hernández SB, Arroyo-Díez J, Vacas MA, Nóbrega C, Manco L, Rodríguez-López R. Novel Variants in theMC4RandLEPRGenes among Severely Obese Children from the Iberian Population. Ann Hum Genet 2014; 78:195-207. [DOI: 10.1111/ahg.12058] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Accepted: 01/21/2014] [Indexed: 12/12/2022]
Affiliation(s)
- David Albuquerque
- Research Centre for Anthropology and Health (CIAS); Department of Life Sciences; University of Coimbra; Portugal
| | | | - Pilar Beato Víbora
- Department of Dietician; Endocrinologist Service; Infanta Cristina Hospital; Badajoz Spain
| | - Plácida Sánchez Giralt
- Department of Dietician; Endocrinologist Service; Infanta Cristina Hospital; Badajoz Spain
| | | | - Pedro Gil Cortés
- Department of Dietician; Endocrinologist Service; Infanta Cristina Hospital; Badajoz Spain
| | - Mercedes Jiménez López
- Department of Medical & Surgical Therapeutics; Medical School; University of Extremadura; Badajoz Spain
| | - Luis Miguel Luego
- Department of Dietician; Endocrinologist Service; Infanta Cristina Hospital; Badajoz Spain
| | - Guillermo Gervasini
- Department of Medical & Surgical Therapeutics; Medical School; University of Extremadura; Badajoz Spain
| | | | | | | | - Clévio Nóbrega
- Center for Neurosciences & Cell Biology; University of Coimbra; Portugal
| | - Licínio Manco
- Research Centre for Anthropology and Health (CIAS); Department of Life Sciences; University of Coimbra; Portugal
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Acosta A, Camilleri M, Shin A, Carlson P, Burton D, O'Neill J, Eckert D, Zinsmeister AR. Association of melanocortin 4 receptor gene variation with satiation and gastric emptying in overweight and obese adults. GENES AND NUTRITION 2014; 9:384. [PMID: 24458996 DOI: 10.1007/s12263-014-0384-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Accepted: 01/11/2014] [Indexed: 12/14/2022]
Abstract
Melanocortin 4 receptor (MC4R) has a major role in energy homeostasis. The rs17782313 polymorphism, mapped 188 kb downstream from MC4R, has been associated with satiety, higher body mass index (BMI) and total calorie intake in adults. To assess the association of rs17782313 with gastric functions, satiation, or satiety, we studied 178 predominantly Caucasian overweight and obese people: 120 females, 58 males; mean BMI 33.4 ± 5.3 kg/m(2) (SD); age 37.7 ± 11.2 years. Quantitative traits assessed were gastric emptying (GE) of solids and liquids; fasting and postprandial gastric volume; satiation by maximum tolerated volume and 4 symptoms by 100-mm visual analog scales (VAS); and satiety by ad libitum buffet meal. Associations of genotype and quantitative traits were assessed by analysis of covariance (using gender and BMI as covariates), based on a dominant [TC (n = 72) - CC (n = 12) vs. TT (n = 94)] genetic model. rs17782313(C) was associated with postprandial satiation symptoms (median Δ total VAS 26.5 mm, p = 0.036), reduced proportion of solid GE at 2 h (median Δ 6.7 %, p = 0.008) and 4 h (median Δ 3.2 %, p = 0.006), and longer t ½ (median Δ 6 min, p = 0.034). Associations of rs17782313 with obesity may be explained by reduced satiation and GE. The role of MC4R mechanisms in satiation and gastric function deserves further study.
