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Monteil A, Guérineau NC, Gil-Nagel A, Parra-Diaz P, Lory P, Senatore A. New insights into the physiology and pathophysiology of the atypical sodium leak channel NALCN. Physiol Rev 2024; 104:399-472. [PMID: 37615954 DOI: 10.1152/physrev.00014.2022] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 07/13/2023] [Accepted: 08/15/2023] [Indexed: 08/25/2023] Open
Abstract
Cell excitability and its modulation by hormones and neurotransmitters involve the concerted action of a large repertoire of membrane proteins, especially ion channels. Unique complements of coexpressed ion channels are exquisitely balanced against each other in different excitable cell types, establishing distinct electrical properties that are tailored for diverse physiological contributions, and dysfunction of any component may induce a disease state. A crucial parameter controlling cell excitability is the resting membrane potential (RMP) set by extra- and intracellular concentrations of ions, mainly Na+, K+, and Cl-, and their passive permeation across the cell membrane through leak ion channels. Indeed, dysregulation of RMP causes significant effects on cellular excitability. This review describes the molecular and physiological properties of the Na+ leak channel NALCN, which associates with its accessory subunits UNC-79, UNC-80, and NLF-1/FAM155 to conduct depolarizing background Na+ currents in various excitable cell types, especially neurons. Studies of animal models clearly demonstrate that NALCN contributes to fundamental physiological processes in the nervous system including the control of respiratory rhythm, circadian rhythm, sleep, and locomotor behavior. Furthermore, dysfunction of NALCN and its subunits is associated with severe pathological states in humans. The critical involvement of NALCN in physiology is now well established, but its study has been hampered by the lack of specific drugs that can block or agonize NALCN currents in vitro and in vivo. Molecular tools and animal models are now available to accelerate our understanding of how NALCN contributes to key physiological functions and the development of novel therapies for NALCN channelopathies.
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Affiliation(s)
- Arnaud Monteil
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, Montpellier, France
- LabEx "Ion Channel Science and Therapeutics," Montpellier, France
- Department of Physiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Nathalie C Guérineau
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, Montpellier, France
- LabEx "Ion Channel Science and Therapeutics," Montpellier, France
| | - Antonio Gil-Nagel
- Department of Neurology, Epilepsy Program, Hospital Ruber Internacional, Madrid, Spain
| | - Paloma Parra-Diaz
- Department of Neurology, Epilepsy Program, Hospital Ruber Internacional, Madrid, Spain
| | - Philippe Lory
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, Montpellier, France
- LabEx "Ion Channel Science and Therapeutics," Montpellier, France
| | - Adriano Senatore
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada
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2
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Singh S, Choudhury A, Hazelhurst S, Crowther NJ, Boua PR, Sorgho H, Agongo G, Nonterah EA, Micklesfield LK, Norris SA, Kisiangani I, Mohamed S, Gómez-Olivé FX, Tollman SM, Choma S, Brandenburg JT, Ramsay M. Genome-wide association study meta-analysis of blood pressure traits and hypertension in sub-Saharan African populations: an AWI-Gen study. Nat Commun 2023; 14:8376. [PMID: 38104120 PMCID: PMC10725455 DOI: 10.1038/s41467-023-44079-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 11/29/2023] [Indexed: 12/19/2023] Open
Abstract
Most hypertension-related genome-wide association studies (GWASs) focus on non-African populations, despite hypertension (a major risk factor for cardiovascular disease) being highly prevalent in Africa. The AWI-Gen study GWAS meta-analysis for blood pressure (BP)-related traits (systolic and diastolic BP, pulse pressure, mean-arterial pressure and hypertension) from three sub-Saharan African geographic regions (N = 10,775), identifies two novel genome-wide significant signals (p < 5E-08): systolic BP near P2RY1 (rs77846204; intergenic variant, p = 4.95E-08) and pulse pressure near LINC01256 (rs80141533; intergenic variant, p = 1.76E-08). No genome-wide signals are detected for the AWI-Gen GWAS meta-analysis with previous African-ancestry GWASs (UK Biobank (African), Uganda Genome Resource). Suggestive signals (p < 5E-06) are observed for all traits, with 29 SNPs associating with more than one trait and several replicating known associations. Polygenic risk scores (PRSs) developed from studies on different ancestries have limited transferability, with multi-ancestry PRS providing better prediction. This study provides insights into the genetics of BP variation in African populations.
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Affiliation(s)
- Surina Singh
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, 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
| | - 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
| | - Nigel J Crowther
- Department of Chemical Pathology, National Health Laboratory Service, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Palwendé R Boua
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Clinical Research Unit of Nanoro, Institut de Recherche en Sciences de la Sante, Ouagadougou, Burkina Faso
| | - Hermann Sorgho
- Clinical Research Unit of Nanoro, Institut de Recherche en Sciences de la Sante, Ouagadougou, Burkina Faso
| | - Godfred Agongo
- Department of Biochemistry and Forensic Sciences, School of Chemical and Biochemical Sciences, C.K. Tedam University of Technology and Applied Sciences, Navrongo, Ghana
- Navrongo Health Research Centre, Ghana Health Service, Navrongo, Ghana
| | - Engelbert A Nonterah
- Navrongo Health Research Centre, Ghana Health Service, Navrongo, Ghana
- Julius Global Health, Julius Centre for Health Sciences and Primary Care, University Medical Centre Utrecht, Utrecht, Netherlands
| | - Lisa K Micklesfield
- SAMRC Developmental Pathways for Health Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Shane A Norris
- SAMRC Developmental Pathways for Health Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- School of Health and Human Development, University of Southampton, Southampton, UK
| | | | - Shukri Mohamed
- African Population and Health Research Center, Nairobi, Kenya
| | - Francesc X Gómez-Olivé
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Stephen M Tollman
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Solomon Choma
- Department of Medical Science, Public Health and Health Promotion, School of Health Care Sciences, Faculty of Health Sciences, University of Limpopo, Polokwane, South Africa
| | - J-T Brandenburg
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Strengthening Oncology Services, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Michèle Ramsay
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
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3
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Shriner D, Bentley AR, Gouveia MH, Heuston EF, Doumatey AP, Chen G, Zhou J, Adeyemo A, Rotimi CN. Universal genome-wide association studies: Powerful joint ancestry and association testing. HGG ADVANCES 2023; 4:100235. [PMID: 37653728 PMCID: PMC10507155 DOI: 10.1016/j.xhgg.2023.100235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 08/28/2023] [Accepted: 08/28/2023] [Indexed: 09/02/2023] Open
Abstract
The vast majority of human populations and individuals have mixed ancestry. Consequently, adjustment for locus-specific ancestry is essential for genetic association studies. To empower association studies for all populations, it is necessary to integrate effects of locus-specific ancestry and genotype. We developed a joint test of ancestry and association that can be performed with summary statistics, is independent of study design, can take advantage of locus-specific ancestry effects to boost power in association testing, and can utilize association effects to fine map admixture peaks. We illustrate the test using the association between serum triglycerides and LPL. By combining data from African Americans, European Americans, and West Africans, we identify three conditionally independent variants with varying amounts of ancestrally differentiated allele frequencies. Using out-of-sample data, we demonstrate improved prediction achievable by accounting for multiple causal variants and locus-specific ancestry effects at a single locus.
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Affiliation(s)
- Daniel Shriner
- 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
| | - Mateus H Gouveia
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, MD 20892, USA
| | - Elisabeth F Heuston
- 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
| | - Jie Zhou
- 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
| | - Charles N Rotimi
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, MD 20892, USA.
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4
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Doumatey AP, Bentley AR, Akinyemi R, Olanrewaju TO, Adeyemo A, Rotimi C. Genes, environment, and African ancestry in cardiometabolic disorders. Trends Endocrinol Metab 2023; 34:601-621. [PMID: 37598069 PMCID: PMC10548552 DOI: 10.1016/j.tem.2023.07.007] [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: 05/19/2023] [Revised: 07/24/2023] [Accepted: 07/25/2023] [Indexed: 08/21/2023]
Abstract
The past two decades have been characterized by a substantial global increase in cardiometabolic diseases, but the prevalence and incidence of these diseases and related traits differ across populations. African ancestry populations are among the most affected yet least included in research. Populations of African descent manifest significant genetic and environmental diversity and this under-representation is a missed opportunity for discovery and could exacerbate existing health disparities and curtail equitable implementation of precision medicine. Here, we discuss cardiometabolic diseases and traits in the context of African descent populations, including both genetic and environmental contributors and emphasizing novel discoveries. We also review new initiatives to include more individuals of African descent in genomics to address current gaps in the field.
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Affiliation(s)
- Ayo P Doumatey
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Amy R Bentley
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Rufus Akinyemi
- Neuroscience and Ageing Research Unit, Institute for Advanced Medical Research and Training and Centre for Genomic and Precision Medicine, College of Medicine, University of Ibadan, Ibadan, Nigeria; Department of Neurology, University College Hospital, Ibadan, Nigeria
| | - Timothy O Olanrewaju
- Division of Nephrology, Department of Medicine, University of Ilorin & University of Ilorin Teaching Hospital, Ilorin, Nigeria
| | - Adebowale Adeyemo
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Charles Rotimi
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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5
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Linares-Pineda T, Peña-Montero N, Fragoso-Bargas N, Gutiérrez-Repiso C, Lima-Rubio F, Suarez-Arana M, Sánchez-Pozo A, Tinahones FJ, Molina-Vega M, Picón-César MJ, Sommer C, Morcillo S. Epigenetic marks associated with gestational diabetes mellitus across two time points during pregnancy. Clin Epigenetics 2023; 15:110. [PMID: 37415231 PMCID: PMC10324212 DOI: 10.1186/s13148-023-01523-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 06/23/2023] [Indexed: 07/08/2023] Open
Abstract
An adverse intrauterine or periconceptional environment, such as hyperglycemia during pregnancy, can affect the DNA methylation pattern both in mothers and their offspring. In this study, we explored the epigenetic profile in maternal peripheral blood samples through pregnancy to find potential epigenetic biomarkers for gestational diabetes mellitus (GDM), as well as candidate genes involved in GDM development. We performed an epigenome-wide association study in maternal peripheral blood samples in 32 pregnant women (16 with GDM and 16 non-GDM) at pregnancy week 24-28 and 36-38. Biochemical, anthropometric, and obstetrical variables were collected from all the participants. The main results were validated in an independent cohort with different ethnic origin (European = 307; South Asians = 165). Two hundred and seventy-two CpGs sites remained significantly different between GDM and non-GDM pregnant women across two time points during pregnancy. The significant CpG sites were related to pathways associated with type I diabetes mellitus, insulin resistance and secretion. Cg01459453 (SELP gene) was the most differentiated in the GDM group versus non-GDM (73.6 vs. 60.9, p = 1.06E-11; FDR = 7.87E-06). Three CpG sites (cg01459453, cg15329406, and cg04095097) were able to discriminate between GDM cases and controls (AUC = 1; p = 1.26E-09). Three differentially methylated positions (DMPs) were replicated in an independent cohort. To conclude, epigenetic marks during pregnancy differed between GDM cases and controls suggesting a role for these genes in GDM development. Three CpGs were able to discriminate GDM and non-GDM groups with high specificity and sensitivity, which may be biomarker candidates for diagnosis or prediction of GDM.
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Affiliation(s)
- Teresa Linares-Pineda
- Unidad de Gestión Clínica de Endocrinología y Nutrición, Instituto de Investigación Biomédica de Málaga-IBIMA_Plataforma Bionand, Hospital Universitario Virgen de la Victoria, 29010, Málaga, Spain
- Departamento de Bioquímica y Biología Molecular 2, Universidad de Granada, Granada, Spain
| | - Nerea Peña-Montero
- Unidad de Gestión Clínica de Endocrinología y Nutrición, Instituto de Investigación Biomédica de Málaga-IBIMA_Plataforma Bionand, Hospital Universitario Virgen de la Victoria, 29010, Málaga, Spain
| | - Nicolás Fragoso-Bargas
- Department of Endocrinology Morbid Obesity and Preventive Medicine, Oslo University Hospital, Oslo, Norway
- Faculty of Medicine, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Carolina Gutiérrez-Repiso
- Unidad de Gestión Clínica de Endocrinología y Nutrición, Instituto de Investigación Biomédica de Málaga-IBIMA_Plataforma Bionand, Hospital Universitario Virgen de la Victoria, 29010, Málaga, Spain
- Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición (CIBERObn), Instituto de Salud Carlos III, 29029, Madrid, Spain
| | - Fuensanta Lima-Rubio
- Unidad de Gestión Clínica de Endocrinología y Nutrición, Instituto de Investigación Biomédica de Málaga-IBIMA_Plataforma Bionand, Hospital Universitario Virgen de la Victoria, 29010, Málaga, Spain
| | - María Suarez-Arana
- Departamento de Obstetricia y Ginecología, Instituto de Investigación Biomédica de Málaga-IBIMA_Plataforma Bionand, Hospital Regional Universitario de Málaga, 29009, Málaga, Spain
| | - Antonio Sánchez-Pozo
- Departamento de Bioquímica y Biología Molecular 2, Universidad de Granada, Granada, Spain
| | - Francisco J Tinahones
- Unidad de Gestión Clínica de Endocrinología y Nutrición, Instituto de Investigación Biomédica de Málaga-IBIMA_Plataforma Bionand, Hospital Universitario Virgen de la Victoria, 29010, Málaga, Spain
- Department of Endocrinology Morbid Obesity and Preventive Medicine, Oslo University Hospital, Oslo, Norway
- Departamento de Medicina y Dermatología, Universidad de Málaga, 29010, Málaga, Spain
| | - María Molina-Vega
- Unidad de Gestión Clínica de Endocrinología y Nutrición, Instituto de Investigación Biomédica de Málaga-IBIMA_Plataforma Bionand, Hospital Universitario Virgen de la Victoria, 29010, Málaga, Spain
| | - María José Picón-César
- Unidad de Gestión Clínica de Endocrinología y Nutrición, Instituto de Investigación Biomédica de Málaga-IBIMA_Plataforma Bionand, Hospital Universitario Virgen de la Victoria, 29010, Málaga, Spain.
| | - Christine Sommer
- Department of Endocrinology Morbid Obesity and Preventive Medicine, Oslo University Hospital, Oslo, Norway
- Faculty of Medicine, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Sonsoles Morcillo
- Unidad de Gestión Clínica de Endocrinología y Nutrición, Instituto de Investigación Biomédica de Málaga-IBIMA_Plataforma Bionand, Hospital Universitario Virgen de la Victoria, 29010, Málaga, Spain.
- Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición (CIBERObn), Instituto de Salud Carlos III, 29029, Madrid, Spain.
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6
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Adua E. Decoding the mechanism of hypertension through multiomics profiling. J Hum Hypertens 2023; 37:253-264. [PMID: 36329155 PMCID: PMC10063442 DOI: 10.1038/s41371-022-00769-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 08/24/2022] [Accepted: 10/17/2022] [Indexed: 11/06/2022]
Abstract
Hypertension, characterised by a constant high blood pressure, is the primary risk factor for multiple cardiovascular events and a major cause of death in adults. Excitingly, innovations in high-throughput technologies have enabled the global exploration of the whole genome (genomics), revealing dysregulated genes that are linked to hypertension. Moreover, post-genomic biomarkers, from the emerging fields of transcriptomics, proteomics, glycomics and lipidomics, have provided new insights into the molecular underpinnings of hypertension. In this paper, we review the pathophysiology of hypertension, and highlight the multi-omics approaches for hypertension prediction and diagnosis.
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Affiliation(s)
- Eric Adua
- School of Clinical Medicine, Medicine & Health, Rural Clinical Campus, University of New South Wales, Wagga Wagga, NSW, Australia.
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia.
