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Huang Q, Hu Z, Zheng Q, Mao X, Lv W, Wu F, Fu D, Lu C, Zeng C, Wang F, Zeng Q, Fang Q, Hood L. A Proactive Intervention Study in Metabolic Syndrome High-Risk Populations Using Phenome-Based Actionable P4 Medicine Strategy. PHENOMICS (CHAM, SWITZERLAND) 2024; 4:91-108. [PMID: 38884061 PMCID: PMC11169348 DOI: 10.1007/s43657-023-00115-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 06/13/2023] [Accepted: 06/16/2023] [Indexed: 06/18/2024]
Abstract
The integration of predictive, preventive, personalized, and participatory (P4) healthcare advocates proactive intervention, including dietary supplements and lifestyle interventions for chronic disease. Personal profiles include deep phenotypic data and genetic information, which are associated with chronic diseases, can guide proactive intervention. However, little is known about how to design an appropriate intervention mode to precisely intervene with personalized phenome-based data. Here, we report the results of a 3-month study on 350 individuals with metabolic syndrome high-risk that we named the Pioneer 350 Wellness project (P350). We examined: (1) longitudinal (two times) phenotypes covering blood lipids, blood glucose, homocysteine (HCY), and vitamin D3 (VD3), and (2) polymorphism of genes related to folic acid metabolism. Based on personalized data and questionnaires including demographics, diet and exercise habits information, coaches identified 'actionable possibilities', which combined exercise, diet, and dietary supplements. After a 3-month proactive intervention, two-thirds of the phenotypic markers were significantly improved in the P350 cohort. Specifically, we found that dietary supplements and lifestyle interventions have different effects on phenotypic improvement. For example, dietary supplements can result in a rapid recovery of abnormal HCY and VD3 levels, while lifestyle interventions are more suitable for those with high body mass index (BMI), but almost do not help the recovery of HCY. Furthermore, although people who implemented only one of the exercise or diet interventions also benefited, the effect was not as good as the combined exercise and diet interventions. In a subgroup of 226 people, we examined the association between the polymorphism of genes related to folic acid metabolism and the benefits of folate supplementation to restore a normal HCY level. We found people with folic acid metabolism deficiency genes are more likely to benefit from folate supplementation to restore a normal HCY level. Overall, these results suggest: (1) phenome-based data can guide the formulation of more precise and comprehensive interventions, and (2) genetic polymorphism impacts clinical responses to interventions. Notably, we provide a proactive intervention example that is operable in daily life, allowing people with different phenome-based data to design the appropriate intervention protocol including dietary supplements and lifestyle interventions. Supplementary Information The online version contains supplementary material available at 10.1007/s43657-023-00115-z.
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Affiliation(s)
- Qiongrong Huang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Key Laboratory of Standardization and Measurement for Nanotechnology, National Center for Nanoscience and Technology, CAS Center for Excellence in Nanoscience, Beijing, 100190 China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049 China
| | - Zhiyuan Hu
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Key Laboratory of Standardization and Measurement for Nanotechnology, National Center for Nanoscience and Technology, CAS Center for Excellence in Nanoscience, Beijing, 100190 China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049 China
- Beijing P4 Healthcare Institute, 316 Wanfeng Road, Beijing, 100161 China
- Health Management Institute, The Second Medical Center, National Clinical Research Center for Geriatric Diseases, Chinese People's Liberation Army (PLA) General Hospital, 28 Fuxing Road, Beijing, 100853 China
- School of Nanoscience and Technology, Sino-Danish College, University of Chinese Academy of Sciences, Beijing, 100049 China
- Fujian Provincial Key Laboratory of Brain Aging and Neurodegenerative Diseases, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, 350108 Fujian China
- School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan, 430205 Hubei China
| | - Qiwen Zheng
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101 China
| | - Xuemei Mao
- Beijing P4 Healthcare Institute, 316 Wanfeng Road, Beijing, 100161 China
| | - Wenxi Lv
- Beijing P4 Healthcare Institute, 316 Wanfeng Road, Beijing, 100161 China
| | - Fei Wu
- Beijing P4 Healthcare Institute, 316 Wanfeng Road, Beijing, 100161 China
| | - Dapeng Fu
- Beijing Zhongguancun Hospital, No. 12, Zhongguancun South Road, Haidian District, Beijing, 100190 China
| | - Cuihong Lu
- Beijing Zhongguancun Hospital, No. 12, Zhongguancun South Road, Haidian District, Beijing, 100190 China
| | - Changqing Zeng
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101 China
| | - Fei Wang