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Affiliation(s)
- Andres Acosta
- Clinical Enteric Neuroscience Translational and Epidemiological Research (C.E.N.T.E.R.), Division of Gastroenterology and Hepatology, Department of Medicine, Mayo Clinic, Charlton 8-110, 200 First St. S.W., Rochester, MN, 55905, USA
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Chew SC, Lim J, Singh O, Chen X, Tan EH, Lee EJD, Chowbay B. Pharmacogenetic effects of regulatory nuclear receptors (PXR, CAR, RXRα and HNF4α) on docetaxel disposition in Chinese nasopharyngeal cancer patients. Eur J Clin Pharmacol 2013; 70:155-66. [PMID: 24193570 DOI: 10.1007/s00228-013-1596-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Accepted: 09/30/2013] [Indexed: 11/28/2022]
Abstract
PURPOSE This exploratory study was aimed at elucidating the pharmacogenetics of regulatory nuclear receptors (PXR, CAR, RXRα and HNF4α) and their implications on docetaxel pharmacokinetics and pharmacodynamics in local Chinese nasopharyngeal cancer patients. METHODS A total of 59 single nucleotide polymorphisms (SNPs), including tag-SNPs and functionally relevant SNPs of the genes encoding these regulatory nuclear receptors (PXR/NR1I2, CAR/NR1I3, RXRα/NR2B1 and HNF4α/NR2A1), were profiled in the patients enrolled in our study by direct sequencing (N = 50). The generalized linear model was employed to estimate the haplotypic effects on the pharmacokinetics and pharmacodynamics of the patients. RESULTS The pharmacokinetic profiles of docetaxel in these patients were characterized by marked interindividual variability, with approximately four- to sixfold variations observed in Cmax, AUC0-∞ and CL. Individual SNP association tests revealed that polymorphisms in NR2B1 and NR2A1 were significantly correlated with altered docetaxel pharmacokinetics. Subsequent haplotype association analysis identified the NR2B1 LD block 2 AG haplotype [*+4458G>A(rs3132291) and *+4988A>G(rs4842198)] to be significantly associated with altered pharmacokinetics, in which patients carrying two copies of the AG haplotype had approximately a 20 % decreased Cmax and AUC0-∞ and a 21 % increased CL compared to those who carried only one copy or no copies of the haplotype. A number of SNPs in NR1I2, NR1I3, NR2B1 and NR2A1 were also associated with a significant decrease in blood counts from baseline. No haplotype was found to exert any effects on the pharmacodynamics parameters. CONCLUSIONS The present exploratory study identified several SNPs in the genes encoding regulatory nuclear receptors which may account for the interpatient variability in docetaxel pharmacokinetics and pharmacodynamics. These findings highlight the important role of regulatory nuclear receptors on the disposition of docetaxel.
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Affiliation(s)
- Sin-Chi Chew
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, 10 Medical Drive, Singapore, Singapore, 117597
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29
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San-Cristobal R, Milagro FI, Martínez JA. Future Challenges and Present Ethical Considerations in the Use of Personalized Nutrition Based on Genetic Advice. J Acad Nutr Diet 2013; 113:1447-1454. [DOI: 10.1016/j.jand.2013.05.028] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Accepted: 05/23/2013] [Indexed: 01/06/2023]
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Li MH, Tiirikka T, Kantanen J. A genome-wide scan study identifies a single nucleotide substitution in ASIP associated with white versus non-white coat-colour variation in sheep (Ovis aries). Heredity (Edinb) 2013; 112:122-31. [PMID: 24022497 DOI: 10.1038/hdy.2013.83] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Revised: 07/02/2013] [Accepted: 07/04/2013] [Indexed: 12/21/2022] Open
Abstract
In sheep, coat colour (and pattern) is one of the important traits of great biological, economic and social importance. However, the genetics of sheep coat colour has not yet been fully clarified. We conducted a genome-wide association study of sheep coat colours by genotyping 47 303 single-nucleotide polymorphisms (SNPs) in the Finnsheep population in Finland. We identified 35 SNPs associated with all the coat colours studied, which cover genomic regions encompassing three known pigmentation genes (TYRP1, ASIP and MITF) in sheep. Eighteen of these associations were confirmed in further tests between white versus non-white individuals, but none of the 35 associations were significant in the analysis of only non-white colours. Across the tests, the s66432.1 in ASIP showed significant association (P=4.2 × 10(-11) for all the colours; P=2.3 × 10(-11) for white versus non-white colours) with the variation in coat colours and strong linkage disequilibrium with other significant variants surrounding the ASIP gene. The signals detected around the ASIP gene were explained by differences in white versus non-white alleles. Further, a genome scan for selection for white coat pigmentation identified a strong and striking selection signal spanning ASIP. Our study identified the main candidate gene for the coat colour variation between white and non-white as ASIP, an autosomal gene that has been directly implicated in the pathway regulating melanogenesis. Together with ASIP, the two other newly identified genes (TYRP1 and MITF) in the Finnsheep, bordering associated SNPs, represent a new resource for enriching sheep coat-colour genetics and breeding.
