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Shang L, Zhao W, Wang YZ, Li Z, Choi JJ, Kho M, Mosley TH, Kardia SLR, Smith JA, Zhou X. meQTL mapping in the GENOA study reveals genetic determinants of DNA methylation in African Americans. Nat Commun 2023; 14:2711. [PMID: 37169753 PMCID: PMC10175543 DOI: 10.1038/s41467-023-37961-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 04/07/2023] [Indexed: 05/13/2023] Open
Abstract
Identifying genetic variants that are associated with variation in DNA methylation, an analysis commonly referred to as methylation quantitative trait locus (meQTL) mapping, is an important first step towards understanding the genetic architecture underlying epigenetic variation. Most existing meQTL mapping studies have focused on individuals of European ancestry and are underrepresented in other populations, with a particular absence of large studies in populations with African ancestry. We fill this critical knowledge gap by performing a large-scale cis-meQTL mapping study in 961 African Americans from the Genetic Epidemiology Network of Arteriopathy (GENOA) study. We identify a total of 4,565,687 cis-acting meQTLs in 320,965 meCpGs. We find that 45% of meCpGs harbor multiple independent meQTLs, suggesting potential polygenic genetic architecture underlying methylation variation. A large percentage of the cis-meQTLs also colocalize with cis-expression QTLs (eQTLs) in the same population. Importantly, the identified cis-meQTLs explain a substantial proportion (median = 24.6%) of methylation variation. In addition, the cis-meQTL associated CpG sites mediate a substantial proportion (median = 24.9%) of SNP effects underlying gene expression. Overall, our results represent an important step toward revealing the co-regulation of methylation and gene expression, facilitating the functional interpretation of epigenetic and gene regulation underlying common diseases in African Americans.
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Affiliation(s)
- Lulu Shang
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Wei Zhao
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Yi Zhe Wang
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Zheng Li
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Jerome J Choi
- Population Health Sciences, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI, 53726, USA
| | - Minjung Kho
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Thomas H Mosley
- Memory Impairment and Neurodegenerative Dementia (MIND) Center, University of Mississippi Medical Center, Jackson, MS, 39126, USA
| | - Sharon L R Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Jennifer A Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, 48109, USA.
| | - Xiang Zhou
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, 48109, USA.
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Yu T, Yu Y, Li X, Xue P, Yu X, Chen Y, Kong H, Lin C, Wang X, Mei H, Wang D, Liu S. Effects of childhood obesity and related genetic factors on precocious puberty: protocol for a multi-center prospective cohort study. BMC Pediatr 2022; 22:310. [PMID: 35624438 PMCID: PMC9135982 DOI: 10.1186/s12887-022-03350-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 05/11/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Childhood obesity has important effects on the onset and development of puberty. Although a number of studies have confirmed the relationship between obesity and precocious puberty, little is known about the pleiotropic genes of obesity and precocious puberty and the interaction between genes and environment. There are four objectives: (1) to analyze the incidence of precocious puberty in the general population in China; (2) to verify the direct effect of obesity on children's precocious puberty using a variety of methods; (3) to verify the effect of obesity and its risk gene polymorphism on precocious puberty in a prospective cohort study; and (4) to analyze the interaction effect of genes and environment on pubertal development. METHODS We will conduct a multi-center prospective cohort study in three cities, which are selected in southern, central, and northern China, respectively. Primary schools in these cities will be selected by a stratified cluster random sampling method. Primary school students from grade 1 to grade 3 (6 to 10 years old) will be selected for the cohort with extensive baseline data collection, including assessment of pubertal development, family demographic information, early development, sleep pattern, dietary pattern, and physical activity. Participants will be followed up for at least three years, and long-term follow-up will depend on future funding. DISCUSSION The findings of this multicenter prospective population-based cohort study may expand previous related puberty development research as well as provide important information on the mechanism of early puberty. Targeted interventions can also be developed to improve adolescent health problems related to puberty development based on the available evidence. TRIAL REGISTRATION ClinicalTrials.gov Identifier: NCT04113070 , prospectively registered on October 2, 2019.
