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Keller M, Svensson SIA, Rohde-Zimmermann K, Kovacs P, Böttcher Y. Genetics and Epigenetics in Obesity: What Do We Know so Far? Curr Obes Rep 2023; 12:482-501. [PMID: 37819541 DOI: 10.1007/s13679-023-00526-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/07/2023] [Indexed: 10/13/2023]
Abstract
PURPOSE OF REVIEW Enormous progress has been made in understanding the genetic architecture of obesity and the correlation of epigenetic marks with obesity and related traits. This review highlights current research and its challenges in genetics and epigenetics of obesity. RECENT FINDINGS Recent progress in genetics of polygenic traits, particularly represented by genome-wide association studies, led to the discovery of hundreds of genetic variants associated with obesity, which allows constructing polygenic risk scores (PGS). In addition, epigenome-wide association studies helped identifying novel targets and methylation sites being important in the pathophysiology of obesity and which are essential for the generation of methylation risk scores (MRS). Despite their great potential for predicting the individual risk for obesity, the use of PGS and MRS remains challenging. Future research will likely discover more loci being involved in obesity, which will contribute to better understanding of the complex etiology of human obesity. The ultimate goal from a clinical perspective will be generating highly robust and accurate prediction scores allowing clinicians to predict obesity as well as individual responses to body weight loss-specific life-style interventions.
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Affiliation(s)
- Maria Keller
- Medical Department III-Endocrinology, Nephrology, Rheumatology, Medical Center, University of Leipzig, 04103, Leipzig, Germany
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Center Munich at the University of Leipzig, University Hospital Leipzig, 04103, Leipzig, Germany
| | - Stina Ingrid Alice Svensson
- EpiGen, Department of Clinical Molecular Biology, Institute of Clinical Medicine, University of Oslo, 0316, Oslo, Norway
| | - Kerstin Rohde-Zimmermann
- Medical Department III-Endocrinology, Nephrology, Rheumatology, Medical Center, University of Leipzig, 04103, Leipzig, Germany
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Center Munich at the University of Leipzig, University Hospital Leipzig, 04103, Leipzig, Germany
| | - Peter Kovacs
- Medical Department III-Endocrinology, Nephrology, Rheumatology, Medical Center, University of Leipzig, 04103, Leipzig, Germany
| | - Yvonne Böttcher
- EpiGen, Department of Clinical Molecular Biology, Institute of Clinical Medicine, University of Oslo, 0316, Oslo, Norway.
- EpiGen, Medical Division, Akershus University Hospital, 1478, Lørenskog, Norway.
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Anwar MY, Graff M, Highland HM, Smit R, Wang Z, Buchanan VL, Young KL, Kenny EE, Fernandez-Rhodes L, Liu S, Assimes T, Garcia DO, Daeeun K, Gignoux CR, Justice AE, Haiman CA, Buyske S, Peters U, Loos RJF, Kooperberg C, North KE. Assessing efficiency of fine-mapping obesity-associated variants through leveraging ancestry architecture and functional annotation using PAGE and UKBB cohorts. Hum Genet 2023; 142:1477-1489. [PMID: 37658231 DOI: 10.1007/s00439-023-02593-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 08/10/2023] [Indexed: 09/03/2023]
Abstract
Inadequate representation of non-European ancestry populations in genome-wide association studies (GWAS) has limited opportunities to isolate functional variants. Fine-mapping in multi-ancestry populations should improve the efficiency of prioritizing variants for functional interrogation. To evaluate this hypothesis, we leveraged ancestry architecture to perform comparative GWAS and fine-mapping of obesity-related phenotypes in European ancestry populations from the UK Biobank (UKBB) and multi-ancestry samples from the Population Architecture for Genetic Epidemiology (PAGE) consortium with comparable sample sizes. In the investigated regions with genome-wide significant associations for obesity-related traits, fine-mapping in our ancestrally diverse sample led to 95% and 99% credible sets (CS) with fewer variants than in the European ancestry sample. Lead fine-mapped variants in PAGE regions had higher average coding scores, and higher average posterior probabilities for causality compared to UKBB. Importantly, 99% CS in PAGE loci contained strong expression quantitative trait loci (eQTLs) in adipose tissues or harbored more variants in tighter linkage disequilibrium (LD) with eQTLs. Leveraging ancestrally diverse populations with heterogeneous ancestry architectures, coupled with functional annotation, increased fine-mapping efficiency and performance, and reduced the set of candidate variants for consideration for future functional studies. Significant overlap in genetic causal variants across populations suggests generalizability of genetic mechanisms underpinning obesity-related traits across populations.