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Affiliation(s)
- M-H Li
- 1] Biotechnology and Food Research, MTT Agrifood Research Finland, Jokioinen, Finland [2] Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - T Tiirikka
- Biotechnology and Food Research, MTT Agrifood Research Finland, Jokioinen, Finland
| | - J Kantanen
- 1] Biotechnology and Food Research, MTT Agrifood Research Finland, Jokioinen, Finland [2] Department of Biology, University of Eastern Finland, Kuopio, Finland
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Switonski M, Mankowska M. Dog obesity--the need for identifying predisposing genetic markers. Res Vet Sci 2013; 95:831-6. [PMID: 24034586 DOI: 10.1016/j.rvsc.2013.08.015] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Revised: 08/14/2013] [Accepted: 08/17/2013] [Indexed: 11/24/2022]
Abstract
Incidence of overweight and obesity in dogs exceeds 30%, and several breeds are predisposed to this heritable phenotype. Rapid progress of canine genomics and advanced knowledge on the genetic background of human obesity bring a unique opportunity to perform such studies in dogs. Natural candidate genes for obesity are these encoding adipokines. Extended studies in humans indicated that polymorphisms of three of them, i.e. ADIPOQ, IL1 and TNF, are associated with predisposition to obesity. On the other hand, the use of genome-wide association studies revealed an association between human obesity and polymorphism of more than 50 other genes. Until now only few preliminary reports on polymorphism of canine FTO, MC4R, MC3R and PPARG genes have been published. Since the dog is a valuable model organism for human diseases one can foresee that such studies may also contribute to an in-depth understanding of human obesity pathogenesis.
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Affiliation(s)
- M Switonski
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Wołynska 33, 60-637 Poznan, Poland.
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Wagner MJ. Rare-variant genome-wide association studies: a new frontier in genetic analysis of complex traits. Pharmacogenomics 2013; 14:413-24. [DOI: 10.2217/pgs.13.36] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Genome-wide association studies have, in the last few years, identified thousands of common genetic variants associated with common complex traits and diseases, implicating many genes not previously known to be involved in the biology of those traits. However, these variants have so far explained little of the population variance in trait values or disease susceptibility. As large-scale genome sequencing efforts have revealed the extent of genetic variation at the low end of the frequency range in human populations, the effects of rare variants have been proposed as an explanation of the ‘missing genetic variance.’ Improved technologies for genotyping rare variants, including inexpensive whole-genome and whole-exome sequencing and rare-variant genotyping chips, coupled with novel analytical methods, are making genome-wide scans for the effects of rare variants possible, and seem likely to usher in a new era in the genetic analysis of complex traits.
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Affiliation(s)
- Michael J Wagner
- Institute for Pharmacogenomics & Individualized Therapy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7361, USA
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Melanocortin-4 Receptor in Energy Homeostasis and Obesity Pathogenesis. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2013; 114:147-91. [DOI: 10.1016/b978-0-12-386933-3.00005-4] [Citation(s) in RCA: 115] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Singh O, Chan JY, Lin K, Heng CCT, Chowbay B. SLC22A1-ABCB1 haplotype profiles predict imatinib pharmacokinetics in Asian patients with chronic myeloid leukemia. PLoS One 2012; 7:e51771. [PMID: 23272163 PMCID: PMC3525665 DOI: 10.1371/journal.pone.0051771] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2012] [Accepted: 11/07/2012] [Indexed: 12/27/2022] Open
Abstract
OBJECTIVE This study aimed to explore the influence of SLC22A1, PXR, ABCG2, ABCB1 and CYP3A5 3 genetic polymorphisms on imatinib mesylate (IM) pharmacokinetics in Asian patients with chronic myeloid leukemia (CML). PATIENTS AND METHODS Healthy subjects belonging to three Asian populations (Chinese, Malay, Indian; n = 70 each) and CML patients (n = 38) were enrolled in a prospective pharmacogenetics study. Imatinib trough (C(0h)) and clearance (CL) were determined in the patients at steady state. Haplowalk method was applied to infer the haplotypes and generalized linear model (GLM) to estimate haplotypic effects on IM pharmacokinetics. Association of haplotype copy numbers with IM pharmacokinetics was defined by Mann-Whitney U test. RESULTS Global haplotype score statistics revealed a SLC22A1 sub-haplotypic region encompassing three polymorphisms (rs3798168, rs628031 and IVS7+850C>T), to be significantly associated with IM clearance (p = 0.013). Haplotype-specific GLM estimated that the haplotypes AGT and CGC were both associated with 22% decrease in clearance compared to CAC [CL (10(-2) L/hr/mg): CAC vs AGT: 4.03 vs 3.16, p = 0.017; CAC vs CGC: 4.03 vs 3.15, p = 0.017]. Patients harboring 2 copies of AGT or CGC haplotypes had 33.4% lower clearance and 50% higher C(0h) than patients carrying 0 or 1 copy [CL (10(-2) L/hr/mg): 2.19 vs 3.29, p = 0.026; C(0h) (10(-6) 1/ml): 4.76 vs 3.17, p = 0.013, respectively]. Further subgroup analysis revealed SLC22A1 and ABCB1 haplotypic combinations to be significantly associated with clearance and C(0h) (p = 0.002 and 0.009, respectively). CONCLUSION This exploratory study suggests that SLC22A1-ABCB1 haplotypes may influence IM pharmacokinetics in Asian CML patients.
