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Cheng PL, Wang H, Dombroski BA, Farrell JJ, Horng I, Chung T, Tosto G, Kunkle BW, Bush WS, Vardarajan B, Schellenberg GD, Lee WP. A Specialized Reference Panel with Structural Variants Integration for Improving Genotype Imputation in Alzheimer's Disease and Related Dementias (ADRD). MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.07.22.24310827. [PMID: 39108532 PMCID: PMC11302603 DOI: 10.1101/2024.07.22.24310827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 08/12/2024]
Abstract
We developed an imputation panel for Alzheimer's disease (AD) and related dementias (ADRD) using whole-genome sequencing (WGS) data from the Alzheimer's Disease Sequencing Project (ADSP). Recognizing the significant associations between structural variants (SVs) and AD, and their underrepresentation in existing public reference panels, our panel uniquely integrates single nucleotide variants (SNVs), short insertions and deletions (indels), and SVs. This panel enhances the imputation of disease susceptibility, including rare AD-associated SNVs, indels, and SVs, onto genotype array data, offering a cost-effective alternative to whole-genome sequencing while significantly augmenting statistical power. Notably, we discovered 10 rare indels nominal significant related to AD that are absent in the TOPMed-r2 panel and identified three suggestive significant (p-value < 1E-05) AD-associated SVs in the genes EXOC3L2 and DMPK, were identified. These findings provide new insights into AD genetics and underscore the critical role of imputation panels in advancing our understanding of complex diseases like ADRD.
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Affiliation(s)
- Po-Liang Cheng
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Hui Wang
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Beth A Dombroski
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - John J Farrell
- Biomedical Genetics, Department of Medicine, Boston University Medical School, Boston, MA, USA
| | - Iris Horng
- Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Tingting Chung
- Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Giuseppe Tosto
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, NY 10032, USA
- Department of Neurology, College of Physicians and Surgeons, Columbia University and the New York Presbyterian Hospital, NY 10032, USA
| | - Brian W Kunkle
- John P Hussman Institute for Human Genomics, Miami, FL, USA
- John T Macdonald Department of Human Genetics, Miami, FL, USA
| | - William S Bush
- Cleveland Institute for Computational Biology, Cleveland, OH, USA
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Badri Vardarajan
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, NY 10032, USA
- Department of Neurology, College of Physicians and Surgeons, Columbia University and the New York Presbyterian Hospital, NY 10032, USA
| | - Gerard D Schellenberg
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Wan-Ping Lee
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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De Serres-Bérard T, Ait Benichou S, Jauvin D, Boutjdir M, Puymirat J, Chahine M. Recent Progress and Challenges in the Development of Antisense Therapies for Myotonic Dystrophy Type 1. Int J Mol Sci 2022; 23:13359. [PMID: 36362145 PMCID: PMC9657934 DOI: 10.3390/ijms232113359] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 10/20/2022] [Accepted: 10/25/2022] [Indexed: 08/01/2023] Open
Abstract
Myotonic dystrophy type 1 (DM1) is a dominant genetic disease in which the expansion of long CTG trinucleotides in the 3' UTR of the myotonic dystrophy protein kinase (DMPK) gene results in toxic RNA gain-of-function and gene mis-splicing affecting mainly the muscles, the heart, and the brain. The CUG-expanded transcripts are a suitable target for the development of antisense oligonucleotide (ASO) therapies. Various chemical modifications of the sugar-phosphate backbone have been reported to significantly enhance the affinity of ASOs for RNA and their resistance to nucleases, making it possible to reverse DM1-like symptoms following systemic administration in different transgenic mouse models. However, specific tissue delivery remains to be improved to achieve significant clinical outcomes in humans. Several strategies, including ASO conjugation to cell-penetrating peptides, fatty acids, or monoclonal antibodies, have recently been shown to improve potency in muscle and cardiac tissues in mice. Moreover, intrathecal administration of ASOs may be an advantageous complementary administration route to bypass the blood-brain barrier and correct defects of the central nervous system in DM1. This review describes the evolution of the chemical design of antisense oligonucleotides targeting CUG-expanded mRNAs and how recent advances in the field may be game-changing by forwarding laboratory findings into clinical research and treatments for DM1 and other microsatellite diseases.