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Affiliation(s)
- Mohammad Yaser Anwar
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
| | - Mariaelisa Graff
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Heather M Highland
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Roelof Smit
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Zhe Wang
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Victoria L Buchanan
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Kristin L Young
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Eimear E Kenny
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lindsay Fernandez-Rhodes
- Department of Biobehavioral Health, College of Health and Human Development, Pennsylvania State University, University Park, PA, 16802, USA
| | - Simin Liu
- Department of Epidemiology and Center for Global Cardiometabolic Health, School of Public Health, Brown University, Providence, RI, 02903, USA
| | - Themistocles Assimes
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - David O Garcia
- Department of Health Promotion Sciences, Mel & Enid Zuckerman College of Public Health, University of Arizona, Tucson, AZ, 85724, USA
| | - Kim Daeeun
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Christopher R Gignoux
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Anne E Justice
- Department of Population Health Sciences, Geisinger Health, Danville, PA, 17822, USA
| | - Christopher A Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Steve Buyske
- Department of Statistics, Rutgers University, Piscataway, NJ, 08854, USA
| | - Ulrike Peters
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
| | - Ruth J F Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
| | - Kari E North
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
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Li D, Zhang B, Cheng J, Chen D, Wu Y, Luo Q, Zhou L. Obesity-related genetic polymorphisms are associated with the risk of early puberty in Han Chinese girls. Clin Endocrinol (Oxf) 2022; 96:319-327. [PMID: 34761429 DOI: 10.1111/cen.14631] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 10/19/2021] [Accepted: 10/31/2021] [Indexed: 11/28/2022]
Abstract
OBJECTIVE To explore the association between obesity and precocious puberty from the perspective of genetic polymorphism. DESIGN Two hundred and ninety-eight pairs of girls in early puberty and age-matched controls (±3 months) were recruited. The genotypes of four obesity-related single-nucleotide polymorphism (SNP) loci (rs10968576, rs12935153, rs4674340 and rs7635103) were determined and the effect of variation on early puberty in Chinese Han girls was evaluated. The unstimulated luteinizing hormone (LH), follicle-stimulating hormone and estradiol levels were also measured to determine the relationship with SNP polymorphisms. RESULTS The effect allele A of rs12935153 was associated with early puberty (odds ratio [OR] = 1.256, 95% confidence interval [CI]: 1.010-1.585), but the significance disappeared after multiple comparisons. After adjusting for body mass index, rs12935153 variation increased the risk of early puberty in additive (OR = 1.589, 95% CI: 1.222-2.066), dominant (OR = 1.788, 95% CI: 1.210-2.642) and recessive (OR = 1.915, 95% CI: 1.207-3.038) models of inheritance. Individuals harbouring AA genotype in rs12935153 had a risk of higher LH levels than that of wild type (OR = 1.668, 95% CI: 1.093-2.546). CONCLUSIONS The association between obesity and precocity can be explained from a genetic perspective. Our study suggests that variations in rs12935153 increase the risk of early puberty in Chinese girls. Further studies are needed to verify our findings.
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Affiliation(s)
- Di Li
- Department of School Hygiene, Shenzhen Center for Disease Control and Prevention, Shenzhen, Guangdong, China
- Department of Clinical Nutrition, Shenzhen University General Hospital, Shenzhen University, Shenzhen, Guangdong, China
| | - Boxian Zhang
- Department of School Hygiene, Shenzhen Center for Disease Control and Prevention, Shenzhen, Guangdong, China
- Medical department, Hospital of Stomatology, SunYat-sen University, Guangzhou, Guangdong, China
| | - Jinquan Cheng
- Department of School Hygiene, Shenzhen Center for Disease Control and Prevention, Shenzhen, Guangdong, China
| | - Dingyan Chen
- Department of School Hygiene, Shenzhen Center for Disease Control and Prevention, Shenzhen, Guangdong, China
| | - Yu Wu
- Department of School Hygiene, Shenzhen Center for Disease Control and Prevention, Shenzhen, Guangdong, China
| | - Qingshan Luo
- Department of School Hygiene, Shenzhen Center for Disease Control and Prevention, Shenzhen, Guangdong, China
| | - Li Zhou
- Department of School Hygiene, Shenzhen Center for Disease Control and Prevention, Shenzhen, Guangdong, China
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CYP1A2 polymorphisms modify the association of habitual coffee consumption with appetite, macronutrient intake, and body mass index: results from an observational cohort and a cross-over randomized study. Int J Obes (Lond) 2021; 46:162-168. [PMID: 34564706 DOI: 10.1038/s41366-021-00972-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 09/07/2021] [Accepted: 09/15/2021] [Indexed: 01/14/2023]
Abstract
