1
|
Zhou F, Tian G, Cui Y, He S, Yan Y. Development of genome-wide association studies on childhood obesity and its indicators: A scoping review and enrichment analysis. Pediatr Obes 2023; 18:e13077. [PMID: 37800454 DOI: 10.1111/ijpo.13077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 08/31/2023] [Accepted: 09/16/2023] [Indexed: 10/07/2023]
Abstract
BACKGROUND The progress of genome-wide association studies (GWAS) in childhood obesity and its indicators is challenging and there are differences in genetic studies in children and adults. OBJECTIVE To illustrate the history of the development of GWAS in childhood obesity and its indicators and summarize the GWAS loci. METHODS PubMed, Web of Science, Embase and GWAS Catalog databases were systematically searched from 1 January 2005 to 19 October 2022 for literature related to GWAS of childhood BMI, body fatness and obesity. The nearest genes were used as positional genes to perform gene set analyses including the enrichment of pathways, tissues and diseases. RESULTS Twenty articles published between 2007 and 2021 were included in this scoping review, which identified 116 SNPs reaching genome-wide significance with childhood BMI (n = 50), body fatness (n = 31) and obesity (n = 35). The study populations were European in 16 studies, non-European in three studies (1 East Asian; 1 American; 1 Mexican) and trans-ancestry in one study. Several enriched pathways, tissues and diseases were identified through enrichment analysis of genes associated with childhood obesity and its indicators. CONCLUSIONS The innovations in tools and methods enable GWAS to better explore the genetic characteristics of obesity in children and adolescents. However, the number of GWAS in American, Asian and African populations is limited compared to the European population.
Collapse
Affiliation(s)
- Feixiang Zhou
- Department of Epidemiology and Health Statistics, Xiangya School of Public Health, Central South University, Changsha, China
| | - Gang Tian
- Department of Epidemiology and Health Statistics, Xiangya School of Public Health, Central South University, Changsha, China
| | - Yiran Cui
- Department of Epidemiology and Health Statistics, Xiangya School of Public Health, Central South University, Changsha, China
| | - Simin He
- Department of Epidemiology and Health Statistics, Xiangya School of Public Health, Central South University, Changsha, China
| | - Yan Yan
- Department of Epidemiology and Health Statistics, Xiangya School of Public Health, Central South University, Changsha, China
| |
Collapse
|
2
|
Argetsinger LS, Flores A, Svezhova N, Ellis M, Reynolds C, Cote JL, Cline JM, Myers MG, Carter-Su C. Role of the Beta and Gamma Isoforms of the Adapter Protein SH2B1 in Regulating Energy Balance. Endocrinology 2023; 164:bqad032. [PMID: 36799031 PMCID: PMC10282918 DOI: 10.1210/endocr/bqad032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 02/03/2023] [Accepted: 02/15/2023] [Indexed: 02/18/2023]
Abstract
Human variants of the adapter protein SH2B1 are associated with severe childhood obesity, hyperphagia, and insulin resistance-phenotypes mimicked by mice lacking Sh2b1. SH2B1β and γ isoforms are expressed ubiquitously, whereas SH2B1α and δ isoforms are expressed primarily in the brain. Restoring SH2B1β driven by the neuron-specific enolase promoter largely reverses the metabolic phenotype of Sh2b1-null mice, suggesting crucial roles for neuronal SH2B1β in energy balance control. Here we test this hypothesis by using CRISPR/Cas9 gene editing to delete the β and γ isoforms from the neurons of mice (SH2B1βγ neuron-specific knockout [NKO] mice) or throughout the body (SH2B1βγ knockout [KO] mice). While parameters of energy balance were normal in both male and female SH2B1βγ NKO mice, food intake, body weight, and adiposity were increased in male (but not female) SH2B1βγ KO mice. Analysis of long-read single-cell RNA seq data from wild-type mouse brain revealed that neurons express almost exclusively the α and δ isoforms, whereas neuroglial cells express almost exclusively the β and γ isoforms. Our work suggests that neuronal SH2B1β and γ are not primary regulators of energy balance. Rather, non-neuronal SH2B1β and γ in combination with neuronal SH2B1α and δ suffice for body weight maintenance. While SH2B1β/γ and SH2B1α/δ share some functionality, SH2B1β/γ appears to play a larger role in promoting leanness.