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7
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Fan S, Spence JP, Feng Y, Hansen MEB, Terhorst J, Beltrame MH, Ranciaro A, Hirbo J, Beggs W, Thomas N, Nyambo T, Mpoloka SW, Mokone GG, Njamnshi A, Folkunang C, Meskel DW, Belay G, Song YS, Tishkoff SA. Whole-genome sequencing reveals a complex African population demographic history and signatures of local adaptation. Cell 2023; 186:923-939.e14. [PMID: 36868214 PMCID: PMC10568978 DOI: 10.1016/j.cell.2023.01.042] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 10/16/2022] [Accepted: 01/30/2023] [Indexed: 03/05/2023]
Abstract
We conduct high coverage (>30×) whole-genome sequencing of 180 individuals from 12 indigenous African populations. We identify millions of unreported variants, many predicted to be functionally important. We observe that the ancestors of southern African San and central African rainforest hunter-gatherers (RHG) diverged from other populations >200 kya and maintained a large effective population size. We observe evidence for ancient population structure in Africa and for multiple introgression events from "ghost" populations with highly diverged genetic lineages. Although currently geographically isolated, we observe evidence for gene flow between eastern and southern Khoesan-speaking hunter-gatherer populations lasting until ∼12 kya. We identify signatures of local adaptation for traits related to skin color, immune response, height, and metabolic processes. We identify a positively selected variant in the lightly pigmented San that influences pigmentation in vitro by regulating the enhancer activity and gene expression of PDPK1.
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Affiliation(s)
- Shaohua Fan
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, School of Life Science, Fudan University, Shanghai, 200438, China; Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jeffrey P Spence
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Yuanqing Feng
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Matthew E B Hansen
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jonathan Terhorst
- Department of Statistics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Marcia H Beltrame
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Alessia Ranciaro
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jibril Hirbo
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - William Beggs
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Neil Thomas
- Computer Science Division, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Thomas Nyambo
- Department of Biochemistry, Kampala International University in Tanzania, P.O. Box 9790, Dar es Salaam, Tanzania
| | - Sununguko Wata Mpoloka
- Department of Biological Sciences, Faculty of Science, University of Botswana Gaborone, Private Bag UB 0022, Gaborone, Botswana
| | - Gaonyadiwe George Mokone
- Department of Biomedical Sciences, Faculty of Medicine, University of Botswana Gaborone, Private Bag UB 0022, Gaborone, Botswana
| | - Alfred Njamnshi
- Department of Neurology, Central Hospital Yaoundé; Brain Research Africa Initiative (BRAIN), Neuroscience Lab, Faculty of Medicine and Biomedical Sciences, The University of Yaoundé I, P.O. Box 337, Yaoundé, Cameroon
| | - Charles Folkunang
- Department of Pharmacotoxicology and Pharmacokinetics, Faculty of Medicine and Biomedical Sciences, The University of Yaoundé I, P.O. Box 337, Yaoundé, Cameroon
| | - Dawit Wolde Meskel
- Department of Microbial Cellular and Molecular Biology, Addis Ababa University, P.O. Box 1176, Addis Ababa, Ethiopia
| | - Gurja Belay
- Department of Microbial Cellular and Molecular Biology, Addis Ababa University, P.O. Box 1176, Addis Ababa, Ethiopia
| | - Yun S Song
- Computer Science Division, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Statistics, University of California, Berkeley, Berkeley, CA 94720, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Sarah A Tishkoff
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA.
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8
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Singh S, Choudhury A, Hazelhurst S, Crowther N, Boua P, Sorgho H, Agongo G, Nonterah E, Micklesfield L, Norris S, Kisiangani I, Mohamed S, Gomez-Olive F, Tollman S, Choma S, Brandenburg JT, Ramsay M. Genome-wide Association Study Meta-analysis of Blood Pressure Traits and Hypertension in Sub-Saharan African Populations: An AWI-Gen Study. RESEARCH SQUARE 2023:rs.3.rs-2532794. [PMID: 36824767 PMCID: PMC9949264 DOI: 10.21203/rs.3.rs-2532794/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Most hypertension-related genome-wide association studies (GWAS) focus on non-African populations, despite hypertension (a major risk factor for cardiovascular disease) being highly prevalent in Africa. The AWI-Gen study GWAS meta-analysis for blood pressure-related traits (systolic and diastolic blood pressure, pulse pressure, mean-arterial pressure and hypertension) from three sub-Saharan African geographic regions (N=10,775), identified two genome-wide significant signals (p<5E-08): systolic blood pressure near P2RY1 (rs77846204; intergenic variant, p=4.25E-08) and pulse pressure near Linc01256 (rs80141533; intergenic variant, p=4.25E-08). No genome-wide signals were detected for the AWI-Gen GWAS meta-analysis with previous African-ancestry GWASs (UK Biobank (African), Uganda Genome Resource). Suggestive signals (p<5E-06) were observed for all traits, with 29 displaying pleiotropic effects and several replicating known associations. Polygenic risk scores developed from studies on different ancestries had limited transferability, with multi-ancestry models providing better prediction. This study provides insights into the genetics and physiology of blood pressure variation in African populations.
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Affiliation(s)
- Surina Singh
- Sydney Brenner Institute for Molecular Bioscience (SBIMB), University of the Witwatersrand
| | | | - Scott Hazelhurst
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences & School of Electrical & Information Engineering, University of the Witwatersrand
| | - Nigel Crowther
- 11Department of Chemical Pathology, National Health Laboratory Service
| | - Palwende Boua
- Clinical Research Unit of Nanoro, Institut de Recherche en Sciences de la Santé
| | - Hermann Sorgho
- Clinical Research Unit of Nanoro, Institut de Recherche en Sciences de la Santé
| | | | | | | | - Shane Norris
- SAMRC Developmental Pathways For Health Research Unit, Department of Paediatrics & Child Health, University of the Witwatersrand, Johannesburg, South Africa
| | | | | | - Francesc Gomez-Olive
- 8MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand
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Abstract
Sickle cell disease (SCD) is the most-common monogenic recessive disease in humans, annually affecting almost 300,000 newborns worldwide, 75% of whom live in Africa. Genomics research can accelerate the development of curative therapies for SCD in three ways. First, research should explore the missing heritability of foetal haemoglobin (HbF) - the strongest known modifier of SCD clinical expression - among highly genetically heterogenous and understudied African populations, to provide novel therapeutics targets for HbF induction. Second, SCD research should invest in RNA therapies, either by using microRNA to target the production of HbF proteins by binding to the transcription machinery in a cell, or by directly mediating production of HbF or adult haemoglobin through injection of messenger RNA. Third, investigators should aim to identify currently unknown genetic risk factors for SCD cardiovascular complications, which will address mortality, particularly in adults. Now is the time for global research programs to uncover genomic keys to unlock SCD therapeutics.
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Affiliation(s)
- Ambroise Wonkam
- McKusick-Nathans Institute and Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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10
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Abstract
Admixture mapping is a powerful method of gene mapping for diseases or traits that show differential risk by ancestry. Admixture mapping has been applied most often to Americans who trace ancestry to various combinations of Native Americans, Europeans, and West Africans. Recent developments in admixture mapping include improvements in the methods and reference data needed to make inferences about ancestry as well as extensions of the mapping approach in the framework of linear mixed models. This overview outlines the key concepts of admixture mapping. It describes approaches for inferring local ancestry and provides strategies for performing admixture mapping depending on the study design. Finally, linkage analysis, association analysis, and admixture mapping are compared, with an emphasis on integrating admixture mapping and association testing. Published 2023. This article is a U.S. Government work and is in the public domain in the USA.
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Affiliation(s)
- Daniel Shriner
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, Maryland
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11
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Udosen B, Soremekun O, Kamiza A, Machipisa T, Cheickna C, Omotuyi O, Soliman M, Wélé M, Nashiru O, Chikowore T, Fatumo S. Meta-Analysis and Multivariate GWAS Analyses in 80,950 Individuals of African Ancestry Identify Novel Variants Associated with Blood Pressure Traits. Int J Mol Sci 2023; 24:2164. [PMID: 36768488 PMCID: PMC9916484 DOI: 10.3390/ijms24032164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 12/24/2022] [Accepted: 01/03/2023] [Indexed: 01/25/2023] Open
Abstract
High blood pressure (HBP) has been implicated as a major risk factor for cardiovascular diseases in several populations, including individuals of African ancestry. Despite the elevated burden of HBP-induced cardiovascular diseases in Africa and other populations of African descent, limited genetic studies have been carried out to explore the genetic mechanism driving this phenomenon. We performed genome-wide association univariate and multivariate analyses of both systolic (SBP) and diastolic blood pressure (DBP) traits in 80,950 individuals of African ancestry. We used summary statistics data from six independent cohorts, including the African Partnership for Chronic Disease Research (APCDR), the UK Biobank, and the Million Veteran Program (MVP). FUMA was used to annotate, prioritize, visualize, and interpret our findings to gain a better understanding of the molecular mechanism(s) underlying the genetics of BP traits. Finally, we undertook a Bayesian fine-mapping analysis to identify potential causal variants. Our meta-analysis identified 10 independent variants associated with SBP and 9 with DBP traits. Whilst our multivariate GWAS method identified 21 independent signals, 18 of these SNPs have been previously identified. SBP was linked to gene sets involved in biological processes such as synapse assembly and cell-cell adhesion via plasma membrane adhesion. Of the 19 independent SNPs identified in the BP meta-analysis, only 11 variants had posterior probability (PP) of > 50%, including one novel variant: rs562545 (MOBP, PP = 77%). To facilitate further research and fine-mapping of high-risk loci/variants in highly susceptible groups for cardiovascular disease and other related traits, large-scale genomic datasets are needed. Our findings highlight the importance of including ancestrally diverse populations in large GWASs and the need for diversity in genetic research.
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Affiliation(s)
- Brenda Udosen
- The African Computational Genomics (TACG) Research Group, MRC/UVRI and LSHTM, Entebbe 7545, Uganda; (B.U.); (O.S.); (A.K.)
- The African Center of Excellence in Bioinformatics of Bamako (ACE-B), University of Sciences, Techniques and Technologies of Bamako, Bamako 3206, Mali; (C.C.); (M.W.)
- H3Africa Bioinformatics Network (H3ABioNet) Node, Centre for Genomics Research and Innovation, NABDA/FMST, Abuja 901101, Nigeria;
| | - Opeyemi Soremekun
- The African Computational Genomics (TACG) Research Group, MRC/UVRI and LSHTM, Entebbe 7545, Uganda; (B.U.); (O.S.); (A.K.)
- Molecular Bio-Computation and Drug Design Laboratory, School of Health Sciences, Westville Campus, University of KwaZulu-Natal, Durban 4001, South Africa;
| | - Abram Kamiza
- The African Computational Genomics (TACG) Research Group, MRC/UVRI and LSHTM, Entebbe 7545, Uganda; (B.U.); (O.S.); (A.K.)
- Malawi Epidemiology and Intervention Research Unit, Lilongwe P.O. Box 46, Malawi
| | - Tafadzwa Machipisa
- Hatter Institute for Cardiovascular Diseases Research in Africa (HICRA), Department of Medicine, University of Cape Town, Cape Town 7701, South Africa;
- Population Health Research Institute, David Braley Cardiac, Vascular and Stroke Research Institute, Hamilton, ON L8L 2X2, Canada
| | - Cisse Cheickna
- The African Center of Excellence in Bioinformatics of Bamako (ACE-B), University of Sciences, Techniques and Technologies of Bamako, Bamako 3206, Mali; (C.C.); (M.W.)
- Department of Biological Sciences, Faculty of Sciences and Techniques, University of Sciences, Techniques and Technologies of Bamako, Bamako 3206, Mali
| | - Olaposi Omotuyi
- Institute for Drug Research and Development, S.E. Bogoro Center, Afe Babalola University, Ado Ekiti 360101, Nigeria;
| | - Mahmoud Soliman
- Molecular Bio-Computation and Drug Design Laboratory, School of Health Sciences, Westville Campus, University of KwaZulu-Natal, Durban 4001, South Africa;
| | - Mamadou Wélé
- The African Center of Excellence in Bioinformatics of Bamako (ACE-B), University of Sciences, Techniques and Technologies of Bamako, Bamako 3206, Mali; (C.C.); (M.W.)
- Department of Biological Sciences, Faculty of Sciences and Techniques, University of Sciences, Techniques and Technologies of Bamako, Bamako 3206, Mali
| | - Oyekanmi Nashiru
- H3Africa Bioinformatics Network (H3ABioNet) Node, Centre for Genomics Research and Innovation, NABDA/FMST, Abuja 901101, Nigeria;
| | - Tinashe Chikowore
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2050, South Africa;
- MRC/Wits Developmental Pathways for Health Research Unit, Department of Pediatrics, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2050, South Africa
| | - Segun Fatumo
- The African Computational Genomics (TACG) Research Group, MRC/UVRI and LSHTM, Entebbe 7545, Uganda; (B.U.); (O.S.); (A.K.)
- H3Africa Bioinformatics Network (H3ABioNet) Node, Centre for Genomics Research and Innovation, NABDA/FMST, Abuja 901101, Nigeria;
- Segun Fatumo, Department of Non-Communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
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12
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Al-Khannaq M, Lytton J. Regulation of K +-Dependent Na +/Ca 2+-Exchangers (NCKX). Int J Mol Sci 2022; 24:ijms24010598. [PMID: 36614039 PMCID: PMC9820825 DOI: 10.3390/ijms24010598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 12/23/2022] [Accepted: 12/24/2022] [Indexed: 12/31/2022] Open
Abstract
Potassium-dependent sodium-calcium exchangers (NCKX) have emerged as key determinants of calcium (Ca2+) signaling and homeostasis, especially in environments where ion concentrations undergo large changes, such as excitatory cells and transport epithelia. The regulation of NCKX transporters enables them to respond to the changing cellular environment thereby helping to shape the extent and kinetics of Ca2+ signals. This review examines the current knowledge of the different ways in which NCKX activity can be modulated. These include (i) cellular and dynamic subcellular location (ii); changes in protein expression mediated at the gene, transcript, or protein level (iii); genetic changes resulting in altered protein structure or expression (iv); regulation via changes in substrate concentration (v); and post-translational modification, partner protein interactions, and allosteric regulation. Detailed mechanistic understanding of NCKX regulation is an emerging area of research with the potential to provide important new insights into transporter function, the control of Ca2+ signals, and possible interventions for dysregulated Ca2+ homeostasis.
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13
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Malinowska JK, Żuradzki T. Towards the multileveled and processual conceptualisation of racialised individuals in biomedical research. SYNTHESE 2022; 201:11. [PMID: 36591336 PMCID: PMC9795162 DOI: 10.1007/s11229-022-04004-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 12/09/2022] [Indexed: 06/17/2023]
Abstract
In this paper, we discuss the processes of racialisation on the example of biomedical research. We argue that applying the concept of racialisation in biomedical research can be much more precise, informative and suitable than currently used categories, such as race and ethnicity. For this purpose, we construct a model of the different processes affecting and co-shaping the racialisation of an individual, and consider these in relation to biomedical research, particularly to studies on hypertension. We finish with a discussion on the potential application of our proposition to institutional guidelines on the use of racial categories in biomedical research.
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Affiliation(s)
| | - Tomasz Żuradzki
- Institute of Philosophy & Interdisciplinary Centre for Ethics, Jagiellonian University, ul. Grodzka 52, 31-044 Kraków, Poland
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14
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Fujii R, Hishida A, Nakatochi M, Tsuboi Y, Suzuki K, Kondo T, Ikezaki H, Hara M, Okada R, Tamura T, Shimoshikiryo I, Suzuki S, Koyama T, Kuriki K, Takashima N, Arisawa K, Momozawa Y, Kubo M, Takeuchi K, Wakai K, Matsuo K, Tanaka K, Miura K, Kita Y, Takezaki T, Nagase H, Mikami H, Uehara R, Narimatsu H. Associations of Genome-Wide Polygenic Risk Score and Risk Factors With Hypertension in a Japanese Population. Circ Genom Precis Med 2022; 15:e003612. [DOI: 10.1161/circgen.121.003612] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Background:
Although many polygenic risk scores (PRS) for cardiovascular traits have been developed in European populations, it is an urgent task to construct a PRS and to evaluate its ability in non-European populations. We developed a genome-wide PRS for blood pressure in a Japanese population and examined the associations between this PRS and hypertension prevalence.
