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Cogan G, Daida K, Billingsley KJ, Tesson C, Forlani S, Jornea L, Arnaud L, Tissier L, LeGuern E, Singleton AB, Ferrien M, Gervais Bernard H, Lesage S, Blauwendraat C, Brice A. Long-read sequencing unravels the complexity of structural variants in PRKN in two individuals with early-onset Parkinson's disease. medRxiv 2024:2024.05.02.24306523. [PMID: 38746197 PMCID: PMC11092742 DOI: 10.1101/2024.05.02.24306523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Background PRKN biallelic pathogenic variants are the most common cause of autosomal recessive early-onset Parkinson's disease (PD). However, the variants responsible for suspected PRKN- PD individuals are not always identified with standard genetic testing. Objectives Identify the genetic cause in two siblings with a PRKN -PD phenotype using long-read sequencing (LRS). Methods The genetic investigation involved standard testing using successively multiple ligation probe amplification (MLPA), Sanger sequencing, targeted sequencing, whole-exome sequencing and LRS. Results MLPA and targeted sequencing identified one copy of exon four in PRKN but no other variants were identified. Subsequently, LRS unveiled a large deletion encompassing exon 3 to 4 on one allele and a duplication of exon 3 on the second allele; explaining the siblings' phenotype. MLPA could not identify the balanced rearrangement of exon 3. Conclusions This study highlights the potential utility of long-read sequencing in the context of unsolved typical PRKN- PD individuals.
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2
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Miano-Burkhardt A, Alvarez Jerez P, Daida K, Bandres Ciga S, Billingsley KJ. The Role of Structural Variants in the Genetic Architecture of Parkinson's Disease. Int J Mol Sci 2024; 25:4801. [PMID: 38732020 PMCID: PMC11084710 DOI: 10.3390/ijms25094801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 04/17/2024] [Accepted: 04/22/2024] [Indexed: 05/13/2024] Open
Abstract
Parkinson's disease (PD) significantly impacts millions of individuals worldwide. Although our understanding of the genetic foundations of PD has advanced, a substantial portion of the genetic variation contributing to disease risk remains unknown. Current PD genetic studies have primarily focused on one form of genetic variation, single nucleotide variants (SNVs), while other important forms of genetic variation, such as structural variants (SVs), are mostly ignored due to the complexity of detecting these variants with traditional sequencing methods. Yet, these forms of genetic variation play crucial roles in gene expression and regulation in the human brain and are causative of numerous neurological disorders, including forms of PD. This review aims to provide a comprehensive overview of our current understanding of the involvement of coding and noncoding SVs in the genetic architecture of PD.
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Affiliation(s)
- Abigail Miano-Burkhardt
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD 20892, USA; (A.M.-B.); (K.D.)
- Center for Alzheimer’s and Related Dementias, National Institute on Aging, Bethesda, MD 20892, USA; (P.A.J.); (S.B.C.)
| | - Pilar Alvarez Jerez
- Center for Alzheimer’s and Related Dementias, National Institute on Aging, Bethesda, MD 20892, USA; (P.A.J.); (S.B.C.)
| | - Kensuke Daida
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD 20892, USA; (A.M.-B.); (K.D.)
- Center for Alzheimer’s and Related Dementias, National Institute on Aging, Bethesda, MD 20892, USA; (P.A.J.); (S.B.C.)
| | - Sara Bandres Ciga
- Center for Alzheimer’s and Related Dementias, National Institute on Aging, Bethesda, MD 20892, USA; (P.A.J.); (S.B.C.)
| | - Kimberley J. Billingsley
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD 20892, USA; (A.M.-B.); (K.D.)
- Center for Alzheimer’s and Related Dementias, National Institute on Aging, Bethesda, MD 20892, USA; (P.A.J.); (S.B.C.)
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3
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Rodriguez I, Rossi NM, Keskus AG, Xie Y, Ahmad T, Bryant A, Lou H, Paredes JG, Milano R, Rao N, Tulsyan S, Boland JF, Luo W, Liu J, O'Hanlon T, Bess J, Mukhina V, Gaykalova D, Yuki Y, Malik L, Billingsley KJ, Blauwendraat C, Carrington M, Yeager M, Mirabello L, Kolmogorov M, Dean M. Insights into the mechanisms and structure of breakage-fusion-bridge cycles in cervical cancer using long-read sequencing. Am J Hum Genet 2024; 111:544-561. [PMID: 38307027 PMCID: PMC10940022 DOI: 10.1016/j.ajhg.2024.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 12/20/2023] [Accepted: 01/04/2024] [Indexed: 02/04/2024] Open
Abstract
Cervical cancer is caused by human papillomavirus (HPV) infection, has few approved targeted therapeutics, and is the most common cause of cancer death in low-resource countries. We characterized 19 cervical and four head and neck cancer cell lines using long-read DNA and RNA sequencing and identified the HPV types, HPV integration sites, chromosomal alterations, and cancer driver mutations. Structural variation analysis revealed telomeric deletions associated with DNA inversions resulting from breakage-fusion-bridge (BFB) cycles. BFB is a common mechanism of chromosomal alterations in cancer, and our study applies long-read sequencing to this important chromosomal rearrangement type. Analysis of the inversion sites revealed staggered ends consistent with exonuclease digestion of the DNA after breakage. Some BFB events are complex, involving inter- or intra-chromosomal insertions or rearrangements. None of the BFB breakpoints had telomere sequences added to resolve the dicentric chromosomes, and only one BFB breakpoint showed chromothripsis. Five cell lines have a chromosomal region 11q BFB event, with YAP1-BIRC3-BIRC2 amplification. Indeed, YAP1 amplification is associated with a 10-year-earlier age of diagnosis of cervical cancer and is three times more common in African American women. This suggests that individuals with cervical cancer and YAP1-BIRC3-BIRC2 amplification, especially those of African ancestry, might benefit from targeted therapy. In summary, we uncovered valuable insights into the mechanisms and consequences of BFB cycles in cervical cancer using long-read sequencing.
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Affiliation(s)
- Isabel Rodriguez
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Nicole M Rossi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Ayse G Keskus
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Yi Xie
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Tanveer Ahmad
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Asher Bryant
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Hong Lou
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Jesica Godinez Paredes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Rose Milano
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Nina Rao
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA; Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Sonam Tulsyan
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Joseph F Boland
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Wen Luo
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Jia Liu
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Tim O'Hanlon
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Jazmyn Bess
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Vera Mukhina
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Maryland School of Medical Center, Baltimore, MD, USA
| | - Daria Gaykalova
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA; Marlene & Stewart Greenebaum Comprehensive Cancer Center, University of Maryland Medical System, Baltimore, MD, USA; Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Yuko Yuki
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Laksh Malik
- Center for Alzheimer's and Related Dementias, National Institute on Aging, Bethesda, MD, USA
| | | | - Cornelis Blauwendraat
- Center for Alzheimer's and Related Dementias, National Institute on Aging, Bethesda, MD, USA; Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA
| | - Mary Carrington
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA; Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Meredith Yeager
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Lisa Mirabello
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Mikhail Kolmogorov
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Michael Dean
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA.
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4
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Genner R, Akeson S, Meredith M, Jerez PA, Malik L, Baker B, Miano-Burkhardt A, Paten B, Billingsley KJ, Blauwendraat C, Jain M. Assessing methylation detection for primary human tissue using Nanopore sequencing. bioRxiv 2024:2024.02.29.581569. [PMID: 38464144 PMCID: PMC10925257 DOI: 10.1101/2024.02.29.581569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
DNA methylation most commonly occurs as 5-methylcytosine (5-mC) in the human genome and has been associated with human diseases. Recent developments in single-molecule sequencing technologies (Oxford Nanopore Technologies (ONT) and Pacific Biosciences) have enabled readouts of long, native DNA molecules, including cytosine methylation. ONT recently upgraded their Nanopore sequencing chemistry and kits from R9 to the R10 version, which yielded increased accuracy and sequencing throughput. However the effects on methylation detection have not yet been documented. Here we performed a series of computational analyses to characterize differences in Nanopore-based 5mC detection between the ONT R9 and R10 chemistries. We compared 5mC calls in R9 and R10 for three human genome datasets: a cell line, a frontal cortex brain sample, and a blood sample. We performed an in-depth analysis on CpG islands and homopolymer regions, and documented high concordance for methylation detection among sequencing technologies. The strongest correlation was observed between Nanopore R10 and Illumina bisulfite technologies for cell line-derived datasets. Subtle differences in methylation datasets between technologies can impact analysis tools such as differential methylation calling software. Our findings show that comparisons can be drawn between methylation data from different Nanopore chemistries using guided hypotheses. This work will facilitate comparison among Nanopore data cohorts derived using different chemistries from large scale sequencing efforts, such as the NIH CARD Long Read Initiative.
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Affiliation(s)
- Rylee Genner
- Center for Alzheimer’s and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Stuart Akeson
- Department of Bioengineering, Northeastern University, Boston, MA, USA
| | - Melissa Meredith
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Pilar Alvarez Jerez
- Center for Alzheimer’s and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Laksh Malik
- Center for Alzheimer’s and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Breeana Baker
- Center for Alzheimer’s and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | | | | | - Benedict Paten
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Kimberley J Billingsley
- Center for Alzheimer’s and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA
| | - Cornelis Blauwendraat
- Center for Alzheimer’s and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA
| | - Miten Jain
- Center for Alzheimer’s and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Department of Bioengineering, Northeastern University, Boston, MA, USA
- Department of Physics, Northeastern University, Boston, MA, USA
- Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA
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5
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Hall A, Middlehurst B, Cadogan MAM, Reed X, Billingsley KJ, Bubb VJ, Quinn JP. A SINE-VNTR-Alu at the LRIG2 locus is associated with proximal and distal gene expression in CRISPR and population models. Sci Rep 2024; 14:792. [PMID: 38191889 PMCID: PMC10774264 DOI: 10.1038/s41598-023-50307-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 12/18/2023] [Indexed: 01/10/2024] Open
Abstract
SINE-VNTR-Alu (SVA) retrotransposons represent mobile regulatory elements that have the potential to influence the surrounding genome when they insert into a locus. Evolutionarily recent mobilisation has resulted in loci in the human genome where a given retrotransposon might be observed to be present or absent, termed a retrotransposon insertion polymorphism (RIP). We previously observed that an SVA RIP ~ 2 kb upstream of LRIG2 on chromosome 1, the 'LRIG2 SVA', was associated with differences in local gene expression and methylation, and that the two were correlated. Here, we have used CRISPR-mediated deletion of the LRIG2 SVA in a cell line model to validate that presence of the retrotransposon is directly affecting local expression and provide evidence that is suggestive of a modest role for the SVA in modulating nearby methylation. Additionally, in leveraging an available Hi-C dataset we observed that the LRIG2 SVA was also involved in long-range chromatin interactions with a cluster of genes ~ 300 kb away, and that expression of these genes was to varying degrees associated with dosage of the SVA in both CRISPR cell line and population models. Altogether, these data support a regulatory role for SVAs in the modulation of gene expression, with the latter potentially involving chromatin looping, consistent with the model that RIPs may contribute to interpersonal differences in transcriptional networks.