BACKGROUND/OBJECTIVES Evidence regarding the influence of coffee on appetite and weight control is equivocal and the influence of covariates, such as genetic variation in caffeine metabolism, remains unknown. Herein, we addressed the novel hypothesis that genetic variation in CYP1A2, a gene responsible for more than 95% of caffeine metabolism, differentially impacts the association of coffee consumption with appetite and BMI among individuals with different genetic predispositions to obesity. SUBJECTS/METHODS A cross-over randomized intervention study involving 18 volunteers assessed the effects of coffee consumption on dietary intake, appetite, and levels of the appetite-controlling hormones asprosin and leptin. Data on habitual coffee intake, BMI, and perceived appetite were obtained from an observational cohort of 284 volunteers using validated questionnaires. Participants were stratified according to a validated genetic risk score (GRS) for obesity and to the -163C > A (rs762551) polymorphism of CYP1A2 as rapid (AA), intermediate (AC), or slow (CC) caffeine metabolizers. RESULTS Coffee consumption led to lower energy and dietary fat intake and circulating asprosin levels (P for interaction of rs762551 genotype*coffee consumption=0.056, 0.039, and 0.043, respectively) as compared to slow/intermediate metabolizers. High coffee consumption was more prevalent in rapid compared to slow metabolizers (P = 0.008 after adjustment for age, sex, and BMI) and was associated with lower appetite perception and lower BMI only in rapid metabolizers (P for interaction of rs762551 genotype*coffee consumption = 0.002 and 0.048, respectively). This differential association of rs762551 genotype and coffee consumption with BMI was more evident in individuals at higher genetic risk of obesity (mean adjusted difference in BMI = -5.82 kg/m2 for rapid versus slow/intermediate metabolizers who consumed more than 14 cups of coffee per week). CONCLUSIONS CYP1A2 rs762551 polymorphism modifies the association of habitual coffee consumption with BMI, in part by influencing appetite, energy intake and circulating levels of the orexigenic hormone asprosin. This association is more evident in subjects with high genetic predisposition to obesity. ClinicalTrials.gov: registered Clinical Trial NCT04514588.
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Pham C, Muñoz-Martín N, Lodder EM. The Diverse Roles of TNNI3K in Cardiac Disease and Potential for Treatment. Int J Mol Sci 2021; 22:6422. [PMID: 34203974 PMCID: PMC8232738 DOI: 10.3390/ijms22126422] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/11/2021] [Accepted: 06/14/2021] [Indexed: 12/25/2022] Open
Abstract
In the two decades since the discovery of TNNI3K it has been implicated in multiple cardiac phenotypes and physiological processes. TNNI3K is an understudied kinase, which is mainly expressed in the heart. Human genetic variants in TNNI3K are associated with supraventricular arrhythmias, conduction disease, and cardiomyopathy. Furthermore, studies in mice implicate the gene in cardiac hypertrophy, cardiac regeneration, and recovery after ischemia/reperfusion injury. Several new papers on TNNI3K have been published since the last overview, broadening the clinical perspective of TNNI3K variants and our understanding of the underlying molecular biology. We here provide an overview of the role of TNNI3K in cardiomyopathy and arrhythmia covering both a clinical perspective and basic science advancements. In addition, we review the potential of TNNI3K as a target for clinical treatments in different cardiac diseases.
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Affiliation(s)
| | | | - Elisabeth M. Lodder
- Department of Clinical and Experimental Cardiology, Heart Center, University of Amsterdam, Amsterdam UMC, 1105 AZ Amsterdam, The Netherlands; (C.P.); (N.M.-M.)
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Anguita-Ruiz A, Bustos-Aibar M, Plaza-Díaz J, Mendez-Gutierrez A, Alcalá-Fdez J, Aguilera CM, Ruiz-Ojeda FJ. Omics Approaches in Adipose Tissue and Skeletal Muscle Addressing the Role of Extracellular Matrix in Obesity and Metabolic Dysfunction. Int J Mol Sci 2021; 22:2756. [PMID: 33803198 PMCID: PMC7963192 DOI: 10.3390/ijms22052756] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/03/2021] [Accepted: 03/05/2021] [Indexed: 12/14/2022] Open
Abstract
Extracellular matrix (ECM) remodeling plays important roles in both white adipose tissue (WAT) and the skeletal muscle (SM) metabolism. Excessive adipocyte hypertrophy causes fibrosis, inflammation, and metabolic dysfunction in adipose tissue, as well as impaired adipogenesis. Similarly, disturbed ECM remodeling in SM has metabolic consequences such as decreased insulin sensitivity. Most of described ECM molecular alterations have been associated with DNA sequence variation, alterations in gene expression patterns, and epigenetic modifications. Among others, the most important epigenetic mechanism by which cells are able to modulate their gene expression is DNA methylation. Epigenome-Wide Association Studies (EWAS) have become a powerful approach to identify DNA methylation variation associated with biological traits in humans. Likewise, Genome-Wide Association Studies (GWAS) and gene expression microarrays have allowed the study of whole-genome genetics and transcriptomics patterns in obesity and metabolic diseases. The aim of this review is to explore the molecular basis of ECM in WAT and SM remodeling in obesity and the consequences of metabolic complications. For that purpose, we reviewed scientific literature including all omics approaches reporting genetic, epigenetic, and transcriptomic (GWAS, EWAS, and RNA-seq or cDNA arrays) ECM-related alterations in WAT and SM as associated with metabolic dysfunction and obesity.