Methods:
We performed a cross-sectional study in 11 252 Japanese individuals who participated in the J-MICC (Japan Multi-Institutional Collaborative Cohort) study. Using publicly available GWAS summary statistics from Biobank Japan, we developed the PRS in the target data (n=7876). With >30 000 single nucleotide polymorphisms, we evaluated PRS performance in the test data (n=3376). Hypertension was defined as systolic blood pressure of 130 mm Hg or more, or diastolic blood pressure of 85 mm Hg or more, or taking an antihypertensive drug.
Results:
Compared with the middle PRS quintile, the prevalence of hypertension at the top PRS quintile was higher independently from traditional risk factors (odds ratio, 1.73 [95% CI, 1.32–2.27]). The difference of mean systolic blood pressure and diastolic blood pressure between the middle and the top PRS quintile was 4.55 (95% CI, 2.26–6.85) and 2.32 (95% CI, 0.86–3.78) mm Hg, respectively. Subgroups reflecting combinations of Japanese PRS and modifiable lifestyles and factors (smoking, alcohol intake, sedentary time, and obesity) were associated with the prevalence of hypertension. A European-derived PRS was not associated with hypertension in our participants.
Conclusions:
A PRS for blood pressure was significantly associated with hypertension and BP traits in a general Japanese population. Our findings also highlighted the importance of a combination of PRS and risk factors for identifying high-risk subgroups.
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Affiliation(s)
- Ryosuke Fujii
- Department of Preventive Medical Sciences, Fujita Health University School of Medical Sciences, Toyoake, Japan (R.F., Y.T., K.S.), Nagoya University Graduate School of Medicine, Nagoya, Japan
- Division of interactive Medical & Healthcare Systems, Department of Integrated Health Sciences (R.F., T. Kondo), Nagoya University Graduate School of Medicine, Nagoya, Japan
- Institute for Biomedicine, Eurac Research (affiliated to the University of Lübeck), Bolzano/Bozen, Italy (R.F.)
| | - Asahi Hishida
- Department of Preventive Medicine (A.H., R.O., T.T., K.T., K.W.), Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Masahiro Nakatochi
- Public Health Informatics Unit, Department of Integrated Health Sciences (M.N.), Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yoshiki Tsuboi
- Department of Preventive Medical Sciences, Fujita Health University School of Medical Sciences, Toyoake, Japan (R.F., Y.T., K.S.), Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Koji Suzuki
- Department of Preventive Medical Sciences, Fujita Health University School of Medical Sciences, Toyoake, Japan (R.F., Y.T., K.S.), Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Takaaki Kondo
- Division of interactive Medical & Healthcare Systems, Department of Integrated Health Sciences (R.F., T. Kondo), Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Hiroaki Ikezaki
- Department of Comprehensive General Internal Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan (H.I.)
| | - Megumi Hara
- Department of Preventive Medicine, Faculty of Medicine, Saga University, Saga, Japan (M.H.)
| | - Rieko Okada
- Department of Preventive Medicine (A.H., R.O., T.T., K.T., K.W.), Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Takashi Tamura
- Department of Preventive Medicine (A.H., R.O., T.T., K.T., K.W.), Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Ippei Shimoshikiryo
- Department of International Island & Community Medicine, Kagoshima University Graduate School of Medical & Dental Sciences, Kagoshima, Japan (I.S.)
| | - Sadao Suzuki
- Department of Public Health, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan (S.S.)
| | - Teruhide Koyama
- Department of Epidemiology for Community Health & Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan (T. Koyama)
| | - Kiyonori Kuriki
- Laboratory of Public Health, Division of Nutritional Sciences, School of Food & Nutritional Sciences, University of Shizuoka, Shizuoka, Shizuoka (K.K.)
| | - Naoyuki Takashima
- Department of Public Health, Shiga University of Medical Science, Otsu, Japan (N.T.)
- Department of Public Health, Kindai University Faculty of Medicine, Osaka, Japan (N.T.)
| | - Kokichi Arisawa
- Department of Preventive Medicine, Tokushima University Graduate School of Biomedical Scinces, Tokushima, Japan (K.A.)
| | - Yukihide Momozawa
- Laboratory for Genotyping Development, Center for Integrative Medical Sciences, RIKEN, Kanagawa, Japan (Y.M., M.K.)
| | - Michiaki Kubo
- Laboratory for Genotyping Development, Center for Integrative Medical Sciences, RIKEN, Kanagawa, Japan (Y.M., M.K.)
| | - Kenji Takeuchi
- Department of Preventive Medicine (A.H., R.O., T.T., K.T., K.W.), Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kenji Wakai
- Department of Preventive Medicine (A.H., R.O., T.T., K.T., K.W.), Nagoya University Graduate School of Medicine, Nagoya, Japan
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15
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Armstrong ND, Srinivasasainagendra V, Chekka LMS, Nguyen NHK, Nahid NA, Jones AC, Tanner RM, Hidalgo BA, Limdi NA, Claas SA, Gong Y, McDonough CW, Cooper-DeHoff RM, Johnson JA, Tiwari HK, Arnett DK, Irvin MR. Genetic Contributors of Efficacy and Adverse Metabolic Effects of Chlorthalidone in African Americans from the Genetics of Hypertension Associated Treatments (GenHAT) Study. Genes (Basel) 2022; 13:genes13071260. [PMID: 35886043 PMCID: PMC9319619 DOI: 10.3390/genes13071260] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 07/01/2022] [Accepted: 07/07/2022] [Indexed: 02/05/2023] Open
Abstract
Hypertension is a leading risk factor for cardiovascular disease mortality. African Americans (AAs) have the highest prevalence of hypertension in the United States, and to alleviate the burden of hypertension in this population, better control of blood pressure (BP) is needed. Previous studies have shown considerable interpersonal differences in BP response to antihypertensive treatment, suggesting a genetic component. Utilizing data from 4297 AA participants randomized to chlorthalidone from the Genetics of Hypertension Associated Treatments (GenHAT) study, we aimed to identify variants associated with the efficacy of chlorthalidone. An additional aim was to find variants that contributed to changes in fasting glucose (FG) in these individuals. We performed genome-wide association analyses on the change of systolic and diastolic BP (SBP and DBP) over six months and FG levels over 24 months of treatment. We sought replication in the International Consortia of Pharmacogenomics Studies. We identified eight variants statistically associated with BP response and nine variants associated with FG response. One suggestive LINC02211-CDH9 intergenic variant was marginally replicated with the same direction of effect. Given the impact of hypertension in AAs, this study implies that understanding the genetic background for BP control and glucose changes during chlorthalidone treatment may help prevent adverse cardiovascular events in this population.
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Affiliation(s)
- Nicole D Armstrong
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | | | - Lakshmi Manasa S Chekka
- Division of Applied Regulatory Sciences, Center for Drug Evaluation and Research, Silver Spring, MD 20903, USA
| | - Nam H K Nguyen
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Gainesville, FL 32611, USA
| | - Noor A Nahid
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Gainesville, FL 32611, USA
| | - Alana C Jones
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Medical Scientist Training Program, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Rikki M Tanner
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Bertha A Hidalgo
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Nita A Limdi
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Steven A Claas
- Department of Epidemiology, College of Public Health, University of Kentucky, Lexington, KY 40506, USA
| | - Yan Gong
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Gainesville, FL 32611, USA
| | - Caitrin W McDonough
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Gainesville, FL 32611, USA
| | - Rhonda M Cooper-DeHoff
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Gainesville, FL 32611, USA
- Division of Cardiovascular Medicine, Department of Medicine, University of Florida, Gainesville, FL 32611, USA
| | - Julie A Johnson
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Gainesville, FL 32611, USA
- Division of Cardiovascular Medicine, Department of Medicine, University of Florida, Gainesville, FL 32611, USA
| | - Hemant K Tiwari
- Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Donna K Arnett
- Department of Epidemiology, College of Public Health, University of Kentucky, Lexington, KY 40506, USA
- Deans Office, College of Public Health, University of Kentucky, Lexington, KY 40506, USA
| | - Marguerite R Irvin
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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16
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Chilunga FP, Meeks KAC, Henneman P, Agyemang C, Doumatey AP, Rotimi CN, Adeyemo AA. An epigenome-wide association study of insulin resistance in African Americans. Clin Epigenetics 2022; 14:88. [PMID: 35836279 PMCID: PMC9281172 DOI: 10.1186/s13148-022-01309-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 07/04/2022] [Indexed: 11/18/2022] Open
Abstract
Background African Americans have a high risk for type 2 diabetes (T2D) and insulin resistance. Studies among other population groups have identified DNA methylation loci associated with insulin resistance, but data in African Americans are lacking. Using DNA methylation profiles of blood samples obtained from the Illumina Infinium® HumanMethylation450 BeadChip, we performed an epigenome-wide association study to identify DNA methylation loci associated with insulin resistance among 136 non-diabetic, unrelated African American men (mean age 41.6 years) from the Howard University Family Study. Results We identified three differentially methylated positions (DMPs) for homeostatic model assessment of insulin resistance (HOMA-IR) at 5% FDR. One DMP (cg14013695, HOXA5) is a known locus among Mexican Americans, while the other two DMPs are novel—cg00456326 (OSR1; beta = 0.027) and cg20259981 (ST18; beta = 0.010). Although the cg00456326 DMP is novel, the OSR1 gene has previously been found associated with both insulin resistance and T2D in Europeans. The genes HOXA5 and ST18 have been implicated in biological processes relevant to insulin resistance. Differential methylation at the significant HOXA5 and OSR1 DMPs is associated with differences in gene expression in the iMETHYL database. Analysis of differentially methylated regions (DMRs) did not identify any epigenome-wide DMRs for HOMA-IR. We tested transferability of HOMA-IR associated DMPs from five previous EWAS in Mexican Americans, Indian Asians, Europeans, and European ancestry Americans. Out of the 730 previously reported HOMA-IR DMPs, 47 (6.4%) were associated with HOMA-IR in this cohort of African Americans. Conclusions The findings from our study suggest substantial differences in DNA methylation patterns associated with insulin resistance across populations. Two of the DMPs we identified in African Americans have not been reported in other populations, and we found low transferability of HOMA-IR DMPs reported in other populations in African Americans. More work in African-ancestry populations is needed to confirm our findings as well as functional analyses to understand how such DNA methylation alterations contribute to T2D pathology. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-022-01309-4.
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Affiliation(s)
- Felix P Chilunga
- Department of Public & Occupational Health, Amsterdam Public Health Research Institute, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Karlijn A C Meeks
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Peter Henneman
- Department of Human Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Charles Agyemang
- Department of Public & Occupational Health, Amsterdam Public Health Research Institute, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Ayo P Doumatey
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Charles N Rotimi
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Adebowale A Adeyemo
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
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17
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Barriers to up-titrated antihypertensive strategies in 12 sub-Saharan African countries: the Multination Evaluation of hypertension in Sub-Saharan Africa Study. J Hypertens 2022; 40:1411-1420. [PMID: 35762480 DOI: 10.1097/hjh.0000000000003169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND Sub-Saharan Africa (SSA) faces the highest rate of hypertension worldwide. The high burden of elevated blood pressure (BP) in black people has been emphasized. Guidelines recommend two or more antihypertensive medications to achieve a BP control. We aimed to identify factors associated with prescription of up-titrated antihypertensive strategies in Africa. METHODS We conducted a cross-sectional study on outpatient consultations for hypertension across 12 SSA countries. Collected data included socioeconomic status, antihypertensive drugs classes, BP measures, cardiovascular risk factors and complication of hypertension. We used ordinal logistic regression to assess factors associated with prescription of up-titrated strategies. RESULTS The study involved 2123 treated patients with hypertension. Patients received monotherapy in 36.3 vs. 25.9%, two-drug in 42.2 vs. 45% and three and more drugs strategies in 21.5 vs. 29.1% in low (LIC) and middle (MIC) income countries, respectively. Patients with sedentary lifestyle [OR 1.4 (1.11-1.77)], complication of hypertension [OR 2.4 (1.89-3.03)], former hypertension [OR 3.12 (2.3-4.26)], good adherence [OR 1.98 (1.47-2.66)], from MIC [OR 1.38 (1.10-1.74)] and living in urban areas [OR 1.52 (1.16-1.99)] were more likely to be treated with up-titrated strategies. Stratified analysis shows that in LIC, up-titrated strategies were less frequent in rural than in urban patients (P for trend <0.01) whereas such difference was not observed in MIC. CONCLUSION In this African setting, in addition to expected factors, up-titrated drug strategies were associated with country-level income, patient location and finally, the interplay between both in LIC. These results highlight the importance of developing policies that seek to make multiple drug classes accessible particularly in rural and LIC.
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18
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Parcha V, Irvin MR, Lange LA, Armstrong ND, Pampana A, Meyer M, Judd SE, Arora G, Arora P. Corin Missense Variants, Blood Pressure, and Hypertension in 11 322 Black Individuals: Insights From REGARDS and the Jackson Heart Study. J Am Heart Assoc 2022; 11:e025582. [PMID: 35699180 PMCID: PMC9238660 DOI: 10.1161/jaha.121.025582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 04/27/2022] [Indexed: 11/18/2022]
Abstract
Background Corin enzyme contributes to the processing of inactive natriuretic peptides to bioactive hormones. In Black individuals, Corin gene variants (rs111253292 [Q568P] and rs75770792 [T555I]) have been previously reported to have a modest association with blood pressure (BP) and hypertension. Methods and Results We evaluated the association of Corin genotype with BP traits, prevalent hypertension, and incident hypertension among self-identified 11 322 Black Americans in the REGARDS (Reasons for Geographic and Racial Differences in Stroke) study and the JHS (Jackson Heart Study) using multivariable-adjusted regression modeling. Multivariable-adjusted genotype-stratified differences in NT-proBNP (N-terminal pro-B-type natriuretic peptide) and BNP (B-type natriuretic peptide) levels were assessed. Genotype-stratified NPPA and NPPB expression differences in healthy organ donor left atrial and left ventricular heart tissue (N=15) were also examined. The rs111253292 genotype was not associated with systolic BP (β±SE, 0.42±0.58; -1.24±0.82), diastolic BP (0.51±0.33; -0.41±0.46), mean arterial pressure (0.48±0.38; -0.68±0.51), and prevalent hypertension (odds ratio [OR], 0.93 [95% CI, 0.80-1.09]; OR, 0.79 [95% CI, 0.61-1.01]) in both REGARDS and JHS, respectively. The rs75770792 genotype was not associated with systolic BP (0.48±0.58; -1.26±0.81), diastolic BP (0.52±0.33; -0.33±0.45), mean arterial pressure (0.50±0.38; -0.63±0.50), and prevalent hypertension (OR, 1.02 [95% CI, 0.84-1.23]; OR, 0.87 [95% CI, 0.67-1.13]) in both cohorts, respectively. The Corin genotype was also not associated with incident hypertension (OR, 1.35 [95% CI, 0.94-1.93]; OR, 0.95 [95% CI, 0.64-1.39]) in the study cohorts. The NT-proBNP levels in REGARDS and BNP levels in JHS were similar between the Corin genotype groups. In heart tissue, the NPPA and NPPB expression was similar between the genotype groups. Conclusions Corin gene variants observed more commonly in Black individuals are not associated with differences in NP expression, circulating NP levels, and BP or hypertension as previously reported in candidate gene studies. Understanding the genetic determinants of complex cardiovascular traits in underrepresented populations requires further evaluation.