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Affiliation(s)
- Ashley Hall
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7BE, UK
| | - Ben Middlehurst
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7BE, UK
| | - Max A M Cadogan
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7BE, UK
| | - Xylena Reed
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, 20892, USA
- Center for Alzheimer's and Related Dementias, National Institute on Aging, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Kimberley J Billingsley
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, 20892, USA
- Center for Alzheimer's and Related Dementias, National Institute on Aging, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Vivien J Bubb
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7BE, UK
| | - John P Quinn
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7BE, UK.
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6
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Daida K, Funayama M, Billingsley KJ, Malik L, Miano-Burkhardt A, Leonard HL, Makarious MB, Iwaki H, Ding J, Gibbs JR, Ishiguro M, Yoshino H, Ogaki K, Oyama G, Nishioka K, Nonaka R, Akamatsu W, Blauwendraat C, Hattori N. Long-Read Sequencing Resolves a Complex Structural Variant in PRKN Parkinson's Disease. Mov Disord 2023; 38:2249-2257. [PMID: 37926948 PMCID: PMC10843047 DOI: 10.1002/mds.29610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 08/17/2023] [Accepted: 09/11/2023] [Indexed: 11/07/2023] Open
Abstract
BACKGROUND Parkin RBR E3 ubiquitin-protein ligase (PRKN) mutations are the most common cause of young onset and autosomal recessive Parkinson's disease (PD). PRKN is located in FRA6E, which is one of the common fragile sites in the human genome, making this region prone to structural variants. However, complex structural variants such as inversions of PRKN are seldom reported, suggesting that there are potentially unrevealed complex pathogenic PRKN structural variants. OBJECTIVES To identify complex structural variants in PRKN using long-read sequencing. METHODS We investigated the genetic cause of monozygotic twins presenting with a young onset dystonia-parkinsonism using targeted sequencing, whole exome sequencing, multiple ligation probe amplification, and long-read sequencing. We assessed the presence and frequency of complex inversions overlapping PRKN using whole-genome sequencing data of Accelerating Medicines Partnership Parkinson's disease (AMP-PD) and United Kingdom (UK)-Biobank datasets. RESULTS Multiple ligation probe amplification identified a heterozygous exon three deletion in PRKN and long-read sequencing identified a large novel inversion spanning over 7 Mb, including a large part of the coding DNA sequence of PRKN. We could diagnose the affected subjects as compound heterozygous carriers of PRKN. We analyzed whole genome sequencing data of 43,538 participants of the UK-Biobank and 4941 participants of the AMP-PD datasets. Nine inversions in the UK-Biobank and two in AMP PD were identified and were considered potentially damaging and likely to affect PRKN expression. CONCLUSIONS This is the first report describing a large 7 Mb inversion involving breakpoints outside of PRKN. This study highlights the importance of using long-read sequencing for structural variant analysis in unresolved young-onset PD cases. © 2023 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.
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Affiliation(s)
- Kensuke Daida
- Integrative Neurogenomics Unit, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- 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
- Department of Neurology, Faculty of Medicine, Juntendo University, Hongo, Tokyo, Japan
| | - Manabu Funayama
- Department of Neurology, Faculty of Medicine, Juntendo University, Hongo, Tokyo, Japan
- Research Institute for Diseases of Old Age, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Kimberley J Billingsley
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - 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
| | - Abigail Miano-Burkhardt
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Hampton L. 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
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Data Tecnica International LLC, Washington, DC, USA
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Mary B. Makarious
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK, WC1N 3BG
- UCL Movement Disorders Centre, University College London, London, UK, WC1N 3BG
| | - 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
- Data Tecnica International LLC, Washington, DC, USA
| | - Jinhui Ding
- Computational Biology Group, Laboratory of Neurogenetics,National Institute on Aging, NIH, PorterNeuroscience ResearchCenter,Bethesda, MD, USA
| | - J. Raphael Gibbs
- Computational Biology Group, Laboratory of Neurogenetics,National Institute on Aging, NIH, PorterNeuroscience ResearchCenter,Bethesda, MD, USA
| | - Mayu Ishiguro
- Department of Neurology, Faculty of Medicine, Juntendo University, Hongo, Tokyo, Japan
| | - Hiroyo Yoshino
- Research Institute for Diseases of Old Age, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Kotaro Ogaki
- Department of Neurology, Faculty of Medicine, Juntendo University, Hongo, Tokyo, Japan
| | - Genko Oyama
- Department of Neurology, Faculty of Medicine, Juntendo University, Hongo, Tokyo, Japan
| | - Kenya Nishioka
- Department of Neurology, Juntendo Tokyo Koto Geriatric Medical Center 3-3-20 Shinsuna, Koto-ku, Tokyo 136-0075
| | - Risa Nonaka
- Department of Neurology, Faculty of Medicine, Juntendo University, Hongo, Tokyo, Japan
- Department of Clinical Data of Parkinson’s Disease, Graduate School of Medicine, Juntendo University, Tokyo, Japan
- Center for Genomic and Regenerative Medicine, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Wado Akamatsu
- Center for Genomic and Regenerative Medicine, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Cornelis Blauwendraat
- Integrative Neurogenomics Unit, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- 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
| | - Nobutaka Hattori
- Department of Neurology, Faculty of Medicine, Juntendo University, Hongo, Tokyo, Japan
- Research Institute for Diseases of Old Age, Graduate School of Medicine, Juntendo University, Tokyo, Japan
- Neurodegenerative Disorders Collaborative Laboratory, RIKEN Center for Brain Science, Wako, Saitama, Japan
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7
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Makarious MB, Lake J, Pitz V, Ye Fu A, Guidubaldi JL, Solsberg CW, Bandres-Ciga S, Leonard HL, Kim JJ, Billingsley KJ, Grenn FP, Jerez PA, Alvarado CX, Iwaki H, Ta M, Vitale D, Hernandez D, Torkamani A, Ryten M, Hardy J, Scholz SW, Traynor BJ, Dalgard CL, Ehrlich DJ, Tanaka T, Ferrucci L, Beach TG, Serrano GE, Real R, Morris HR, Ding J, Gibbs JR, Singleton AB, Nalls MA, Bhangale T, Blauwendraat C. Large-scale rare variant burden testing in Parkinson's disease. Brain 2023; 146:4622-4632. [PMID: 37348876 PMCID: PMC10629770 DOI: 10.1093/brain/awad214] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 05/01/2023] [Accepted: 05/30/2023] [Indexed: 06/24/2023] Open
Abstract
Parkinson's disease has a large heritable component and genome-wide association studies have identified over 90 variants with disease-associated common variants, providing deeper insights into the disease biology. However, there have not been large-scale rare variant analyses for Parkinson's disease. To address this gap, we investigated the rare genetic component of Parkinson's disease at minor allele frequencies <1%, using whole genome and whole exome sequencing data from 7184 Parkinson's disease cases, 6701 proxy cases and 51 650 healthy controls from the Accelerating Medicines Partnership Parkinson's disease (AMP-PD) initiative, the National Institutes of Health, the UK Biobank and Genentech. We performed burden tests meta-analyses on small indels and single nucleotide protein-altering variants, prioritized based on their predicted functional impact. Our work identified several genes reaching exome-wide significance. Two of these genes, GBA1 and LRRK2, have variants that have been previously implicated as risk factors for Parkinson's disease, with some variants in LRRK2 resulting in monogenic forms of the disease. We identify potential novel risk associations for variants in B3GNT3, AUNIP, ADH5, TUBA1B, OR1G1, CAPN10 and TREML1 but were unable to replicate the observed associations across independent datasets. Of these, B3GNT3 and TREML1 could provide new evidence for the role of neuroinflammation in Parkinson's disease. To date, this is the largest analysis of rare genetic variants in Parkinson's disease.