Collapse
Affiliation(s)
- Lawrence S Argetsinger
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Anabel Flores
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Nadezhda Svezhova
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Michael Ellis
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Caitlin Reynolds
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Jessica L Cote
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Joel M Cline
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Martin G Myers
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Christin Carter-Su
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| |
Collapse
|
3
|
Dlamini SN, Choudhury A, Ramsay M, Micklesfield LK, Norris SA, Crowther NJ, Crawford AA, Walker BR, Lombard Z, Goedecke JH. Associations Between CYP17A1 and SERPINA6/A1 Polymorphisms, and Cardiometabolic Risk Factors in Black South Africans. Front Genet 2021; 12:687335. [PMID: 34484290 PMCID: PMC8414563 DOI: 10.3389/fgene.2021.687335] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 07/20/2021] [Indexed: 01/11/2023] Open
Abstract
Research in European and Asian populations has reported associations between single nucleotide polymorphisms (SNPs) in CYP17A1 and SERPINA6/A1 and circulating glucocorticoid concentrations, and some key cardiometabolic risk factors. This study aimed to investigate these associations in black South African adults, who are disproportionally affected by the metabolic syndrome and its related cardiometabolic risk factors. The dataset included black South African adults (n = 4,431; 56.7% women) from the AWI-Gen study, genotyped on the H3A genotyping array and imputed using the African reference panel at the Sanger imputation service. From the imputed data, 31 CYP17A1 SNPs and 550 SERPINA6/A1 SNPs were extracted. The metabolic syndrome and its components were defined using the 2009 harmonized guidelines. Serum glucocorticoid concentrations were measured in a subset of 304 men and 573 women, using a liquid chromatography-mass spectrometry method. Genetic associations were detected using PLINK. Bonferroni correction was used to control for multiple testing. A SNP at SERPINA6/A1, rs17090691 (effect allele G), was associated with higher diastolic blood pressure (BP) in all adults combined (p = 9.47 × 10-6). Sex-stratified analyses demonstrated an association between rs1051052 (effect allele G), another SERPINA6/A1 SNP, and higher high-density lipoprotein (HDL) cholesterol concentrations in women (p = 1.23 × 10-5). No association was observed between these variants and glucocorticoids or between any of the CYP17A1 SNPs and metabolic outcomes after adjusting for multiple testing. Furthermore, there were no associations between any of the SNPs tested and the metabolic syndrome. This study reports novel genetic associations between two SNPs at SERPINA6/A1 and key cardiometabolic risk factors in black South Africans. Future replication and functional studies in larger populations are required to confirm the role of the identified SNPs in the metabolic syndrome and assess if these associations are mediated by circulating glucocorticoids.
Collapse
Affiliation(s)
- Siphiwe N. Dlamini
- South African Medical Research Council/Wits Developmental Pathways for Health Research Unit, Department of Paediatrics, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Non-communicable Diseases Research Unit, South African Medical Research Council, Cape Town, South Africa
| | - Ananyo Choudhury
- Faculty of Health Sciences, Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
| | - Michèle Ramsay
- Faculty of Health Sciences, Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
| | - Lisa K. Micklesfield
- South African Medical Research Council/Wits Developmental Pathways for Health Research Unit, Department of Paediatrics, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Shane A. Norris
- South African Medical Research Council/Wits Developmental Pathways for Health Research Unit, Department of Paediatrics, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Nigel J. Crowther
- Department of Chemical Pathology, National Health Laboratory Service, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Andrew A. Crawford
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
- BHF Centre for Cardiovascular Science, University of Edinburgh, Edinburgh, United Kingdom
| | - Brian R. Walker
- BHF Centre for Cardiovascular Science, University of Edinburgh, Edinburgh, United Kingdom