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MESH Headings
- ATP Binding Cassette Transporter, Subfamily B
- ATP Binding Cassette Transporter, Subfamily B, Member 1/genetics
- Adolescent
- Adult
- Aged
- Antineoplastic Agents/administration & dosage
- Antineoplastic Agents/pharmacokinetics
- Antineoplastic Agents/therapeutic use
- Asian People/genetics
- Benzamides/administration & dosage
- Benzamides/pharmacokinetics
- Benzamides/therapeutic use
- Female
- Haplotypes
- Humans
- Imatinib Mesylate
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Linkage Disequilibrium
- Malaysia/ethnology
- Male
- Middle Aged
- Organic Cation Transporter 1/genetics
- Pharmacogenetics
- Piperazines/administration & dosage
- Piperazines/pharmacokinetics
- Piperazines/therapeutic use
- Polymorphism, Single Nucleotide
- Protein Kinase Inhibitors/administration & dosage
- Protein Kinase Inhibitors/pharmacokinetics
- Protein Kinase Inhibitors/therapeutic use
- Pyrimidines/administration & dosage
- Pyrimidines/pharmacokinetics
- Pyrimidines/therapeutic use
- Treatment Outcome
- Young Adult
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Affiliation(s)
- Onkar Singh
- Laboratory of Clinical Pharmacology, Division of Medical Sciences, Humphrey Oei Institute of Cancer Research, National Cancer Centre Singapore, Singapore, Singapore
| | - Jason Yongsheng Chan
- Laboratory of Clinical Pharmacology, Division of Medical Sciences, Humphrey Oei Institute of Cancer Research, National Cancer Centre Singapore, Singapore, Singapore
| | - Keegan Lin
- Laboratory of Clinical Pharmacology, Division of Medical Sciences, Humphrey Oei Institute of Cancer Research, National Cancer Centre Singapore, Singapore, Singapore
| | | | - Balram Chowbay
- Laboratory of Clinical Pharmacology, Division of Medical Sciences, Humphrey Oei Institute of Cancer Research, National Cancer Centre Singapore, Singapore, Singapore
- * E-mail:
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Malhotra AK, Correll CU, Chowdhury NI, Müller DJ, Gregersen PK, Lee AT, Tiwari AK, Kane JM, Fleischhacker WW, Kahn RS, Ophoff RA, Meltzer HY, Lencz T, Kennedy JL. Association between common variants near the melanocortin 4 receptor gene and severe antipsychotic drug-induced weight gain. ACTA ACUST UNITED AC 2012; 69:904-12. [PMID: 22566560 DOI: 10.1001/archgenpsychiatry.2012.191] [Citation(s) in RCA: 137] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
CONTEXT Second-generation antipsychotics (SGAs) are increasingly used in the treatment of many psychotic and nonpsychotic disorders. Unfortunately, SGAs are often associated with substantial weight gain, with no means to predict which patients are at greatest risk. OBJECTIVE To identify single-nucleotide polymorphisms associated with antipsychotic drug–induced weight gain. DESIGN Pharmacogenetic association study. SETTING The discovery cohort was from a US general psychiatric hospital. Three additional cohorts were from psychiatric hospitals in the United States and Germany and from a European antipsychotic drug trial. PARTICIPANTS The discovery cohort consisted of 139 pediatric patients undergoing first exposure to SGAs. The 3 additional cohorts consisted of 73, 40, and 92 subjects. INTERVENTION Patients in the discovery cohort were treated with SGAs for 12 weeks. Additional cohorts were treated for 6 and 12 weeks. MAIN OUTCOME MEASURES We conducted a genomewide association study assessing weight gain associated with 12 weeks of SGA treatment in patients undergoing first exposure to antipsychotic drugs. We next genotyped 3 independent cohorts of subjects assessed for antipsychotic drug-induced weight gain. RESULTS Our genome-wide association study yielded 20 single-nucleotide polymorphisms at a single locus exceeding a statistical threshold of P<10(-5). This locus, near the melanocortin 4 receptor (MC4R) gene, overlaps a region previously identified by large-scale genome-wide association studies of obesity in the general population. Effects were recessive, with minor allele homozygotes gaining extreme amounts of weight during the 12-week trial. These results were replicated in 3 additional cohorts, with rs489693 demonstrating consistent recessive effects; meta-analysis revealed a genome-wide significant effect (P=5.59 X 10 (-12). Moreover, we observed consistent effects on related metabolic indices, including triglyceride, leptin, and insulin levels. CONCLUSIONS These data implicate MC4R in extreme SGA-induced weight gain and related metabolic disturbances. A priori identification of high-risk subjects could lead to alternative treatment strategies in this population.