- Health Management Institute, The Second Medical Center, National Clinical Research Center for Geriatric Diseases, Chinese People's Liberation Army (PLA) General Hospital, 28 Fuxing Road, Beijing, 100853 China
| | - Qiang Zeng
- Health Management Institute, The Second Medical Center, National Clinical Research Center for Geriatric Diseases, Chinese People's Liberation Army (PLA) General Hospital, 28 Fuxing Road, Beijing, 100853 China
| | - Qiaojun Fang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Key Laboratory of Standardization and Measurement for Nanotechnology, National Center for Nanoscience and Technology, CAS Center for Excellence in Nanoscience, Beijing, 100190 China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049 China
- School of Nanoscience and Technology, Sino-Danish College, University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Leroy Hood
- Health Management Institute, The Second Medical Center, National Clinical Research Center for Geriatric Diseases, Chinese People's Liberation Army (PLA) General Hospital, 28 Fuxing Road, Beijing, 100853 China
- Institute for Systems Biology, Seattle, WA 98109 USA
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Nwamekang Belinga L, Espourteille J, Wepnyu Njamnshi Y, Zafack Zeukang A, Rouaud O, Kongnyu Njamnshi A, Allali G, Richetin K. Circulating Biomarkers for Alzheimer's Disease: Unlocking the Diagnostic Potential in Low- and Middle-Income Countries, Focusing on Africa. NEURODEGENER DIS 2024; 24:26-40. [PMID: 38555638 PMCID: PMC11251669 DOI: 10.1159/000538623] [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: 12/13/2023] [Accepted: 03/28/2024] [Indexed: 04/02/2024] Open
Abstract
BACKGROUND Alzheimer's disease (AD) is emerging as a significant public health challenge in Africa, with predictions indicating a tripling in incidence by 2050. The diagnosis of AD on the African continent is notably difficult, leading to late detection that severely limits treatment options and significantly impacts the quality of life for patients and their families. SUMMARY This review focuses on the potential of high-sensitivity specific blood biomarkers as promising tools for improving AD diagnosis and management globally, particularly in Africa. These advances are particularly pertinent in the continent, where access to medical and technical resources is often limited. KEY MESSAGES Identifying precise, sensitive, and specific blood biomarkers could contribute to the biological characterization and management of AD in Africa. Such advances promise to improve patient care and pave the way for new regional opportunities in pharmaceutical research and drug trials on the continent for AD.
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Affiliation(s)
- Luc Nwamekang Belinga
- Department of Psychiatry, Center for Psychiatric Neurosciences, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland
- Leenaards Memory Center, Department of Clinical Neurosciences, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
- Department of Translational Neuroscience, Brain Research Africa Initiative (BRAIN), Geneva, Switzerland
- Department of Translational Neuroscience, Brain Research Africa Initiative (BRAIN), Yaoundé, Cameroon
| | - Jeanne Espourteille
- Department of Psychiatry, Center for Psychiatric Neurosciences, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland
| | - Yembe Wepnyu Njamnshi
- Department of Translational Neuroscience, Brain Research Africa Initiative (BRAIN), Geneva, Switzerland
- Department of Translational Neuroscience, Brain Research Africa Initiative (BRAIN), Yaoundé, Cameroon
- Neuroscience Lab, Faculty of Medicine and Biomedical Sciences, The University of Yaoundé I, Yaoundé, Cameroon
- Division of Health Operations Research, Ministry of Public Health, Yaoundé, Cameroon
| | - Ariole Zafack Zeukang
- Department of Translational Neuroscience, Brain Research Africa Initiative (BRAIN), Geneva, Switzerland
- Department of Translational Neuroscience, Brain Research Africa Initiative (BRAIN), Yaoundé, Cameroon
| | - Olivier Rouaud
- Leenaards Memory Center, Department of Clinical Neurosciences, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Alfred Kongnyu Njamnshi
- Department of Translational Neuroscience, Brain Research Africa Initiative (BRAIN), Geneva, Switzerland
- Department of Translational Neuroscience, Brain Research Africa Initiative (BRAIN), Yaoundé, Cameroon
- Neuroscience Lab, Faculty of Medicine and Biomedical Sciences, The University of Yaoundé I, Yaoundé, Cameroon
- Department of Clinical Neuroscience and Neurology, Yaoundé Central Hospital, Yaoundé, Cameroon
| | - Gilles Allali
- Leenaards Memory Center, Department of Clinical Neurosciences, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Kevin Richetin
- Department of Psychiatry, Center for Psychiatric Neurosciences, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland
- Leenaards Memory Center, Department of Clinical Neurosciences, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