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Zané Lombard
- Division of Human Genetics, National Health Laboratory Service, Faculty of Health Sciences, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Julia H. Goedecke
- South African Medical Research Council/Wits Developmental Pathways for Health Research Unit, Department of Paediatrics, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Non-communicable Diseases Research Unit, South African Medical Research Council, Cape Town, South Africa
| |
Collapse
|
4
|
Pereira SC, Martins AD, Monteiro MP, Pinto S, Barros A, Oliveira PF, Alves MG. Expression of obesity-related genes in human spermatozoa affects the outcomes of reproductive treatments. F&S SCIENCE 2021; 2:164-175. [PMID: 35559751 DOI: 10.1016/j.xfss.2021.03.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 03/18/2021] [Accepted: 03/22/2021] [Indexed: 12/13/2022]
Abstract
OBJECTIVE To study the abundance of obesity-related gene (ORG) mRNA in human spermatozoa and its association with sperm quality parameters, embryonic development, and pregnancy rates after assisted reproduction treatment (ART). DESIGN Cross-sectional study of spermatozoa ORG mRNA expression, and sperm and embryonic development parameters of infertile couples attending a single ART center. SETTING University, in collaboration with a medically assisted reproduction center. PATIENT(S) One hundred six couples seeking fertility treatment and receiving ART. INTERVENTION(S) Expression of spermatozoa ORG mRNA was assessed by quantitative reverse transcription-polymerase chain reaction. Sperm and embryonic development parameters were measured by board-certified embryologists. Serum β-human chorionic gonadotropin levels and fetal heartbeat detection on ultrasound were used to document biochemical and clinical pregnancy, respectively. MAIN OUTCOME MEASURE(S) Correlations between the abundance of ORG transcripts in spermatozoa and sperm quality, embryonic development, and achievement of pregnancy. RESULTS The abundance of spermatozoa FTO mRNA was positively correlated with total sperm count (r = 0.5030), fertilization rate (r = 0.4854), embryo cleavage rate (r = 0.5705), and high-quality embryo rate (r = 0.6982). The abundance of spermatozoa MC4R transcript was negatively correlated with sperm viability (r = -0.3111) and positively correlated with biochemical pregnancy (r = 0.4420). The abundance of MC4R and GNPDA2 transcripts was higher in spermatozoa of men with asthenozoospermia and teratozoospermia than in those with normozoospermia. CONCLUSION To our knowledge, this is the first report showing that the abundance of MC4R and FTO transcripts in spermatozoa is associated with sperm and embryo quality parameters, as well as pregnancy rates. Overall, these results further support the view that male factors beyond classic sperm quality parameters, namely the abundance of ORG transcripts, also affect the outcome of ART.
Collapse
Affiliation(s)
- Sara C Pereira
- Clinical and Experimental Endocrinology, Department of Anatomy, Unit for Multidisciplinary Research in Biomedicine, Institute of Biomedical Sciences Abel Salazar, University of Porto, Porto, Portugal
| | - Ana D Martins
- Clinical and Experimental Endocrinology, Department of Anatomy, Unit for Multidisciplinary Research in Biomedicine, Institute of Biomedical Sciences Abel Salazar, University of Porto, Porto, Portugal; Química Orgânica, Produtos Naturais e Agroalimentares (QOPNA) and Laboratório Associado para a Química Verde (LAQV), Department of Chemistry, University of Aveiro, Portugal
| | - Mariana P Monteiro
- Clinical and Experimental Endocrinology, Department of Anatomy, Unit for Multidisciplinary Research in Biomedicine, Institute of Biomedical Sciences Abel Salazar, University of Porto, Porto, Portugal
| | - Soraia Pinto
- Center for Reproductive Genetics Professor Alberto Barros, Porto, Portugal
| | - Alberto Barros
- Center for Reproductive Genetics Professor Alberto Barros, Porto, Portugal; Department of Genetics, Faculty of Medicine, University of Porto, Porto, Portugal; Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
| | - Pedro F Oliveira
- Química Orgânica, Produtos Naturais e Agroalimentares (QOPNA) and Laboratório Associado para a Química Verde (LAQV), Department of Chemistry, University of Aveiro, Portugal
| | - Marco G Alves
- Clinical and Experimental Endocrinology, Department of Anatomy, Unit for Multidisciplinary Research in Biomedicine, Institute of Biomedical Sciences Abel Salazar, University of Porto, Porto, Portugal.