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Affiliation(s)
- Tingting Yu
- Sanya Women and Children's Hospital, managed by Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, 339 Yingbin Road, Sanya, 572022, China.,Office of Hospital Infection Management, The Fourth Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Ying Yu
- Sanya Women and Children's Hospital, managed by Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, 339 Yingbin Road, Sanya, 572022, China
| | - Xiaoqing Li
- Sanya Women and Children's Hospital, managed by Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, 339 Yingbin Road, Sanya, 572022, China.,School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Peng Xue
- Sanya Women and Children's Hospital, managed by Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, 339 Yingbin Road, Sanya, 572022, China.,School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaodan Yu
- Department of Developmental and Behavioral Pediatrics, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yao Chen
- Department of Endocrinology and Genetic Metabolism, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Huijun Kong
- Department of Pediatrics, Qu Fu People's Hospital, Qufu, Shandong, China
| | - Cuilan Lin
- Boai Hospital of Zhongshan, Southern Medical University, Zhongshan, Guangdong, China
| | - Xiumin Wang
- Department of Endocrinology and Genetic Metabolism, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hao Mei
- Department of Data Science, School of Population Health, University of Mississippi Medical Center, Jackson, MS, USA
| | - Dan Wang
- Sanya Women and Children's Hospital, managed by Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, 339 Yingbin Road, Sanya, 572022, China.
| | - Shijian Liu
- Sanya Women and Children's Hospital, managed by Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, 339 Yingbin Road, Sanya, 572022, China. .,School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China. .,Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, 1678 Dongfang Road, Shanghai, 200127, China.
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Velazquez-Roman J, Angulo-Zamudio UA, León-Sicairos N, Medina-Serrano J, DeLira-Bustillos N, Villamil-Ramírez H, Canizales-Quinteros S, Macías-Kauffer L, Campos-Romero A, Alcántar-Fernández J, Canizalez-Roman A. Association of FTO, ABCA1, ADRB3, and PPARG variants with obesity, type 2 diabetes, and metabolic syndrome in a Northwest Mexican adult population. J Diabetes Complications 2021; 35:108025. [PMID: 34420811 DOI: 10.1016/j.jdiacomp.2021.108025] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 08/10/2021] [Accepted: 08/14/2021] [Indexed: 11/28/2022]
Abstract
AIM To identify associations among allelic variants of the genes FTO, ABCA1, ADRB3, and PPARG with anthropometric and biochemical traits, metabolic diseases (obesity, T2D or metabolic syndrome) in an adult population from Northwest Mexico. METHODS Blood samples were collected from 846 subjects including 266 normal weight subjects, 285 with obesity, and 295 with T2D. Of the 846 persons in the study, 365 presented metabolic syndrome diagnostic criteria. Anthropometric and biochemical traits were recorded and 4 single nucleotide polymorphisms (SNPs): FTO rs9939609 A-allele, ABCA1 rs9282541 A-allele, ADRB3 rs4994 G-allele, and PPARG rs1801282 G-allele were genotyped by real-time PCR. RESULTS FTO rs9939609 A-allele was significantly associated with obesity (p: 8.3 × 10-4), and metabolic syndrome (p: 0.001), but no individual SNPs were significantly associated with T2D. Finally, the cumulative risk of the four SNPs was significantly associated with obesity (p: 1.95 × 10-4). CONCLUSION Associations in FTO, ABCA, ADRB3, and PPARG SNPs presented in this study with obesity and metabolic syndrome could represent a risk for developing metabolic diseases in Northwest Mexican adult subjects.
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Affiliation(s)
- Jorge Velazquez-Roman
- School of Medicine, CIASaP, Autonomous University of Sinaloa, 80246 Culiacan, Sinaloa, Mexico
| | - Uriel A Angulo-Zamudio
- School of Medicine, CIASaP, Autonomous University of Sinaloa, 80246 Culiacan, Sinaloa, Mexico
| | - Nidia León-Sicairos
- School of Medicine, CIASaP, Autonomous University of Sinaloa, 80246 Culiacan, Sinaloa, Mexico; Pediatric Hospital of Sinaloa, 80200 Culiacan, Sinaloa, Mexico
| | - Julio Medina-Serrano
- Programa de Maestría en Ciencias en Biomedicina Molecular, UAS, 80246 Culiacan, Sinaloa, Mexico; Coordinación de Planeación y Enlace Institucional, Órgano de Operación Administrativa Desconcentrada (OOAD) de Sinaloa, Instituto Mexicano del Seguro Social (IMSS), Culiacan Sinaloa, Mexico
| | - Nora DeLira-Bustillos
- Programa de Maestría en Ciencias en Biomedicina Molecular, UAS, 80246 Culiacan, Sinaloa, Mexico
| | - Hugo Villamil-Ramírez
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM/INMEGEN, Mexico City, Mexico
| | - Samuel Canizales-Quinteros
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM/INMEGEN, Mexico City, Mexico
| | - Luis Macías-Kauffer
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM/INMEGEN, Mexico City, Mexico
| | | | | | - Adrian Canizalez-Roman
- School of Medicine, CIASaP, Autonomous University of Sinaloa, 80246 Culiacan, Sinaloa, Mexico; The Women's Hospital, Secretariat of Health, 80020 Culiacan, Sinaloa, Mexico.