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Kong F, Wu T, Dai J, Cai J, Zhai Z, Zhu Z, Xu Y, Sun T. Knowledge domains and emerging trends of Genome-wide association studies in Alzheimer's disease: A bibliometric analysis and visualization study from 2002 to 2022. PLoS One 2024; 19:e0295008. [PMID: 38241287 PMCID: PMC10798548 DOI: 10.1371/journal.pone.0295008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 11/13/2023] [Indexed: 01/21/2024] Open
Abstract
OBJECTIVES Alzheimer's disease (AD) is a neurodegenerative disorder characterized by a progressive decline in cognitive and behavioral function. Studies have shown that genetic factors are one of the main causes of AD risk. genome-wide association study (GWAS), as a novel and effective tool for studying the genetic risk of diseases, has attracted attention from researchers in recent years and a large number of studies have been conducted. This study aims to summarize the literature on GWAS in AD by bibliometric methods, analyze the current status, research hotspots and future trends in this field. METHODS We retrieved articles on GWAS in AD published between 2002 and 2022 from Web of Science. CiteSpace and VOSviewer software were applied to analyze the articles for the number of articles published, countries/regions and institutions of publication, authors and cited authors, highly cited literature, and research hotspots. RESULTS We retrieved a total of 2,751 articles. The United States had the highest number of publications in this field, and Columbia University was the institution with the most published articles. The identification of AD-related susceptibility genes and their effects on AD is one of the current research hotspots. Numerous risk genes have been identified, among which APOE, CLU, CD2AP, CD33, EPHA1, PICALM, CR1, ABCA7 and TREM2 are the current genes of interest. In addition, risk prediction for AD and research on other related diseases are also popular research directions in this field. CONCLUSION This study conducted a comprehensive analysis of GWAS in AD and identified the current research hotspots and research trends. In addition, we also pointed out the shortcomings of current research and suggested future research directions. This study can provide researchers with information about the knowledge structure and emerging trends in the field of GWAS in AD and provide guidance for future research.
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Affiliation(s)
- Fanjing Kong
- School of Intelligent Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Tianyu Wu
- School of Acupuncture-Moxibustion and Tuina, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Jingyi Dai
- School of Intelligent Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Jie Cai
- School of Intelligent Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Zhenwei Zhai
- School of Intelligent Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Zhishan Zhu
- School of Intelligent Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Ying Xu
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Tao Sun
- School of Intelligent Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
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Reagan AM, Christensen KE, Graham LC, Bedwell AA, Eldridge K, Speedy R, Figueiredo LL, Persohn SC, Bottiglieri T, Nho K, Sasner M, Territo PR, Rozen R, Howell GR. The 677C > T variant in methylenetetrahydrofolate reductase causes morphological and functional cerebrovascular deficits in mice. J Cereb Blood Flow Metab 2022; 42:2333-2350. [PMID: 36050860 PMCID: PMC9670012 DOI: 10.1177/0271678x221122644] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 06/30/2022] [Accepted: 07/12/2022] [Indexed: 02/03/2023]
Abstract
Vascular contributions to cognitive impairment and dementia (VCID) particularly Alzheimer's disease and related dementias (ADRDs) are increasing; however, mechanisms driving cerebrovascular decline are poorly understood. Methylenetetrahydrofolate reductase (MTHFR) is a critical enzyme in the folate and methionine cycles. Variants in MTHFR, notably 677 C > T, are associated with dementias, but no mouse model existed to identify mechanisms by which MTHFR677C > T increases risk. Therefore, MODEL-AD created a novel knock-in (KI) strain carrying the Mthfr677C > T allele on the C57BL/6J background (Mthfr677C > T) to characterize morphology and function perturbed by the variant. Consistent with human clinical data, Mthfr677C > T mice have reduced enzyme activity in the liver and elevated plasma homocysteine levels. MTHFR enzyme activity is also reduced in the Mthfr677C > T brain. Mice showed reduced tissue perfusion in numerous brain regions by PET/CT as well as significantly reduced vascular density, pericyte number and increased GFAP-expressing astrocytes in frontal cortex. Electron microscopy revealed cerebrovascular damage including endothelial and pericyte apoptosis, reduced luminal size, and increased astrocyte and microglial presence in the microenvironment. Collectively, these data support a mechanism by which variations in MTHFR perturb cerebrovascular health laying the foundation to incorporate our new Mthfr677C > T mouse model in studies examining genetic susceptibility for cerebrovascular dysfunction in ADRDs.