| |
Collapse
|
5
|
Sun C, Kovacs P, Guiu-Jurado E. Genetics of Obesity in East Asians. Front Genet 2020; 11:575049. [PMID: 33193685 PMCID: PMC7606890 DOI: 10.3389/fgene.2020.575049] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 09/17/2020] [Indexed: 12/31/2022] Open
Abstract
Obesity has become a public health problem worldwide. Compared with Europe, people in Asia tend to suffer from type 2 diabetes with a lower body mass index (BMI). Genome-wide association studies (GWASs) have identified over 750 loci associated with obesity. Although the majority of GWAS results were conducted in individuals of European ancestry, a recent GWAS in individuals of Asian ancestry has made a significant contribution to the identification of obesity susceptibility loci. Indeed, owing to the multifactorial character of obesity with a strong environmental component, the revealed loci may have distinct contributions in different ancestral genetic backgrounds and in different environments as presented through diet and exercise among other factors. Uncovering novel, yet unrevealed genes in non-European ancestries may further contribute to explaining the missing heritability for BMI. In this review, we aimed to summarize recent advances in obesity genetics in individuals of Asian ancestry. We therefore compared proposed mechanisms underlying susceptibility loci for obesity associated with individuals of European and Asian ancestries and discussed whether known genetic variants might explain ethnic differences in obesity risk. We further acknowledged that GWAS implemented in individuals of Asian ancestries have not only validated the potential role of previously specified obesity susceptibility loci but also exposed novel ones, which have been missed in the initial genetic studies in individuals of European ancestries. Thus, multi-ethnic studies have a great potential not only to contribute to a better understanding of the complex etiology of human obesity but also potentially of ethnic differences in the prevalence of obesity, which may ultimately pave new avenues in more targeted and personalized obesity treatments.
Collapse
Affiliation(s)
| | - Peter Kovacs
- Medical Department III – Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany
| | | |
Collapse
|
6
|
Mchiza ZJR, Parker WA, Hossin MZ, Heshmati A, Labadarios D, Falkstedt D, Koupil I. Social and Psychological Predictors of Body Mass Index among South Africans 15 Years and Older: SANHANES-1. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2019; 16:ijerph16203919. [PMID: 31618952 PMCID: PMC6843690 DOI: 10.3390/ijerph16203919] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 09/20/2019] [Accepted: 09/21/2019] [Indexed: 12/01/2022]
Abstract
This study investigated how psychological distress and the proxies for social position combine to influence the risk of both underweight and overweight in South Africans aged 15 years and older. This was a cross-sectional study that included 2254 men and 4170 women participating in the first South African National Health and Nutrition Examination Survey (SANHANES-1). An analysis exploring the associations of social and mental health characteristics with body mass index (BMI) was conducted using binary and multinomial logistic regressions. Results suggested that, overall, women had a higher risk of overweight/obesity compared to men (age-adjusted odds ratio [AOR] 4.65; 95% confidence intervals [CI] 3.94–5.50). The gender effect on BMI was smaller in non-African participants (AOR 3.02; 95% CI 2.41–3.79; p-value for interaction = 0.004). Being employed and having a higher level of education were associated with higher risks of overweight and obesity and a lower risk of underweight. Being single or without a spouse and poor mental health were found to increase the odds of being underweight, especially in men. To conclude, there are strong social gradients and important gender and ethnic differences in how BMI is distributed in the South African population.
Collapse
Affiliation(s)
| | - Whadi-Ah Parker
- Social Aspects of Public Health (SAPH), Human Sciences Research Council, Cape Town 8000, South Africa.
| | - Muhammad Zakir Hossin
- Department of Public Health Sciences, Karolinska Institutet, Stockholm SE-171 76, Sweden.
| | - Amy Heshmati
- Department of Public Health Sciences, Stockholm University, Stockholm SE-106 91, Sweden.
- Centre for Health Equity Studies, Stockholm University, Stockholm SE-106 91, Sweden.
| | - Demetre Labadarios
- Faculty of Medicine and Health Sciences, Stellenbosch University, Francie van Zijl Drive, Tygerberg 7505, South Africa.
| | - Daniel Falkstedt
- Department of Public Health Sciences, Karolinska Institutet, Stockholm SE-171 76, Sweden.
| | - Ilona Koupil
- Department of Public Health Sciences, Karolinska Institutet, Stockholm SE-171 76, Sweden.
- Department of Public Health Sciences, Stockholm University, Stockholm SE-106 91, Sweden.