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Affiliation(s)
- Augusto Anguita-Ruiz
- Department of Biochemistry and Molecular Biology II, School of Pharmacy, University of Granada, 18071 Granada, Spain; (A.A.-R.); (M.B.-A.); (J.P.-D.); (A.M.-G.); (F.J.R.-O.)
- Instituto de Investigación Biosanitaria IBS.GRANADA, Complejo Hospitalario Universitario de Granada, 18014 Granada, Spain
- Institute of Nutrition and Food Technology “José Mataix”, Center of Biomedical Research, University of Granada, Avda. del Conocimiento s/n., 18016 Granada, Spain
- CIBEROBN (CIBER Physiopathology of Obesity and Nutrition), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Mireia Bustos-Aibar
- Department of Biochemistry and Molecular Biology II, School of Pharmacy, University of Granada, 18071 Granada, Spain; (A.A.-R.); (M.B.-A.); (J.P.-D.); (A.M.-G.); (F.J.R.-O.)
- Institute of Nutrition and Food Technology “José Mataix”, Center of Biomedical Research, University of Granada, Avda. del Conocimiento s/n., 18016 Granada, Spain
| | - Julio Plaza-Díaz
- Department of Biochemistry and Molecular Biology II, School of Pharmacy, University of Granada, 18071 Granada, Spain; (A.A.-R.); (M.B.-A.); (J.P.-D.); (A.M.-G.); (F.J.R.-O.)
- Instituto de Investigación Biosanitaria IBS.GRANADA, Complejo Hospitalario Universitario de Granada, 18014 Granada, Spain
- Institute of Nutrition and Food Technology “José Mataix”, Center of Biomedical Research, University of Granada, Avda. del Conocimiento s/n., 18016 Granada, Spain
- Children’s Hospital of Eastern Ontario Research Institute, Ottawa, ON K1H 8L1, Canada
| | - Andrea Mendez-Gutierrez
- Department of Biochemistry and Molecular Biology II, School of Pharmacy, University of Granada, 18071 Granada, Spain; (A.A.-R.); (M.B.-A.); (J.P.-D.); (A.M.-G.); (F.J.R.-O.)
- Instituto de Investigación Biosanitaria IBS.GRANADA, Complejo Hospitalario Universitario de Granada, 18014 Granada, Spain
- Institute of Nutrition and Food Technology “José Mataix”, Center of Biomedical Research, University of Granada, Avda. del Conocimiento s/n., 18016 Granada, Spain
- CIBEROBN (CIBER Physiopathology of Obesity and Nutrition), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Jesús Alcalá-Fdez
- Department of Computer Science and Artificial Intelligence, University of Granada, 18071 Granada, Spain;
| | - Concepción María Aguilera
- Department of Biochemistry and Molecular Biology II, School of Pharmacy, University of Granada, 18071 Granada, Spain; (A.A.-R.); (M.B.-A.); (J.P.-D.); (A.M.-G.); (F.J.R.-O.)
- Instituto de Investigación Biosanitaria IBS.GRANADA, Complejo Hospitalario Universitario de Granada, 18014 Granada, Spain
- Institute of Nutrition and Food Technology “José Mataix”, Center of Biomedical Research, University of Granada, Avda. del Conocimiento s/n., 18016 Granada, Spain
- CIBEROBN (CIBER Physiopathology of Obesity and Nutrition), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Francisco Javier Ruiz-Ojeda
- Department of Biochemistry and Molecular Biology II, School of Pharmacy, University of Granada, 18071 Granada, Spain; (A.A.-R.); (M.B.-A.); (J.P.-D.); (A.M.-G.); (F.J.R.-O.)