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Affiliation(s)
- Anil K Malhotra
- Psychiatry Research, Zucker Hillside Hospital, 75-59 263rd St, Glen Oaks, NY 11004, USA.
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Omoyinmi E, Forabosco P, Hamaoui R, Bryant A, Hinks A, Ursu S, Wedderburn LR, Thomson W, Lewis CM, Woo P. Association of the IL-10 gene family locus on chromosome 1 with juvenile idiopathic arthritis (JIA). PLoS One 2012; 7:e47673. [PMID: 23094074 PMCID: PMC3475696 DOI: 10.1371/journal.pone.0047673] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2012] [Accepted: 09/14/2012] [Indexed: 12/14/2022] Open
Abstract
Background The cytokine IL-10 and its family members have been implicated in autoimmune diseases and we have previously reported that genetic variants in IL-10 were associated with a rare group of diseases called juvenile idiopathic arthritis (JIA). The aim of this study was to fine map genetic variants within the IL-10 cytokine family cluster on chromosome 1 using linkage disequilibrium (LD)-tagging single nucleotide polymorphisms (tSNPs) approach with imputation and conditional analysis to test for disease associations. Methodology/Principal Findings Fifty-three tSNPs were tested for association between Caucasian paediatric cohorts [219 systemic JIA (sJIA), 187 persistent oligoarticular JIA (pOJIA), and 139 extended OJIA (eOJIA) patients], and controls (Wellcome Trust control cohort, WTCCC2). Significant association with sJIA was detected at rs1400986 in the promoter of IL-20 (odds ratio 1.53; 95% CI 1.21–1.93; p = 0.0004), but in no other subtypes. Imputation analysis identified additional associated SNPs for pOJIA at IL-20 and IL-24, including a rare, functional, missense variant at IL-24 with a p = 0.0002. Penalised logistic regression analysis with HyperLasso and conditional analysis identified several further associations with JIA subtypes. In particular, haplotype analysis refined the sJIA association, with a joint effect at rs1400986 and rs4129024 in intron 1 of MAPKAPK2 (p = 3.2E−5). For pOJIA, a 3-SNP haplotype including rs1878672 in intron 3 of IL-10 showed evidence for association (p = 0.0018). In eOJIA, rs10863962 (3′UTR of FCAMR) and rs12409577 (intron of IL-19) haplotype showed some evidence of association (p = 0.0003). Conclusions This study supports previous association of IL-20 with sJIA. Haplotype analyses provided stronger association signals than single point analyses, while a penalised logistic regression approach also suggested multiple independent association signals. Replication studies are required to confirm or refute these findings. The results indicate that combined effects with unknown/rare variants remain to be characterised in JIA, and represent a possible example of synthetic association in this region.
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Affiliation(s)
- Ebun Omoyinmi
- Department of Immunology and Molecular Pathology, University College London, London, United Kingdom.