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Affiliation(s)
- Mary B Makarious
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20814, USA
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
- UCL Movement Disorders Centre, University College London, London WC1N 3BG, UK
| | - Julie Lake
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20814, USA
| | - Vanessa Pitz
- Integrative Neurogenomics Unit, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20814, USA
| | - Allen Ye Fu
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20814, USA
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ 08854, USA
| | - Joseph L Guidubaldi
- Integrative Neurogenomics Unit, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20814, USA
- 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 20814, USA
| | - Caroline Warly Solsberg
- Memory and Aging Center, Department of Neurology, University of California San Francisco, San Francisco, CA 94158, USA
- Pharmaceutical Sciences and Pharmacogenomics, University of California San Francisco, San Francisco, CA 94143, USA
| | - 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 20814, USA
| | - Hampton L Leonard
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20814, USA
- 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 20814, USA
- Data Tecnica International, Washington, DC 20812, USA
| | - Jonggeol Jeffrey Kim
- Integrative Neurogenomics Unit, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20814, USA
- Preventive Neurology Unit, Wolfson Institute of Preventive Medicine, Queen Mary University of London, London EC1M 6BQ, UK
| | - Kimberley J Billingsley
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20814, USA
- 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 20814, USA
| | - Francis P Grenn
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20814, USA
| | - Pilar Alvarez Jerez
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20814, USA
- 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 20814, 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 20814, USA
- Data Tecnica International, Washington, DC 20812, USA
| | - Hirotaka Iwaki
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20814, USA
- 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 20814, USA
- Data Tecnica International, Washington, DC 20812, USA
| | - Michael Ta
- 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 20814, USA
- Data Tecnica International, Washington, DC 20812, USA
| | - Dan Vitale
- 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 20814, USA
- Data Tecnica International, Washington, DC 20812, USA
| | - Dena Hernandez
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20814, USA
| | - Ali Torkamani
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Mina Ryten
- NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London WC1N 1EH, UK
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
| | - John Hardy
- UK Dementia Research Institute and Department of Neurodegenerative Disease and Reta Lila Weston Institute, UCL Queen Square Institute of Neurology and UCL Movement Disorders Centre, University College London, London WC1N 3BG, UK
- Institute for Advanced Study, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | | | - Sonja W Scholz
- Neurodegenerative Diseases Research Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD 20814, USA
- Department of Neurology, Johns Hopkins University Medical Center, Baltimore, MD 21287, USA
| | - Bryan J Traynor
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20814, USA
- Department of Neurology, Johns Hopkins University Medical Center, Baltimore, MD 21287, USA
| | - Clifton L Dalgard
- The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Debra J Ehrlich
- Parkinson’s Disease Clinic, Office of the Clinical Director, National Institute of Neurological Disorders and Stroke, Bethesda, MD 20814, USA
| | - Toshiko Tanaka
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Luigi Ferrucci
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Thomas G Beach
- Civin Laboratory for Neuropathology, Banner Sun Health Research Institute, Sun City, AZ 85351, USA
| | - Geidy E Serrano
- Civin Laboratory for Neuropathology, Banner Sun Health Research Institute, Sun City, AZ 85351, USA
| | - Raquel Real
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
- UCL Movement Disorders Centre, University College London, London WC1N 3BG, UK
| | - Huw R Morris
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
- UCL Movement Disorders Centre, University College London, London WC1N 3BG, UK
| | - Jinhui Ding
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20814, USA
| | - J Raphael Gibbs
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20814, USA
| | - Andrew B Singleton
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20814, USA
- 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 20814, USA
| | - Mike A Nalls
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20814, USA
- 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 20814, USA
- Data Tecnica International, Washington, DC 20812, USA
| | - Tushar Bhangale
- Department of Human Genetics, Genentech, Inc., South San Francisco, CA 94080, USA
| | - Cornelis Blauwendraat
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20814, USA
- Integrative Neurogenomics Unit, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20814, USA
- 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 20814, USA
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8
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Rizig M, Bandres-Ciga S, Makarious MB, Ojo OO, Crea PW, Abiodun OV, Levine KS, Abubakar SA, Achoru CO, Vitale D, Adeniji OA, Agabi OP, Koretsky MJ, Agulanna U, Hall DA, Akinyemi RO, Xie T, Ali MW, Shamim EA, Ani-Osheku I, Padmanaban M, Arigbodi OM, Standaert DG, Bello AH, Dean MN, Erameh CO, Elsayed I, Farombi TH, Okunoye O, Fawale MB, Billingsley KJ, Imarhiagbe FA, Jerez PA, Iwuozo EU, Baker B, Komolafe MA, Malik L, Nwani PO, Daida K, Nwazor EO, Miano-Burkhardt A, Nyandaiti YW, Fang ZH, Obiabo YO, Kluss JH, Odeniyi OA, Hernandez DG, Odiase FE, Tayebi N, Ojini FI, Sidranksy E, Onwuegbuzie GA, D'Souza AM, Osaigbovo GO, Berhe B, Osemwegie N, Reed X, Oshinaike OO, Leonard HL, Otubogun FM, Alvarado CX, Oyakhire SI, Ozomma SI, Samuel SC, Taiwo FT, Wahab KW, Zubair YA, Iwaki H, Kim JJ, Morris HR, Hardy J, Nalls MA, Heilbron K, Norcliffe-Kaufmann L, Blauwendraat C, Houlden H, Singleton A, Okubadejo NU. Identification of genetic risk loci and causal insights associated with Parkinson's disease in African and African admixed populations: a genome-wide association study. Lancet Neurol 2023; 22:1015-1025. [PMID: 37633302 PMCID: PMC10593199 DOI: 10.1016/s1474-4422(23)00283-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 06/15/2023] [Accepted: 07/18/2023] [Indexed: 08/28/2023]
Abstract
BACKGROUND An understanding of the genetic mechanisms underlying diseases in ancestrally diverse populations is an important step towards development of targeted treatments. Research in African and African admixed populations can enable mapping of complex traits, because of their genetic diversity, extensive population substructure, and distinct linkage disequilibrium patterns. We aimed to do a comprehensive genome-wide assessment in African and African admixed individuals to better understand the genetic architecture of Parkinson's disease in these underserved populations. METHODS We performed a genome-wide association study (GWAS) in people of African and African admixed ancestry with and without Parkinson's disease. Individuals were included from several cohorts that were available as a part of the Global Parkinson's Genetics Program, the International Parkinson's Disease Genomics Consortium Africa, and 23andMe. A diagnosis of Parkinson's disease was confirmed clinically by a movement disorder specialist for every individual in each cohort, except for 23andMe, in which it was self-reported based on clinical diagnosis. We characterised ancestry-specific risk, differential haplotype structure and admixture, coding and structural genetic variation, and enzymatic activity. FINDINGS We included 197 918 individuals (1488 cases and 196 430 controls) in our genome-wide analysis. We identified a novel common risk factor for Parkinson's disease (overall meta-analysis odds ratio for risk of Parkinson's disease 1·58 [95% CI 1·37-1·80], p=2·397 × 10-14) and age at onset at the GBA1 locus, rs3115534-G (age at onset β=-2·00 [SE=0·57], p=0·0005, for African ancestry; and β=-4·15 [0·58], p=0·015, for African admixed ancestry), which was rare in non-African or non-African admixed populations. Downstream short-read and long-read whole-genome sequencing analyses did not reveal any coding or structural variant underlying the GWAS signal. The identified signal seems to be associated with decreased glucocerebrosidase activity. INTERPRETATION Our study identified a novel genetic risk factor in GBA1 in people of African ancestry, which has not been seen in European populations, and it could be a major mechanistic basis of Parkinson's disease in African populations. This population-specific variant exerts substantial risk on Parkinson's disease as compared with common variation identified through GWAS and it was found to be present in 39% of the cases assessed in this study. This finding highlights the importance of understanding ancestry-specific genetic risk in complex diseases, a particularly crucial point as the Parkinson's disease field moves towards targeted treatments in clinical trials. The distinctive genetics of African populations highlights the need for equitable inclusion of ancestrally diverse groups in future trials, which will be a valuable step towards gaining insights into novel genetic determinants underlying the causes of Parkinson's disease. This finding opens new avenues towards RNA-based and other therapeutic strategies aimed at reducing lifetime risk of Parkinson's disease. FUNDING The Global Parkinson's Genetics Program, which is funded by the Aligning Science Across Parkinson's initiative, and The Michael J Fox Foundation for Parkinson's Research.
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Affiliation(s)
- Mie Rizig
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Sara Bandres-Ciga
- Center for Alzheimer's and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Mary B Makarious
- UCL Movement Disorders Centre, University College London, London, UK; Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | | | - Peter Wild Crea
- Center for Alzheimer's and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA; Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | | | - Kristin S Levine
- Center for Alzheimer's and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA; Data Tecnica International, Washington, DC, USA
| | | | | | - Dan Vitale
- Data Tecnica International, Washington, DC, USA
| | | | - Osigwe Paul Agabi
- College of Medicine, University of Lagos, Idi Araba, Lagos State, Nigeria
| | - Mathew J Koretsky
- Center for Alzheimer's and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - 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 Olusola 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, IL, USA
| | | | - Ejaz A Shamim
- Human Motor Control Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA; Kaiser Permanente Mid-Atlantic States, Largo, MD, USA; MidAtlantic Permanente Research Institute, Rockville, MD, USA
| | | | - Mahesh Padmanaban
- Department of Neurology, University of Chicago Medicine, Chicago, IL, USA
| | | | - David G Standaert
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Marissa N Dean
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Inas Elsayed
- Faculty of Pharmacy, University of Gezira, Wadmadani, Sudan
| | | | - Olaitan Okunoye
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | | | - Kimberley J Billingsley
- Center for Alzheimer's and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA; 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, UK; Center for Alzheimer's and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | | | - Breeana Baker
- Center for Alzheimer's and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | | | - Laksh Malik
- Center for Alzheimer's and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Paul Osemeke Nwani
- Nnamdi Azikiwe University Teaching Hospital, Nnewi, Anambra State, Nigeria
| | - Kensuke Daida
- Center for Alzheimer's and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA; Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | | | - Abigail Miano-Burkhardt
- Center for Alzheimer's and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA; Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | | | - Zih-Hua Fang
- German Center for Neurodegenerative Diseases, Tuebingen, Germany
| | | | - Jillian H Kluss
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | | | - Dena G 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, MD, USA
| | - Francis Ibe 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, MD, USA
| | | | - Andrea M D'Souza
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Bahafta Berhe
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Xylena Reed
- Center for Alzheimer's and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | | | - Hampton L Leonard
- Center for Alzheimer's and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA; Data Tecnica International, Washington, DC, USA
| | | | - Chelsea X Alvarado
- Center for Alzheimer's and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA; Data Tecnica International, Washington, DC, USA
| | | | | | | | | | - Kolawole Wasiu Wahab
- University of Ilorin Teaching Hospital, Ilorin, Kwara State, Nigeria; University of Ilorin, Ilorin, Kwara State, Nigeria
| | | | - Hirotaka Iwaki
- Center for Alzheimer's and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA; Data Tecnica International, Washington, DC, USA
| | - Jonggeol Jeffrey Kim
- Center for Alzheimer's and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA; 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, UK
| | - John Hardy
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
| | | | | | | | - Cornelis Blauwendraat
- Center for Alzheimer's and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA; 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, UK
| | - Andrew Singleton
- Center for Alzheimer's and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA; Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA.
| | - Njideka Ulunma Okubadejo
- College of Medicine, University of Lagos, Idi Araba, Lagos State, Nigeria; Lagos University Teaching Hospital, Idi Araba, Lagos State, Nigeria.