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Leak-Johnson T, Yan F, Daniels P. What the Jackson Heart Study Has Taught Us About Diabetes and Cardiovascular Disease in the African American Community: a 20-year Appreciation. Curr Diab Rep 2021; 21:39. [PMID: 34495422 DOI: 10.1007/s11892-021-01413-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/25/2021] [Indexed: 01/10/2023]
Abstract
PURPOSE OF REVIEW The burden of cardiometabolic diseases such as cardiovascular disease (CVD) and type 2 diabetes (T2D) is pronounced among African Americans. Research has shown that behavioral, social, metabolic, psychosocial, and genetic risk factors of CVD and T2D are closely interwoven. Approximately 20 years ago, the Jackson Heart Study (JHS) was established to investigate this constellation of risk factors. RECENT FINDINGS Findings from neighborhood studies emphasize the importance of social cohesion and physical environment in the context CVD and T2D risk. Socioeconomic status factors such as income and education were significant predictors for CVD and T2D. Behavioral studies indicate that modifiable risk factors such as smoking, physical inactivity, lack of sleep, and poor nutrition are associated with CVD risk and all-cause mortality. Mental health also was found to be associated with CVD and T2D. Genetic influences are associated with disease etiology. This review summarizes the joint contributions of CVD and cardiometabolic risk factors in an African American population.
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Affiliation(s)
- Tennille Leak-Johnson
- Cardiovascular Research Institute, Morehouse School of Medicine, Atlanta, GA, 30310, USA.
- Department of Physiology, Morehouse School of Medicine, Atlanta, GA, USA.
| | - Fengxia Yan
- The Research Design and Biostatistics Core, Morehouse School of Medicine, Atlanta, GA, USA
- Community Health & Preventive Medicine, Morehouse School of Medicine, Atlanta, GA, USA
| | - Pamela Daniels
- The Research Design and Biostatistics Core, Morehouse School of Medicine, Atlanta, GA, USA
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Tchio C, Musani SK, Quarshie A, Tosini G. Association between MTNR1B polymorphisms and obesity in African American: findings from the Jackson Heart Study. BMC Med Genomics 2021; 14:136. [PMID: 34020621 PMCID: PMC8138980 DOI: 10.1186/s12920-021-00983-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 05/13/2021] [Indexed: 01/02/2023] Open
Abstract
Background Melatonin is a hormone that is secreted at night by the pineal gland. It exerts its function by binding to the MT1 and MT2 receptors, which are encoded by the MTNR1A and MTNR1B genes, respectively. Previous studies reveal that MTNR1B variants are associated with insulin secretion impairments and an increased body mass index (BMI) in individuals of European and Asian ancestries. Obesity is highly prevalent in the US and disproportionately affects African Americans. Here, we hypothesized that common single nucleotide polymorphisms (SNPs) imputed in 1000 Genomes in the MTNR1B gene are associated with adiposity in African American adult men and women and that the association is modified by insomnia. Methods We used an additive genetic model to describe the association between the adiposity traits (BMI and waist circumference) and selected MTNR1B variants in 3,029 Jackson Heart Study participants, with an average age of 55.13 ± 12.84 years, and 62% were women. We regressed the adiposity measures on the estimated allelic or genotypic dosage at every selected SNP and adjusted for age, sex, population stratification, and insomnia. Thirty common SNPs, spanning the MTNR1B gene, with a minor allele frequency ≥ 5%, a call rate ≥ 90%, a Hardy–Weinberg equilibrium p value > 10–6, were available for the analysis. Results The allele T of rs76371840 was associated with adiposity (OR = 1.47 [1.13—1.82]; PFDR-adjusted = 0.0499), and the allele A of rs8192552 showed a significant association with waist circumference (β = 0.023 ± 0.007; PFDR-adjusted = 0.0077) after correcting for multiple testing. When insomnia was included in the adiposity analysis model, the following four variants became significantly associated with adiposity: rs6483208; rs4388843; rs4601728; and rs12804291. Conclusions Our data indicate that polymorphisms in the MTNR1B gene are associated with obesity traits in African Americans. To the best of our knowledge, this is the first study to explore the effect of insomnia on the association between the circadian MTNR1B genetic variants and metabolic traits in an African American sample population. We observed that insomnia affected the association between the MTNR1B variants and adiposity.