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Affiliation(s)
- Vibhu Parcha
- Division of Cardiovascular DiseaseUniversity of Alabama at BirminghamBirminghamAL
| | | | - Leslie A. Lange
- Division of Biomedical Informatics and Personalized MedicineDepartment of MedicineUniversity of Colorado School of MedicineAuroraCO
- Department of EpidemiologyUniversity of Colorado School of Public HealthAuroraCO
| | | | - Akhil Pampana
- Division of Cardiovascular DiseaseUniversity of Alabama at BirminghamBirminghamAL
| | - Mariah Meyer
- Division of Biomedical Informatics and Personalized MedicineDepartment of MedicineUniversity of Colorado School of MedicineAuroraCO
| | - Suzanne E. Judd
- Department of BiostatisticsUniversity of Alabama at BirminghamBirminghamAL
| | - Garima Arora
- Division of Cardiovascular DiseaseUniversity of Alabama at BirminghamBirminghamAL
| | - Pankaj Arora
- Division of Cardiovascular DiseaseUniversity of Alabama at BirminghamBirminghamAL
- Section of CardiologyBirmingham Veterans Affairs Medical CenterBirminghamAL
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19
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Chen G, Shriner D, Zhang J, Zhou J, Adikaram P, Doumatey AP, Bentley AR, Adeyemo A, Rotimi CN. Additive genetic effect of GCKR, G6PC2, and SLC30A8 variants on fasting glucose levels and risk of type 2 diabetes. PLoS One 2022; 17:e0269378. [PMID: 35657990 PMCID: PMC9165855 DOI: 10.1371/journal.pone.0269378] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 05/19/2022] [Indexed: 01/11/2023] Open
Abstract
Impaired glucose tolerance is a major risk factor for type 2 diabetes (T2D) and several cardiometabolic disorders. To identify genetic loci underlying fasting glucose levels, we conducted an analysis of 9,232 individuals of European ancestry who at enrollment were either nondiabetic or had untreated type 2 diabetes. Multivariable linear mixed models were used to test for associations between fasting glucose and 7.9 million SNPs, with adjustment for age, body mass index (BMI), sex, significant principal components of the genotypes, and cryptic relatedness. Three previously discovered loci were genome-wide significant, with the lead SNPs being rs1260326, a missense variant in GCKR (p = 1.06×10−8); rs560887, an intronic variant in G6PC2 (p = 3.39×10−11); and rs13266634, a missense variant in SLC30A8 (p = 4.28×10−10). Fine mapping, genome-wide conditional analysis, and functional annotation indicated that the three loci were independently associated with fasting glucose. Each copy of an alternate allele at any of these three SNPs was associated with a reduction of 0.012 mmol/L in fasting glucose levels (p = 8.0×10−28), and this association was replicated in trans-ethnic analysis of 14,303 individuals (p = 2.2×10−16). The three SNPs were jointly associated with significantly reduced T2D risk, with an odds ratio (95% CI) of 0.93 (0.88, 0.98) per protective allele. Our findings implicate additive effects across pathophysiological pathways involved in type 2 diabetes, including glycolysis, gluconeogenesis, and insulin secretion. Since none of the individuals homozygous for the alternate alleles at all three loci has T2D, it might be possible to use a genetic predictor of fasting glucose levels to identify individuals at low vs. high risk of developing type 2 diabetes.
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Affiliation(s)
- Guanjie Chen
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, Maryland, United States of America
| | - Daniel Shriner
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, Maryland, United States of America
| | - Jianhua Zhang
- Metabolic Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland, United States of America
| | - Jie Zhou
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, Maryland, United States of America
| | - Poorni Adikaram
- Advanced BioScience Laboratories, Rockville, Maryland, United States of America
| | - Ayo P. Doumatey
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, Maryland, United States of America
| | - Amy R. Bentley
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, Maryland, United States of America
| | - Adebowale Adeyemo
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, Maryland, United States of America
| | - Charles N. Rotimi
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, Maryland, United States of America
- * E-mail:
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20
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Jung J, Kim H. Shared genetic etiology and antagonistic relationship of plasma renin activity and systolic blood pressure in a Korean cohorts. Genomics 2022; 114:110334. [PMID: 35278618 DOI: 10.1016/j.ygeno.2022.110334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 02/11/2022] [Accepted: 03/06/2022] [Indexed: 01/14/2023]
Abstract
Despite extensive studies on blood pressure, its genetic risk factors remain uncertain. Even one of the most researched blood pressure-related traits - renin - is not fully understood genetically. Here, we determine the genetic relationship and associated predisposition between blood pressure and baseline renin. In 8840 Korean individuals, we observed a strong negative genome-wide genetic correlation (rg = -0.484) between systolic blood pressure (SBP) and plasma renin activity (PRA), suggesting that antagonistic genetic signals explain the variance in the two traits. We found 51 significant pleiotropic SNPs affecting the two traits, which could contribute to the Renin-Angiotensin-Aldosterone System (RAAS). Our findings provide insight into studies on RAAS by identifying the genome-wide relationship and susceptibility loci of SBP and PRA.
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Affiliation(s)
- Jaehoon Jung
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 151-742, Republic of Korea; eGnome, 26 Beobwon-ro, Songpa-gu, Seoul 05836, Republic of Korea.
| | - Heebal Kim
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 151-742, Republic of Korea; eGnome, 26 Beobwon-ro, Songpa-gu, Seoul 05836, Republic of Korea; Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 151-742, Republic of Korea.
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21
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Mariano VS, Boer PA, Gontijo JAR. Fetal Undernutrition Programming, Sympathetic Nerve Activity, and Arterial Hypertension Development. Front Physiol 2021; 12:704819. [PMID: 34867434 PMCID: PMC8635863 DOI: 10.3389/fphys.2021.704819] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 10/14/2021] [Indexed: 12/11/2022] Open
Abstract
A wealth of evidence showed that low birth weight is associated with environmental disruption during gestation, triggering embryotic or fetal adaptations and increasing the susceptibility of progeny to non-communicable diseases, including metabolic and cardiovascular diseases, obesity, and arterial hypertension. In addition, dietary disturbance during pregnancy in animal models has highlighted mechanisms that involve the genesis of arterial hypertension, particularly severe maternal low-protein intake (LP). Functional studies demonstrated that maternal low-protein intake leads to the renal decrease of sodium excretion and the dysfunction of the renin-angiotensin-aldosterone system signaling of LP offspring. The antinatriuretic effect is accentuated by a reduced number of nephron units and glomerulosclerosis, which are critical in establishing arterial hypertension phenotype. Also, in this way, studies have shown that the overactivity of the central and peripheral sympathetic nervous system occurs due to reduced sensory (afferent) renal nerve activity. As a result of this reciprocal and abnormal renorenal reflex, there is an enhanced tubule sodium proximal sodium reabsorption, which, at least in part, contributes directly to arterial hypertension development in some of the programmed models. A recent study has observed that significant changes in adrenal medulla secretion could be involved in the pathophysiological process of increasing blood pressure. Thus, this review aims to compile studies that link the central and peripheral sympathetic system activity mechanisms on water and salt handle and blood pressure control in the maternal protein-restricted offspring. Besides, these pathophysiological mechanisms mainly may involve the modulation of neurokinins and catecholamines pathways.
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Affiliation(s)
- Vinícius Schiavinatto Mariano
- Fetal Programming and Hydroelectrolyte Metabolism Laboratory, Nucleus of Medicine and Experimental Surgery, Department of Internal Medicine, Faculty of Medical Sciences, State University of Campinas, São Paulo, Brazil
| | - Patrícia Aline Boer
- Fetal Programming and Hydroelectrolyte Metabolism Laboratory, Nucleus of Medicine and Experimental Surgery, Department of Internal Medicine, Faculty of Medical Sciences, State University of Campinas, São Paulo, Brazil
| | - José Antônio Rocha Gontijo
- Fetal Programming and Hydroelectrolyte Metabolism Laboratory, Nucleus of Medicine and Experimental Surgery, Department of Internal Medicine, Faculty of Medical Sciences, State University of Campinas, São Paulo, Brazil
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22
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Kaur H, Crawford DC, Liang J, Benchek P, Zhu X, Kallianpur AR, Bush WS. Replication of European hypertension associations in a case-control study of 9,534 African Americans. PLoS One 2021; 16:e0259962. [PMID: 34793544 PMCID: PMC8601554 DOI: 10.1371/journal.pone.0259962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 10/29/2021] [Indexed: 12/01/2022] Open
Abstract
Objective Hypertension is more prevalent in African Americans (AA) than other ethnic groups. Genome-wide association studies (GWAS) have identified loci associated with hypertension and other cardio-metabolic traits like type 2 diabetes, coronary artery disease, and body mass index (BMI), however the AA population is underrepresented in these studies. In this study, we examined a large AA cohort for the generalizability of 14 Metabochip array SNPs with previously reported European hypertension associations. Methods To evaluate associations, we analyzed genotype data of 14 SNPs for their associations with a diagnosis of hypertension, systolic blood pressure (SBP), and diastolic blood pressure (DBP) in a case-control study of an AA population (N = 9,534). We also performed an age-stratified analysis (>30, 30≥59 and ≥60 years) following the hypertension definition described by the 8th Joint National Committee (JNC). Associations were adjusted for BMI, age, age2, sex, clinical confounders, and genetic ancestry using multivariable regression models to estimate odds ratios (ORs) and beta-coefficients. Analyses stratified by sex were also conducted. Meta-analyses (including both BioVU and COGENT-BP cohorts) were performed using a random-effects model. Results We found rs880315 to be associated with systolic hypertension (SBP≥140 mmHg) in the entire cohort (OR = 1.14, p = 0.003) and within women only (OR = 1.16, p = 0.012). Variant rs17080093 associated with lower SBP and DBP (β = -2.99, p = 0.0352 and - β = 1.69, p = 0.0184) among younger individuals, particularly in younger women (β = -3.92, p = 0.0025 and β = -1.87, p = 0.0241 for SBP and DBP respectively). SNP rs1530440 associated with higher SBP and DBP measurements (younger individuals β = 4.1, p = 0.039 and β = 2.5, p = 0.043 for SBP and DBP; (younger women β = 4.5, p = 0.025 and β = 2.9, p = 0.028 for SBP and DBP), and hypertension risk in older women (OR = 1.4, p = 0.050). rs16948048 increases hypertension risk in younger individuals (OR = 1.31, p = 0.011). Among mid-age women rs880315 associated with higher risk of hypertension (OR = 1.20, p = 0.027). rs1361831 associated with DBP (β = -1.96, p = 0.02) among individuals older than 60 years. rs3096277 increases hypertension risk among older individuals (OR = 1.26 p = 0.0015), however, this variant also reduces SBP among younger women (β = -2.63, p = 0.0102). Conclusion These findings suggest that European-descent and AA populations share genetic loci that contribute to blood pressure traits and hypertension. However, the OR and beta-coefficient estimates differ, and some are age-dependent. Additional genetic studies of hypertension in AA are warranted to identify new loci associated with hypertension and blood pressure traits in this population.
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Affiliation(s)
- Harpreet Kaur
- Genomic Medicine Institute, Cleveland Clinic/Lerner Research Institute, Cleveland, OH, United States of America
- Department of Population and Quantitative Health Sciences, Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, United States of America
| | - Dana C. Crawford
- Department of Population and Quantitative Health Sciences, Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, United States of America
| | - Jingjing Liang
- Department of Population and Quantitative Health Sciences, Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, United States of America
| | - Penelope Benchek
- Department of Population and Quantitative Health Sciences, Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, United States of America
| | | | - Xiaofeng Zhu
- Department of Population and Quantitative Health Sciences, Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, United States of America
| | - Asha R. Kallianpur
- Genomic Medicine Institute, Cleveland Clinic/Lerner Research Institute, Cleveland, OH, United States of America
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH, United States of America
| | - William S. Bush
- Genomic Medicine Institute, Cleveland Clinic/Lerner Research Institute, Cleveland, OH, United States of America
- Department of Population and Quantitative Health Sciences, Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, United States of America
- * E-mail:
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23
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Singh S, Brandenburg JT, Choudhury A, Gómez-Olivé FX, Ramsay M. Systematic Review of Genomic Associations with Blood Pressure and Hypertension in Populations with African-Ancestry. Front Genet 2021; 12:699445. [PMID: 34745203 PMCID: PMC8564494 DOI: 10.3389/fgene.2021.699445] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 09/10/2021] [Indexed: 11/25/2022] Open
Abstract
Background: Despite hypertension being highly prevalent in individuals with African-ancestry, they are under-represented in large genome-wide association studies. Inclusion of African participants is essential to better understand genetic associations with blood pressure-related traits in Africans. This systematic review critically evaluates existing studies with African-ancestry participants and identifies knowledge gaps. Methods: We followed the PRISMA protocol, HuGE Review handbook to identify literature on original research, in English, on genetic association studies for blood pressure-related traits (systolic and diastolic blood pressure, pulse and mean-arterial pressure, and hypertension) in populations with African-ancestry (January 2007 to April 2020). A narrative synthesis of the evidence was conducted. Results: Twelve studies with African-ancestry participants met the eligibility criteria, within which 10 studies met the additional genetic association data criteria (i.e., reporting only on African-ancestry participants). Across the five blood pressure-related traits, 26 genome-wide significantly associated SNPs were identified, with six SNPs linked to more than one trait, illustrating pleiotropic effects. Among the SNP associations, 12 had not previously been described in non-African studies. Discussion: The limited number of relevant studies highlights the dearth of genomic association studies on participants with African-ancestry, especially those located within Africa. Variations in study methodology, participant inclusion, adjustment for covariates (e.g., antihypertensive medication) and relatively small sample sizes make comparisons challenging, and have resulted in fewer significant associations, compared to large European studies. Regional variation in the prevalence and associated risk factors of hypertension across Africa makes a compelling argument to develop African cohorts to facilitate large genomic studies, using African-centric arrays. Data harmonisation and comparable study designs, such as described in the H3Africa CHAIR initiative, provide a good example toward achieving this goal. Other relevant information: SS and J-TB were funded by the South African National Research Foundation. MR is a South African Research Chair in Genomics and Bioinformatics of African populations hosted by the University of the Witwatersrand, funded by the Department of Science and Innovation, and administered by the NRF. This review was registered at PROSPERO (registration number: CRD42020179221) and OSF (registration DOI: 10.17605/OSF.IO/QT2HA).
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Affiliation(s)
- S Singh
- Sydney Brenner Institute for Molecular Bioscience (SBIMB), Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Division of Human Genetics, School of Pathology, National Health Laboratory Service and Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - J-T Brandenburg
- Sydney Brenner Institute for Molecular Bioscience (SBIMB), Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - A Choudhury
- Sydney Brenner Institute for Molecular Bioscience (SBIMB), Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - F X Gómez-Olivé
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, University of the Witwatersrand, Johannesburg, South Africa
| | - M Ramsay
- Sydney Brenner Institute for Molecular Bioscience (SBIMB), Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Division of Human Genetics, School of Pathology, National Health Laboratory Service and Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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24
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Bentley AR, Chen G, Doumatey AP, Shriner D, Meeks KAC, Gouveia MH, Ekoru K, Zhou J, Adeyemo A, Rotimi CN. GWAS in Africans identifies novel lipids loci and demonstrates heterogenous association within Africa. Hum Mol Genet 2021; 30:2205-2214. [PMID: 34196372 PMCID: PMC8561421 DOI: 10.1093/hmg/ddab174] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 06/22/2021] [Accepted: 06/23/2021] [Indexed: 01/11/2023] Open
Abstract
Serum lipids are biomarkers of cardiometabolic disease risk, and understanding genomic factors contributing to their distribution is of interest. Studies of lipids in Africans are rare, though it is expected that such studies could identify novel loci. We conducted a GWAS of 4317 Africans enrolled from Nigeria, Ghana and Kenya. We evaluated linear mixed models of high-density lipoprotein cholesterol (HDLC), low-density lipoprotein cholesterol (LDLC), total cholesterol (CHOL), triglycerides (TG) and TG/HDLC. Replication was attempted in 9542 African Americans (AA). In our main analysis, we identified 28 novel associations in Africans. Of the 18 of these that could be tested in AA, three associations replicated (GPNMB-TG, ENPP1-TG and SMARCA4-LDLC). Five additional novel loci were discovered upon meta-analysis with AA (rs138282551-TG, PGBD5-HDLC, CD80-TG/HDLC, SLC44A1-CHOL and TLL2-CHOL). Analyses considering only those with predominantly West African ancestry (Nigeria, Ghana and AA) yielded new insights: ORC5-LDLC and chr20:60973327-CHOL. Among our novel findings are some loci with known connections to lipids pathways. For instance, rs147706369 (TLL2) alters a regulatory motif for sterol regulatory element-binding proteins, a family of transcription factors that control the expression of a range of enzymes involved in cholesterol, fatty acid and TG synthesis, and rs115749422 (SMARCA4), an independent association near the known LDLR locus that is rare or absent in populations without African ancestry. These findings demonstrate the utility of conducting genomic analyses in Africans for discovering novel loci and provide some preliminary evidence for caution against treating 'African ancestry' as a monolithic category.