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9
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Kolmogorov M, Billingsley KJ, Mastoras M, Meredith M, Monlong J, Lorig-Roach R, Asri M, Alvarez Jerez P, Malik L, Dewan R, Reed X, Genner RM, Daida K, Behera S, Shafin K, Pesout T, Prabakaran J, Carnevali P, Yang J, Rhie A, Scholz SW, Traynor BJ, Miga KH, Jain M, Timp W, Phillippy AM, Chaisson M, Sedlazeck FJ, Blauwendraat C, Paten B. Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation. Nat Methods 2023; 20:1483-1492. [PMID: 37710018 DOI: 10.1038/s41592-023-01993-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 08/04/2023] [Indexed: 09/16/2023]
Abstract
Long-read sequencing technologies substantially overcome the limitations of short-reads but have not been considered as a feasible replacement for population-scale projects, being a combination of too expensive, not scalable enough or too error-prone. Here we develop an efficient and scalable wet lab and computational protocol, Napu, for Oxford Nanopore Technologies long-read sequencing that seeks to address those limitations. We applied our protocol to cell lines and brain tissue samples as part of a pilot project for the National Institutes of Health Center for Alzheimer's and Related Dementias. Using a single PromethION flow cell, we can detect single nucleotide polymorphisms with F1-score comparable to Illumina short-read sequencing. Small indel calling remains difficult within homopolymers and tandem repeats, but achieves good concordance to Illumina indel calls elsewhere. Further, we can discover structural variants with F1-score on par with state-of-the-art de novo assembly methods. Our protocol phases small and structural variants at megabase scales and produces highly accurate, haplotype-specific methylation calls.
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Affiliation(s)
- Mikhail Kolmogorov
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Kimberley J Billingsley
- Center for Alzheimer's and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA.
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA.
| | - Mira Mastoras
- UC Santa Cruz Genomics Institute, Santa Cruz, CA, USA
| | | | - Jean Monlong
- UC Santa Cruz Genomics Institute, Santa Cruz, CA, USA
| | | | - Mobin Asri
- UC Santa Cruz Genomics Institute, Santa Cruz, CA, USA
| | - Pilar Alvarez Jerez
- Center for Alzheimer's and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Laksh Malik
- Center for Alzheimer's and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Ramita Dewan
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Xylena Reed
- Center for Alzheimer's and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Rylee M Genner
- Center for Alzheimer's and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Kensuke Daida
- Center for Alzheimer's and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Sairam Behera
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | | | - Trevor Pesout
- UC Santa Cruz Genomics Institute, Santa Cruz, CA, USA
| | - Jeshuwin Prabakaran
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD, USA
| | | | - Jianzhi Yang
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Arang Rhie
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sonja W Scholz
- Neurodegenerative Diseases Research Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Department of Neurology, Johns Hopkins University Medical Center, Baltimore, MD, USA
| | - Bryan J Traynor
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Department of Neurology, Johns Hopkins University Medical Center, Baltimore, MD, USA
| | - Karen H Miga
- UC Santa Cruz Genomics Institute, Santa Cruz, CA, USA
| | - Miten Jain
- Department of Bioengineering, Northeastern University, Boston, MA, USA
- Department of Physics, Northeastern University, Boston, MA, USA
| | - Winston Timp
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Adam M Phillippy
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mark Chaisson
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Cornelis Blauwendraat
- Center for Alzheimer's and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA.
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA.
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10
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Daida K, Funayama M, Billingsley KJ, Malik L, Miano-Burkhardt A, Leonard HL, Makarious MB, Iwaki H, Ding J, Gibbs JR, Ishiguro M, Yoshino H, Ogaki K, Oyama G, Nishioka K, Nonaka R, Akamatsu W, Blauwendraat C, Hattori N. Long-read sequencing resolves a complex structural variant in PRKN Parkinson's disease. medRxiv 2023:2023.08.14.23293948. [PMID: 37790330 PMCID: PMC10543050 DOI: 10.1101/2023.08.14.23293948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Background PRKN mutations are the most common cause of young onset and autosomal recessive Parkinson's disease (PD). PRKN is located in FRA6E which is one of the common fragile sites in the human genome, making this region prone to structural variants. However, complex structural variants such as inversions of PRKN are seldom reported, suggesting that there are potentially unrevealed complex pathogenic PRKN structural variants. Objectives To identify complex structural variants in PRKN using long-read sequencing. Methods We investigated the genetic cause of monozygotic twins presenting with a young onset dystonia-parkinsonism using targeted sequencing, whole exome sequencing, multiple ligation probe amplification, and long-read. We assessed the presence and frequency of complex inversions overlapping PRKN using whole-genome sequencing data of AMP-PD and UK-Biobank datasets. Results Multiple ligation probe amplification identified a heterozygous exon 3 deletion in PRKN and long-read sequencing identified a large novel inversion spanning over 7Mb, including a large part of the coding DNA sequence of PRKN. We could diagnose the affected subjects as compound heterozygous carriers of PRKN. We analyzed whole genome sequencing data of 43,538 participants of the UK-Biobank and 4,941 participants of the AMP-PD datasets. Nine inversions in the UK-Biobank and two in AMP PD were identified and were considered potentially damaging and likely to affect PRKN isoforms. Conclusions This is the first report describing a large 7Mb inversion involving breakpoints outside of PRKN. This study highlights the importance of using long-read whole genome sequencing for structural variant analysis in unresolved young-onset PD cases.
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Affiliation(s)
- Kensuke Daida
- Integrative Neurogenomics Unit, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- 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
- Department of Neurology, Juntendo University School of Medicine, Hongo, Tokyo, Japan
| | - Manabu Funayama
- Department of Neurology, Juntendo University School of Medicine, Hongo, Tokyo, Japan
- Research Institute for Diseases of Old Age, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Kimberley J Billingsley
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - 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
| | - Abigail Miano-Burkhardt
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Hampton L. 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
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Data Tecnica International LLC, Washington, DC, USA
- German Center for Neurodegenerative Diseases (DZNE), Tubingen, Germany
| | - Mary B. Makarious
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK, WC1N 3BG
- UCL Movement Disorders Centre, University College London, London, UK, WC1N 3BG
| | - 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
- Data Tecnica International LLC, Washington, DC, USA
| | - Jinhui Ding
- BiocomputationalGroup, Laboratory of Neurogenetics,National Institute on Aging, NIH, PorterNeuroscience ResearchCenter,Bethesda, MD, USA
| | - J. Raphael Gibbs
- BiocomputationalGroup, Laboratory of Neurogenetics,National Institute on Aging, NIH, PorterNeuroscience ResearchCenter,Bethesda, MD, USA
| | - Mayu Ishiguro
- Department of Neurology, Juntendo University School of Medicine, Hongo, Tokyo, Japan
| | - Hiroyo Yoshino
- Research Institute for Diseases of Old Age, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Kotaro Ogaki
- Department of Neurology, Juntendo University School of Medicine, Hongo, Tokyo, Japan
| | - Genko Oyama
- Department of Neurology, Juntendo University School of Medicine, Hongo, Tokyo, Japan
| | - Kenya Nishioka
- Department of Neurology, Juntendo University School of Medicine, Hongo, Tokyo, Japan
| | - Risa Nonaka
- Department of Neurology, Juntendo University School of Medicine, Hongo, Tokyo, Japan
- Department of Clinical Data of Parkinson’s Disease, Graduate School of Medicine, Juntendo University, Tokyo, Japan
- Center for Genomic and Regenerative Medicine, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Wado Akamatsu
- Center for Genomic and Regenerative Medicine, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Cornelis Blauwendraat
- Integrative Neurogenomics Unit, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- 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
| | - Nobutaka Hattori
- Department of Neurology, Juntendo University School of Medicine, Hongo, Tokyo, Japan
- Research Institute for Diseases of Old Age, Graduate School of Medicine, Juntendo University, Tokyo, Japan
- Neurodegenerative Disorders Collaborative Laboratory, RIKEN Center for Brain Science, Wako, Saitama, Japan
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11
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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 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] [What about the content of this article? (0)] [Affiliation(s)] [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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12
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Billingsley KJ, Ding J, Jerez PA, Illarionova A, Levine K, Grenn FP, Makarious MB, Moore A, Vitale D, Reed X, Hernandez D, Torkamani A, Ryten M, Hardy J, Chia R, Scholz SW, Traynor BJ, Dalgard CL, Ehrlich DJ, Tanaka T, Ferrucci L, Beach T, Serrano GE, Quinn JP, Bubb VJ, Collins RL, Zhao X, Walker M, Pierce-Hoffman E, Brand H, Talkowski ME, Casey B, Cookson MR, Markham A, Nalls MA, Mahmoud M, Sedlazeck FJ, Blauwendraat C, Gibbs JR, Singleton AB. Genome-Wide Analysis of Structural Variants in Parkinson Disease. Ann Neurol 2023; 93:1012-1022. [PMID: 36695634 PMCID: PMC10192042 DOI: 10.1002/ana.26608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 01/03/2023] [Accepted: 01/16/2023] [Indexed: 01/26/2023]
Abstract
OBJECTIVE Identification of genetic risk factors for Parkinson disease (PD) has to date been primarily limited to the study of single nucleotide variants, which only represent a small fraction of the genetic variation in the human genome. Consequently, causal variants for most PD risk are not known. Here we focused on structural variants (SVs), which represent a major source of genetic variation in the human genome. We aimed to discover SVs associated with PD risk by performing the first large-scale characterization of SVs in PD. METHODS We leveraged a recently developed computational pipeline to detect and genotype SVs from 7,772 Illumina short-read whole genome sequencing samples. Using this set of SV variants, we performed a genome-wide association study using 2,585 cases and 2,779 controls and identified SVs associated with PD risk. Furthermore, to validate the presence of these variants, we generated a subset of matched whole-genome long-read sequencing data. RESULTS We genotyped and tested 3,154 common SVs, representing over 412 million nucleotides of previously uncatalogued genetic variation. Using long-read sequencing data, we validated the presence of three novel deletion SVs that are associated with risk of PD from our initial association analysis, including a 2 kb intronic deletion within the gene LRRN4. INTERPRETATION We identified three SVs associated with genetic risk of PD. This study represents the most comprehensive assessment of the contribution of SVs to the genetic risk of PD to date. ANN NEUROL 2023;93:1012-1022.