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Affiliation(s)
- Thiéry De Serres-Bérard
- CERVO Research Center, Institut Universitaire en Santé Mentale de Québec, Quebec City, QC G1J 2G3, Canada
| | - Siham Ait Benichou
- LOEX, CHU de Québec-Université Laval Research Center, Quebec City, QC G1J 1Z4, Canada
| | - Dominic Jauvin
- CERVO Research Center, Institut Universitaire en Santé Mentale de Québec, Quebec City, QC G1J 2G3, Canada
| | - Mohamed Boutjdir
- Cardiovascular Research Program, VA New York Harbor Healthcare System, New York, NY 11209, USA
- Department of Medicine, Cell Biology and Pharmacology, State University of New York Downstate Health Science University, New York, NY 11203, USA
- Department of Medicine, NYU School of Medicine, New York, NY 10016, USA
| | - Jack Puymirat
- LOEX, CHU de Québec-Université Laval Research Center, Quebec City, QC G1J 1Z4, Canada
- Department of Medicine, Faculty of Medicine, Université Laval, Quebec City, QC G1V 0A6, Canada
| | - Mohamed Chahine
- CERVO Research Center, Institut Universitaire en Santé Mentale de Québec, Quebec City, QC G1J 2G3, Canada
- Department of Medicine, Faculty of Medicine, Université Laval, Quebec City, QC G1V 0A6, Canada
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De Serres-Bérard T, Pierre M, Chahine M, Puymirat J. Deciphering the mechanisms underlying brain alterations and cognitive impairment in congenital myotonic dystrophy. Neurobiol Dis 2021; 160:105532. [PMID: 34655747 DOI: 10.1016/j.nbd.2021.105532] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/24/2021] [Accepted: 10/11/2021] [Indexed: 12/13/2022] Open
Abstract
Myotonic dystrophy type 1 (DM1) is a multisystemic and heterogeneous disorder caused by the expansion of CTG repeats in the 3' UTR of the myotonic dystrophy protein kinase (DMPK) gene. There is a congenital form (CDM1) of the disease characterized by severe hypotonia, respiratory insufficiency as well as developmental delays and intellectual disabilities. CDM1 infants manifest important brain structure abnormalities present from birth while, in contrast, older patients with adult-onset DM1 often present neurodegenerative features and milder progressive cognitive deficits. Promising therapies targeting central molecular mechanisms contributing to the symptoms of adult-onset DM1 are currently in development, but their relevance for treating cognitive impairment in CDM1, which seems to be a partially distinct neurodevelopmental disorder, remain to be elucidated. Here, we provide an update on the clinical presentation of CDM1 and review recent in vitro and in vivo models that have provided meaningful insights on its consequences in development, with a particular focus on the brain. We discuss how enhanced toxic gain-of-function of the mutated DMPK transcripts with larger CUG repeats and the resulting dysregulation of RNA-binding proteins may affect the developing cortex in utero. Because the methylation of CpG islets flanking the trinucleotide repeats has emerged as a strong biomarker of CDM1, we highlight the need to investigate the tissue-specific impacts of these chromatin modifications in the brain. Finally, we outline promising potential therapeutic treatments for CDM1 and propose future in vitro and in vivo models with great potential to shed light on this disease.
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Affiliation(s)
- Thiéry De Serres-Bérard
- LOEX, CHU de Québec-Université Laval Research Center, Quebec City, Canada; CERVO Brain Research Center, Institut universitaire en santé mentale de Québec, Quebec City, Canada
| | - Marion Pierre
- CERVO Brain Research Center, Institut universitaire en santé mentale de Québec, Quebec City, Canada
| | - Mohamed Chahine
- CERVO Brain Research Center, Institut universitaire en santé mentale de Québec, Quebec City, Canada; Department of Medicine, Faculty of Medicine, Université Laval, Quebec City, Canada.
| | - Jack Puymirat
- LOEX, CHU de Québec-Université Laval Research Center, Quebec City, Canada; Department of Medicine, Faculty of Medicine, Université Laval, Quebec City, Canada
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