- Instituto de Investigación Biosanitaria IBS.GRANADA, Complejo Hospitalario Universitario de Granada, 18014 Granada, Spain
- RG Adipocytes and Metabolism, Institute for Diabetes and Obesity, Helmholtz Diabetes Center at Helmholtz Center Munich, Neuherberg, 85764 Munich, Germany
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Vázquez-Moreno M, Zeng H, Locia-Morales D, Peralta-Romero J, Asif H, Maharaj A, Tam V, Romero-Figueroa MDS, Sosa-Bustamante GP, Méndez-Martínez S, Mejía-Benítez A, Valladares-Salgado A, Wacher-Rodarte N, Cruz M, Meyre D. The Melanocortin 4 Receptor p.Ile269Asn Mutation Is Associated with Childhood and Adult Obesity in Mexicans. J Clin Endocrinol Metab 2020; 105:5679482. [PMID: 31841602 DOI: 10.1210/clinem/dgz276] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 12/13/2019] [Indexed: 12/19/2022]
Abstract
CONTEXT Rare partial/complete loss-of-function mutations in the melanocortin-4 receptor (MC4R) gene are the most common cause of Mendelian obesity in European populations, but their contribution to obesity in the Mexican population is unclear. OBJECTIVE AND DESIGN We investigated whether deleterious mutations in MC4R contribute to obesity in Mexican children and adults. RESULTS We provide evidence that the MC4R p.Ile269Asn (rs79783591) mutation may have arisen in modern human populations from a founder event in native Mexicans. The MC4R Isoleucine 269 is perfectly conserved across 184 species, which suggests a critical role for the amino acid in MC4R activity. Four in silico tools (SIFT, PolyPhen-2, CADD, MutPred2) predicted a deleterious impact of the p.Ile269Asn substitution on MC4R function. The MC4R p.Ile269Asn mutation was associated with childhood (Ncontrols = 952, Ncases = 661, odds ratio (OR) = 3.06, 95% confidence interval (95%CI) [1.94-4.85]) and adult obesity (Ncontrols = 1445, Ncases = 2,487, OR = 2.58, 95%CI [1.52-4.39]). The frequency of the MC4R p.Ile269Asn mutation ranged from 0.52 to 0.59% and 1.53 to 1.59% in children and adults with normal weight and obesity, respectively. The MC4R p.Ile269Asn mutation co-segregated perfectly with obesity in 5 multigenerational Mexican pedigrees. While adults with obesity carrying the p.Ile269Asn mutation had higher BMI values than noncarriers, this trend was not observed in children. The MC4R p.Ile269Asn mutation accounted for a population attributable risk of 1.28% and 0.68% for childhood and adult obesity, respectively, in the Mexican population. CONCLUSION The MC4R p.Ile269Asn mutation may have emerged as a founder mutation in native Mexicans and is associated with childhood and adult obesity in the modern Mexican population.
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Affiliation(s)
- Miguel Vázquez-Moreno
- Unidad de Investigación Médica en Bioquímica, Hospital de Especialidades, Centro Médico Nacional Siglo XXI del Instituto Mexicano del Seguro Social, Ciudad de México, México
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, Canada
| | - Helen Zeng
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, Canada
| | - Daniel Locia-Morales
- Unidad de Investigación Médica en Bioquímica, Hospital de Especialidades, Centro Médico Nacional Siglo XXI del Instituto Mexicano del Seguro Social, Ciudad de México, México
| | - Jesús Peralta-Romero
- Unidad de Investigación Médica en Bioquímica, Hospital de Especialidades, Centro Médico Nacional Siglo XXI del Instituto Mexicano del Seguro Social, Ciudad de México, México
| | - Hamza Asif
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, Canada
| | - Arjuna Maharaj
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, Canada
| | - Vivian Tam
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, Canada
| | - María D S Romero-Figueroa
- Centro de Investigación en Ciencias de la Salud (CICSA), Facultad de Ciencias de la Salud, Universidad Anáhuac, Campus Norte, Huixquilucan, México
| | | | - Socorro Méndez-Martínez
- Coordinación de Investigación en Salud, Instituto Mexicano del Seguro Social Puebla, Puebla, México
| | - Aurora Mejía-Benítez
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, Canada
| | - Adan Valladares-Salgado
- Unidad de Investigación Médica en Bioquímica, Hospital de Especialidades, Centro Médico Nacional Siglo XXI del Instituto Mexicano del Seguro Social, Ciudad de México, México
| | - Niels Wacher-Rodarte
- Unidad de Investigación en Epidemiología Clínica, Hospital de Especialidades Bernardo Sepúlveda, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de México, México
| | | | - Miguel Cruz
- Unidad de Investigación Médica en Bioquímica, Hospital de Especialidades, Centro Médico Nacional Siglo XXI del Instituto Mexicano del Seguro Social, Ciudad de México, México
| | - David Meyre
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, Canada
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Canada
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8
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Costa-Urrutia P, Abud C, Franco-Trecu V, Colistro V, Rodríguez-Arellano ME, Alvarez-Fariña R, Acuña Alonso V, Bertoni B, Granados J. Effect of 15 BMI-Associated Polymorphisms, Reported for Europeans, across Ethnicities and Degrees of Amerindian Ancestry in Mexican Children. Int J Mol Sci 2020; 21:E374. [PMID: 31936053 PMCID: PMC7013683 DOI: 10.3390/ijms21020374] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 12/20/2019] [Accepted: 01/03/2020] [Indexed: 12/22/2022] Open