| |
Collapse
|
7
|
Sahibdeen V, Crowther NJ, Soodyall H, Hendry LM, Munthali RJ, Hazelhurst S, Choudhury A, Norris SA, Ramsay M, Lombard Z. Genetic variants in SEC16B are associated with body composition in black South Africans. Nutr Diabetes 2018; 8:43. [PMID: 30026463 PMCID: PMC6053407 DOI: 10.1038/s41387-018-0050-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 05/14/2018] [Accepted: 05/23/2018] [Indexed: 12/12/2022] Open
Abstract
Objective The latest genome-wide association studies of obesity-related traits have identified several genetic loci contributing to body composition (BC). These findings have not been robustly replicated in African populations, therefore, this study aimed to assess whether European BC-associated gene loci played a similar role in a South African black population. Methods A replication and fine-mapping study was performed in participants from the Birth to Twenty cohort (N = 1,926) using the Metabochip. Measurements included body mass index (BMI), waist and hip circumference, waist-to-hip ratio (WHR), total fat mass, total lean mass and percentage fat mass (PFM). Results SNPs in several gene loci, including SEC16B (Padj < 9.48 × 10−7), NEGR1 (Padj < 1.64 × 10−6), FTO (Padj < 2.91 × 10−5), TMEM18 (Padj < 2.27 × 10−5), and WARS2(Padj < 3.25 × 10−5) were similarly associated (albeit not at array-wide signficance (P ≤ 6.7 × 10−7) with various phenotypes including fat mass, PFM, WHR linked to BC in this African cohort, however the associations were driven by different sentinel SNPs. More importantly, DXA-derived BC measures revealed stronger genetic associations than simple anthropometric measures. Association signals generated in this study were shared by European and African populations, as well as unique to this African cohort. Moreover, sophisticated estimates like DXA measures enabled an enhanced characterisation of genetic associations for BC traits. Conclusion Results from this study suggest that in-depth genomic studies in larger African cohorts may reveal novel SNPs for body composition and adiposity, which will provide greater insight into the aetiology of obesity.
Collapse
Affiliation(s)
- Venesa Sahibdeen
- Division of Human Genetics, School of Pathology, Faculty of Health Sciences, National Health Laboratory Service & University of the Witwatersrand, Johannesburg, South Africa. .,Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
| | - Nigel J Crowther
- Department of Chemical Pathology, School of Pathology, Faculty of Health Sciences, National Health Laboratory Service & University of the Witwatersrand, Johannesburg, South Africa
| | - Himla Soodyall
- Division of Human Genetics, School of Pathology, Faculty of Health Sciences, National Health Laboratory Service & University of the Witwatersrand, Johannesburg, South Africa
| | - Liesl M Hendry
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,School of Molecular and Cell Biology, Faculty of Science, University of the Witwatersrand, Johannesburg, South Africa
| | - Richard J Munthali
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,School of Molecular and Cell Biology, Faculty of Science, University of the Witwatersrand, Johannesburg, South Africa.,MRC/Wits Developmental Pathways for Health Research Unit, Department of Paediatrics, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Scott Hazelhurst
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,School of Electrical and Information Engineering, University of the Witwatersrand, Johannesburg, South Africa
| | - Ananyo Choudhury
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Shane A Norris
- MRC/Wits Developmental Pathways for Health Research Unit, Department of Paediatrics, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Michèle Ramsay
- Division of Human Genetics, School of Pathology, Faculty of Health Sciences, National Health Laboratory Service & University of the Witwatersrand, Johannesburg, South Africa.,Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Zané Lombard
- Division of Human Genetics, School of Pathology, Faculty of Health Sciences, National Health Laboratory Service & University of the Witwatersrand, Johannesburg, South Africa.,Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,School of Molecular and Cell Biology, Faculty of Science, University of the Witwatersrand, Johannesburg, South Africa
| |
Collapse
|
8
|
Rotimi CN, Bentley AR, Doumatey AP, Chen G, Shriner D, Adeyemo A. The genomic landscape of African populations in health and disease. Hum Mol Genet 2017; 26:R225-R236. [PMID: 28977439 PMCID: PMC6075021 DOI: 10.1093/hmg/ddx253] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 06/19/2017] [Accepted: 06/29/2017] [Indexed: 12/12/2022] Open
Abstract
A deeper appreciation of the complex architecture of African genomes is critical to the global effort to understand human history, biology and differential distribution of disease by geography and ancestry. Here, we report on how the growing engagement of African populations in genome science is providing new insights into the forces that shaped human genomes before and after the Out-of-Africa migrations. As a result of this human evolutionary history, African ancestry populations have the greatest genomic diversity in the world, and this diversity has important ramifications for genomic research. In the case of pharmacogenomics, for instance, variants of consequence are not limited to those identified in other populations, and diversity within African ancestry populations precludes summarizing risk across different African ethnic groups. Exposure of Africans to fatal pathogens, such as Plasmodium falciparum, Lassa Virus and Trypanosoma brucei rhodesiense, has resulted in elevated frequencies of alleles conferring survival advantages for infectious diseases, but that are maladaptive in modern-day environments. Illustrating with cardiometabolic traits, we show that while genomic research in African ancestry populations is still in early stages, there are already many examples of novel and African ancestry-specific disease loci that have been discovered. Furthermore, the shorter haplotypes in African genomes have facilitated fine-mapping of loci discovered in other human ancestry populations. Given the insights already gained from the interrogation of African genomes, it is imperative to continue and increase our efforts to describe genomic risk in and across African ancestry populations.