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Affiliation(s)
| | - Karen E Christensen
- Departments of Human Genetics and Pediatrics, McGill University,
Research Institute of the Health Center, Montreal, QC, Canada
| | | | - Amanda A Bedwell
- Department of Medicine, Division of Clinical Pharmacology,
Indiana University School of Medicine, Indianapolis, IN, USA
| | - Kierra Eldridge
- Department of Medicine, Division of Clinical Pharmacology,
Indiana University School of Medicine, Indianapolis, IN, USA
| | - Rachael Speedy
- Department of Medicine, Division of Clinical Pharmacology,
Indiana University School of Medicine, Indianapolis, IN, USA
| | - Lucas L Figueiredo
- Department of Medicine, Division of Clinical Pharmacology,
Indiana University School of Medicine, Indianapolis, IN, USA
| | - Scott C Persohn
- Department of Medicine, Division of Clinical Pharmacology,
Indiana University School of Medicine, Indianapolis, IN, USA
| | - Teodoro Bottiglieri
- Center of Metabolomics, Institute of Metabolic Disease, Baylor
Scott & White Research Institute, Dallas, TX, USA
| | - Kwangsik Nho
- Center for Neuroimaging, Indiana Alzheimer’s Disease Research
Center, Department of Radiology and Imaging Sciences, Indiana University School
of Medicine, Indianapolis, IN, USA
| | | | - Paul R Territo
- Department of Medicine, Division of Clinical Pharmacology,
Indiana University School of Medicine, Indianapolis, IN, USA
| | - Rima Rozen
- Departments of Human Genetics and Pediatrics, McGill University,
Research Institute of the Health Center, Montreal, QC, Canada
| | - Gareth R Howell
- The Jackson Laboratory, Bar Harbor, ME, USA
- Graduate School of Biomedical Sciences, Tufts University School
of Medicine, Boston, MA, USA
- Graduate School of Biomedical Sciences and Engineering,
University of Maine, Orono, ME, USA
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5
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Noren Hooten N, Pacheco NL, Smith JT, Evans MK. The accelerated aging phenotype: The role of race and social determinants of health on aging. Ageing Res Rev 2022; 73:101536. [PMID: 34883202 PMCID: PMC10862389 DOI: 10.1016/j.arr.2021.101536] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 11/12/2021] [Accepted: 12/03/2021] [Indexed: 02/06/2023]
Abstract
The pursuit to discover the fundamental biology and mechanisms of aging within the context of the physical and social environment is critical to designing interventions to prevent and treat its complex phenotypes. Aging research is critically linked to understanding health disparities because these inequities shape minority aging, which may proceed on a different trajectory than the overall population. Health disparities are characteristically seen in commonly occurring age-associated diseases such as cardiovascular and cerebrovascular disease as well as diabetes mellitus and cancer. The early appearance and increased severity of age-associated disease among African American and low socioeconomic status (SES) individuals suggests that the factors contributing to the emergence of health disparities may also induce a phenotype of 'premature aging' or 'accelerated aging' or 'weathering'. In marginalized and low SES populations with high rates of early onset age-associated disease the interaction of biologic, psychosocial, socioeconomic and environmental factors may result in a phenotype of accelerated aging biologically similar to premature aging syndromes with increased susceptibility to oxidative stress, premature accumulation of oxidative DNA damage, defects in DNA repair and higher levels of biomarkers of oxidative stress and inflammation. Health disparities, therefore, may be the end product of this complex interaction in populations at high risk. This review will examine the factors that drive both health disparities and the accelerated aging phenotype that ultimately contributes to premature mortality.
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Affiliation(s)
- Nicole Noren Hooten
- Laboratory of Epidemiology and Population Science, National Institute on Aging, National Institutes of Health, 251 Bayview Boulevard, Baltimore, MD 21224, USA
| | - Natasha L Pacheco
- Laboratory of Epidemiology and Population Science, National Institute on Aging, National Institutes of Health, 251 Bayview Boulevard, Baltimore, MD 21224, USA
| | - Jessica T Smith
- Laboratory of Epidemiology and Population Science, National Institute on Aging, National Institutes of Health, 251 Bayview Boulevard, Baltimore, MD 21224, USA
| | - Michele K Evans
- Laboratory of Epidemiology and Population Science, National Institute on Aging, National Institutes of Health, 251 Bayview Boulevard, Baltimore, MD 21224, USA.