Abstract
In Mexico, the genetic mechanisms underlying childhood obesity are poorly known. We evaluated the effect of loci, known to be associated with childhood body mass index (BMI) in Europeans, in Mexican children from different ethnic groups. We performed linear and logistic analyses of BMI and obesity, respectively, in Mestizos and Amerindians (Seris, Yaquis and Nahuatl speakers) from Northern (n = 369) and Central Mexico (n = 8545). We used linear models to understand the effect of degree of Amerindian ancestry (AMA) and genetic risk score (GRS) on BMI z-score. Northern Mexican Mestizos showed the highest overweight-obesity prevalence (47.4%), followed by Seri (36.2%) and Central Mexican (31.5%) children. Eleven loci (SEC16B/rs543874, OLFM4/rs12429545/rs9568856, FTO/rs9939609, MC4R/rs6567160, GNPDA2/rs13130484, FAIM2/rs7132908, FAM120AOS/rs944990, LMX1B/rs3829849, ADAM23/rs13387838, HOXB5/rs9299) were associated with BMI and seven (SEC16B/rs543874, OLFM4/rs12429545/rs9568856, FTO/rs9939609, MC4R/rs6567160, GNPDA2 rs13130484, LMX1B/rs3829849) were associated with obesity in Central Mexican children. One SNP was associated with obesity in Northern Mexicans and Yaquis (SEC16B/rs543874). We found higher BMI z-score at higher GRS (β = 0.11, p = 0.2 × 10-16) and at lower AMA (β = -0.05, p = 6.8 × 10-7). The GRS interacts with AMA to increase BMI (β = 0.03, p = 6.08 × 10-3). High genetic BMI susceptibility increase the risk of higher BMI, including in Amerindian children.
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Affiliation(s)
- Paula Costa-Urrutia
- Laboratorio de Medicina Genómica del Hospital Regional Lic. Adolfo López Mateos, ISSSTE, Ciudad de México 01030, Mexico;
- Integrigen de Mexico SAPI de CV. Patriotismo 12, Ciudad de México 06100, Mexico; (C.A.); (R.A.-F.)
| | - Carolina Abud
- Integrigen de Mexico SAPI de CV. Patriotismo 12, Ciudad de México 06100, Mexico; (C.A.); (R.A.-F.)
| | - Valentina Franco-Trecu
- Departamento de Ecología y Evolución, Facultad de Ciencias, Universidad de la República. Iguá 4225, Montevideo 11400, Uruguay;
| | - Valentina Colistro
- Departamento de Métodos Cuantitativos, Facultad de Medicina, Universidad de la República. Avda. General Flores 2125, Montevideo 11800, Uruguay;
| | | | - Rafael Alvarez-Fariña
- Integrigen de Mexico SAPI de CV. Patriotismo 12, Ciudad de México 06100, Mexico; (C.A.); (R.A.-F.)
| | - Víctor Acuña Alonso
- Instituto Nacional de Antropología e Historia. Periférico Sur y Zapote, Tlalpan, Ciudad de México 14030, Mexico;
| | - Bernardo Bertoni
- Departamento de Genetica, Facultad de Medicina, Universidad de la República. Avda. General Flores 2125, Montevideo 11800, Uruguay;
| | - Julio Granados
- División de Inmunogenética, Departamento de Trasplantes, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán. Avda. Vasco de Quiroga, Ciudad de México14080, Mexico;
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9
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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: 933] [Impact Index Per Article: 186.6] [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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10
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Ramírez Á, Hernández M, Suárez-Sánchez R, Ortega C, Peralta J, Gómez J, Valladares A, Cruz M, Vázquez-Moreno MA, Suárez-Sánchez F. Type 2 diabetes-associated polymorphisms correlate with SIRT1 and TGF-β1 gene expression. Ann Hum Genet 2019; 84:185-194. [PMID: 31799723 DOI: 10.1111/ahg.12363] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 08/08/2019] [Accepted: 10/10/2019] [Indexed: 12/27/2022]
Abstract
The polymorphisms rs3758391 and rs1800470 located in SIRT1 and TGF-β1 have been associated with type 2 diabetes in different populations but its functional effect is not clear. In this study, we evaluated their effect on the expression of SIRT1 and TGF-β1 in peripheral blood as well as their participation in the formation of DNA-protein complexes in a pancreas-derived cell line. It has been described that SIRT1 and TGF-β1 participate in cell growth and regulation of production and secretion of insulin in the pancreas. Anthropometric and biochemical profiles of 127 adults were measured. Genotypes for rs3758391 and rs1800470 were determined using TaqMan assays. Expression analysis of SIRT1 and TGF-β1 were performed using real-time PCR. Gene expression of these genes increased 1.8 ± 0.6- and 1.3 ± 0.6-fold in patients carrying the TT genotype of rs3758391 and rs1800470 when compared to carriers of the CC genotype. Then, we tested whether these single-nucleotide polymorphisms (SNPs) (and rs932658, which is in linkage disequilibrium with rs3758391) are located in regulatory DNA-protein binding sites by electrophoretic mobility shift assays using nuclear extract from the pancreas-derived cell line BxPC-3. The electrophoretic mobility shift assay showed no binding of nuclear proteins to DNA. In conclusion, the genotypes of rs3758391 and rs1800470 are associated with modifications in the expression of the genes SIRT1 and TGF-β1, respectively, but none of the tested SNPs are located in regulatory DNA-protein binding sites.
