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Rizig M, Bandres-Ciga S, Makarious MB, Ojo O, Crea PW, Abiodun O, Levine KS, Abubakar S, Achoru C, Vitale D, Adeniji O, Agabi O, Koretsky MJ, Agulanna U, Hall DA, Akinyemi R, Xie T, Ali M, Shamim EA, Ani-Osheku I, Padmanaban M, Arigbodi O, Standaert DG, Bello A, Dean M, Erameh C, Elsayed I, Farombi T, Okunoye O, Fawale M, Billingsley KJ, Imarhiagbe F, Jerez PA, Iwuozo E, Baker B, Komolafe M, Malik L, Nwani P, Daida K, Nwazor E, Miano-Burkhardt A, Nyandaiti Y, Fang ZH, Obiabo Y, Kluss JH, Odeniyi O, Hernandez D, Odiase F, Tayebi N, Ojini F, Sidranksy E, Onwuegbuzie G, D’Souza AM, Osaigbovo G, Berhe B, Osemwegie N, Reed X, Oshinaike O, Leonard H, Otubogun F, Alvarado CX, Oyakhire S, Ozomma S, Samuel S, Taiwo F, Wahab K, Zubair Y, Iwaki H, Kim JJ, Morris HR, Hardy J, Nalls M, Heilbron K, Norcliffe-Kaufmann L, Blauwendraat C, Houlden H, Singleton A, Okubadejo N. Genome-wide Association Identifies Novel Etiological Insights Associated with Parkinson's Disease in African and African Admixed Populations. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.05.05.23289529. [PMID: 37398408 PMCID: PMC10312852 DOI: 10.1101/2023.05.05.23289529] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Background Understanding the genetic mechanisms underlying diseases in ancestrally diverse populations is a critical step towards the realization of the global application of precision medicine. The African and African admixed populations enable mapping of complex traits given their greater levels of genetic diversity, extensive population substructure, and distinct linkage disequilibrium patterns. Methods Here we perform a comprehensive genome-wide assessment of Parkinson's disease (PD) in 197,918 individuals (1,488 cases; 196,430 controls) of African and African admixed ancestry, characterizing population-specific risk, differential haplotype structure and admixture, coding and structural genetic variation and polygenic risk profiling. Findings We identified a novel common risk factor for PD and age at onset at the GBA1 locus (risk, rs3115534-G; OR=1.58, 95% CI = 1.37 - 1.80, P=2.397E-14; age at onset, BETA =-2.004, SE =0.57, P = 0.0005), that was found to be rare in non-African/African admixed populations. Downstream short- and long-read whole genome sequencing analyses did not reveal any coding or structural variant underlying the GWAS signal. However, we identified that this signal mediates PD risk via expression quantitative trait locus (eQTL) mechanisms. While previously identified GBA1 associated disease risk variants are coding mutations, here we suggest a novel functional mechanism consistent with a trend in decreasing glucocerebrosidase activity levels. Given the high population frequency of the underlying signal and the phenotypic characteristics of the homozygous carriers, we hypothesize that this variant may not cause Gaucher disease. Additionally, the prevalence of Gaucher's disease in Africa is low. Interpretation The present study identifies a novel African-ancestry genetic risk factor in GBA1 as a major mechanistic basis of PD in the African and African admixed populations. This striking result contrasts to previous work in Northern European populations, both in terms of mechanism and attributable risk. This finding highlights the importance of understanding population-specific genetic risk in complex diseases, a particularly crucial point as the field moves toward precision medicine in PD clinical trials and while recognizing the need for equitable inclusion of ancestrally diverse groups in such trials. Given the distinctive genetics of these underrepresented populations, their inclusion represents a valuable step towards insights into novel genetic determinants underlying PD etiology. This opens new avenues towards RNA-based and other therapeutic strategies aimed at reducing lifetime risk. Research in Context Evidence Before this Study Our current understanding of Parkinson's disease (PD) is disproportionately based on studying populations of European ancestry, leading to a significant gap in our knowledge about the genetics, clinical characteristics, and pathophysiology in underrepresented populations. This is particularly notable in individuals of African and African admixed ancestries. Over the last two decades, we have witnessed a revolution in the research area of complex genetic diseases. In the PD field, large-scale genome-wide association studies in the European, Asian, and Latin American populations have identified multiple risk loci associated with disease. These include 78 loci and 90 independent signals associated with PD risk in the European population, nine replicated loci and two novel population-specific signals in the Asian population, and a total of 11 novel loci recently nominated through multi-ancestry GWAS efforts.Nevertheless, the African and African admixed populations remain completely unexplored in the context of PD genetics. Added Value of this Study To address the lack of diversity in our research field, this study aimed to conduct the first genome-wide assessment of PD genetics in the African and African admixed populations. Here, we identified a genetic risk factor linked to PD etiology, dissected African-specific differences in risk and age at onset, characterized known genetic risk factors, and highlighted the utility of the African and African admixed risk haplotype substructure for future fine-mapping efforts. We identified a novel disease mechanism via expression changes consistent with decreased GBA1 activity levels. Future large scale single cell expression studies should investigate the neuronal populations in which expression differences are most prominent. This novel mechanism may hold promise for future efficient RNA-based therapeutic strategies such as antisense oligonucleotides or short interfering RNAs aimed at preventing and decreasing disease risk. We envisage that these data generated under the umbrella of the Global Parkinson's Genetics Program (GP2) will shed light on the molecular mechanisms involved in the disease process and might pave the way for future clinical trials and therapeutic interventions. This work represents a valuable resource in an underserved population, supporting pioneering research within GP2 and beyond. Deciphering causal and genetic risk factors in all these ancestries will help determine whether interventions, potential targets for disease modifying treatment, and prevention strategies that are being studied in the European populations are relevant to the African and African admixed populations. Implications of all the Available Evidence We nominate a novel signal impacting GBA1 as the major genetic risk factor for PD in the African and African admixed populations. The present study could inform future GBA1 clinical trials, improving patient stratification. In this regard, genetic testing can help to design trials likely to provide meaningful and actionable answers. It is our hope that these findings may ultimately have clinical utility for this underrepresented population.