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6
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Rubin L, Ingram LA, Resciniti NV, Ashford-Carroll B, Leith KH, Rose A, Ureña S, McCollum Q, Friedman DB. Genetic Risk Factors for Alzheimer's Disease in Racial/Ethnic Minority Populations in the U.S.: A Scoping Review. Front Public Health 2021; 9:784958. [PMID: 35004586 PMCID: PMC8739784 DOI: 10.3389/fpubh.2021.784958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 11/23/2021] [Indexed: 11/13/2022] Open
Abstract
Objectives: As the United States (U.S.) population rapidly ages, the incidence of Alzheimer's Disease and Related Dementias (ADRDs) is rising, with racial/ethnic minorities affected at disproportionate rates. Much research has been undertaken to test, sequence, and analyze genetic risk factors for ADRDs in Caucasian populations, but comparatively little has been done with racial/ethnic minority populations. We conducted a scoping review to examine the nature and extent of the research that has been published about the genetic factors of ADRDs among racial/ethnic minorities in the U.S. Design: Using an established scoping review methodological framework, we searched electronic databases for articles describing peer-reviewed empirical studies or Genome-Wide Association Studies that had been published 2005-2018 and focused on ADRD-related genes or genetic factors among underrepresented racial/ethnic minority population in the U.S. Results: Sixty-six articles met the inclusion criteria for full text review. Well-established ADRD genetic risk factors for Caucasian populations including APOE, APP, PSEN1, and PSEN2 have not been studied to the same degree in minority U.S. populations. Compared to the amount of research that has been conducted with Caucasian populations in the U.S., racial/ethnic minority communities are underrepresented. Conclusion: Given the projected growth of the aging population and incidence of ADRDs, particularly among racial/ethnic minorities, increased focus on this important segment of the population is warranted. Our review can aid researchers in developing fundamental research questions to determine the role that ADRD risk genes play in the heavier burden of ADRDs in racial/ethnic minority populations.
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Affiliation(s)
- Lindsey Rubin
- Department of Health Promotion, Education, and Behavior, University of South Carolina, Columbia, SC, United States
| | - Lucy A. Ingram
- Department of Health Promotion, Education, and Behavior, University of South Carolina, Columbia, SC, United States
| | - Nicholas V. Resciniti
- Department of Epidemiology and Biostatistics, University of South Carolina, Columbia, SC, United States
| | - Brianna Ashford-Carroll
- Department of Health Promotion, Education, and Behavior, University of South Carolina, Columbia, SC, United States
| | - Katherine Henrietta Leith
- Department of Health Promotion, Education, and Behavior, University of South Carolina, Columbia, SC, United States
| | - Aubrey Rose
- School of Medicine, University of South Carolina, Columbia, SC, United States
| | - Stephanie Ureña
- Department of Health Promotion, Education, and Behavior, University of South Carolina, Columbia, SC, United States
| | - Quentin McCollum
- College of Social Work, University of South Carolina, Columbia, SC, United States
| | - Daniela B. Friedman
- Department of Health Promotion, Education, and Behavior, University of South Carolina, Columbia, SC, United States
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7
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Liu T, Momin M, Zhou H, Zheng Q, Fan F, Jia J, Liu M, Bao M, Li J, Huo Y, Liu J, Zhang Y, Mao X, Han X, Hu Z, Zeng C, Liu F, Zhang Y. Exome-Wide Association Study Identifies East Asian-Specific Missense Variant MTHFR C136T Influencing Homocysteine Levels in Chinese Populations RH: ExWAS of tHCY in a Chinese Population. Front Genet 2021; 12:717621. [PMID: 34707639 PMCID: PMC8542906 DOI: 10.3389/fgene.2021.717621] [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: 06/02/2021] [Accepted: 09/02/2021] [Indexed: 02/01/2023] Open
Abstract
Plasma total homocysteine (tHCY) is a known risk factor of a wide range of complex diseases. No genome scans for tHCY have been conducted in East Asian populations. Here, we conducted an exome-wide association study (ExWAS) for tHCY in 5,175 individuals of Chinese Han origin, followed by a replication study in 668 Chinese individuals. The ExWAS identified two loci, 1p36.22 (lead single-nucleotide polymorphism (SNP) rs1801133, MTHFR C677T) and 16q24.3 (rs1126464, DPEP1), showing exome-wide significant association with tHCY (p < 5E-7); and both loci have been previously associated with tHCY in non-East Asian populations. Both SNPs were replicated in the replication study (p < 0.05). Conditioning on the genotype of C677T and rs1126464, we identified a novel East Asian-specific missense variant rs138189536 (C136T) of MTHFR (p = 6.53E-10), which was also significant in the replication study (p = 9.8E-3). The C136T and C677T variants affect tHCY in a compound heterozygote manner, where compound heterozygote and homozygote genotype carriers had on average 43.4% increased tHCY than had other genotypes. The frequency of the homozygote C677T genotype showed an inverse-U-shaped geospatial pattern globally with a pronounced frequency in northern China, which coincided with the high prevalence of hyperhomocysteinemia (HHCY) in northern China. A logistic regression model of HHCY status considering sex, age, and the genotypes of the three identified variants reached an area under the receiver operating characteristic curve (AUC) value of 0.74 in an independent validation cohort. These genetic observations provide new insights into the presence of multiple causal mutations at the MTHFR locus, highlight the role of genetics in HHCY epidemiology among different populations, and provide candidate loci for future functional studies.