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Affiliation(s)
- Kimberley J. Billingsley
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, Maryland, USA
- Center for Alzheimer’s and Related Dementias, National Institute on Aging, Bethesda, Maryland, USA
| | - Jinhui Ding
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, Maryland, USA
| | - Pilar Alvarez Jerez
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, Maryland, USA
- Center for Alzheimer’s and Related Dementias, National Institute on Aging, Bethesda, Maryland, USA
| | | | | | - Francis P. Grenn
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, Maryland, USA
| | - Mary B. Makarious
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, Maryland, USA
| | - Anni Moore
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, Maryland, USA
| | - Daniel Vitale
- Center for Alzheimer’s and Related Dementias, National Institute on Aging, Bethesda, Maryland, USA
- Data Tecnica International, Washington, DC, USA
| | - Xylena Reed
- Center for Alzheimer’s and Related Dementias, National Institute on Aging, Bethesda, Maryland, USA
| | - Dena Hernandez
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, Maryland, USA
| | - Ali Torkamani
- The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Mina Ryten
- NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, UK
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - John Hardy
- UK Dementia Research Institute and Department of Neurodegenerative Disease and Reta Lila Weston Institute, UCL Queen Square Institute of Neurology and UCL Movement Disorders Centre, University College London, London, UK
- Institute for Advanced Study, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | | | - Ruth Chia
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, Maryland, USA
| | - Sonja W. Scholz
- Neurodegenerative Diseases Research Unit, National Institute of Neurological Disorders and Stroke, Bethesda, Maryland, USA
- Department of Neurology, Johns Hopkins University Medical Center, Baltimore, Maryland, USA
| | - Bryan J. Traynor
- Department of Neurology, Johns Hopkins University Medical Center, Baltimore, Maryland, USA
- Neuromuscular Diseases Research Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA
- Therapeutic Development Branch, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
- National Institute of Neurological Disorders and Stroke, Bethesda, MD 20892
- Reta Lila Weston Institute, UCL Queen Square Institute of Neurology, University College London, London WC1N 1PJ, UK
| | - Clifton L. Dalgard
- Department of Anatomy Physiology & Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Debra J. Ehrlich
- Parkinson’s Disease Clinic, Office of the Clinical Director, National Institute of Neurological Disorders and Stroke, Bethesda, Maryland, USA
| | - Toshiko Tanaka
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Luigi Ferrucci
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Thomas.G. Beach
- Civin Laboratory for Neuropathology, Banner Sun Health Research Institute, Sun City, AZ
| | - Geidy E. Serrano
- Civin Laboratory for Neuropathology, Banner Sun Health Research Institute, Sun City, AZ
| | - John P. Quinn
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3BX, UK
| | - Vivien J. Bubb
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3BX, UK
| | - Ryan L Collins
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology (M.I.T) and Harvard USA Cambridge, MA 02142, USA
- Division of Medical Sciences and Department of Medicine, Harvard Medical School, Boston, MA 02115
| | - Xuefang Zhao
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology (M.I.T) and Harvard USA Cambridge, MA 02142, USA
| | - Mark Walker
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology (M.I.T) and Harvard USA Cambridge, MA 02142, USA
- Data Sciences Platform, Broad Institute of Massachusetts Institute of Technology (M.I.T) and Harvard USA Cambridge, MA 02142, USA
| | - Emma Pierce-Hoffman
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology (M.I.T) and Harvard USA Cambridge, MA 02142, USA
- Data Sciences Platform, Broad Institute of Massachusetts Institute of Technology (M.I.T) and Harvard USA Cambridge, MA 02142, USA
| | - Harrison Brand
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology (M.I.T) and Harvard USA Cambridge, MA 02142, USA
- Division of Medical Sciences and Department of Medicine, Harvard Medical School, Boston, MA 02115
| | - Michael E. Talkowski
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology (M.I.T) and Harvard USA Cambridge, MA 02142, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Bradford Casey
- The Michael J. Fox Foundation for Parkinson’s Research, New York, NY 10001
| | - Mark R Cookson
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, Maryland, USA
| | | | - Mike A. Nalls
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, Maryland, USA
- Center for Alzheimer’s and Related Dementias, National Institute on Aging, Bethesda, Maryland, USA
- Data Tecnica International, Washington, DC, USA
| | - Medhat Mahmoud
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030
- Department of Computer Science, Rice University, 6100 Main Street, Houston, TX, 77005, US
| | - Cornelis Blauwendraat
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, Maryland, USA
- Center for Alzheimer’s and Related Dementias, National Institute on Aging, Bethesda, Maryland, USA
| | - J. Raphael Gibbs
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, Maryland, USA
| | - Andrew B. Singleton
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, Maryland, USA
- Center for Alzheimer’s and Related Dementias, National Institute on Aging, Bethesda, Maryland, USA
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Alvarez Jerez P, Alcantud JL, de Los Reyes-Ramírez L, Moore A, Ruz C, Vives Montero F, Rodriguez-Losada N, Saini P, Gan-Or Z, Alvarado CX, Makarious MB, Billingsley KJ, Blauwendraat C, Noyce AJ, Singleton AB, Duran R, Bandres-Ciga S. Exploring the genetic and genomic connection underlying neurodegeneration with brain iron accumulation and the risk for Parkinson's disease. NPJ Parkinsons Dis 2023; 9:54. [PMID: 37024536 PMCID: PMC10079978 DOI: 10.1038/s41531-023-00496-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 03/16/2023] [Indexed: 04/08/2023] Open
Abstract
Neurodegeneration with brain iron accumulation (NBIA) represents a group of neurodegenerative disorders characterized by abnormal iron accumulation in the brain. In Parkinson's Disease (PD), iron accumulation is a cardinal feature of degenerating regions in the brain and seems to be a key player in mechanisms that precipitate cell death. The aim of this study was to explore the genetic and genomic connection between NBIA and PD. We screened for known and rare pathogenic mutations in autosomal dominant and recessive genes linked to NBIA in a total of 4481 PD cases and 10,253 controls from the Accelerating Medicines Partnership Parkinsons' Disease Program and the UKBiobank. We examined whether a genetic burden of NBIA variants contributes to PD risk through single-gene, gene-set, and single-variant association analyses. In addition, we assessed publicly available expression quantitative trait loci (eQTL) data through Summary-based Mendelian Randomization and conducted transcriptomic analyses in blood of 1886 PD cases and 1285 controls. Out of 29 previously reported NBIA screened coding variants, four were associated with PD risk at a nominal p value < 0.05. No enrichment of heterozygous variants in NBIA-related genes risk was identified in PD cases versus controls. Burden analyses did not reveal a cumulative effect of rare NBIA genetic variation on PD risk. Transcriptomic analyses suggested that DCAF17 is differentially expressed in blood from PD cases and controls. Due to low mutation occurrence in the datasets and lack of replication, our analyses suggest that NBIA and PD may be separate molecular entities.
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Affiliation(s)
- Pilar Alvarez Jerez
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- 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
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Jose Luis Alcantud
- Institute of Neurosciences "Federico Olóriz", Centro de Investigación Biomédica, Universidad de Granada, Granada, Spain
| | - Lucia de Los Reyes-Ramírez
- Laboratory of Neuropharmacology. Dept. Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Anni Moore
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Clara Ruz
- Institute of Neurosciences "Federico Olóriz", Centro de Investigación Biomédica, Universidad de Granada, Granada, Spain
| | - Francisco Vives Montero
- Institute of Neurosciences "Federico Olóriz", Centro de Investigación Biomédica, Universidad de Granada, Granada, Spain
| | - Noela Rodriguez-Losada
- Department Human Physiology, Faculty of Medicine, Biomedicine Research Institute of Malaga (IBIMA C07), University of Malaga, Malaga, Spain
| | - Prabhjyot Saini
- Montreal Neurological Institute, McGill University, Montréal, QC, Canada
- Department of Human Genetics, McGill University, Montréal, QC, Canada
| | - Ziv Gan-Or
- Montreal Neurological Institute, McGill University, Montréal, QC, Canada
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- Department of Neurology and Neurosurgery, McGill University, Montréal, QC, Canada
| | - 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
- Data Tecnica International, Washington, DC, USA
| | - Mary B Makarious
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
| | - Kimberley J Billingsley
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- 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
| | - Cornelis Blauwendraat
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- 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
| | - Alastair J Noyce
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
- Preventive Neurology Unit, Centre for Prevention, Detection and Diagnosis, Wolfson Institute of Population Health, Queen Mary University of London, London, UK
| | - Andrew B Singleton
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- 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
| | - Raquel Duran
- Institute of Neurosciences "Federico Olóriz", Centro de Investigación Biomédica, Universidad de Granada, Granada, Spain
| | - Sara Bandres-Ciga
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA.
- 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.
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14
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Kolmogorov M, Billingsley KJ, Mastoras M, Meredith M, Monlong J, Lorig-Roach R, Asri M, Jerez PA, Malik L, Dewan R, Reed X, Genner RM, Daida K, Behera S, Shafin K, Pesout T, Prabakaran J, Carnevali P, Yang J, Rhie A, Scholz SW, Traynor BJ, Miga KH, Jain M, Timp W, Phillippy AM, Chaisson M, Sedlazeck FJ, Blauwendraat C, Paten B. Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation. bioRxiv 2023:2023.01.12.523790. [PMID: 36711673 PMCID: PMC9882142 DOI: 10.1101/2023.01.12.523790] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Long-read sequencing technologies substantially overcome the limitations of short-reads but to date have not been considered as feasible replacement at scale due to a combination of being too expensive, not scalable enough, or too error-prone. Here, we develop an efficient and scalable wet lab and computational protocol for Oxford Nanopore Technologies (ONT) long-read sequencing that seeks to provide a genuine alternative to short-reads for large-scale genomics projects. We applied our protocol to cell lines and brain tissue samples as part of a pilot project for the NIH Center for Alzheimer's and Related Dementias (CARD). Using a single PromethION flow cell, we can detect SNPs with F1-score better than Illumina short-read sequencing. Small indel calling remains to be difficult inside homopolymers and tandem repeats, but is comparable to Illumina calls elsewhere. Further, we can discover structural variants with F1-score comparable to state-of the-art methods involving Pacific Biosciences HiFi sequencing and trio information (but at a lower cost and greater throughput). Using ONT based phasing, we can then combine and phase small and structural variants at megabase scales. Our protocol also produces highly accurate, haplotype-specific methylation calls. Overall, this makes large-scale long-read sequencing projects feasible; the protocol is currently being used to sequence thousands of brain-based genomes as a part of the NIH CARD initiative. We provide the protocol and software as open-source integrated pipelines for generating phased variant calls and assemblies.