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Affiliation(s)
- Mie Rizig
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
- UCL Movement Disorders Centre, University College London, London, WC1N 3BG, UK
| | - Sara Bandres-Ciga
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA, 20814
| | - Mary B Makarious
- UCL Movement Disorders Centre, University College London, London, WC1N 3BG, UK
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Oluwadamilola Ojo
- College of Medicine, University of Lagos, Idi Araba, Lagos State, Nigeria
| | - Peter Wild Crea
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA, 20814
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | | | - Kristin S Levine
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA, 20814
- Data Tecnica International, Washington, DC, USA
| | - Sani Abubakar
- Ahmadu Bello University, Zaria, Kaduna State, Nigeria
| | - Charles Achoru
- Jos University Teaching Hospital, Jos, Plateau State, Nigeria
| | - Dan Vitale
- Data Tecnica International, Washington, DC, USA
| | | | - Osigwe Agabi
- College of Medicine, University of Lagos, Idi Araba, Lagos State, Nigeria
| | - Mathew J Koretsky
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA, 20814
| | - Uchechi Agulanna
- Lagos University Teaching Hospital, Idi Araba, Lagos State, Nigeria
| | - Deborah A. Hall
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, USA
| | - Rufus Akinyemi
- Neuroscience and Ageing Research Unit, Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - Tao Xie
- Department of Neurology, University of Chicago Medicine, Chicago, Illinois, USA
| | - Mohammed Ali
- Federal Teaching Hospital Gombe, Gombe State, Nigeria
| | - Ejaz A. Shamim
- Human Motor Control Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
- Kaiser Permanente Mid-Atlantic States, Largo, Maryland, USA
- MidAtlantic Permanente Research Institute, Rockville, Maryland, USA
| | | | - Mahesh Padmanaban
- Department of Neurology, University of Chicago Medicine, Chicago, Illinois, USA
| | | | - David G Standaert
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Abiodun Bello
- University of Ilorin Teaching Hospital, Ilorin, Kwara State, Nigeria
| | - Marissa Dean
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Cyril Erameh
- Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria
| | - Inas Elsayed
- Faculty of Pharmacy, University of Gezira, Wadmadani, 20, Sudan
| | | | - Olaitan Okunoye
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Michael Fawale
- Obafemi Awolowo University, Ile-Ife, Osun State, Nigeria
| | - Kimberley J Billingsley
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA, 20814
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | | | - Pilar Alvarez Jerez
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA, 20814
| | | | - Breeana Baker
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA, 20814
| | | | - Laksh Malik
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA, 20814
| | - Paul Nwani
- Nnamdi Azikiwe University Teaching Hospital, Nnewi, Anambra State, Nigeria
| | - Kensuke Daida
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA, 20814
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Ernest Nwazor
- Rivers State University Teaching Hospital, Port Harcourt, Rivers State, Nigeria
| | - Abigail Miano-Burkhardt
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA, 20814
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Yakub Nyandaiti
- University of Maiduguri Teaching Hospital, Maiduguri, Borno State, Nigeria
| | - Zih-Hua Fang
- German Center for Neurodegenerative Diseases (DZNE), Tuebingen, Germany
| | - Yahaya Obiabo
- Federal University of Health Sciences, Otukpo, Benue State, Nigeria
| | - Jillian H. Kluss
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | | | - Dena Hernandez
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | | | - Nahid Tayebi
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Francis Ojini
- College of Medicine, University of Lagos, Idi Araba, Lagos State, Nigeria
| | - Ellen Sidranksy
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | | | - Andrea M. D’Souza
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | | | - Bahafta Berhe
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | | | - Xylena Reed
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA, 20814
| | | | - Hampton Leonard
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA, 20814
- Data Tecnica International, Washington, DC, USA
| | | | - Chelsea X Alvarado
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA, 20814
- Data Tecnica International, Washington, DC, USA
| | | | - Simon Ozomma
- University of Calabar Teaching Hospital, Calabar, Cross River State, Nigeria
| | - Sarah Samuel
- University of Maiduguri Teaching Hospital, Maiduguri, Borno State, Nigeria
| | | | - Kolawole Wahab
- University of Ilorin Teaching Hospital, Ilorin, Kwara State, Nigeria
- University of Ilorin, Ilorin, Kwara State, Nigeria
| | - Yusuf Zubair
- National Hospital, Abuja, Federal Capital Territory, Nigeria
| | - Hirotaka Iwaki
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA, 20814
- Data Tecnica International, Washington, DC, USA
| | - Jonggeol Jeffrey Kim
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA, 20814
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Huw R Morris
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
- UCL Movement Disorders Centre, University College London, London, WC1N 3BG, UK
| | - John Hardy
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Mike Nalls
- Data Tecnica International, Washington, DC, USA
| | | | | | | | - Cornelis Blauwendraat
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA, 20814
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Henry Houlden
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Andrew Singleton
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA, 20814
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Njideka Okubadejo
- College of Medicine, University of Lagos, Idi Araba, Lagos State, Nigeria
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