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Xi B, Chandak GR, Shen Y, Wang Q, Zhou D. Association between common polymorphism near the MC4R gene and obesity risk: a systematic review and meta-analysis. PLoS One 2012; 7:e45731. [PMID: 23049848 PMCID: PMC3458070 DOI: 10.1371/journal.pone.0045731] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2012] [Accepted: 08/21/2012] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Genome-wide association studies on Europeans have shown that two polymorphisms (rs17782313, rs12970134) near the melanocortin 4 receptor (MC4R) gene were associated with increased risk of obesity. Subsequently studies among different ethnic populations have shown mixed results with some confirming and others showing inconsistent results, especially among East Asians and Africans. We performed a comprehensive meta-analysis of various studies from different ethnic populations to assess the association of the MC4R polymorphism with obesity risk. METHODS We retrieved all published literature that investigated association of MC4R variants with obesity from PubMed and Embase. Pooled odds ratio (OR) with 95% confidence interval (CI) was calculated using fixed- or random-effects model. RESULTS A total of 61 studies (80,957 cases/220,223 controls) for rs17782313 polymorphism (or proxy) were included in the meta-analysis. The results suggested that rs17782313 polymorphism was significantly associated with obesity risk (OR=1.18, 95%CI=1.15-1.21, p<0.001). Similar trends were observed among subgroups of Europeans and East Asians, adults and children, studies with high quality score, and for each five MC4R polymorphisms independently. CONCLUSIONS The present meta-analysis confirms the significant association of MC4R polymorphism with risk of obesity. Further studies should be conducted to identify the causal variant and the underlying mechanisms of the identified association.
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Affiliation(s)
- Bo Xi
- Department of Maternal and Child Health Care, School of Public Health, Shandong University, Jinan, Shandong, People's Republic of China
- * E-mail: (BX); (DZ)
| | - Giriraj R. Chandak
- Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Hyderabad, Andhra Pradesh, India
| | - Yue Shen
- Department of Epidemiology, Capital Institute of Pediatrics, Beijing, People's Republic of China
| | - Qijuan Wang
- Department of Maternal and Child Health Care, School of Public Health, Shandong University, Jinan, Shandong, People's Republic of China
| | - Donghao Zhou
- Department of Endocrinology, Linyi People's Hospital, Linyi, Shandong, People's Republic of China
- * E-mail: (BX); (DZ)
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Chew SC, Sandanaraj E, Singh O, Chen X, Tan EH, Lim WT, Lee EJD, Chowbay B. Influence of SLCO1B3 haplotype-tag SNPs on docetaxel disposition in Chinese nasopharyngeal cancer patients. Br J Clin Pharmacol 2012; 73:606-18. [PMID: 21995462 DOI: 10.1111/j.1365-2125.2011.04123.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
WHAT IS ALREADY KNOWN ABOUT THIS SUBJECT SLCO1B3 is an influx transporter located at the hepatocyte basolateral membrane and it is involved in the uptake of a broad range of drug substrates including docetaxel. The pharmacogenetics of SLCO1B3 is not well characterized and previous in vivo and in vitro studies reported conflicting results with regards to the functional effects of the limited number of SLCO1B3 polymorphisms that were studied. Docetaxel displays a wide interindividual variability in its pharmacokinetics and pharmacodynamics and an understanding of SLCO1B3 pharmacogenetics might provide clinical benefits in guiding docetaxel dosing. WHAT THIS STUDY ADDS The SLCO1B3 gene was comprehensively screened in the local healthy Asian populations (n= 168). A strong linkage disequilibrium pattern was detected across a total of 88 polymorphisms and 15 haplotype-tag SNPs (htSNPs) were identified. These htSNPs were profiled in a cohort of Chinese nasopharyngeal cancer (NPC) patients (n= 50). Genotypic-phenotypic analysis showed that a haplotypic construct comprising of four variants [IVS4+76G>A, 699G>A(Met233Ile), IVS12-5676A>G, and *347_*348insA] was the critical determinant of docetaxel disposition. This study suggests that the comprehensive screening and haplotypic linkage analysis of SLCO1B3 can better elucidate its pharmacogenetic effects on interpatient variability of docetaxel and other putative drug substrates. Further studies are warranted in cancer patients belonging to other ethnic groups. AIMS To completely screen the SLCO1B3 gene in three distinct healthy Asian populations (Chinese, Malay and Indian, n= 168) and investigate the influence of haplotype-tag SNPs (htSNPs) on docetaxel disposition in 50 nasopharyngeal carcinoma patients. METHODS Genomic DNA of individuals was screened for SLCO1B3 polymorphisms by direct sequencing. htSNPs were derived based on the sequence clustering algorithm and profiled in the patients. Population based genetic association analysis was performed using Haplostats package implemented in R and PLINK. RESULTS A strong linkage disequilibrium pattern was detected across a total of 88 polymorphisms and 15-htSNPs were identified. The SLCO1B3 haplotypic region comprising seven htSNPs was found to be significantly associated with docetaxel clearance (P= 0.003). Conditional haplotype analyses revealed that the haplotypic constructs comprising the IVS4+76G>A, 699G>A(Met233Ile), IVS12-5676A>G, and *347_*348insA polymorphisms were critical determinants of variability in docetaxel disposition [clearance and area under the plasma concentration-time curve (AUC(0,∞)): r(2) = 29% and 22%, respectively]. Patients harbouring the GAG*347insA haplotype were significantly associated with a 30% decrease in clearance and a 40% increase in AUC(0,∞) of docetaxel compared with patients harbouring the reference haplotype, GGA*347wt (P= 0.025 and 0.018, respectively). In contrast, a 50% higher clearance was observed in patients carrying the GAG*347wt haplotype compared with those with the reference haplotype (P= 0.002). The functional SLCO1B3 haplotypic constructs included the widely studied Met233Ile variant and *347_*348insA located in the putative miR-890 binding site in the 3'-untranslated region which may influence the transport characteristics of SLCO1B3. CONCLUSIONS This study highlights the importance of SLCO1B3 polymorphic variations in influencing docetaxel disposition in nasopharyngeal carcinoma patients.