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Affiliation(s)
- Tianzi Liu
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,China National Center for Bioinformation, Beijing, China
| | - Mohetaboer Momin
- Department of Cardiology, Peking University First Hospital, Beijing, China.,Institute of Cardiovascular Disease, Peking University First Hospital, Beijing, China
| | - Huiyue Zhou
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,China National Center for Bioinformation, Beijing, China
| | - Qiwen Zheng
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,China National Center for Bioinformation, Beijing, China
| | - Fangfang Fan
- Department of Cardiology, Peking University First Hospital, Beijing, China.,Institute of Cardiovascular Disease, Peking University First Hospital, Beijing, China
| | - Jia Jia
- Department of Cardiology, Peking University First Hospital, Beijing, China.,Institute of Cardiovascular Disease, Peking University First Hospital, Beijing, China
| | - Mengyuan Liu
- Department of Cardiology, Peking University First Hospital, Beijing, China.,Institute of Cardiovascular Disease, Peking University First Hospital, Beijing, China
| | - Minghui Bao
- Department of Cardiology, Peking University First Hospital, Beijing, China.,Institute of Cardiovascular Disease, Peking University First Hospital, Beijing, China
| | - Jianping Li
- Department of Cardiology, Peking University First Hospital, Beijing, China.,Institute of Cardiovascular Disease, Peking University First Hospital, Beijing, China
| | - Yong Huo
- Department of Cardiology, Peking University First Hospital, Beijing, China.,Institute of Cardiovascular Disease, Peking University First Hospital, Beijing, China
| | - Jialin Liu
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,China National Center for Bioinformation, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yaning Zhang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,China National Center for Bioinformation, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xuemei Mao
- Beijing P4 Healthcare Institute, Beijing, China
| | - Xiao Han
- Beijing P4 Healthcare Institute, Beijing, China
| | - Zhiyuan Hu
- Beijing P4 Healthcare Institute, Beijing, China.,CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing, China.,School of Nanoscience and Technology, Sino-Danish College, University of Chinese Academy of Sciences, Beijing, China
| | - Changqing Zeng
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,China National Center for Bioinformation, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Fan Liu
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,China National Center for Bioinformation, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yan Zhang
- Department of Cardiology, Peking University First Hospital, Beijing, China.,Institute of Cardiovascular Disease, Peking University First Hospital, Beijing, China
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8
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Khan MJ, Desaire H, Lopez OL, Kamboh MI, Robinson RA. Why Inclusion Matters for Alzheimer’s Disease Biomarker Discovery in Plasma. J Alzheimers Dis 2021; 79:1327-1344. [DOI: 10.3233/jad-201318] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Background: African American/Black adults have a disproportionate incidence of Alzheimer’s disease (AD) and are underrepresented in biomarker discovery efforts. Objective: This study aimed to identify potential diagnostic biomarkers for AD using a combination of proteomics and machine learning approaches in a cohort that included African American/Black adults. Methods: We conducted a discovery-based plasma proteomics study on plasma samples (N = 113) obtained from clinically diagnosed AD and cognitively normal adults that were self-reported African American/Black or non-Hispanic White. Sets of differentially-expressed proteins were then classified using a support vector machine (SVM) to identify biomarker candidates. Results: In total, 740 proteins were identified of which, 25 differentially-expressed proteins in AD came from comparisons within a single racial and ethnic background group. Six proteins were differentially-expressed in AD regardless of racial and ethnic background. Supervised classification by SVM yielded an area under the curve (AUC) of 0.91 and accuracy of 86%for differentiating AD in samples from non-Hispanic White adults when trained with differentially-expressed proteins unique to that group. However, the same model yielded an AUC of 0.49 and accuracy of 47%for differentiating AD in samples from African American/Black adults. Other covariates such as age, APOE4 status, sex, and years of education were found to improve the model mostly in the samples from non-Hispanic White adults for classifying AD. Conclusion: These results demonstrate the importance of study designs in AD biomarker discovery, which must include diverse racial and ethnic groups such as African American/Black adults to develop effective biomarkers.
