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Pedicone C, Weitzman SA, Renton AE, Goate AM. Unraveling the complex role of MAPT-containing H1 and H2 haplotypes in neurodegenerative diseases. Mol Neurodegener 2024; 19:43. [PMID: 38812061 PMCID: PMC11138017 DOI: 10.1186/s13024-024-00731-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Accepted: 05/11/2024] [Indexed: 05/31/2024] Open
Abstract
A ~ 1 Mb inversion polymorphism exists within the 17q21.31 locus of the human genome as direct (H1) and inverted (H2) haplotype clades. This inversion region demonstrates high linkage disequilibrium, but the frequency of each haplotype differs across ancestries. While the H1 haplotype exists in all populations and shows a normal pattern of genetic variability and recombination, the H2 haplotype is enriched in European ancestry populations, is less frequent in African ancestry populations, and nearly absent in East Asian ancestry populations. H1 is a known risk factor for several neurodegenerative diseases, and has been associated with many other traits, suggesting its importance in cellular phenotypes of the brain and entire body. Conversely, H2 is protective for these diseases, but is associated with predisposition to recurrent microdeletion syndromes and neurodevelopmental disorders such as autism. Many single nucleotide variants and copy number variants define H1/H2 haplotypes and sub-haplotypes, but identifying the causal variant(s) for specific diseases and phenotypes is complex due to the extended linkage equilibrium. In this review, we assess the current knowledge of this inversion region regarding genomic structure, gene expression, cellular phenotypes, and disease association. We discuss recent discoveries and challenges, evaluate gaps in knowledge, and highlight the importance of understanding the effect of the 17q21.31 haplotypes to promote advances in precision medicine and drug discovery for several diseases.
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Affiliation(s)
- Chiara Pedicone
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sarah A Weitzman
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alan E Renton
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alison M Goate
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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Awamleh Z, Choufani S, Wu W, Rots D, Dingemans AJM, Nadif Kasri N, Boronat S, Ibañez-Mico S, Cuesta Herraiz L, Ferrer I, Martínez Carrascal A, Pérez-Jurado LA, Aznar Lain G, Ortigoza-Escobar JD, de Vries BBA, Koolen DA, Weksberg R. A new blood DNA methylation signature for Koolen-de Vries syndrome: Classification of missense KANSL1 variants and comparison to fibroblast cells. Eur J Hum Genet 2024; 32:324-332. [PMID: 38282074 PMCID: PMC10923882 DOI: 10.1038/s41431-024-01538-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 12/27/2023] [Accepted: 01/09/2024] [Indexed: 01/30/2024] Open
Abstract
Pathogenic variants in KANSL1 and 17q21.31 microdeletions are causative of Koolen-de Vries syndrome (KdVS), a neurodevelopmental syndrome with characteristic facial dysmorphia. Our previous work has shown that syndromic conditions caused by pathogenic variants in epigenetic regulatory genes have identifiable patterns of DNA methylation (DNAm) change: DNAm signatures or episignatures. Given the role of KANSL1 in histone acetylation, we tested whether variants underlying KdVS are associated with a DNAm signature. We profiled whole-blood DNAm for 13 individuals with KANSL1 variants, four individuals with 17q21.31 microdeletions, and 21 typically developing individuals, using Illumina's Infinium EPIC array. In this study, we identified a robust DNAm signature of 456 significant CpG sites in 8 individuals with KdVS, a pattern independently validated in an additional 7 individuals with KdVS. We also demonstrate the diagnostic utility of the signature and classify two KANSL1 VUS as well as four variants in individuals with atypical clinical presentation. Lastly, we investigated tissue-specific DNAm changes in fibroblast cells from individuals with KdVS. Collectively, our findings contribute to the understanding of the epigenetic landscape related to KdVS and aid in the diagnosis and classification of variants in this structurally complex genomic region.