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Affiliation(s)
- Sin Chi Chew
- Laboratory of Clinical Pharmacology, Division of Medical Sciences, Humphrey Oei Institute of Cancer Research, National Cancer Centre, 11 Hospital Drive, Singapore
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Creemers JW, Choquet H, Stijnen P, Vatin V, Pigeyre M, Beckers S, Meulemans S, Than ME, Yengo L, Tauber M, Balkau B, Elliott P, Jarvelin MR, Van Hul W, Van Gaal L, Horber F, Pattou F, Froguel P, Meyre D. Heterozygous mutations causing partial prohormone convertase 1 deficiency contribute to human obesity. Diabetes 2012; 61:383-90. [PMID: 22210313 PMCID: PMC3266396 DOI: 10.2337/db11-0305] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Null mutations in the PCSK1 gene, encoding the proprotein convertase 1/3 (PC1/3), cause recessive monogenic early onset obesity. Frequent coding variants that modestly impair PC1/3 function mildly increase the risk for common obesity. The aim of this study was to determine the contribution of rare functional PCSK1 mutations to obesity. PCSK1 exons were sequenced in 845 nonconsanguineous extremely obese Europeans. Eight novel nonsynonymous PCSK1 mutations were identified, all heterozygous. Seven mutations had a deleterious effect on either the maturation or the enzymatic activity of PC1/3 in cell lines. Of interest, five of these novel mutations, one of the previously described frequent variants (N221D), and the mutation found in an obese mouse model (N222D), affect residues at or near the structural calcium binding site Ca-1. The prevalence of the newly identified mutations was assessed in 6,233 obese and 6,274 lean European adults and children, which showed that carriers of any of these mutations causing partial PCSK1 deficiency had an 8.7-fold higher risk to be obese than wild-type carriers. These results provide the first evidence of an increased risk of obesity in heterozygous carriers of mutations in the PCSK1 gene. Furthermore, mutations causing partial PCSK1 deficiency are present in 0.83% of extreme obesity phenotypes.