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Affiliation(s)
- Amy R Bentley
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Guanjie Chen
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Ayo P Doumatey
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Daniel Shriner
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Karlijn A C Meeks
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Mateus H Gouveia
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Kenneth Ekoru
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Jie Zhou
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Adebowale Adeyemo
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Charles N Rotimi
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
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25
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Meeks KAC, Bentley AR, Gouveia MH, Chen G, Zhou J, Lei L, Adeyemo AA, Doumatey AP, Rotimi CN. Genome-wide analyses of multiple obesity-related cytokines and hormones informs biology of cardiometabolic traits. Genome Med 2021; 13:156. [PMID: 34620218 PMCID: PMC8499470 DOI: 10.1186/s13073-021-00971-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 09/16/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND A complex set of perturbations occur in cytokines and hormones in the etiopathogenesis of obesity and related cardiometabolic conditions such as type 2 diabetes (T2D). Evidence for the genetic regulation of these cytokines and hormones is limited, particularly in African-ancestry populations. In order to improve our understanding of the biology of cardiometabolic traits, we investigated the genetic architecture of a large panel of obesity- related cytokines and hormones among Africans with replication analyses in African Americans. METHODS We performed genome-wide association studies (GWAS) in 4432 continental Africans, enrolled from Ghana, Kenya, and Nigeria as part of the Africa America Diabetes Mellitus (AADM) study, for 13 obesity-related cytokines and hormones, including adipsin, glucose-dependent insulinotropic peptide (GIP), glucagon-like peptide-1 (GLP-1), interleukin-1 receptor antagonist (IL1-RA), interleukin-6 (IL-6), interleukin-10 (IL-10), leptin, plasminogen activator inhibitor-1 (PAI-1), resistin, visfatin, insulin, glucagon, and ghrelin. Exact and local replication analyses were conducted in African Americans (n = 7990). The effects of sex, body mass index (BMI), and T2D on results were investigated through stratified analyses. RESULTS GWAS identified 39 significant (P value < 5 × 10-8) loci across all 13 traits. Notably, 14 loci were African-ancestry specific. In this first GWAS for adipsin and ghrelin, we detected 13 and 4 genome-wide significant loci respectively. Stratified analyses by sex, BMI, and T2D showed a strong effect of these variables on detected loci. Eight novel loci were successfully replicated: adipsin (3), GIP (1), GLP-1 (1), and insulin (3). Annotation of these loci revealed promising links between these adipocytokines and cardiometabolic outcomes as illustrated by rs201751833 for adipsin and blood pressure and locus rs759790 for insulin level and T2D in lean individuals. CONCLUSIONS Our study identified genetic variants underlying variation in multiple adipocytokines, including the first loci for adipsin and ghrelin. We identified population differences in variants associated with adipocytokines and highlight the importance of stratification for discovery of loci. The high number of African-specific loci detected emphasizes the need for GWAS in African-ancestry populations, as these loci could not have been detected in other populations. Overall, our work contributes to the understanding of the biology linking adipocytokines to cardiometabolic traits.
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Affiliation(s)
- Karlijn A C Meeks
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, 12 South Drive Bldg 12A rm 4047, Bethesda, MD, 20814, USA
| | - Amy R Bentley
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, 12 South Drive Bldg 12A rm 4047, Bethesda, MD, 20814, USA
| | - Mateus H Gouveia
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, 12 South Drive Bldg 12A rm 4047, Bethesda, MD, 20814, USA
| | - Guanjie Chen
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, 12 South Drive Bldg 12A rm 4047, Bethesda, MD, 20814, USA
| | - Jie Zhou
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, 12 South Drive Bldg 12A rm 4047, Bethesda, MD, 20814, USA
| | - Lin Lei
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, 12 South Drive Bldg 12A rm 4047, Bethesda, MD, 20814, USA
| | - Adebowale A Adeyemo
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, 12 South Drive Bldg 12A rm 4047, Bethesda, MD, 20814, USA
| | - Ayo P Doumatey
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, 12 South Drive Bldg 12A rm 4047, Bethesda, MD, 20814, USA.
| | - Charles N Rotimi
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, 12 South Drive Bldg 12A rm 4047, Bethesda, MD, 20814, USA.
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26
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Otte KA, Nolte V, Mallard F, Schlötterer C. The genetic architecture of temperature adaptation is shaped by population ancestry and not by selection regime. Genome Biol 2021; 22:211. [PMID: 34271951 PMCID: PMC8285869 DOI: 10.1186/s13059-021-02425-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Accepted: 06/29/2021] [Indexed: 12/28/2022] Open
Abstract
Background Understanding the genetic architecture of temperature adaptation is key for characterizing and predicting the effect of climate change on natural populations. One particularly promising approach is Evolve and Resequence, which combines advantages of experimental evolution such as time series, replicate populations, and controlled environmental conditions, with whole genome sequencing. Recent analysis of replicate populations from two different Drosophila simulans founder populations, which were adapting to the same novel hot environment, uncovered very different architectures—either many selection targets with large heterogeneity among replicates or fewer selection targets with a consistent response among replicates. Results Here, we expose the founder population from Portugal to a cold temperature regime. Although almost no selection targets are shared between the hot and cold selection regime, the adaptive architecture was similar. We identify a moderate number of targets under strong selection (19 selection targets, mean selection coefficient = 0.072) and parallel responses in the cold evolved replicates. This similarity across different environments indicates that the adaptive architecture depends more on the ancestry of the founder population than the specific selection regime. Conclusions These observations will have broad implications for the correct interpretation of the genomic responses to a changing climate in natural populations. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-021-02425-9.
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Affiliation(s)
- Kathrin A Otte
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria.,Present address: Institute for Zoology, University of Cologne, Cologne, Germany
| | - Viola Nolte
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria
| | - François Mallard
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria.,Present address: Institut de Biologie de l'École Normale Supérieure, CNRS UMR 8197, Inserm U1024, PSL Research University, F-75005, Paris, France
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27
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Cheng CF, Hsieh AR, Liang WM, Chen CC, Chen CH, Wu JY, Lin TH, Liao CC, Huang SM, Huang YC, Ban B, Lin YJ, Tsai FJ. Genome-Wide and Candidate Gene Association Analyses Identify a 14-SNP Combination for Hypertension in Patients With Type 2 Diabetes. Am J Hypertens 2021; 34:651-661. [PMID: 33276381 DOI: 10.1093/ajh/hpaa203] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 10/19/2020] [Accepted: 12/02/2020] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND High blood pressure is common and comorbid with type 2 diabetes (T2D). Almost 50% of patients with T2D have high blood pressure. Patients with both conditions of hypertension (HTN) and T2D are at risk for cardiovascular diseases and mortality. The study aim was to investigate genetic risk factors for HTN in T2D patients. METHODS This study included 999 T2D (cohort 1) patients for the first genome scan stage and 922 T2D (cohort 2) patients for the replication stage. Here, we investigated the genetic susceptibility and cumulative weighted genetic risk score for HTN in T2D patients of Han Chinese descent in Taiwan. RESULTS Thirty novel genetic single nucleotide polymorphisms (SNPs) were associated with HTN in T2D after adjusting for age and body mass index (P value <1 × 10-4). Eight blood pressure-related and/or HTN-related genetic SNPs were associated with HTN in T2D after adjusting for age and body mass index (P value <0.05). Linkage disequilibrium and cumulative weighted genetic risk score analyses showed that 14 of the 38 SNPs were associated with risk of HTN in a dose-dependent manner in T2D (Cochran-Armitage trend test: P value <0.0001). The 14-SNP cumulative weighted genetic risk score was also associated with increased regression tendency of systolic blood pressure in T2D (SBP = 122.05 + 0.8 × weighted genetic risk score; P value = 0.0001). CONCLUSIONS A cumulative weighted genetic risk score composed of 14 SNPs is important for HTN, increased tendency of systolic blood pressure, and may contribute to HTN risk in T2D in Taiwan.
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Affiliation(s)
- Chi-Fung Cheng
- Graduate Institute of Biostatistics, School of Public Health, China Medical University, Taichung, Taiwan
- Genetic Center, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan
| | - Ai-Ru Hsieh
- Department of Statistics, Tamkang University, New Taipei City, Taiwan
| | - Wen-Miin Liang
- Graduate Institute of Biostatistics, School of Public Health, China Medical University, Taichung, Taiwan
| | - Ching-Chu Chen
- Division of Endocrinology and Metabolism, Department of Medicine, China Medical University Hospital, Taichung, Taiwan
| | - Chien-Hsiun Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
- School of Chinese Medicine, China Medical University, Taichung, Taiwan
| | - Jer-Yuarn Wu
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
- School of Chinese Medicine, China Medical University, Taichung, Taiwan
| | - Ting-Hsu Lin
- Genetic Center, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan
| | - Chiu-Chu Liao
- Genetic Center, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan
| | - Shao-Mei Huang
- Genetic Center, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan
| | - Yu-Chuen Huang
- Genetic Center, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan
- School of Chinese Medicine, China Medical University, Taichung, Taiwan
| | - Bo Ban
- Chinese Research Center for Behavior Medicine in Growth and Development, Jining, Shandong, China
| | - Ying-Ju Lin
- Genetic Center, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan
- School of Chinese Medicine, China Medical University, Taichung, Taiwan
| | - Fuu-Jen Tsai
- Genetic Center, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan
- School of Chinese Medicine, China Medical University, Taichung, Taiwan
- Department of Biotechnology and Bioinformatics, Asia University, Taichung, Taiwan
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28
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Chen G, Adeyemo A, Zhou J, Doumatey AP, Bentley AR, Ekoru K, Shriner D, Rotimi CN. A UGT1A1 variant is associated with serum total bilirubin levels, which are causal for hypertension in African-ancestry individuals. NPJ Genom Med 2021; 6:44. [PMID: 34117260 PMCID: PMC8196001 DOI: 10.1038/s41525-021-00208-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 04/15/2021] [Indexed: 02/05/2023] Open
Abstract
Serum bilirubin is associated with several clinical outcomes, including hypertension, type 2 diabetes (T2D), and drug metabolism. Here, we describe findings from our genome-wide association studies (GWAS) of serum (TBIL) using a generalized linear mixed model in West Africans (n = 1127), with adjustment for age, sex, body mass index, T2D, significant principal components of population structure, and cryptic relatedness. Genome-wide conditional analysis and CAVIARBF were used to fine map significant loci. The causal effect of TBIL on hypertension was assessed by Mendelian randomization (MR) using the GWAS findings as instrumental variables (IVs) in African Americans (n = 3,067). The SNP rs887829 (UGT1A1) was significantly associated with TBIL levels (effect allele (T) frequency = 0.49, β (SE) = 0.59 (0.04), p = 9.13 × 10-54). Genome-wide conditional analysis and regional fine mapping pointed to rs887829 as a possible causal variant with a posterior inclusion probability of 0.99. The T allele of rs887829 is associated with lower hepatic expression of UGT1A1. Using rs887829 as an IV, two-stage least-squares MR showed a causal effect of bilirubin on hypertension (β = -0.76, 95% CI [-1.52, -0.01], p = 0.0459). Our finding confirms that UGT1A1 influences bilirubin levels. Notably, lower TBIL is causally associated with the increased risk of hypertension.
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Affiliation(s)
- Guanjie Chen
- grid.280128.10000 0001 2233 9230Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD USA
| | - Adebowale Adeyemo
- grid.280128.10000 0001 2233 9230Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD USA
| | - Jie Zhou
- grid.280128.10000 0001 2233 9230Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD USA
| | - Ayo P. Doumatey
- grid.280128.10000 0001 2233 9230Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD USA
| | - Amy R. Bentley
- grid.280128.10000 0001 2233 9230Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD USA
| | - Kenneth Ekoru
- grid.280128.10000 0001 2233 9230Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD USA
| | - Daniel Shriner
- grid.280128.10000 0001 2233 9230Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD USA
| | - Charles N. Rotimi
- grid.280128.10000 0001 2233 9230Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD USA
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29
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Plasma lipidome is dysregulated in Alzheimer's disease and is associated with disease risk genes. Transl Psychiatry 2021; 11:344. [PMID: 34092785 PMCID: PMC8180517 DOI: 10.1038/s41398-021-01362-2] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 03/10/2021] [Accepted: 04/06/2021] [Indexed: 01/11/2023] Open
Abstract
Lipidomics research could provide insights of pathobiological mechanisms in Alzheimer's disease. This study explores a battery of plasma lipids that can differentiate Alzheimer's disease (AD) patients from healthy controls and determines whether lipid profiles correlate with genetic risk for AD. AD plasma samples were collected from the Sydney Memory and Ageing Study (MAS) Sydney, Australia (aged range 75-97 years; 51.2% male). Untargeted lipidomics analysis was performed by liquid chromatography coupled-mass spectrometry (LC-MS/MS). We found that several lipid species from nine lipid classes, particularly sphingomyelins (SMs), cholesterol esters (ChEs), phosphatidylcholines (PCs), phosphatidylethanolamines (PIs), phosphatidylinositols (PIs), and triglycerides (TGs) are dysregulated in AD patients and may help discriminate them from healthy controls. However, when the lipid species were grouped together into lipid subgroups, only the DG group was significantly higher in AD. ChEs, SMs, and TGs resulted in good classification accuracy using the Glmnet algorithm (elastic net penalization for the generalized linear model [glm]) with more than 80% AUC. In general, group lipids and the lipid subclasses LPC and PE had less classification accuracy compared to the other subclasses. We also found significant increases in SMs, PIs, and the LPE/PE ratio in human U251 astroglioma cell lines exposed to pathophysiological concentrations of oligomeric Aβ42. This suggests that oligomeric Aβ42 plays a contributory, if not causal role, in mediating changes in lipid profiles in AD that can be detected in the periphery. In addition, we evaluated the association of plasma lipid profiles with AD-related single nucleotide polymorphisms (SNPs) and polygenic risk scores (PRS) of AD. We found that FERMT2 and MS4A6A showed a significantly differential association with lipids in all lipid classes across disease and control groups. ABCA7 had a differential association with more than half of the DG lipids (52.63%) and PI lipids (57.14%), respectively. Additionally, 43.4% of lipids in the SM class were differentially associated with CLU. More than 30% of lipids in ChE, PE, and TG classes had differential associations with separate genes (ChE-PICALM, SLC24A4, and SORL1; PE-CLU and CR1; TG-BINI) between AD and control group. These data may provide renewed insights into the pathobiology of AD and the feasibility of identifying individuals with greater AD risk.