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Affiliation(s)
- Zain Awamleh
- Genetics and Genome Biology Program, Research Institute, the Hospital for Sick Children, Toronto, ON, M5G 1×8, Canada
| | - Sanaa Choufani
- Genetics and Genome Biology Program, Research Institute, the Hospital for Sick Children, Toronto, ON, M5G 1×8, Canada
| | - Wendy Wu
- Genetics and Genome Biology Program, Research Institute, the Hospital for Sick Children, Toronto, ON, M5G 1×8, Canada
| | - Dmitrijs Rots
- Department of Human Genetics, Radboud university medical center, Donders Institute for Brain, Cognition, and Behavior, Nijmegen, The Netherlands
| | - Alexander J M Dingemans
- Department of Human Genetics, Radboud university medical center, Donders Institute for Brain, Cognition, and Behavior, Nijmegen, The Netherlands
| | - Nael Nadif Kasri
- Department of Human Genetics, Radboud university medical center, Donders Institute for Brain, Cognition, and Behavior, Nijmegen, The Netherlands
| | - Susana Boronat
- Department of Pediatrics, Hospital del Santa Creu y Sant Pau, Barcelona, Spain
| | - Salvador Ibañez-Mico
- Department of Pediatric Neurology, Hospital Virgen de la Arrixaca, Murcia, Madrid, Spain
| | | | - Irene Ferrer
- Department of Genetics, Consorcio Hospital General de Valencia, Valencia, Spain
| | | | - Luis A Pérez-Jurado
- Genetics Unit, Universitat Pompeu Fabra, Hospital del Mar Research Institute (IMIM) and CIBERER, Barcelona, Spain
| | - Gemma Aznar Lain
- Genetics Unit, Universitat Pompeu Fabra, Hospital del Mar Research Institute (IMIM) and CIBERER, Barcelona, Spain
| | - Juan Dario Ortigoza-Escobar
- Movement Disorders Unit, Institut de Recerca Sant Joan de Déu, CIBERER-ISCIII and European Reference Network for Rare Neurological Diseases (ERN-RND), Barcelona, Spain
| | - Bert B A de Vries
- Department of Human Genetics, Radboud university medical center, Donders Institute for Brain, Cognition, and Behavior, Nijmegen, The Netherlands
| | - David A Koolen
- Department of Human Genetics, Radboud university medical center, Donders Institute for Brain, Cognition, and Behavior, Nijmegen, The Netherlands.
| | - Rosanna Weksberg
- Genetics and Genome Biology Program, Research Institute, the Hospital for Sick Children, Toronto, ON, M5G 1×8, Canada.
- Division of Clinical and Metabolic Genetics, Department of Pediatrics, the Hospital for Sick Children, University of Toronto, Toronto, ON, M5G 1×8, Canada.
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Cao H, Baranova A, Song Y, Chen JH, Zhang F. Causal associations and genetic overlap between COVID-19 and intelligence. QJM 2023; 116:766-773. [PMID: 37286376 PMCID: PMC10559337 DOI: 10.1093/qjmed/hcad122] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 05/19/2023] [Accepted: 05/30/2023] [Indexed: 06/09/2023] Open
Abstract
OBJECTIVE COVID-19 might cause neuroinflammation in the brain, which could decrease neurocognitive function. We aimed to evaluate the causal associations and genetic overlap between COVID-19 and intelligence. METHODS We performed Mendelian randomization (MR) analyses to assess potential associations between three COVID-19 outcomes and intelligence (N = 269 867). The COVID phenotypes included severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection (N = 2 501 486), hospitalized COVID-19 (N = 1 965 329) and critical COVID-19 (N = 743 167). Genome-wide risk genes were compared between the genome-wide association study (GWAS) datasets on hospitalized COVID-19 and intelligence. In addition, functional pathways were constructed to explore molecular connections between COVID-19 and intelligence. RESULTS The MR analyses indicated that genetic liabilities to SARS-CoV-2 infection (odds ratio [OR]: 0.965, 95% confidence interval [CI]: 0.939-0.993) and critical COVID-19 (OR: 0.989, 95% CI: 0.979-0.999) confer causal effects on intelligence. There was suggestive evidence supporting the causal effect of hospitalized COVID-19 on intelligence (OR: 0.988, 95% CI: 0.972-1.003). Hospitalized COVID-19 and intelligence share 10 risk genes within 2 genomic loci, including MAPT and WNT3. Enrichment analysis showed that these genes are functionally connected within distinct subnetworks of 30 phenotypes linked to cognitive decline. The functional pathway revealed that COVID-19-driven pathological changes within the brain and multiple peripheral systems may lead to cognitive impairment. CONCLUSIONS Our study suggests that COVID-19 may exert a detrimental effect on intelligence. The tau protein and Wnt signaling may mediate the influence of COVID-19 on intelligence.