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Affiliation(s)
- Mostafa J. Khan
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA
| | - Heather Desaire
- Department of Chemistry, University of Kansas, Lawrence, KS, USA
| | - Oscar L. Lopez
- Department of Neurology, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
| | - M. Ilyas Kamboh
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Epidemiology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Renã A.S. Robinson
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA
- Vanderbilt Memory and Alzheimer’s Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN, USA
- Vanderbilt Brain Institute, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN, USA
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9
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A critical evaluation of results from genome-wide association studies of micronutrient status and their utility in the practice of precision nutrition. Br J Nutr 2019; 122:121-130. [DOI: 10.1017/s0007114519001119] [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]
Abstract
AbstractRapid advances in ‘omics’ technologies have paved the way forward to an era where more ‘precise’ approaches – ‘precision’ nutrition – which leverage data on genetic variability alongside the traditional indices, have been put forth as the state-of-the-art solution to redress the effects of malnutrition across the life course. We purport that this inference is premature and that it is imperative to first review and critique the existing evidence from large-scale epidemiological findings. We set out to provide a critical evaluation of findings from genome-wide association studies (GWAS) in the roadmap to precision nutrition, focusing on GWAS of micronutrient disposition. We found that a large number of loci associated with biomarkers of micronutrient status have been identified. Mean estimates of heritability of micronutrient status ranged between 20 and 35 % for minerals, 56–59 % for water-soluble and 30–70 % for fat-soluble vitamins. With some exceptions, the majority of the identified genetic variants explained little of the overall variance in status for each micronutrient, ranging between 1·3 and 8 % (minerals), <0·1–12 % (water-soluble) and 1·7–2·3 % for (fat-soluble) vitamins. However, GWAS have provided some novel insight into mechanisms that underpin variability in micronutrient status. Our findings highlight obvious gaps that need to be addressed if the full scope of precision nutrition is ever to be realised, including research aimed at (i) dissecting the genetic basis of micronutrient deficiencies or ‘response’ to intake/supplementation (ii) identifying trans-ethnic and ethnic-specific effects (iii) identifying gene–nutrient interactions for the purpose of unravelling molecular ‘behaviour’ in a range of environmental contexts.
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10
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Raffield LM, Ellis J, Olson NC, Duan Q, Li J, Durda P, Pankratz N, Keating BJ, Wassel CL, Cushman M, Wilson JG, Gross MD, Tracy RP, Rich SS, Reiner AP, Li Y, Willis MS, Lange EM, Lange LA. Genome-wide association study of homocysteine in African Americans from the Jackson Heart Study, the Multi-Ethnic Study of Atherosclerosis, and the Coronary Artery Risk in Young Adults study. J Hum Genet 2018; 63:327-337. [PMID: 29321517 PMCID: PMC5826839 DOI: 10.1038/s10038-017-0384-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 09/26/2017] [Accepted: 10/22/2017] [Indexed: 12/21/2022]
Abstract
Homocysteine (Hcy) is a heritable biomarker for CVD, peripheral artery disease, stroke, and dementia. Little is known about genetic associations with Hcy in individuals of African ancestry. We performed a genome-wide association study for Hcy in 4927 AAs from the Jackson Heart Study (JHS), the Multi-Ethnic Study of Atherosclerosis (MESA), and the Coronary Artery Risk in Young Adults (CARDIA) study. Analyses were stratified by sex and results were meta-analyzed within and across sex. In the sex-combined meta-analysis, we observed genome-wide significant evidence (p < 5.0 × 10-8) for the NOX4 locus (lead variant rs2289125, β = -0.15, p = 5.3 × 1011). While the NOX4 locus was previously reported as associated with Hcy in European-American populations, rs2289125 remained genome-wide significant when conditioned on the previously reported lead variants. Previously reported genome-wide significant associations at NOX4, MTR, CBS, and MMACHC were also nominally (p < 0.050) replicated in AAs. Associations at the CPS1 locus, previously reported in females only, also was replicated specifically in females in this analysis, supporting sex-specific effects for this locus. These results suggest that there may be a combination of cross-population and population-specific genetic effects, as well as differences in genetic effects between males and females, in the regulation of Hcy levels.