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Affiliation(s)
- Ángeles Ramírez
- Unidad de Investigación Médica en Bioquímica, Hospital de Especialidades, Ciudad de México, México
| | - Miriam Hernández
- Unidad de Investigación Médica en Bioquímica, Hospital de Especialidades, Ciudad de México, México
| | - Rocío Suárez-Sánchez
- Laboratorio de Medicina Genómica, Departamento de Genética, Instituto Nacional de Rehabilitación LGII, Ciudad de México
| | - Clara Ortega
- Unidad de Investigación Médica en Bioquímica, Hospital de Especialidades, Ciudad de México, México
| | - Jesús Peralta
- Unidad de Investigación Médica en Bioquímica, Hospital de Especialidades, Ciudad de México, México
| | - Jaime Gómez
- Unidad de Investigación Médica en Bioquímica, Hospital de Especialidades, Ciudad de México, México
| | - Adán Valladares
- Unidad de Investigación Médica en Bioquímica, Hospital de Especialidades, Ciudad de México, México
| | - Miguel Cruz
- Unidad de Investigación Médica en Bioquímica, Hospital de Especialidades, Ciudad de México, México
| | | | - Fernando Suárez-Sánchez
- Unidad de Investigación Médica en Bioquímica, Hospital de Especialidades, Ciudad de México, México
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11
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Costa-Urrutia P, Colistro V, Jiménez-Osorio AS, Cárdenas-Hernández H, Solares-Tlapechco J, Ramirez-Alcántara M, Granados J, Ascencio-Montiel IDJ, Rodríguez-Arellano ME. Genome-Wide Association Study of Body Mass Index and Body Fat in Mexican-Mestizo Children. Genes (Basel) 2019; 10:E945. [PMID: 31752434 PMCID: PMC6895864 DOI: 10.3390/genes10110945] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 11/12/2019] [Accepted: 11/15/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Childhood obesity is a major health problem in Mexico. Obesity prevalence estimated by body mass index (BMI) is almost half than that estimated by percent body fat (%BF) in the Childhood Obesity pediatric cohort (COIPIS). OBJECTIVE We performed a genome-wide association study (GWAS) of BMI and %BF in 828 children from the COIPIS to identify markers of predisposition to high values for both phenotypes used for obesity classification. METHODS For the GWAS we used the LAT Axiom 1, Affymetrix and 2.5 million single loci from the 1000 Genomes Phase 3 imputation panel. We used a linear model, adjusted by age, sex, and Amerindian ancestry assuming an additive inheritance model. RESULTS Genome-wide significance (p ≤ 5.0 × 10-8) and 80% of statistical power was reached for associations of two loci in two genes (CERS3 and CYP2E1) to BMI. Also, 11 loci in six genes (ANKS1B, ARNTL2, KCNS3, LMNB1, SRGAP3, TRPC7) reached genome-wide significance for associations to %BF, though not 80% of statistical power. DISCUSSION None of the SNPs were previously reported as being associated to BMI or %BF. In addition, different loci were found for BMI and %BF. These results highlight the importance of gaining deeper understanding of genetic markers of predisposition to high values for the phenotypes used for obesity diagnosis.