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Affiliation(s)
- John W.M. Creemers
- Department of Human Genetics, University of Leuven, Leuven, Belgium
- Corresponding authors: John W.M. Creemers, , and Philippe Froguel,
| | - Hélène Choquet
- Centre National de la Recherche Scientifique (CNRS) 8199, Lille North of France University, Pasteur Institute, Lille, France
| | - Pieter Stijnen
- Department of Human Genetics, University of Leuven, Leuven, Belgium
| | - Vincent Vatin
- Centre National de la Recherche Scientifique (CNRS) 8199, Lille North of France University, Pasteur Institute, Lille, France
| | - Marie Pigeyre
- Department of Nutrition, Hospital University, Lille, France
| | - Sigri Beckers
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Sandra Meulemans
- Department of Human Genetics, University of Leuven, Leuven, Belgium
| | - Manuel E. Than
- Leibniz Institute for Age Research, Fritz Lipmann Institute, Jena, Germany
| | - Loïc Yengo
- Centre National de la Recherche Scientifique (CNRS) 8199, Lille North of France University, Pasteur Institute, Lille, France
| | - Maithé Tauber
- INSERM U563, Children’s Hospital, Centre Hospitalier Universitaire, Toulouse, France
| | - Beverley Balkau
- INSERM U1018, Villejuif, France
- University Paris Sud 11, UMRS 1018, Villejuif, France
| | - Paul Elliott
- Department of Epidemiology and Biostatistics, and MRC-HPA Centre for Environment and Health, Imperial College London, London, U.K
| | - Marjo-Riitta Jarvelin
- Department of Epidemiology and Biostatistics, and MRC-HPA Centre for Environment and Health, Imperial College London, London, U.K
- Department of Child and Adolescent Health, National Public Health Institute, Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Wim Van Hul
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Luc Van Gaal
- Department of Endocrinology, Antwerp University Hospital, Antwerp, Belgium
| | - Fritz Horber
- Department of Surgery and Internal Medicine, Clinic Lindberg, Winterthur, Switzerland
| | - François Pattou
- INSERM U859, Lille North of France University, Lille, France
| | - Philippe Froguel
- Centre National de la Recherche Scientifique (CNRS) 8199, Lille North of France University, Pasteur Institute, Lille, France
- Department of Genomics of Common Disease, School of Public Health, Imperial College London, London, U.K
- Corresponding authors: John W.M. Creemers, , and Philippe Froguel,
| | - David Meyre
- Centre National de la Recherche Scientifique (CNRS) 8199, Lille North of France University, Pasteur Institute, Lille, France
- Department of Clinical Epidemiology & Biostatistics, McMaster University, Hamilton, Ontario, Canada
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D'Angelo CS, Koiffmann CP. Copy number variants in obesity-related syndromes: review and perspectives on novel molecular approaches. J Obes 2012; 2012:845480. [PMID: 23316347 PMCID: PMC3534325 DOI: 10.1155/2012/845480] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Accepted: 10/09/2012] [Indexed: 02/07/2023] Open
Abstract
In recent decades, obesity has reached epidemic proportions worldwide and became a major concern in public health. Despite heritability estimates of 40 to 70% and the long-recognized genetic basis of obesity in a number of rare cases, the list of common obesity susceptibility variants by the currently published genome-wide association studies (GWASs) only explain a small proportion of the individual variation in risk of obesity. It was not until very recently that GWASs of copy number variants (CNVs) in individuals with extreme phenotypes reported a number of large and rare CNVs conferring high risk to obesity, and specifically deletions on chromosome 16p11.2. In this paper, we comment on the recent advances in the field of genetics of obesity with an emphasis on the genes and genomic regions implicated in highly penetrant forms of obesity associated with developmental disorders. Array genomic hybridization in this patient population has afforded discovery opportunities for CNVs that have not previously been detectable. This information can be used to generate new diagnostic arrays and sequencing platforms, which will likely enhance detection of known genetic conditions with the potential to elucidate new disease genes and ultimately help in developing a next-generation sequencing protocol relevant to clinical practice.
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Affiliation(s)
- Carla Sustek D'Angelo
- Human Genome and Stem Cell Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of Sao Paulo, 277 Rua do Matao, Rooms 204 and 209, 05508-090 Sao Paulo, SP, Brazil.
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Choquet H, Meyre D. Genetics of Obesity: What have we Learned? Curr Genomics 2011; 12:169-79. [PMID: 22043165 PMCID: PMC3137002 DOI: 10.2174/138920211795677895] [Citation(s) in RCA: 139] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2011] [Revised: 03/31/2011] [Accepted: 03/31/2011] [Indexed: 12/14/2022] Open
Abstract
Candidate gene and genome-wide association studies have led to the discovery of nine loci involved in Mendelian forms of obesity and 58 loci contributing to polygenic obesity. These loci explain a small fraction of the heritability for obesity and many genes remain to be discovered. However, efforts in obesity gene identification greatly modified our understanding of this disorder. In this review, we propose an overlook of major lessons learned from 15 years of research in the field of genetics and obesity. We comment on the existence of the genetic continuum between monogenic and polygenic forms of obesity that pinpoints the role of genes involved in the central regulation of food intake and genetic predisposition to obesity. We explain how the identification of novel obesity predisposing genes has clarified unsuspected biological pathways involved in the control of energy balance that have helped to understand past human history and to explore causality in epidemiology. We provide evidence that obesity predisposing genes interact with the environment and influence the response to treatment relevant to disease prediction.
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Affiliation(s)
- Hélène Choquet
- Ernest Gallo Clinic and Research Center, Department of Neurology, University of California, San Francisco, Emeryville, California 94608, USA
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