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Affiliation(s)
- Laura M Raffield
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA.
| | - Jaclyn Ellis
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Nels C Olson
- Department of Pathology and Laboratory Medicine, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, VT, 05405, USA
| | - Qing Duan
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Jin Li
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Peter Durda
- Department of Pathology and Laboratory Medicine, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, VT, 05405, USA
| | - Nathan Pankratz
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Brendan J Keating
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Christina L Wassel
- Department of Pathology and Laboratory Medicine, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, VT, 05405, USA
| | - Mary Cushman
- Department of Pathology and Laboratory Medicine, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, VT, 05405, USA
- Department of Medicine, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, VT, 05405, USA
| | - James G Wilson
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, MS, 39216, USA
| | - Myron D Gross
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Russell P Tracy
- Department of Pathology and Laboratory Medicine, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, VT, 05405, USA
- Department of Biochemistry, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, VT, 05405, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908, USA
| | - Alex P Reiner
- Department of Epidemiology, University of Washington, Seattle, WA, 98195, USA
| | - Yun Li
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Monte S Willis
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Ethan M Lange
- Department of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Leslie A Lange
- Department of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, 80045, USA
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11
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Quansah E, McGregor NW. Towards diversity in genomics: The emergence of neurogenomics in Africa? Genomics 2018; 110:1-9. [PMID: 28774809 DOI: 10.1016/j.ygeno.2017.07.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 07/24/2017] [Accepted: 07/30/2017] [Indexed: 12/11/2022]
Abstract
There is a high burden of mental and neurological disorders in Africa. Nevertheless, there appears to be an under-representation of African ancestry populations in large-scale genomic studies. Here, we evaluated the extent of under-representation of Africans in neurogenomic studies in the GWAS Catalog. We found 569 neurogenomic studies, of which 88.9% were exclusively focused on people with European ancestry and the remaining 11.1% having African ancestry cases included. In terms of population, only 1.2% of the total populations involved in these 569 GWAS studies were of African descent. Further, most of the individuals in the African ancestry category were identified to be African-Americans/Afro-Caribbeans, highlighting the huge under-representation of homogenous African populations in large-scale neurogenomic studies. Efforts geared at establishing strong collaborative ties with European/American researchers, maintaining freely accessible biobanks and establishing comprehensive African genome data repositories to track African genome variations are critical for propelling neurogenomics/precision medicine in Africa.
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Affiliation(s)
- Emmanuel Quansah
- Pharmacology, Faculty of Health and Life Sciences, De Montfort University, Leicester LE1 9BH, UK.
| | - Nathaniel W McGregor
- Department of Genetics, Stellenbosch University, Stellenbosch, South Africa; Department of Psychiatry, Stellenbosch University, Tygerberg Medical Campus, Tygerberg, South Africa.
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12
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Diversity and inclusion in genomic research: why the uneven progress? J Community Genet 2017; 8:255-266. [PMID: 28770442 PMCID: PMC5614884 DOI: 10.1007/s12687-017-0316-6] [Citation(s) in RCA: 168] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 06/29/2017] [Indexed: 12/15/2022] Open
Abstract
Conducting genomic research in diverse populations has led to numerous advances in our understanding of human history, biology, and health disparities, in addition to discoveries of vital clinical significance. Conducting genomic research in diverse populations is also important in ensuring that the genomic revolution does not exacerbate health disparities by facilitating discoveries that will disproportionately benefit well-represented populations. Despite the general agreement on the need for genomic research in diverse populations in terms of equity and scientific progress, genomic research remains largely focused on populations of European descent. In this article, we describe the rationale for conducting genomic research in diverse populations by reviewing examples of advances facilitated by their inclusion. We also explore some of the factors that perpetuate the disproportionate attention on well-represented populations. Finally, we discuss ongoing efforts to ameliorate this continuing bias. Collaborative and intensive efforts at all levels of research, from the funding of studies to the publication of their findings, will be necessary to ensure that genomic research does not conserve historical inequalities or curtail the contribution that genomics could make to the health of all humanity.
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