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30
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A Genome-Wide Association Study for Hypertensive Kidney Disease in Korean Men. Genes (Basel) 2021; 12:genes12050751. [PMID: 34067580 PMCID: PMC8155956 DOI: 10.3390/genes12050751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 05/10/2021] [Accepted: 05/14/2021] [Indexed: 11/26/2022] Open
Abstract
Hypertension is one of the major risk factors for chronic kidney disease (CKD), and the coexistence of hypertension and CKD increases morbidity and mortality. Although many genetic factors have been identified separately for hypertension and kidney disease, studies specifically focused on hypertensive kidney disease (HKD) have been rare. Therefore, this study aimed to identify loci or genes associated with HKD. A genome-wide association study (GWAS) was conducted using two Korean cohorts, the Health Examinee (HEXA) and Korean Association REsource (KARE). Consequently, 19 single nucleotide polymorphisms (SNPs) were found to be significantly associated with HKD in the discovery and replication phases (p < 5 × 10−8, p < 0.05, respectively). We further analyzed HKD-related traits such as the estimated glomerular filtration rate (eGFR), creatinine, blood urea nitrogen (BUN), systolic blood pressure (SBP) and diastolic blood pressure (DBP) at the 14q21.2 locus, which showed a strong linkage disequilibrium (LD). Expression quantitative trait loci (eQTL) analysis was also performed to determine whether HKD-related SNPs affect gene expression changes in glomerular and arterial tissues. The results suggested that the FANCM gene may affect the development of HKD through an integrated analysis of eQTL and GWAS and was the most significantly associated candidate gene. Taken together, this study indicated that the FANCM gene is involved in the pathogenesis of HKD. Additionally, our results will be useful in prioritizing other genes for further experiments.
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31
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Ekoru K, Adeyemo AA, Chen G, Doumatey AP, Zhou J, Bentley AR, Shriner D, Rotimi CN. Genetic risk scores for cardiometabolic traits in sub-Saharan African populations. Int J Epidemiol 2021; 50:1283-1296. [PMID: 33729508 DOI: 10.1093/ije/dyab046] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 02/25/2021] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND There is growing support for the use of genetic risk scores (GRS) in routine clinical settings. Due to the limited diversity of current genomic discovery samples, there are concerns that the predictive power of GRS will be limited in non-European ancestry populations. GRS for cardiometabolic traits were evaluated in sub-Saharan Africans in comparison with African Americans and European Americans. METHODS We evaluated the predictive utility of GRS for 12 cardiometabolic traits in sub-Saharan Africans (AF; n = 5200), African Americans (AA; n = 9139) and European Americans (EUR; n = 9594). GRS were constructed as weighted sums of the number of risk alleles. Predictive utility was assessed using the additional phenotypic variance explained and the increase in discriminatory ability over traditional risk factors [age, sex and body mass index (BMI)], with adjustment for ancestry-derived principal components. RESULTS Across all traits, GRS showed up to a 5-fold and 20-fold greater predictive utility in EUR relative to AA and AF, respectively. Predictive utility was most consistent for lipid traits, with percentage increase in explained variation attributable to GRS ranging from 10.6% to 127.1% among EUR, 26.6% to 65.8% among AA and 2.4% to 37.5% among AF. These differences were recapitulated in the discriminatory power, whereby the predictive utility of GRS was 4-fold greater in EUR relative to AA and up to 44-fold greater in EUR relative to AF. Obesity and blood pressure traits showed a similar pattern of greater predictive utility among EUR. CONCLUSIONS This work demonstrates the poorer performance of GRS in AF and highlights the need to improve representation of multiple ethnic populations in genomic studies to ensure equitable clinical translation of GRS.
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Affiliation(s)
- Kenneth Ekoru
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Adebowale A Adeyemo
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Guanjie Chen
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ayo P Doumatey
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jie Zhou
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Amy R Bentley
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Daniel Shriner
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Charles N Rotimi
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
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32
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Wang K, Basu M, Malin J, Hannenhalli S. A transcription-centric model of SNP-age interaction. PLoS Genet 2021; 17:e1009427. [PMID: 33770080 PMCID: PMC7997000 DOI: 10.1371/journal.pgen.1009427] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 02/16/2021] [Indexed: 12/23/2022] Open
Abstract
Complex age-associated phenotypes are caused, in part, by an interaction between an individual's genotype and age. The mechanisms governing such interactions are however not entirely understood. Here, we provide a novel transcriptional mechanism-based framework-SNiPage, to investigate such interactions, whereby a transcription factor (TF) whose expression changes with age (age-associated TF), binds to a polymorphic regulatory element in an allele-dependent fashion, rendering the target gene's expression dependent on both, the age and the genotype. Applying SNiPage to GTEx, we detected ~637 significant TF-SNP-Gene triplets on average across 25 tissues, where the TF binds to a regulatory SNP in the gene's promoter or putative enhancer and potentially regulates its expression in an age- and allele-dependent fashion. The detected SNPs are enriched for epigenomic marks indicative of regulatory activity, exhibit allele-specific chromatin accessibility, and spatial proximity to their putative gene targets. Furthermore, the TF-SNP interaction-dependent target genes have established links to aging and to age-associated diseases. In six hypertension-implicated tissues, detected interactions significantly inform hypertension state of an individual. Lastly, the age-interacting SNPs exhibit a greater proximity to the reported phenotype/diseases-associated SNPs than eSNPs identified in an interaction-independent fashion. Overall, we present a novel mechanism-based model, and a novel framework SNiPage, to identify functionally relevant SNP-age interactions in transcriptional control and illustrate their potential utility in understanding complex age-associated phenotypes.
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Affiliation(s)
- Kun Wang
- Cancer Data Science Laboratory, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, United States of America
| | - Mahashweta Basu
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, United States of America
- Institute for Genome Sciences, University of Maryland, Baltimore, Maryland, United States of America
| | - Justin Malin
- Laboratory of Genome Integrity, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Sridhar Hannenhalli
- Cancer Data Science Laboratory, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, United States of America
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33
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Mapesi H, Gupta R, Wilson HI, Lukau B, Amstutz A, Lyimo A, Muhairwe J, Senkoro E, Byakuzana T, Mphunyane M, Bresser M, Glass TR, Lambiris M, Fink G, Gingo W, Battegay M, Paris DH, Rohacek M, Vanobberghen F, Labhardt ND, Burkard T, Weisser M. The coArtHA trial-identifying the most effective treatment strategies to control arterial hypertension in sub-Saharan Africa: study protocol for a randomized controlled trial. Trials 2021; 22:77. [PMID: 33478567 PMCID: PMC7818218 DOI: 10.1186/s13063-021-05023-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 01/05/2021] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Arterial hypertension is the most prevalent risk factor for cardiovascular disease in sub-Saharan Africa. Only a few and mostly small randomized trials have studied antihypertensive treatments in people of African descent living in sub-Saharan Africa. METHODS In this open-label, three-arm, parallel randomized controlled trial conducted at two rural hospitals in Lesotho and Tanzania, we compare the efficacy and cost-effectiveness of three antihypertensive treatment strategies among participants aged ≥ 18 years. The study includes patients with untreated uncomplicated arterial hypertension diagnosed by a standardized office blood pressure ≥ 140/90 mmHg. The trial encompasses a superiority comparison between a triple low-dose antihypertensive drug combination versus the current standard of care (monotherapy followed by dual treatment), as well as a non-inferiority comparison for a dual drug combination versus standard of care with optional dose titration after 4 and 8 weeks for participants not reaching the target blood pressure. The sample size is 1268 participants with parallel allocation and a randomization ratio of 2:1:2 for the dual, triple and control arms, respectively. The primary endpoint is the proportion of participants reaching a target blood pressure at 12 weeks of ≤ 130/80 mmHg and ≤ 140/90 mmHg among those aged < 65 years and ≥ 65 years, respectively. Clinical manifestations of end-organ damage and cost-effectiveness at 6 months are secondary endpoints. DISCUSSION This trial will help to identify the most effective and cost-effective treatment strategies for uncomplicated arterial hypertension among people of African descent living in rural sub-Saharan Africa and inform future clinical guidelines on antihypertensive management in the region. TRIAL REGISTRATION Clinicaltrials.gov NCT04129840 . Registered on 17 October 2019 ( https://www.clinicaltrials.gov/ ).
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Affiliation(s)
- Herry Mapesi
- Ifakara Health Institute, Ifakara branch, Ifakara, United Republic of Tanzania.,Swiss Tropical and Public Health Institute (Swiss TPH), Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Ravi Gupta
- SolidarMed, Partnerships for Health, Maseru, Lesotho
| | | | - Blaise Lukau
- SolidarMed, Partnerships for Health, Maseru, Lesotho
| | - Alain Amstutz
- Swiss Tropical and Public Health Institute (Swiss TPH), Basel, Switzerland.,University of Basel, Basel, Switzerland.,Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
| | - Aza Lyimo
- St. Francis Referral Hospital, Ifakara, United Republic of Tanzania.,Tanzania Training Center for International Health, Ifakara, United Republic of Tanzania
| | | | - Elizabeth Senkoro
- Ifakara Health Institute, Ifakara branch, Ifakara, United Republic of Tanzania
| | | | | | - Moniek Bresser
- Swiss Tropical and Public Health Institute (Swiss TPH), Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Tracy Renée Glass
- Swiss Tropical and Public Health Institute (Swiss TPH), Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Mark Lambiris
- Swiss Tropical and Public Health Institute (Swiss TPH), Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Günther Fink
- Swiss Tropical and Public Health Institute (Swiss TPH), Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Winfrid Gingo
- St. Francis Referral Hospital, Ifakara, United Republic of Tanzania
| | - Manuel Battegay
- University of Basel, Basel, Switzerland.,Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
| | - Daniel Henry Paris
- Swiss Tropical and Public Health Institute (Swiss TPH), Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Martin Rohacek
- Ifakara Health Institute, Ifakara branch, Ifakara, United Republic of Tanzania.,Swiss Tropical and Public Health Institute (Swiss TPH), Basel, Switzerland.,University of Basel, Basel, Switzerland.,St. Francis Referral Hospital, Ifakara, United Republic of Tanzania
| | - Fiona Vanobberghen
- Swiss Tropical and Public Health Institute (Swiss TPH), Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Niklaus Daniel Labhardt
- Swiss Tropical and Public Health Institute (Swiss TPH), Basel, Switzerland.,University of Basel, Basel, Switzerland.,Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
| | - Thilo Burkard
- Medical Outpatient and Hypertension Clinic, ESH Hypertension Centre of Excellence, University Hospital Basel, Basel, Switzerland.,Department of Cardiology, University Hospital Basel, Basel, Switzerland
| | - Maja Weisser
- Ifakara Health Institute, Ifakara branch, Ifakara, United Republic of Tanzania. .,Swiss Tropical and Public Health Institute (Swiss TPH), Basel, Switzerland. .,University of Basel, Basel, Switzerland. .,Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland.
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34
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Shriner D, Bentley AR, Zhou J, Ekoru K, Doumatey AP, Chen G, Adeyemo A, Rotimi CN. Time-to-event modeling of hypertension reveals the nonexistence of true controls. eLife 2020; 9:62998. [PMID: 33258447 PMCID: PMC7707825 DOI: 10.7554/elife.62998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 11/13/2020] [Indexed: 11/13/2022] Open
Abstract
Given a lifetime risk of ~90% by the ninth decade of life, it is unknown if there are true controls for hypertension in epidemiological and genetic studies. Here, we compared Bayesian logistic and time-to-event approaches to modeling hypertension. The median age at hypertension was approximately a decade earlier in African Americans than in European Americans or Mexican Americans. The probability of being free of hypertension at 85 years of age in African Americans was less than half that in European Americans or Mexican Americans. In all groups, baseline hazard rates increased until nearly 60 years of age and then decreased but did not reach zero. Taken together, modeling of the baseline hazard function of hypertension suggests that there are no true controls and that controls in logistic regression are cases with a late age of onset.
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Affiliation(s)
- Daniel Shriner
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, United States
| | - Amy R Bentley
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, United States
| | - Jie Zhou
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, United States
| | - Kenneth Ekoru
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, United States
| | - Ayo P Doumatey
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, United States
| | - Guanjie Chen
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, United States
| | - Adebowale Adeyemo
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, United States
| | - Charles N Rotimi
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, United States
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35
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Wu T, Wang Y, Shi W, Zhang BQ, Raelson J, Yao YM, Wu HD, Xu ZX, Marois-Blanchet FC, Ledoux J, Blunck R, Sheng JZ, Hu SJ, Luo H, Wu J. A Variant in the Nicotinic Acetylcholine Receptor Alpha 3 Subunit Gene Is Associated With Hypertension Risks in Hypogonadic Patients. Front Genet 2020; 11:539862. [PMID: 33329690 PMCID: PMC7728919 DOI: 10.3389/fgene.2020.539862] [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: 03/02/2020] [Accepted: 11/10/2020] [Indexed: 12/29/2022] Open
Abstract
Ephb6 gene knockout causes hypertension in castrated mice. EPHB6 controls catecholamine secretion by adrenal gland chromaffin cells (AGCCs) in a testosterone-dependent way. Nicotinic acetylcholine receptor (nAChR) is a ligand-gated Ca2+/Na+ channel, and its opening is the first signaling event leading to catecholamine secretion by AGCCs. There is a possibility that nAChR might be involved in EPHB6 signaling, and thus sequence variants of its subunit genes are associated with hypertension risks. CHRNA3 is the major subunit of nAChR used in human and mouse AGCCs. We conducted a human genetic study to assess the association of CHRNA3 variants with hypertension risks in hypogonadic males. The study cohort included 1,500 hypogonadic Chinese males with (750 patients) or without (750 patients) hypertension. The result revealed that SNV rs3743076 in the fourth intron of CHRNA3 was significantly associated with hypertension risks in the hypogonadic males. We further showed that EPHB6 physically interacted with CHRNA3 in AGCCs, providing a molecular basis for nAChR being in the EPHB6 signaling pathway.
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Affiliation(s)
- Tao Wu
- Institute of Cardiology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Yujia Wang
- Research Centre, Centre Hospitalier de l'Université de Montréal (CHUM), Montreal, QC, Canada.,Children's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Wei Shi
- Research Centre, Centre Hospitalier de l'Université de Montréal (CHUM), Montreal, QC, Canada
| | - Bi-Qi Zhang
- Institute of Cardiology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - John Raelson
- Research Centre, Centre Hospitalier de l'Université de Montréal (CHUM), Montreal, QC, Canada
| | - Yu-Mei Yao
- Department of Cardiology, The Third Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China
| | - Huan-Dong Wu
- Institute of Cardiology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Zao-Xian Xu
- Institute of Cardiology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | | | - Jonathan Ledoux
- Montreal Heart Institute, Université de Montréal, Montreal, QC, Canada
| | - Rikard Blunck
- Department of Physics, University of Montreal, Montreal, QC, Canada
| | - Jian-Zhong Sheng
- Department of Pathology and Physiopathology, College of Medicine, Zhejiang University, Hangzhou, China
| | - Shen-Jiang Hu
- Institute of Cardiology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Hongyu Luo
- Research Centre, Centre Hospitalier de l'Université de Montréal (CHUM), Montreal, QC, Canada
| | - Jiangping Wu
- Research Centre, Centre Hospitalier de l'Université de Montréal (CHUM), Montreal, QC, Canada.,Nephrology Service, Centre Hospitalier de l'Université de Montréal (CHUM), Montreal, QC, Canada
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36
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Joseph JJ, Zhou X, Zilbermint M, Stratakis CA, Faucz FR, Lodish MB, Berthon A, Wilson JG, Hsueh WA, Golden SH, Lin S. The Association of ARMC5 with the Renin-Angiotensin-Aldosterone System, Blood Pressure, and Glycemia in African Americans. J Clin Endocrinol Metab 2020; 105:5841631. [PMID: 32436940 PMCID: PMC7308077 DOI: 10.1210/clinem/dgaa290] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 05/18/2020] [Indexed: 12/31/2022]
Abstract
CONTEXT Armadillo repeat containing 5 (ARMC5) on chromosome 16 is an adrenal gland tumor suppressor gene associated with primary aldosteronism, especially among African Americans (AAs). We examined the association of ARMC5 variants with aldosterone, plasma renin activity (PRA), blood pressure, glucose, and glycosylated hemoglobin A1c (HbA1c) in community-dwelling AAs. METHODS The Jackson Heart Study is a prospective cardiovascular cohort study in AAs with baseline data collection from 2000 to 2004. Kernel machine method was used to perform a single joint test to analyze for an overall association between the phenotypes of interest (aldosterone, PRA, systolic and diastolic blood pressure [SBP, DBP], glucose, and HbA1c) and the ARMC5 single nucleotide variants (SNVs) adjusted for age, sex, BMI, and medications; followed by Baysian Lasso methodology to identify sets of SNVs in terms of associated haplotypes with specific phenotypes. RESULTS Among 3223 participants (62% female; mean age 55.6 (SD ± 12.8) years), the average SBP and DBP were 127 and 76 mmHg, respectively. The average fasting plasma glucose and HbA1c were 101 mg/dL and 6.0%, respectively. ARMC5 variants were associated with all 6 phenotypes. Haplotype TCGCC (ch16:31476015-31476093) was negatively associated, whereas haplotype CCCCTTGCG (ch16:31477195-31477460) was positively associated with SBP, DBP, and glucose. Haplotypes GGACG (ch16:31477790-31478013) and ACGCG (ch16:31477834-31478113) were negatively associated with aldosterone and positively associated with HbA1c and glucose, respectively. Haplotype GCGCGAGC (ch16:31471193-ch16:31473597(rs114871627) was positively associated with PRA and negatively associated with HbA1c. CONCLUSIONS ARMC5 variants are associated with aldosterone, PRA, blood pressure, fasting glucose, and HbA1c in community-dwelling AAs, suggesting that germline mutations in ARMC5 may underlie cardiometabolic disease in AAs.