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Affiliation(s)
- Hongbao Cao
- School of Systems Biology, George Mason University, Manassas, VA 20110, USA
| | - Ancha Baranova
- School of Systems Biology, George Mason University, Manassas, VA 20110, USA
- Research Centre for Medical Genetics, Moscow 115478, Russia
| | - Yuqing Song
- Institute of Mental Health, Peking University Sixth Hospital
- NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing 100191, China
| | - Jian-Huan Chen
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi 214122, China
| | - Fuquan Zhang
- Institute of Neuropsychiatry, The Affiliated Brain Hospital of Nanjing Medical University, Nanjing 210029,China
- Department of Psychiatry, The Affiliated Brain Hospital of Nanjing Medical University, Nanjing 210029, China
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Martorell L, Yubero D, Capdevila EC, Fernández Isern G, Salinas D, Mari Vico R, Rebollo M, Muchart J, Armstrong J, Ortigoza-Escobar JD. The diagnosis of the first-documented intragenic KANSL1 microduplication patient broadens the genetic spectrum of Koolen de Vries syndrome. Clin Genet 2022; 101:575-576. [PMID: 35191016 DOI: 10.1111/cge.14124] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 02/14/2022] [Accepted: 02/15/2022] [Indexed: 11/29/2022]
Affiliation(s)
- Loreto Martorell
- Department of Genetic and Molecular Medicine-IPER, Institut de Recerca Sant Joan de Déu, Barcelona, Spain.,U-703 Centre for Biomedical Research on Rare Diseases (CIBER-ER), Instituto de Salud Carlos III, Barcelona, Spain
| | - Delia Yubero
- Department of Genetic and Molecular Medicine-IPER, Institut de Recerca Sant Joan de Déu, Barcelona, Spain.,U-703 Centre for Biomedical Research on Rare Diseases (CIBER-ER), Instituto de Salud Carlos III, Barcelona, Spain
| | | | - Guerau Fernández Isern
- Department of Genetic and Molecular Medicine-IPER, Institut de Recerca Sant Joan de Déu, Barcelona, Spain
| | - Diana Salinas
- Department of Genetic and Molecular Medicine-IPER, Institut de Recerca Sant Joan de Déu, Barcelona, Spain
| | - Rosanna Mari Vico
- Department of Rehabilitation, Institut de Recerca Sant Joan de Déu, Barcelona, Spain
| | - Mónica Rebollo
- Department of Radiology, Institut de Recerca Sant Joan de Déu, Barcelona, Spain
| | - Jordi Muchart
- Department of Radiology, Institut de Recerca Sant Joan de Déu, Barcelona, Spain
| | - Judith Armstrong
- Department of Genetic and Molecular Medicine-IPER, Institut de Recerca Sant Joan de Déu, Barcelona, Spain.,U-703 Centre for Biomedical Research on Rare Diseases (CIBER-ER), Instituto de Salud Carlos III, Barcelona, Spain
| | - Juan Darío Ortigoza-Escobar
- U-703 Centre for Biomedical Research on Rare Diseases (CIBER-ER), Instituto de Salud Carlos III, Barcelona, Spain.,Movement Disorders Unit, Department of Child Neurology, Institut de Recerca Sant Joan de Déu.,European Reference Network for Rare Neurological Diseases (ERN-RND), Barcelona, Spain
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