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Affiliation(s)
- Mikhail Kolmogorov
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, USA
| | - Kimberley J. Billingsley
- Center for Alzheimer’s and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Mira Mastoras
- UC Santa Cruz Genomics Institute, Santa Cruz, CA, USA
| | | | - Jean Monlong
- UC Santa Cruz Genomics Institute, Santa Cruz, CA, USA
| | | | - Mobin Asri
- UC Santa Cruz Genomics Institute, Santa Cruz, CA, USA
| | - Pilar Alvarez Jerez
- Center for Alzheimer’s and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Laksh Malik
- Center for Alzheimer’s and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Ramita Dewan
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Xylena Reed
- Center for Alzheimer’s and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Rylee M. Genner
- Center for Alzheimer’s and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Kensuke Daida
- Center for Alzheimer’s and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Sairam Behera
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Kishwar Shafin
- Google LLC, 1600 Amphitheatre Pkwy, Mountain View, CA, USA
| | - Trevor Pesout
- UC Santa Cruz Genomics Institute, Santa Cruz, CA, USA
| | - Jeshuwin Prabakaran
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, USA
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD, USA
| | | | | | - Jianzhi Yang
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, USA
| | - Arang Rhie
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sonja W. Scholz
- Neurodegenerative Diseases Research Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, USA
- Department of Neurology, Johns Hopkins University Medical Center, Baltimore, MD, USA
| | - Bryan J. Traynor
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Karen H. Miga
- UC Santa Cruz Genomics Institute, Santa Cruz, CA, USA
| | - Miten Jain
- Department of Bioengineering, Department of Physics, Northeastern University, Boston, MA, USA
| | - Winston Timp
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Adam M. Phillippy
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mark Chaisson
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, USA
| | - Fritz J. Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Department of Computer Science, Rice University, Houston, Texas, USA
| | - Cornelis Blauwendraat
- Center for Alzheimer’s and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
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15
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Bressan E, Reed X, Bansal V, Hutchins E, Cobb MM, Webb MG, Alsop E, Grenn FP, Illarionova A, Savytska N, Violich I, Broeer S, Fernandes N, Sivakumar R, Beilina A, Billingsley KJ, Berghausen J, Pantazis CB, Pitz V, Patel D, Daida K, Meechoovet B, Reiman R, Courtright-Lim A, Logemann A, Antone J, Barch M, Kitchen R, Li Y, Dalgard CL, Rizzu P, Hernandez DG, Hjelm BE, Nalls M, Gibbs JR, Finkbeiner S, Cookson MR, Van Keuren-Jensen K, Craig DW, Singleton AB, Heutink P, Blauwendraat C. The Foundational Data Initiative for Parkinson Disease: Enabling efficient translation from genetic maps to mechanism. Cell Genom 2023; 3:100261. [PMID: 36950378 PMCID: PMC10025424 DOI: 10.1016/j.xgen.2023.100261] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 09/22/2022] [Accepted: 01/12/2023] [Indexed: 02/08/2023]
Abstract
The Foundational Data Initiative for Parkinson Disease (FOUNDIN-PD) is an international collaboration producing fundamental resources for Parkinson disease (PD). FOUNDIN-PD generated a multi-layered molecular dataset in a cohort of induced pluripotent stem cell (iPSC) lines differentiated to dopaminergic (DA) neurons, a major affected cell type in PD. The lines were derived from the Parkinson's Progression Markers Initiative study, which included participants with PD carrying monogenic PD variants, variants with intermediate effects, and variants identified by genome-wide association studies and unaffected individuals. We generated genetic, epigenetic, regulatory, transcriptomic, and longitudinal cellular imaging data from iPSC-derived DA neurons to understand molecular relationships between disease-associated genetic variation and proximate molecular events. These data reveal that iPSC-derived DA neurons provide a valuable cellular context and foundational atlas for modeling PD genetic risk. We have integrated these data into a FOUNDIN-PD data browser as a resource for understanding the molecular pathogenesis of PD.
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Affiliation(s)
| | - Xylena Reed
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- 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
| | - Vikas Bansal
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Elizabeth Hutchins
- Division of Neurogenomics, The Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Melanie M. Cobb
- Center for Systems and Therapeutics, Gladstone Institutes, San Francisco, CA, USA
| | - Michelle G. Webb
- Department of Translational Genomics, Keck School of Medicine, University of Southern California, 1450 Biggy Street, Los Angeles, CA, USA
| | - Eric Alsop
- Division of Neurogenomics, The Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Francis P. Grenn
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | | | - Natalia Savytska
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Ivo Violich
- Department of Translational Genomics, Keck School of Medicine, University of Southern California, 1450 Biggy Street, Los Angeles, CA, USA
| | - Stefanie Broeer
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Noémia Fernandes
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Ramiyapriya Sivakumar
- Department of Translational Genomics, Keck School of Medicine, University of Southern California, 1450 Biggy Street, Los Angeles, CA, USA
| | - Alexandra Beilina
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Kimberley J. Billingsley
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Joos Berghausen
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Caroline B. Pantazis
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- 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
| | - Vanessa Pitz
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Dhairya Patel
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Kensuke Daida
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Bessie Meechoovet
- Division of Neurogenomics, The Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Rebecca Reiman
- Division of Neurogenomics, The Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Amanda Courtright-Lim
- Division of Neurogenomics, The Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Amber Logemann
- Division of Neurogenomics, The Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Jerry Antone
- Division of Neurogenomics, The Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Mariya Barch
- Center for Systems and Therapeutics, Gladstone Institutes, San Francisco, CA, USA
| | - Robert Kitchen
- Massachusetts General Hospital, Cardiovascular Research Center, Charlestown, MA, USA
| | - Yan Li
- Protein/Peptide Sequencing Facility, National Institute of Neurological, Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Clifton L. Dalgard
- The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- Department of Anatomy, Physiology & Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - The American Genome Center
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- 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
- Division of Neurogenomics, The Translational Genomics Research Institute, Phoenix, AZ, USA
- Center for Systems and Therapeutics, Gladstone Institutes, San Francisco, CA, USA
- Department of Translational Genomics, Keck School of Medicine, University of Southern California, 1450 Biggy Street, Los Angeles, CA, USA
- Massachusetts General Hospital, Cardiovascular Research Center, Charlestown, MA, USA
- Protein/Peptide Sequencing Facility, National Institute of Neurological, Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- Department of Anatomy, Physiology & Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- Data Tecnica International, Washington, DC, USA
- Departments of Neurology and Physiology, University of California, San Francisco, San Francisco, CA, USA
| | - Patrizia Rizzu
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Dena G. Hernandez
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Brooke E. Hjelm
- Department of Translational Genomics, Keck School of Medicine, University of Southern California, 1450 Biggy Street, Los Angeles, CA, USA
| | - Mike Nalls
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- 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
- Data Tecnica International, Washington, DC, USA
| | - J. Raphael Gibbs
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Steven Finkbeiner
- Center for Systems and Therapeutics, Gladstone Institutes, San Francisco, CA, USA
- Departments of Neurology and Physiology, University of California, San Francisco, San Francisco, CA, USA
| | - Mark R. Cookson
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | | | - David W. Craig
- Department of Translational Genomics, Keck School of Medicine, University of Southern California, 1450 Biggy Street, Los Angeles, CA, USA
| | - Andrew B. Singleton
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- 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
| | - Peter Heutink
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Cornelis Blauwendraat
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- 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
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16
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Dadu A, Satone V, Kaur R, Hashemi SH, Leonard H, Iwaki H, Makarious MB, Billingsley KJ, Bandres‐Ciga S, Sargent LJ, Noyce AJ, Daneshmand A, Blauwendraat C, Marek K, Scholz SW, Singleton AB, Nalls MA, Campbell RH, Faghri F. Identification and prediction of Parkinson's disease subtypes and progression using machine learning in two cohorts. NPJ Parkinsons Dis 2022; 8:172. [PMID: 36526647 PMCID: PMC9758217 DOI: 10.1038/s41531-022-00439-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 11/29/2022] [Indexed: 12/23/2022] Open
Abstract
The clinical manifestations of Parkinson's disease (PD) are characterized by heterogeneity in age at onset, disease duration, rate of progression, and the constellation of motor versus non-motor features. There is an unmet need for the characterization of distinct disease subtypes as well as improved, individualized predictions of the disease course. We used unsupervised and supervised machine learning methods on comprehensive, longitudinal clinical data from the Parkinson's Disease Progression Marker Initiative (n = 294 cases) to identify patient subtypes and to predict disease progression. The resulting models were validated in an independent, clinically well-characterized cohort from the Parkinson's Disease Biomarker Program (n = 263 cases). Our analysis distinguished three distinct disease subtypes with highly predictable progression rates, corresponding to slow, moderate, and fast disease progression. We achieved highly accurate projections of disease progression 5 years after initial diagnosis with an average area under the curve (AUC) of 0.92 (95% CI: 0.95 ± 0.01) for the slower progressing group (PDvec1), 0.87 ± 0.03 for moderate progressors, and 0.95 ± 0.02 for the fast-progressing group (PDvec3). We identified serum neurofilament light as a significant indicator of fast disease progression among other key biomarkers of interest. We replicated these findings in an independent cohort, released the analytical code, and developed models in an open science manner. Our data-driven study provides insights to deconstruct PD heterogeneity. This approach could have immediate implications for clinical trials by improving the detection of significant clinical outcomes. We anticipate that machine learning models will improve patient counseling, clinical trial design, and ultimately individualized patient care.