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Affiliation(s)
- Joshua J Joseph
- The Ohio State University, Columbus, Ohio
- Correspondence and Reprint Requests: Joshua J. Joseph, MD, Department of Medicine, The Ohio State University Wexner Medical Center, 566 McCampbell Hall, 1581 Dodd Drive, Columbus, OH 43210; Phone: 614-346-8878; Fax: 614-366-0345;
| | | | - Mihail Zilbermint
- Division of Endocrinology, Diabetes and Metabolism, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Section on Endocrinology and Genetics, The Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
- Johns Hopkins Community Physicians at Suburban Hospital, Bethesda, Maryland
| | - Constantine A Stratakis
- Section on Endocrinology and Genetics, The Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
| | - Fabio R Faucz
- Section on Endocrinology and Genetics, The Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
| | - Maya B Lodish
- Division of Pediatric Endocrinology and Diabetes, University of California, San Francisco, San Francisco, California
| | - Annabel Berthon
- Institut Cochin, Centre National de la Recherche Scientifique (CNRS), INSERM, Université Paris Descartes, Paris, France
| | - James G Wilson
- Department of Medicine, University of Mississippi Medical Center, Jackson, Mississippi
- Division of Cardiology, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | | | - Sherita H Golden
- Division of Endocrinology, Diabetes and Metabolism, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Shili Lin
- The Ohio State University, Columbus, Ohio
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Wonkam A, Chimusa ER, Mnika K, Pule GD, Ngo Bitoungui VJ, Mulder N, Shriner D, Rotimi CN, Adeyemo A. Genetic modifiers of long-term survival in sickle cell anemia. Clin Transl Med 2020; 10:e152. [PMID: 32898326 PMCID: PMC7423184 DOI: 10.1002/ctm2.152] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 07/30/2020] [Accepted: 07/31/2020] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Sickle cell anemia (SCA) is a clinically heterogeneous, monogenic disorder. Medical care has less-than-optimal impact on clinical outcomes in SCA in Africa due to several factors, including patient accessibility, poor access to resources, and non-availability of specific effective interventions for SCA. METHODS Against this background, we investigated 192 African participants who underwent whole exome sequencing. Participants included 105 SCA patients spanning variable clinical expression: a "long survivor" group (age over 40 years), a "stroke" group (at least one episode of overt stroke), and a "random" group (patients younger than 40 years without overt cerebrovascular disease). Fifty-eight ethnically matched homozygous hemoglobin A controls were also studied. Findings were validated in an independently recruited sample of 29 SCA patients. Statistical significance of the mutational burden of deleterious and loss-of-function variants per gene against a null model was estimated for each group, and gene-set association tests were conducted to test differences between groups. RESULTS In the "long survivor" group, deleterious/loss-of-function variants were enriched in genes including CLCN6 (a voltage-dependent chloride channel for which rare deleterious variants have been associated with lower blood pressure) and OGHDL (important in arginine metabolism, which is a therapeutic target in SCA). In the "stroke" group, significant genes implicated were associated with increased activity of the blood coagulation cascade and increased complement activation, for example, SERPINC1, which encodes antithrombin. Oxidative stress and glutamate biosynthesis pathways were enriched in "long survivors" group. Published transcriptomic evidence provides functional support for the role of the identified pathways. CONCLUSIONS This study provides new gene sets that contribute to variability in clinical expression of SCA. Identified genes and pathways suggest new avenues for other interventions.
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Affiliation(s)
- Ambroise Wonkam
- Division of Human Genetics, Institute of Infectious Disease and Molecular Medicine (IDM), Faculty of Health SciencesUniversity of Cape TownCape TownSouth Africa
- Institute of Infectious Disease and Molecular Medicine (IDM), Faculty of Health SciencesUniversity of Cape TownCape TownSouth Africa
| | - Emile R. Chimusa
- Division of Human Genetics, Institute of Infectious Disease and Molecular Medicine (IDM), Faculty of Health SciencesUniversity of Cape TownCape TownSouth Africa
- Institute of Infectious Disease and Molecular Medicine (IDM), Faculty of Health SciencesUniversity of Cape TownCape TownSouth Africa
| | - Khuthala Mnika
- Division of Human Genetics, Institute of Infectious Disease and Molecular Medicine (IDM), Faculty of Health SciencesUniversity of Cape TownCape TownSouth Africa
| | - Gift Dineo Pule
- Division of Human Genetics, Institute of Infectious Disease and Molecular Medicine (IDM), Faculty of Health SciencesUniversity of Cape TownCape TownSouth Africa
| | - Valentina Josiane Ngo Bitoungui
- Division of Human Genetics, Institute of Infectious Disease and Molecular Medicine (IDM), Faculty of Health SciencesUniversity of Cape TownCape TownSouth Africa
| | - Nicola Mulder
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute for Infectious Disease and Molecular MedicineUniversity of Cape TownCape TownSouth Africa
| | - Daniel Shriner
- Center for Research on Genomics and Global HealthNational Human Genome Research InstituteNational Institutes of HealthBethesdaMarylandUSA
| | - Charles N. Rotimi
- Center for Research on Genomics and Global HealthNational Human Genome Research InstituteNational Institutes of HealthBethesdaMarylandUSA
| | - Adebowale Adeyemo
- Center for Research on Genomics and Global HealthNational Human Genome Research InstituteNational Institutes of HealthBethesdaMarylandUSA
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Rysz J, Franczyk B, Rysz-Górzyńska M, Gluba-Brzózka A. Pharmacogenomics of Hypertension Treatment. Int J Mol Sci 2020; 21:ijms21134709. [PMID: 32630286 PMCID: PMC7369859 DOI: 10.3390/ijms21134709] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 06/21/2020] [Accepted: 06/26/2020] [Indexed: 12/12/2022] Open
Abstract
Hypertension is one of the strongest modifiable cardiovascular risk factors, affecting an increasing number of people worldwide. Apart from poor medication adherence, the low efficacy of some therapies could also be related to inter-individual genetic variability. Genetic studies of families revealed that heritability accounts for 30% to 50% of inter-individual variation in blood pressure (BP). Genetic factors not only affect blood pressure (BP) elevation but also contribute to inter-individual variability in response to antihypertensive treatment. This article reviews the recent pharmacogenomics literature concerning the key classes of antihypertensive drugs currently in use (i.e., diuretics, β-blockers, ACE inhibitors, ARB, and CCB). Due to the numerous studies on this topic and the sometimes-contradictory results within them, the presented data are limited to several selected SNPs that alter drug response. Genetic polymorphisms can influence drug responses through genes engaged in the pathogenesis of hypertension that are able to modify the effects of drugs, modifications in drug–gene mechanistic interactions, polymorphisms within drug-metabolizing enzymes, genes related to drug transporters, and genes participating in complex cascades and metabolic reactions. The results of numerous studies confirm that genotype-based antihypertension therapies are the most effective and may help to avoid the occurrence of major adverse events, as well as decrease the costs of treatment. However, the genetic heritability of drug response phenotypes seems to remain hidden in multigenic and multifactorial complex traits. Therefore, further studies are required to analyze all associations and formulate final genome-based treatment recommendations.
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Affiliation(s)
- Jacek Rysz
- Department of Nephrology, Hypertension and Family Medicine, Medical University of Lodz, 90-549 Lodz, Poland; (J.R.); (B.F.)
| | - Beata Franczyk
- Department of Nephrology, Hypertension and Family Medicine, Medical University of Lodz, 90-549 Lodz, Poland; (J.R.); (B.F.)
| | - Magdalena Rysz-Górzyńska
- Department of Ophthalmology and Visual Rehabilitation, Medical University of Lodz, 90-549 Lodz, Poland;
| | - Anna Gluba-Brzózka
- Department of Nephrology, Hypertension and Family Medicine, Medical University of Lodz, 90-549 Lodz, Poland; (J.R.); (B.F.)
- Correspondence:
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EPHA4 regulates vascular smooth muscle cell contractility and is a sex-specific hypertension risk gene in individuals with type 2 diabetes. J Hypertens 2020; 37:775-789. [PMID: 30817459 DOI: 10.1097/hjh.0000000000001948] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
OBJECTIVE We investigated the association of genetic variants of EPHA4, a receptor tyrosine kinase, with hypertension, and its role in vascular smooth muscle cell (VSMC) contractility. METHODS Data from two human genetic studies, ADVANCE and HCHS/SOL, were analyzed for association of EPHA4 single nucleotide variants (SNVs) with hypertension risks. The effect of EPHA4 signalling on mouse VSMC contractility was assessed. RESULTS We identified a SNV (rs75843691 hg19 chr2:g.222395371 C>G), located in the third intron of EPHA4 gene, being significantly associated with hypertension in human female patients (P value = 8.3 × 10, below the Bonferroni-corrected critical P value) but not male patients with type 2 diabetes from the ADVANCE clinical trial. We found that EPHA4 was expressed in VSMCs and its stimulation by anti-EPHA4 antibody led to reduced VSMC contractility. Estrogen enhanced the contractility-lowering effect of EPHA4 stimulation. Conversely, siRNA knockdown of Epha4 expression in VSMCs resulted in increased contractility of VSMCs from female mice but not from male mice. CONCLUSION EPHA4 appears to be a sex-specific hypertension risk gene in type 2 diabetic patients. Forward EPHA4 signalling reduces VSMC contractility, and estrogen is a modifier of this effect. The effect of EPHA4 on VSMCs contractility explains the association of EPHA4 gene with hypertension risks in female patients.
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Johnson R, Dludla P, Mabhida S, Benjeddou M, Louw J, February F. Pharmacogenomics of amlodipine and hydrochlorothiazide therapy and the quest for improved control of hypertension: a mini review. Heart Fail Rev 2020; 24:343-357. [PMID: 30645721 PMCID: PMC6476827 DOI: 10.1007/s10741-018-09765-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Blood pressure (BP) is a complex trait that is regulated by multiple physiological pathways and include but is not limited to extracellular fluid volume homeostasis, cardiac contractility, and vascular tone through renal, neural, or endocrine systems. Uncontrolled hypertension (HTN) has been associated with an increased mortality risk. Therefore, understanding the genetics that underpins and influence BP regulation will have a major impact on public health. Moreover, uncontrolled HTN has been linked to inter-individual variation in the drugs’ response and this has been associated with an individual’s genetics architecture. However, the identification of candidate genes that underpin the genetic basis of HTN remains a major challenge. To date, few variants associated with inter-individual BP regulation have been identified and replicated. Research in this field has accelerated over the past 5 years as a direct result of on-going genome-wide association studies (GWAS) and the progress in the identification of rare gene variants and mutations, epigenetic markers, and the regulatory pathways involved in the pathophysiology of BP. In this review we describe and enhance our current understanding of how genetic variants account for the observed variability in BP response in patients on first-line antihypertensive drugs, amlodipine and hydrochlorothiazide.
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Affiliation(s)
- Rabia Johnson
- Biomedical Research and Innovation Platform (BRIP), South African Medical Research Council (SAMRC), Tygerberg, 7505 South Africa
- Division of Medical Physiology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, 7505 South Africa
| | - Phiwayinkosi Dludla
- Biomedical Research and Innovation Platform (BRIP), South African Medical Research Council (SAMRC), Tygerberg, 7505 South Africa
| | - Sihle Mabhida
- Biomedical Research and Innovation Platform (BRIP), South African Medical Research Council (SAMRC), Tygerberg, 7505 South Africa
- Department of Biotechnology, Faculty of Natural Science, University of the Western Cape, Private Bag X17, Bellville, Cape Town, 7535 South Africa
| | - Mongi Benjeddou
- Department of Biotechnology, Faculty of Natural Science, University of the Western Cape, Private Bag X17, Bellville, Cape Town, 7535 South Africa
| | - Johan Louw
- Biomedical Research and Innovation Platform (BRIP), South African Medical Research Council (SAMRC), Tygerberg, 7505 South Africa
| | - Faghri February
- Department of Haematology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, 7505 South Africa
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Chen G, Shriner D, Doumatey AP, Zhou J, Bentley AR, Lei L, Adeyemo A, Rotimi CN. Refining genome-wide associated loci for serum uric acid in individuals with African ancestry. Hum Mol Genet 2020; 29:506-514. [PMID: 31841133 PMCID: PMC7015846 DOI: 10.1093/hmg/ddz272] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 10/31/2019] [Accepted: 11/05/2019] [Indexed: 01/11/2023] Open
Abstract
OBJECTIVE Serum uric acid is the end-product of purine metabolism and at high levels is a risk factor for several human diseases including gout and cardiovascular disease. Heritability estimates range from 0.32 to 0.63. Genome-wide association studies (GWAS) provide an unbiased approach to identify loci influencing serum uric acid. Here, we performed the first GWAS for serum uric acid in continental Africans, with replication in African Americans. METHODS Africans (n = 4126) and African Americans (n = 5007) were genotyped on high-density GWAS arrays. Efficient mixed model association, a variance component approach, was used to perform association testing for a total of ~ 18 million autosomal genotyped and imputed variants. CAVIARBF was used to fine map significant regions. RESULTS We identified two genome-wide significant loci: 4p16.1 (SLC2A9) and 11q13.1 (SLC22A12). At SLC2A9, the most strongly associated SNP was rs7683856 (P = 1.60 × 10-44). Conditional analysis revealed a second signal indexed by rs6838021 (P = 5.75 × 10-17). Gene expression and regulatory motif data prioritized a single-candidate causal variant for each signal. At SLC22A12, the most strongly associated SNP was rs147647315 (P = 6.65 × 10-25). Conditional analysis and functional annotation prioritized the missense variant rs147647315 (R (Arg) > H (His)) as the sole causal variant. Functional annotation of these three signals implicated processes in skeletal muscle, subcutaneous adipose tissue and the kidneys, respectively. CONCLUSIONS This first GWAS of serum uric acid in continental Africans identified three associations at two loci, SLC2A9 and SLC22A12. The combination of weak linkage disequilibrium in Africans and functional annotation led to the identification of candidate causal SNPs for all three signals. Each candidate causal variant implicated a different cell type. Collectively, the three associations accounted for 4.3% of the variance of serum uric acid.