Collapse
Affiliation(s)
- Charles N. Rotimi
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, MD 20892, USA
| | - Amy R. Bentley
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, MD 20892, USA
| | - Ayo P. Doumatey
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, MD 20892, USA
| | - Guanjie Chen
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, MD 20892, USA
| | - Daniel Shriner
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, MD 20892, USA
| | - Adebowale Adeyemo
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, MD 20892, USA
| |
Collapse
|
9
|
Foote AP, Zarek CM, Kuehn L, Cunningham HC, Cammack KM, Freetly HC, Lindholm-Perry AK. Effect of abomasal butyrate infusion on gene expression in the duodenum of lambs. J Anim Sci 2017; 95:1191-1196. [DOI: 10.2527/jas.2016.1022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
|
10
|
Ouyang H, Zhang H, Li W, Liang S, Jebessa E, Abdalla BA, Nie Q. Identification, expression and variation of the GNPDA2 gene, and its association with body weight and fatness traits in chicken. PeerJ 2016; 4:e2129. [PMID: 27326383 PMCID: PMC4911950 DOI: 10.7717/peerj.2129] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 05/23/2016] [Indexed: 12/29/2022] Open
Abstract
Background. The GNPDA2 (glucosamine-6-phosphate deaminase 2) gene is a member of Glucosamine-6-phosphate (GlcN6P) deaminase subfamily, which encoded an allosteric enzyme of GlcN6P. Genome-wide association studies (GWAS) have shown that variations of human GNPDA2 are associated with body mass index and obesity risk, but its function and metabolic implications remain to be elucidated.The object of this study was to characterize the gene structure, expression, and biological functions of GNPDA2 in chickens. Methods. Variant transcripts of chicken GNPDA2 and their expression were investigated using rapid amplification of cDNA ends (RACE) system and real-time quantitative PCR technology. We detected the GNPDA2 expression in hypothalamic, adipose, and liver tissue of Xinghua chickens with fasting and high-glucose-fat diet treatments, and performed association analysis of variations of GNPDA2 with productive traits in chicken. The function of GNPDA2 was further studied by overexpression and small interfering RNA (siRNA) methods in chicken preadipocytes. Results.Four chicken GNPDA2 transcripts (cGNPDA2-a∼cGNPDA2-d) were identified in this study. The complete transcript GNPDA2-a was predominantly expressed in adipose tissue (subcutaneous fat and abdominal fat), hypothalamus, and duodenum. In fasting chickens, the mRNA level of GNPDA2 was decreased by 58.8% (P < 0.05) in hypothalamus, and returned to normal level after refeeding. Chicken fed a high-glucose-fat diet increased GNPDA2 gene expression about 2-fold higher in adipose tissue (P < 0.05) than that in the control (fed a basal diet), but decreased its expression in hypothalamus. Two single-nucleotide polymorphisms of the GNPDA2 gene were significantly associated with body weight and a number of fatness traits in chicken (P < 0.05). Conclusion. Our findings indicated that the GNPDA2 gene has a potential role in the regulation of body weight, fat and energy metabolism in chickens.
Collapse
Affiliation(s)
- Hongjia Ouyang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University,Guangzhou,China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding,Guangzhou,China
| | - Huan Zhang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University,Guangzhou,China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding,Guangzhou,China
| | - Weimin Li
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University,Guangzhou,China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding,Guangzhou,China
| | - Sisi Liang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University,Guangzhou,China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding,Guangzhou,China
| | - Endashaw Jebessa
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University,Guangzhou,China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding,Guangzhou,China
| | - Bahareldin A Abdalla
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University,Guangzhou,China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding,Guangzhou,China
| | - Qinghua Nie
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University,Guangzhou,China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding,Guangzhou,China
| |
Collapse
|