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Affiliation(s)
- Anant Dadu
- grid.35403.310000 0004 1936 9991Department of Computer Science, University of Illinois at Urbana-Champaign, Champaign, IL 61820 USA ,grid.94365.3d0000 0001 2297 5165Center 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 20892 USA ,grid.511118.dData Tecnica International, Washington, DC 20812 USA
| | - Vipul Satone
- grid.35403.310000 0004 1936 9991Department of Industrial and Enterprise Systems Engineering, University of Illinois at Urbana-Champaign, Champaign, IL 61820 USA
| | - Rachneet Kaur
- grid.35403.310000 0004 1936 9991Department of Industrial and Enterprise Systems Engineering, University of Illinois at Urbana-Champaign, Champaign, IL 61820 USA
| | - Sayed Hadi Hashemi
- grid.35403.310000 0004 1936 9991Department of Computer Science, University of Illinois at Urbana-Champaign, Champaign, IL 61820 USA
| | - Hampton Leonard
- grid.94365.3d0000 0001 2297 5165Center 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 20892 USA ,grid.511118.dData Tecnica International, Washington, DC 20812 USA ,grid.94365.3d0000 0001 2297 5165Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892 USA
| | - Hirotaka Iwaki
- grid.94365.3d0000 0001 2297 5165Center 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 20892 USA ,grid.511118.dData Tecnica International, Washington, DC 20812 USA ,grid.94365.3d0000 0001 2297 5165Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892 USA
| | - Mary B. Makarious
- grid.94365.3d0000 0001 2297 5165Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892 USA ,grid.83440.3b0000000121901201Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK ,grid.83440.3b0000000121901201UCL Movement Disorders Centre, University College London, London, UK
| | - Kimberley J. Billingsley
- grid.94365.3d0000 0001 2297 5165Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892 USA
| | - Sara Bandres‐Ciga
- grid.94365.3d0000 0001 2297 5165Center 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 20892 USA ,grid.94365.3d0000 0001 2297 5165Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892 USA
| | - Lana J. Sargent
- grid.94365.3d0000 0001 2297 5165Center 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 20892 USA ,grid.224260.00000 0004 0458 8737School of Nursing, Virginia Commonwealth University, Richmond, VA 23298 USA
| | - Alastair J. Noyce
- grid.83440.3b0000000121901201UCL Movement Disorders Centre, University College London, London, UK ,grid.416041.60000 0001 0738 5466Preventive Neurology Unit, Wolfson Institute of Preventive Medicine, Queen Mary University of London and Department of Neurology, Royal London Hospital, London, UK
| | - Ali Daneshmand
- grid.189504.10000 0004 1936 7558Department of Neurology, Boston Medical Center, Boston University School of Medicine, Boston, MA 02118 USA
| | - Cornelis Blauwendraat
- grid.94365.3d0000 0001 2297 5165Center 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 20892 USA ,grid.94365.3d0000 0001 2297 5165Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892 USA
| | - Ken Marek
- grid.452597.8InviCRO LLC, Boston, MA USA ,grid.452597.8Molecular Neuroimaging, A Division of InviCRO, New Haven, CT USA
| | - Sonja W. Scholz
- grid.416870.c0000 0001 2177 357XNeurodegenerative Diseases Research Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD USA ,grid.21107.350000 0001 2171 9311Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Andrew B. Singleton
- grid.94365.3d0000 0001 2297 5165Center 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 20892 USA ,grid.94365.3d0000 0001 2297 5165Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892 USA
| | - Mike A. Nalls
- grid.94365.3d0000 0001 2297 5165Center 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 20892 USA ,grid.511118.dData Tecnica International, Washington, DC 20812 USA ,grid.94365.3d0000 0001 2297 5165Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892 USA
| | - Roy H. Campbell
- grid.35403.310000 0004 1936 9991Department of Computer Science, University of Illinois at Urbana-Champaign, Champaign, IL 61820 USA
| | - Faraz Faghri
- grid.94365.3d0000 0001 2297 5165Center 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 20892 USA ,grid.511118.dData Tecnica International, Washington, DC 20812 USA ,grid.94365.3d0000 0001 2297 5165Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892 USA
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17
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Billingsley KJ, Alvarez Jerez P, Grenn FP, Bandres-Ciga S, Malik L, Hernandez D, Torkamani A, Ryten M, Hardy J, Scholz SW, Traynor BJ, Dalgard CL, Ehrlich DJ, Tanaka T, Ferrucci L, Beach TG, Serrano GE, Ding J, Gibbs JR, Blauwendraat C, Singleton AB. Profiling the NOTCH2NLC GGC Repeat Expansion in Parkinson's Disease in the European Population. Mov Disord 2022; 37:2161-2162. [PMID: 35866887 DOI: 10.1002/mds.29155] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 05/25/2022] [Accepted: 06/13/2022] [Indexed: 11/11/2022] Open
Affiliation(s)
- Kimberley J Billingsley
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, Maryland, USA
- Center for Alzheimer's and Related Dementias, National Institute on Aging, Bethesda, Maryland, USA
| | - Pilar Alvarez Jerez
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, Maryland, USA
- Center for Alzheimer's and Related Dementias, National Institute on Aging, Bethesda, Maryland, USA
| | - Francis P Grenn
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, Maryland, USA
| | - Sara Bandres-Ciga
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, Maryland, USA
- Center for Alzheimer's and Related Dementias, National Institute on Aging, Bethesda, Maryland, USA
| | - Laksh Malik
- Center for Alzheimer's and Related Dementias, National Institute on Aging, Bethesda, Maryland, USA
| | - Dena Hernandez
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, Maryland, USA
| | - Ali Torkamani
- The Scripps Research Institute, La Jolla, California, USA
| | - Mina Ryten
- NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, United Kingdom
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - John Hardy
- UK Dementia Research Institute and Department of Neurodegenerative Disease and Reta Lila Weston Institute, UCL Queen Square Institute of Neurology and UCL Movement Disorders Centre, University College London, London, United Kingdom
- Institute for Advanced Study, The Hong Kong University of Science and Technology, Hong Kong, SAR, China
| | | | - Sonja W Scholz
- Neurodegenerative Diseases Research Unit, National Institute of Neurological Disorders and Stroke, Bethesda, Maryland, USA
- Department of Neurology, Johns Hopkins University Medical Center, Baltimore, Maryland, USA
| | - Bryan J Traynor
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, Maryland, USA
- Department of Neurology, Johns Hopkins University Medical Center, Baltimore, Maryland, USA
| | - Clifton L Dalgard
- Department of Anatomy Physiology and Genetics, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
- The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Debra J Ehrlich
- Parkinson's Disease Clinic, Office of the Clinical Director, National Institute of Neurological Disorders and Stroke, Bethesda, Maryland, USA
| | - Toshiko Tanaka
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, Maryland, USA
| | - Luigi Ferrucci
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, Maryland, USA
| | - Thomas G Beach
- Parkinson's Disease Clinic, Office of the Clinical Director, National Institute of Neurological Disorders and Stroke, Bethesda, Maryland, USA
| | - Geidy E Serrano
- Civin Laboratory for Neuropathology, Banner Sun Health Research Institute, Sun City, Arizona, USA
| | - Jinhui Ding
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, Maryland, USA
| | - J Raphael Gibbs
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, Maryland, USA
| | - Cornelis Blauwendraat
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, Maryland, USA
- Center for Alzheimer's and Related Dementias, National Institute on Aging, Bethesda, Maryland, USA
| | - Andrew B Singleton
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, Maryland, USA
- Center for Alzheimer's and Related Dementias, National Institute on Aging, Bethesda, Maryland, USA
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18
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Hall A, Quinn JP, Billingsley KJ. Letter to the editor regarding "TGM6 variants in Parkinson's disease: clinical findings and functional evidence". J Integr Neurosci 2020; 19:735-737. [PMID: 33378849 DOI: 10.31083/j.jin.2020.04.261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/19/2020] [Accepted: 10/19/2020] [Indexed: 11/06/2022] Open
Abstract
No abstract present.
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Affiliation(s)
- Ashley Hall
- Neurobiology Research Group, Molecular and Clinical Pharmacology, Institute of Systems, Molecular & Integrative Biology, University of Liverpool, Liverpool, L69 3BX, United Kingdom
| | - John P Quinn
- Neurobiology Research Group, Molecular and Clinical Pharmacology, Institute of Systems, Molecular & Integrative Biology, University of Liverpool, Liverpool, L69 3BX, United Kingdom
| | - Kimberley J Billingsley
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA
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19
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Hall A, Bandres-Ciga S, Diez-Fairen M, Quinn JP, Billingsley KJ. Genetic Risk Profiling in Parkinson's Disease and Utilizing Genetics to Gain Insight into Disease-Related Biological Pathways. Int J Mol Sci 2020; 21:E7332. [PMID: 33020390 PMCID: PMC7584037 DOI: 10.3390/ijms21197332] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 09/30/2020] [Accepted: 10/01/2020] [Indexed: 12/18/2022] Open
Abstract
Parkinson's disease (PD) is a complex disorder underpinned by both environmental and genetic factors. The latter only began to be understood around two decades ago, but since then great inroads have rapidly been made into deconvoluting the genetic component of PD. In particular, recent large-scale projects such as genome-wide association (GWA) studies have provided insight into the genetic risk factors associated with genetically ''complex'' PD (PD that cannot readily be attributed to single deleterious mutations). Here, we discuss the plethora of genetic information provided by PD GWA studies and how this may be utilized to generate polygenic risk scores (PRS), which may be used in the prediction of risk and trajectory of PD. We also comment on how pathway-specific genetic profiling can be used to gain insight into PD-related biological pathways, and how this may be further utilized to nominate causal PD genes and potentially druggable therapeutic targets. Finally, we outline the current limits of our understanding of PD genetics and the potential contribution of variation currently uncaptured in genetic studies, focusing here on uncatalogued structural variants.
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Affiliation(s)
- Ashley Hall
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular & Integrative Biology, University of Liverpool, L69 7BE, UK; (A.H.); (J.P.Q.)
| | - Sara Bandres-Ciga
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA;
| | - Monica Diez-Fairen
- Neurogenetics Group, University Hospital MutuaTerrassa, Sant Antoni 19, 08221 Terrassa, Barcelona, Spain;
| | - John P. Quinn
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular & Integrative Biology, University of Liverpool, L69 7BE, UK; (A.H.); (J.P.Q.)
| | - Kimberley J. Billingsley
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA;
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20
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Billingsley KJ, Bandres-Ciga S, Ding J, Hernandez D, Gibbs JR, Blauwendraat C. MIDN locus structural variants and Parkinson's Disease risk. Ann Clin Transl Neurol 2020; 7:602-603. [PMID: 32212230 PMCID: PMC7187709 DOI: 10.1002/acn3.51012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 02/21/2020] [Indexed: 01/24/2023] Open
Affiliation(s)
- Kimberley J Billingsley
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, 35 Convent Drive, Bethesda, 20892, Maryland, United states
| | - Sara Bandres-Ciga
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, 35 Convent Drive, Bethesda, 20892, Maryland, United states
| | - Jinhui Ding
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, 35 Convent Drive, Bethesda, 20892, Maryland, United states
| | - Dena Hernandez
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, 35 Convent Drive, Bethesda, 20892, Maryland, United states
| | - J Raphael Gibbs
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, 35 Convent Drive, Bethesda, 20892, Maryland, United states
| | - Cornelis Blauwendraat
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, 35 Convent Drive, Bethesda, 20892, Maryland, United states
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21
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Gianfrancesco O, Geary B, Savage AL, Billingsley KJ, Bubb VJ, Quinn JP. The Role of SINE-VNTR-Alu (SVA) Retrotransposons in Shaping the Human Genome. Int J Mol Sci 2019; 20:ijms20235977. [PMID: 31783611 PMCID: PMC6928650 DOI: 10.3390/ijms20235977] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 11/16/2019] [Accepted: 11/17/2019] [Indexed: 12/29/2022] Open
Abstract
Retrotransposons can alter the regulation of genes both transcriptionally and post-transcriptionally, through mechanisms such as binding transcription factors and alternative splicing of transcripts. SINE-VNTR-Alu (SVA) retrotransposons are the most recently evolved class of retrotransposable elements, found solely in primates, including humans. SVAs are preferentially found at genic, high GC loci, and have been termed "mobile CpG islands". We hypothesise that the ability of SVAs to mobilise, and their non-random distribution across the genome, may result in differential regulation of certain pathways. We analysed SVA distribution patterns across the human reference genome and identified over-representation of SVAs at zinc finger gene clusters. Zinc finger proteins are able to bind to and repress SVA function through transcriptional and epigenetic mechanisms, and the interplay between SVAs and zinc fingers has been proposed as a major feature of genome evolution. We describe observations relating to the clustering patterns of both reference SVAs and polymorphic SVA insertions at zinc finger gene loci, suggesting that the evolution of this network may be ongoing in humans. Further, we propose a mechanism to direct future research and validation efforts, in which the interplay between zinc fingers and their epigenetic modulation of SVAs may regulate a network of zinc finger genes, with the potential for wider transcriptional consequences.