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Affiliation(s)
- Cynthia Tchio
- Circadian Rhythms and Sleep Disorders Program, Neuroscience Institute, Morehouse School of Medicine, 720 Westview Dr. SW, Atlanta, GA, 30130, USA.,Department of Pharmacology and Toxicology, Morehouse School of Medicine, Atlanta, GA, USA
| | - Solomon K Musani
- Jackson Heart Study, University of Mississippi Medical Center, Jackson, MS, USA
| | - Alexander Quarshie
- Clinical Research Center, Morehouse School of Medicine, Atlanta, GA, USA
| | - Gianluca Tosini
- Circadian Rhythms and Sleep Disorders Program, Neuroscience Institute, Morehouse School of Medicine, 720 Westview Dr. SW, Atlanta, GA, 30130, USA. .,Department of Pharmacology and Toxicology, Morehouse School of Medicine, Atlanta, GA, USA.
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Trifonova EA, Popovich AA, Makeeva OA, Minaycheva LI, Bocharova AV, Vagaitseva KV, Stepanov VA. Replicative Association Analysis of Genetic Markers of Obesity in the Russian Population. RUSS J GENET+ 2021. [DOI: 10.1134/s1022795421050136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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Noh K, Park JC, Han JS, Lee SJ. From Bound Cells Comes a Sound Mind: The Role of Neuronal Growth Regulator 1 in Psychiatric Disorders. Exp Neurobiol 2020; 29:1-10. [PMID: 32122104 PMCID: PMC7075657 DOI: 10.5607/en.2020.29.1.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 02/23/2020] [Accepted: 02/25/2020] [Indexed: 12/21/2022] Open
Abstract
Cell-to-cell adhesion is important for maintenance of brain structure and function. Abnormal neuronal cell adhesion and loss of its connectivity are considered a main cause of psychiatric disorders such as major depressive disorder (MDD). Various cell adhesion molecules (CAMs) are involved in neuronal cell adhesions and thereby affect brain functions such as learning and memory, cognitive functions, and psychiatric functions. Compared with other CAMs, neuronal growth regulator 1 (Negr1) has a distinct functioning mechanism in terms of its cross-talk with cytokine receptor signaling. Negr1 is a member of the immunoglobulin LON (IgLON) family of proteins and is involved in neuronal outgrowth, dendritic arborization, and synapse formation. In humans, Negr1 is a risk gene for obesity based on a genome-wide association study. More recently, accumulating evidence supports that it also plays a critical role in psychiatric disorders. In this review, we discuss the recent findings on the role of Negr1 in MDD, focusing on its regulatory mechanism. We also provide evidence of putative involvement of Negr1 in other psychiatric disorders based on the novel behavioral phenotypes of Negr1 knockout mice.
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Affiliation(s)
- Kyungchul Noh
- Department of Physiology and Neuroscience, Dental Research Institute, Seoul National University School of Dentistry, Seoul 08826, Korea
| | - Jung-Cheol Park
- Department of Biological Science, Konkuk University, Seoul 05029, Korea
| | - Jung-Soo Han
- Department of Biological Science, Konkuk University, Seoul 05029, Korea
| | - Sung Joong Lee
- Department of Physiology and Neuroscience, Dental Research Institute, Seoul National University School of Dentistry, Seoul 08826, Korea
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Abstract
BACKGROUND Age at menarche and age at natural menopause occur significantly earlier in African American women than in other ethnic groups. African American women also have twice the prevalence of cardiometabolic disorders related to the timing of these reproductive traits. OBJECTIVES The objectives of this integrative review were to (a) summarize the genome-wide association studies of reproductive traits in African American women, (b) identify genes that overlap with reproductive traits and cardiometabolic risk factors in African American women, and (c) propose biological mechanisms explaining the link between reproductive traits and cardiometabolic risk factors. METHODS PubMed was searched for genome-wide association studies of genes associated with reproductive traits in African American women. After extracting and summarizing the primary genes, we examined whether any of the associations with reproductive traits had also been identified with cardiometabolic risk factors in African American women. RESULTS Seven studies met the inclusion criteria. Associations with both reproductive and cardiometabolic traits were reported in or near the following genes: FTO, SEC16B, TMEM18, APOE, PHACTR1, KCNQ1, LDLR, PIK3R1, and RORA. Biological pathways implicated include body weight regulation, vascular homeostasis, and lipid metabolism. DISCUSSION A better understanding of the genetic basis of reproductive traits in African American women may provide insight into the biological mechanisms linking variation in these traits with increased risk for cardiometabolic disorders in this population.
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Ye M, Huang R, Min Z, Zhang P, Wang T, Yu B. Comparison of the effect by which gastric plication and sleeve gastrectomy procedures alter metabolic and physical parameters in an obese type 2 diabetes rodent model. Surg Obes Relat Dis 2017. [DOI: 10.1016/j.soard.2017.05.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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