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Affiliation(s)
- Paula Costa-Urrutia
- Laboratorio de Medicina Genómica, Hospital Regional Lic. Adolfo López Mateos, ISSSTE. 1321 Universidad Avenue, Álvaro Obregón, Florida, Mexico City P.C0103, Mexico; (P.C.-U.); (A.S.J.-O.); (H.C.-H.); (J.S.-T.); (M.R.-A.)
| | - Valentina Colistro
- Departamento de Métodos Cuantitativos, Facultad de Medicina, Universidad de la República, 2125 General Flores Avenue, Montevideo P.C11800, Uruguay;
| | - Angélica Saraí Jiménez-Osorio
- Laboratorio de Medicina Genómica, Hospital Regional Lic. Adolfo López Mateos, ISSSTE. 1321 Universidad Avenue, Álvaro Obregón, Florida, Mexico City P.C0103, Mexico; (P.C.-U.); (A.S.J.-O.); (H.C.-H.); (J.S.-T.); (M.R.-A.)
| | - Helios Cárdenas-Hernández
- Laboratorio de Medicina Genómica, Hospital Regional Lic. Adolfo López Mateos, ISSSTE. 1321 Universidad Avenue, Álvaro Obregón, Florida, Mexico City P.C0103, Mexico; (P.C.-U.); (A.S.J.-O.); (H.C.-H.); (J.S.-T.); (M.R.-A.)
| | - Jacqueline Solares-Tlapechco
- Laboratorio de Medicina Genómica, Hospital Regional Lic. Adolfo López Mateos, ISSSTE. 1321 Universidad Avenue, Álvaro Obregón, Florida, Mexico City P.C0103, Mexico; (P.C.-U.); (A.S.J.-O.); (H.C.-H.); (J.S.-T.); (M.R.-A.)
| | - Miryam Ramirez-Alcántara
- Laboratorio de Medicina Genómica, Hospital Regional Lic. Adolfo López Mateos, ISSSTE. 1321 Universidad Avenue, Álvaro Obregón, Florida, Mexico City P.C0103, Mexico; (P.C.-U.); (A.S.J.-O.); (H.C.-H.); (J.S.-T.); (M.R.-A.)
| | - Julio Granados
- División de Inmunogenética, Departamento de Trasplantes, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán. 15 Vasco de Quiroga Avenue. Mexico City P.C.14080, Mexico;
| | - Iván de Jesús Ascencio-Montiel
- Coordinación de Vigilancia de Epidemiología, Instituto Mexicano de Seguro Social, 120 Mier y Pesado Street, del Valle Benito Juárez, Mexico City C.P. 03100 Mexico;
| | - Martha Eunice Rodríguez-Arellano
- Laboratorio de Medicina Genómica, Hospital Regional Lic. Adolfo López Mateos, ISSSTE. 1321 Universidad Avenue, Álvaro Obregón, Florida, Mexico City P.C0103, Mexico; (P.C.-U.); (A.S.J.-O.); (H.C.-H.); (J.S.-T.); (M.R.-A.)
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12
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Kaur Y, Wang DX, Liu HY, Meyre D. Comprehensive identification of pleiotropic loci for body fat distribution using the NHGRI-EBI Catalog of published genome-wide association studies. Obes Rev 2019; 20:385-406. [PMID: 30565845 DOI: 10.1111/obr.12806] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 10/05/2018] [Accepted: 10/15/2018] [Indexed: 12/22/2022]
Abstract
We conducted a hypothesis-free cross-trait analysis for waist-to-hip ratio adjusted for body mass index (WHRadjBMI ) loci derived through genome-wide association studies (GWAS). Summary statistics from published GWAS were used to capture all WHRadjBMI single-nucleotide polymorphisms (SNPs), and their proxy SNPs were identified. These SNPs were used to extract cross-trait associations between WHRadjBMI SNPs and other traits through the NHGRI-EBI GWAS Catalog. Pathway analysis was conducted for pleiotropic WHRadjBMI SNPs. We found 160 WHRadjBMI SNPs and 3675 proxy SNPs. Cross-trait analysis identified 239 associations, of which 100 were for obesity traits. The remaining 139 associations were filtered down to 101 unique linkage disequilibrium block associations, which were grouped into 13 categories: lipids, red blood cell traits, white blood cell counts, inflammatory markers and autoimmune diseases, type 2 diabetes-related traits, adiponectin, cancers, blood pressure, height, neuropsychiatric disorders, electrocardiography changes, urea measurement, and others. The highest number of cross-trait associations were found for triglycerides (n = 10), high-density lipoprotein cholesterol (n = 9), and reticulocyte counts (n = 8). Pathway analysis for WHRadjBMI pleiotropic SNPs found immune function pathways as the top canonical pathways. Results from our original methodology indicate a novel genetic association between WHRadjBMI and reticulocyte counts and highlight the pleiotropy between abdominal obesity, immune pathways, and other traits.
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Affiliation(s)
- Yuvreet Kaur
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, Canada.,Faculty of Medicine, University of Toronto, Toronto, Canada
| | - Dominic X Wang
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, Canada.,Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, Canada
| | - Hsin-Yen Liu
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, Canada.,Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, Canada
| | - David Meyre
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, Canada.,Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Canada
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