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Affiliation(s)
- Olympia Gianfrancesco
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool L69 3GE, UK; (O.G.); (A.L.S.); (K.J.B.); (V.J.B.)
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Bethany Geary
- Division of Molecular and Clinical Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK;
| | - Abigail L. Savage
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool L69 3GE, UK; (O.G.); (A.L.S.); (K.J.B.); (V.J.B.)
| | - Kimberley J. Billingsley
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool L69 3GE, UK; (O.G.); (A.L.S.); (K.J.B.); (V.J.B.)
| | - Vivien J. Bubb
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool L69 3GE, UK; (O.G.); (A.L.S.); (K.J.B.); (V.J.B.)
| | - John P. Quinn
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool L69 3GE, UK; (O.G.); (A.L.S.); (K.J.B.); (V.J.B.)
- Correspondence:
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22
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Billingsley KJ, Barbosa IA, Bandrés-Ciga S, Quinn JP, Bubb VJ, Deshpande C, Botia JA, Reynolds RH, Zhang D, Simpson MA, Blauwendraat C, Gan-Or Z, Gibbs JR, Nalls MA, Singleton A, Ryten M, Koks S. Mitochondria function associated genes contribute to Parkinson's Disease risk and later age at onset. NPJ Parkinsons Dis 2019; 5:8. [PMID: 31123700 PMCID: PMC6531455 DOI: 10.1038/s41531-019-0080-x] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 04/15/2019] [Indexed: 02/06/2023] Open
Abstract
Mitochondrial dysfunction has been implicated in the etiology of monogenic Parkinson's disease (PD). Yet the role that mitochondrial processes play in the most common form of the disease; sporadic PD, is yet to be fully established. Here, we comprehensively assessed the role of mitochondrial function-associated genes in sporadic PD by leveraging improvements in the scale and analysis of PD GWAS data with recent advances in our understanding of the genetics of mitochondrial disease. We calculated a mitochondrial-specific polygenic risk score (PRS) and showed that cumulative small effect variants within both our primary and secondary gene lists are significantly associated with increased PD risk. We further reported that the PRS of the secondary mitochondrial gene list was significantly associated with later age at onset. Finally, to identify possible functional genomic associations we implemented Mendelian randomization, which showed that 14 of these mitochondrial function-associated genes showed functional consequence associated with PD risk. Further analysis suggested that the 14 identified genes are not only involved in mitophagy, but implicate new mitochondrial processes. Our data suggests that therapeutics targeting mitochondrial bioenergetics and proteostasis pathways distinct from mitophagy could be beneficial to treating the early stage of PD.
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Affiliation(s)
- Kimberley J. Billingsley
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, , University of Liverpool, Liverpool, UK
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892 USA
| | - Ines A. Barbosa
- Department of Medical and Molecular Genetics, King’s College London School of Basic and Medical Biosciences, London, SE1 9RT UK
| | - Sara Bandrés-Ciga
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892 USA
| | - John P. Quinn
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, , University of Liverpool, Liverpool, UK
| | - Vivien J. Bubb
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, , University of Liverpool, Liverpool, UK
| | - Charu Deshpande
- Clinical Genetics Unit, Guys and St. Thomas’ NHS Foundation Trust, London, SE1 9RT UK
| | - Juan A. Botia
- Departamento de Ingeniería de la Información y las Comunicaciones, Universidad de Murcia, 30100 Murcia, Spain
- Department of Neurodegenerative Disease, UCL Institute of Neurology, 10-12 Russell Square House, London, UK
| | - Regina H. Reynolds
- Department of Neurodegenerative Disease, UCL Institute of Neurology, 10-12 Russell Square House, London, UK
| | - David Zhang
- Department of Neurodegenerative Disease, UCL Institute of Neurology, 10-12 Russell Square House, London, UK
| | - Michael A. Simpson
- Department of Medical and Molecular Genetics, King’s College London School of Basic and Medical Biosciences, London, SE1 9RT UK
| | - Cornelis Blauwendraat
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892 USA
| | - Ziv Gan-Or
- Montreal Neurological Institute, McGill University, Montréal, QC Canada
- Department of Neurology and Neurosurgery, McGill University, Montréal, QC Canada
- Department of Human Genetics, McGill University, Montréal, QC Canada
| | - J. Raphael Gibbs
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892 USA
| | - Mike A. Nalls
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892 USA
- Data Tecnica International, Glen Echo, MD 20812 USA
| | - Andrew Singleton
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892 USA
| | - Mina Ryten
- Department of Neurodegenerative Disease, UCL Institute of Neurology, 10-12 Russell Square House, London, UK
| | - Sulev Koks
- The Perron Institute for Neurological and Translational Science, 8 Verdun Street, Nedlands, WA 6009 Australia
- Centre for Comparative Genomics, Murdoch University, Murdoch, 6150 Australia
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23
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Billingsley KJ, Manca M, Gianfrancesco O, Collier DA, Sharp H, Bubb VJ, Quinn JP. Regulatory characterisation of the schizophrenia-associated CACNA1C proximal promoter and the potential role for the transcription factor EZH2 in schizophrenia aetiology. Schizophr Res 2018; 199:168-175. [PMID: 29501388 PMCID: PMC6179964 DOI: 10.1016/j.schres.2018.02.036] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Revised: 12/05/2017] [Accepted: 02/19/2018] [Indexed: 12/13/2022]
Abstract
Genomic wide association studies identified the CACNA1C locus as genetically associated with both schizophrenia and bipolar affective disorder. CACNA1C encodes Cav1.2, one of four subunits of L-type voltage gated calcium channels. Variation resides in non-coding regions of CACNA1C which interact with the promoter and are validated expression quantitative trait loci. Using reporter gene constructs we demonstrate the CACNA1C promoter is a major mediator of inducible regulation of CACNA1C activity in the SH-SY5Y neuroblastoma cell line. Exposure of SH-SY5Y cells to lithium and cocaine modulated both the endogenous CACNA1C gene and the promoter in reporter gene constructs. Deletion analysis of the promoter demonstrated the actions of both lithium and cocaine were mediated by the proximal promoter. Initial interrogation of ENCODE ChIP-seq data over the CACNA1C promoter indicated binding of the transcription factor 'Enhancer of zeste homolog 2' (EZH2), which was consistent with our data that overexpression of EZH2 repressed CACNA1C promoter reporter gene expression. Array data from the Human Brain Transcriptome demonstrated that EZH2 was highly expressed across the developing brain, but subsequently maintained at low levels after birth and adulthood. RNA-seq data obtained from PD_NGSAtlas, a reference database for epigenomic and transcriptomic data for psychiatric disorders, demonstrated a 3-fold increase in EZH2 expression in the anterior cingulate cortex of individuals with schizophrenia compared to controls. We propose that EZH2 may contribute to schizophrenia risk at two distinct time points either through disruption in development leading to neurodevelopmental changes, or through anomalous reactivation of expression in the adult brain.
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Affiliation(s)
- Kimberley J Billingsley
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool L69 3BX, UK
| | - Maurizio Manca
- Institute of Psychology, Health and Society, University of Liverpool, Liverpool, UK
| | - Olympia Gianfrancesco
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool L69 3BX, UK
| | | | - Helen Sharp
- Institute of Psychology, Health and Society, University of Liverpool, Liverpool, UK
| | - Vivien J Bubb
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool L69 3BX, UK
| | - John P Quinn
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool L69 3BX, UK.
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24
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Abstract
Over the last two decades, we have witnessed a revolution in the field of Parkinson's disease (PD) genetics. Great advances have been made in identifying many loci that confer a risk for PD, which has subsequently led to an improved understanding of the molecular pathways involved in disease pathogenesis. Despite this success, it is predicted that only a relatively small proportion of the phenotypic variability has been explained by genetics. Therefore, it is clear that common heritable components of disease are still to be identified. Dissecting the genetic architecture of PD constitutes a critical effort in identifying therapeutic targets and although such substantial progress has helped us to better understand disease mechanism, the route to PD disease-modifying drugs is a lengthy one. In this review, we give an overview of the known genetic risk factors in PD, focusing not on individual variants but the larger networks that have been implicated following comprehensive pathway analysis. We outline the challenges faced in the translation of risk loci to pathobiological relevance and illustrate the need for integrating big-data by noting success in recent work which adopts a broad-scale screening approach. Lastly, with PD genetics now progressing from identifying risk to predicting disease, we review how these models will likely have a significant impact in the future.
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Affiliation(s)
- K J Billingsley
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, 35 Convent Drive, Bethesda, MD, 20892, USA
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, University of Liverpool, L69 3BX, Liverpool, UK
| | - S Bandres-Ciga
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, 35 Convent Drive, Bethesda, MD, 20892, USA
| | - S Saez-Atienzar
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, 35 Convent Drive, Bethesda, MD, 20892, USA
| | - A B Singleton
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, 35 Convent Drive, Bethesda, MD, 20892, USA.
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