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Affiliation(s)
- 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
| | - Ayo P Doumatey
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, MD 20892, USA
| | - Jie Zhou
- 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
| | - Lin Lei
- 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
| | - Charles N Rotimi
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, MD 20892, USA
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Vicente M, Jakobsson M, Ebbesen P, Schlebusch CM. Genetic Affinities among Southern Africa Hunter-Gatherers and the Impact of Admixing Farmer and Herder Populations. Mol Biol Evol 2020; 36:1849-1861. [PMID: 31288264 PMCID: PMC6735883 DOI: 10.1093/molbev/msz089] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Southern African indigenous groups, traditionally hunter-gatherers (San) and herders (Khoekhoe), are commonly referred to as “Khoe-San” populations and have a long history in southern Africa. Their ancestors were largely isolated up until ∼2,000 years ago before the arrival of pastoralists and farmers in southern Africa. Assessing relationships among regional Khoe-San groups has been challenging due to admixture with immigrant populations that obscure past population affinities and gene flow among these autochthonous communities. We re-evaluate a combined genome-wide data set of previously published southern Africa Khoe-San populations in conjunction with novel data from Khoe-San individuals collected in Xade (Central Kalahari Game Reserve, Botswana) prior to their resettlement outside the reserve. After excluding regions in the genome that trace their ancestry to recent migrant groups, the genetic diversity of 20 Khoe-San groups fitted an isolation-by-distance model. Even though isolation-by-distance explained most genetic affinities between the different autochthonous groups, additional signals of contact between Khoe-San groups could be detected. For instance, we found stronger genetic affinities, than what would be explained by isolation-by-distance gene flow, between the two geographically separated Khoe-San groups, who speak branches of the Kx’a-language family (ǂHoan and Ju). We also scanned the genome-wide data for signals of adaptive gene flow from farmers/herders into Khoe-San groups and identified a number of genomic regions potentially introduced by the arrival of the new groups. This study provides a comprehensive picture of affinities among Khoe-San groups, prior to the arrival of recent migrants, and found that these affinities are primarily determined by the geographic landscape.
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Affiliation(s)
- Mário Vicente
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Mattias Jakobsson
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden.,Palaeo-Research Institute, University of Johannesburg, Auckland Park, South Africa.,SciLifeLab, Uppsala, Sweden
| | - Peter Ebbesen
- Department of Health Science and Technology, University of Aalborg, Aalborg, Denmark
| | - Carina M Schlebusch
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden.,Palaeo-Research Institute, University of Johannesburg, Auckland Park, South Africa.,SciLifeLab, Uppsala, Sweden
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Galaviz KI, Varughese R, Agan BK, Marconi VC, Chu X, Won SH, Ganesan A, Ali MK, Colasanti J. The Intersection of HIV, Diabetes, and Race: Exploring Disparities in Diabetes Care among People Living with HIV. J Int Assoc Provid AIDS Care 2020; 19:2325958220904241. [PMID: 32162997 PMCID: PMC7068738 DOI: 10.1177/2325958220904241] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 12/08/2019] [Accepted: 01/08/2020] [Indexed: 01/05/2023] Open
Abstract
In a setting of universal health care access, we compared diabetes control between Caucasians and African Americans (AA) living with HIV. This was a cross-sectional analysis of data from a cohort study among military members living with HIV and diabetes. Using adjusted logistic regression models, we compared proportions of Caucasians and AA meeting the following diabetes treatment goals: hemoglobin A1c <7.0%, blood pressure (BP) <140/90 mm Hg, low density lipoprotein cholesterol <100 mg/dL, and not smoking. We included 107 Caucasian (mean age 37 years) and 126 AA (mean age 33 years) participants. A similar proportion of Caucasians and AA were prescribed diabetes (∼60%) and BP (∼80%) medications. Yet, more Caucasians met the BP treatment goal (77% [54%, 90%]) than AA (61% [36%, 82%]). Thus, more Caucasians met the combined A1c, BP, and cholesterol goals for diabetes control (25% [10%, 49%]) than AA (13% [5%, 31%]). Despite having equal access to health care, AA in this study have poorer diabetes control than Caucasians.
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Affiliation(s)
- Karla I. Galaviz
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Rincy Varughese
- Infectious Disease Section, Atlanta VA Medical Center, Atlanta, GA, USA
| | - Brian K. Agan
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
| | - Vincent C. Marconi
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
- Infectious Disease Section, Atlanta VA Medical Center, Atlanta, GA, USA
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
- Infectious Disease Program, Grady Health System, Atlanta, GA, USA
| | - Xiuping Chu
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
| | - Seung Hyun Won
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
| | - Anuradha Ganesan
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
- Division of Infectious Diseases, Walter Reed National Military Medical Center, Bethesda, MD, USA
| | - Mohammed K. Ali
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
- Department of Family and Preventive Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Jonathan Colasanti
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
- Infectious Disease Program, Grady Health System, Atlanta, GA, USA
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HLA and autoantibodies define scleroderma subtypes and risk in African and European Americans and suggest a role for molecular mimicry. Proc Natl Acad Sci U S A 2019; 117:552-562. [PMID: 31871193 PMCID: PMC6955366 DOI: 10.1073/pnas.1906593116] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Systemic sclerosis (SSc) is a clinically heterogeneous autoimmune disease characterized by mutually exclusive autoantibodies directed against distinct nuclear antigens. We examined HLA associations in SSc and its autoantibody subsets in a large, newly recruited African American (AA) cohort and among European Americans (EA). In the AA population, the African ancestry-predominant HLA-DRB1*08:04 and HLA-DRB1*11:02 alleles were associated with overall SSc risk, and the HLA-DRB1*08:04 allele was strongly associated with the severe antifibrillarin (AFA) antibody subset of SSc (odds ratio = 7.4). These African ancestry-predominant alleles may help explain the increased frequency and severity of SSc among the AA population. In the EA population, the HLA-DPB1*13:01 and HLA-DRB1*07:01 alleles were more strongly associated with antitopoisomerase (ATA) and anticentromere antibody-positive subsets of SSc, respectively, than with overall SSc risk, emphasizing the importance of HLA in defining autoantibody subtypes. The association of the HLA-DPB1*13:01 allele with the ATA+ subset of SSc in both AA and EA patients demonstrated a transancestry effect. A direct correlation between SSc prevalence and HLA-DPB1*13:01 allele frequency in multiple populations was observed (r = 0.98, P = 3 × 10-6). Conditional analysis in the autoantibody subsets of SSc revealed several associated amino acid residues, mostly in the peptide-binding groove of the class II HLA molecules. Using HLA α/β allelic heterodimers, we bioinformatically predicted immunodominant peptides of topoisomerase 1, fibrillarin, and centromere protein A and discovered that they are homologous to viral protein sequences from the Mimiviridae and Phycodnaviridae families. Taken together, these data suggest a possible link between HLA alleles, autoantibodies, and environmental triggers in the pathogenesis of SSc.
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Khodayari Moez E, Hajihosseini M, Andrews JL, Dinu I. Longitudinal linear combination test for gene set analysis. BMC Bioinformatics 2019; 20:650. [PMID: 31822265 PMCID: PMC6902471 DOI: 10.1186/s12859-019-3221-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 11/13/2019] [Indexed: 11/12/2022] Open
Abstract
Background Although microarray studies have greatly contributed to recent genetic advances, lack of replication has been a continuing concern in this area. Complex study designs have the potential to address this concern, though they remain undervalued by investigators due to the lack of proper analysis methods. The primary challenge in the analysis of complex microarray study data is handling the correlation structure within data while also dealing with the combination of large number of genetic measurements and small number of subjects that are ubiquitous even in standard microarray studies. Motivated by the lack of available methods for analysis of repeatedly measured phenotypic or transcriptomic data, herein we develop a longitudinal linear combination test (LLCT). Results LLCT is a two-step method to analyze multiple longitudinal phenotypes when there is high dimensionality in response and/or explanatory variables. Alternating between calculating within-subjects and between-subjects variations in two steps, LLCT examines if the maximum possible correlation between a linear combination of the time trends and a linear combination of the predictors given by the gene expressions is statistically significant. A generalization of this method can handle family-based study designs when the subjects are not independent. This method is also applicable to time-course microarray, with the ability to identify gene sets that exhibit significantly different expression patterns over time. Based on the results from a simulation study, LLCT outperformed its alternative: pathway analysis via regression. LLCT was shown to be very powerful in the analysis of large gene sets even when the sample size is small. Conclusions This self-contained pathway analysis method is applicable to a wide range of longitudinal genomics, proteomics, metabolomics (OMICS) data, allows adjusting for potentially time-dependent covariates and works well with unbalanced and incomplete data. An important potential application of this method could be time-course linkage of OMICS, an attractive possibility for future genetic researchers. Availability: R package of LLCT is available at: https://github.com/its-likeli-jeff/LLCT
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Mapesi H, Paris DH. Non-Communicable Diseases on the Rise in Sub-Saharan Africa, the Underappreciated Threat of a Dual Disease Burden. PRAXIS 2019; 108:997-1005. [PMID: 31771492 DOI: 10.1024/1661-8157/a003354] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
In sub-Saharan Africa, the burden of non-communicable diseases (NCDs) remains under appreciated, but emerging evidence suggests it to be substantial. NCDs such as arterial hypertension, heart diseases, diabetes mellitus and chronic kidney diseases are especially relevant, and put additional strain on the already challenged health systems in this region. Moreover, NCDs appear to be associated with higher mortality and morbidity rates and are more common in younger population groups, in people from sub-Saharan Africa when compared to more developed countries. In this review, we summarize the current literature on the burden of NCDs in sub-Saharan Africa, and highlight the clinical implications of the most relevant etiologies, i.e. arterial hypertension, heart diseases, diabetes mellitus and chronic kidney diseases.
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Affiliation(s)
- Herry Mapesi
- Ifakara Health Institute, Ifakara branch, Ifakara,Tanzania
- Swiss Tropical and Public Health Institute, Basel
- University of Basel, Basel
| | - Daniel Henry Paris
- Swiss Tropical and Public Health Institute, Basel
- University of Basel, Basel
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Lule SA, Mentzer AJ, Namara B, Muwenzi AG, Nassanga B, kizito D, Akurut H, Lubyayi L, Tumusiime J, Zziwa C, Akello F, Gurdasani D, Sandhu M, Smeeth L, Elliott AM, Webb EL. A genome-wide association and replication study of blood pressure in Ugandan early adolescents. Mol Genet Genomic Med 2019; 7:e00950. [PMID: 31469255 PMCID: PMC6785527 DOI: 10.1002/mgg3.950] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 04/30/2019] [Accepted: 06/14/2019] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Genetic association studies of blood pressure (BP) have mostly been conducted in non-African populations. Using the Entebbe Mother and Baby Study (EMaBS), we aimed to identify genetic variants associated with BP among Ugandan adolescents. METHODS Systolic and diastolic BP were measured among 10- and 11-year olds. Whole-genome genotype data were generated using Illumina omni 2.5M arrays and untyped variants were imputed. Genome-wide association study (GWAS) was conducted using linear mixed model regression to account for population structure. Linear regression analysis was used to assess whether variants previously associated with BP (p < 5.0 × 10-8 ) in published BP GWASs were replicated in our study. RESULTS Of the 14 million variants analyzed among 815 adolescents, none reached genome-wide significance (p < 5.0×10-8 ) for association with systolic or diastolic BP. The most strongly associated variants were rs181430167 (p = 6.8 × 10-7 ) for systolic BP and rs12991132 (p = 4.0 × 10-7 ) for diastolic BP. Thirty-three (17 single nucleotide polymorphisms (SNPs) for systolic BP, 15 SNPs for diastolic BP and one SNP for both) of 330 variants previously identified as associated with BP were replicated in this study, but none remained significant after accounting for multiple testing. CONCLUSION Variants showing suggestive associations are worthy of future investigation. Replication results suggest that variants influencing adolescent BP may overlap somewhat with those already established in previous studies, largely based on adults in Western settings.
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Affiliation(s)
- Swaib A. Lule
- London School of Hygiene and Tropical MedicineLondonUK
- MRC/UVRI & LSHTM Uganda Research UnitEntebbeUganda
| | - Alexander J. Mentzer
- Wellcome Trust Centre for Human GeneticsUniversity of OxfordOxfordUK
- Big Data Institute, Li Ka Shing Centre for Health Information and DiscoveryUniversity of OxfordOxfordUK
| | | | | | | | | | - Helen Akurut
- MRC/UVRI & LSHTM Uganda Research UnitEntebbeUganda
| | | | | | | | | | - Deept Gurdasani
- Wellcome Trust Sanger InstituteCambridgeUK
- University of CambridgeCambridgeUK
| | - Manjinder Sandhu
- Wellcome Trust Sanger InstituteCambridgeUK
- University of CambridgeCambridgeUK
| | - Liam Smeeth
- London School of Hygiene and Tropical MedicineLondonUK
| | - Alison M. Elliott
- London School of Hygiene and Tropical MedicineLondonUK
- MRC/UVRI & LSHTM Uganda Research UnitEntebbeUganda
| | - Emily L. Webb
- London School of Hygiene and Tropical MedicineLondonUK
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Brown KM, Hui Q, Huang Y, Taylor JY, Prescott L, de Mendoza VB, Crusto C, Sun YV. Association Between Stress and Coping with DNA Methylation of Blood Pressure-Related Genes Among African American Women. CHRONIC STRESS 2019; 3. [PMID: 32395678 PMCID: PMC7213592 DOI: 10.1177/2470547019879088] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Background Exposure to psychosocial stress and employment of high effort coping
strategies have been identified as risk factors that may partially explain
the high prevalence of hypertension among African Americans. One biological
mechanism through which stress and coping may affect risk of hypertension is
via epigenetic modifications (e.g., DNA methylation) in blood
pressure-related genes; however, this area remains understudied in African
Americans. Methods We used data from the ongoing Intergenerational Blood Pressure Study, a
longitudinal study designed to investigate factors that contribute to
hypertension risk in African American women (n = 120) and their young
children, to investigate the association between stress overload,
problem-solving coping, avoidance coping, and social support coping with DNA
methylation in 25 candidate genes related to blood pressure. Multivariable
linear regression and multilevel modeling were used to conduct methylation
site-level and gene-level analyses, respectively. Results In site-level analyses, stress overload, problem-solving coping, social
support coping, and avoidance coping were associated with 47, 63, 66, and 61
sites, respectively, at p < 0.05. However, no associations were
statistically significant after multiple testing correction. There were also
no significant associations in gene-level analyses. Conclusions As human social epigenomics is an emerging, evolving area of research, there
is much to be learned from studies with statistically significant findings
as well as studies with null findings. Factors such as characteristics of
the social stressor, source of DNA, and synchronization of exposure and
outcome are likely important considerations as we move the field
forward.
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Affiliation(s)
| | - Qin Hui
- Emory University (Atlanta, Georgia)
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Bolaji OO, Adehin A, Adeagbo BA. Pharmacogenomics in the Nigerian population: the past, the present and the future. Pharmacogenomics 2019; 20:915-926. [DOI: 10.2217/pgs-2019-0046] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The Nigerian population exhibits huge ethnic and genetic diversity, typical of African populations, which can be harnessed for improved drug-response and disease management. Existing data on genes relevant to drug response, so far generated for the population, indeed confirm the prevalence of some clinically significant pharmacogenes. These reports detail prevailing genetic alleles and metabolic phenotypes of vital drug metabolizing monooxygenases, transferases and drug transporters. While the utilization of existing pharmacogenomic data for healthcare delivery remains unpopular, several past and on-going studies suggest that a future shift toward genotype-stratified dosing of drugs and disease management in the population is imminent. This review discusses the present state of pharmacogenomics in Nigeria and the potential benefits of sustained research in this field for the population.
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Affiliation(s)
- Oluseye O Bolaji
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Obafemi Awolowo University, Ile-Ife, Nigeria
| | - Ayorinde Adehin
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Obafemi Awolowo University, Ile-Ife, Nigeria
- Institute of Biomedical & Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, PR China
| | - Babatunde A Adeagbo
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Obafemi Awolowo University, Ile-Ife, Nigeria
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