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Perrone F, Cacace R, van der Zee J, Van Broeckhoven C. Emerging genetic complexity and rare genetic variants in neurodegenerative brain diseases. Genome Med 2021; 13:59. [PMID: 33853652 PMCID: PMC8048219 DOI: 10.1186/s13073-021-00878-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 03/25/2021] [Indexed: 12/12/2022] Open
Abstract
Knowledge of the molecular etiology of neurodegenerative brain diseases (NBD) has substantially increased over the past three decades. Early genetic studies of NBD families identified rare and highly penetrant deleterious mutations in causal genes that segregate with disease. Large genome-wide association studies uncovered common genetic variants that influenced disease risk. Major developments in next-generation sequencing (NGS) technologies accelerated gene discoveries at an unprecedented rate and revealed novel pathways underlying NBD pathogenesis. NGS technology exposed large numbers of rare genetic variants of uncertain significance (VUS) in coding regions, highlighting the genetic complexity of NBD. Since experimental studies of these coding rare VUS are largely lacking, the potential contributions of VUS to NBD etiology remain unknown. In this review, we summarize novel findings in NBD genetic etiology driven by NGS and the impact of rare VUS on NBD etiology. We consider different mechanisms by which rare VUS can act and influence NBD pathophysiology and discuss why a better understanding of rare VUS is instrumental for deriving novel insights into the molecular complexity and heterogeneity of NBD. New knowledge might open avenues for effective personalized therapies.
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Affiliation(s)
- Federica Perrone
- Neurodegenerative Brain Diseases Group, VIB Center for Molecular Neurology, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp – CDE, Universiteitsplein 1, BE-2610 Antwerp, Belgium
| | - Rita Cacace
- Neurodegenerative Brain Diseases Group, VIB Center for Molecular Neurology, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp – CDE, Universiteitsplein 1, BE-2610 Antwerp, Belgium
| | - Julie van der Zee
- Neurodegenerative Brain Diseases Group, VIB Center for Molecular Neurology, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp – CDE, Universiteitsplein 1, BE-2610 Antwerp, Belgium
| | - Christine Van Broeckhoven
- Neurodegenerative Brain Diseases Group, VIB Center for Molecular Neurology, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp – CDE, Universiteitsplein 1, BE-2610 Antwerp, Belgium
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Cacace R, Heeman B, Van Mossevelde S, De Roeck A, Hoogmartens J, De Rijk P, Gossye H, De Vos K, De Coster W, Strazisar M, De Baets G, Schymkowitz J, Rousseau F, Geerts N, De Pooter T, Peeters K, Sieben A, Martin JJ, Engelborghs S, Salmon E, Santens P, Vandenberghe R, Cras P, P. De Deyn P, C. van Swieten J, M. van Duijn C, van der Zee J, Sleegers K, Van Broeckhoven C. Loss of DPP6 in neurodegenerative dementia: a genetic player in the dysfunction of neuronal excitability. Acta Neuropathol 2019; 137:901-918. [PMID: 30874922 PMCID: PMC6531610 DOI: 10.1007/s00401-019-01976-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [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: 12/03/2018] [Revised: 02/07/2019] [Accepted: 02/13/2019] [Indexed: 12/14/2022]
Abstract
Emerging evidence suggested a converging mechanism in neurodegenerative brain diseases (NBD) involving early neuronal network dysfunctions and alterations in the homeostasis of neuronal firing as culprits of neurodegeneration. In this study, we used paired-end short-read and direct long-read whole genome sequencing to investigate an unresolved autosomal dominant dementia family significantly linked to 7q36. We identified and validated a chromosomal inversion of ca. 4 Mb, segregating on the disease haplotype and disrupting the coding sequence of dipeptidyl-peptidase 6 gene (DPP6). DPP6 resequencing identified significantly more rare variants-nonsense, frameshift, and missense-in early-onset Alzheimer's disease (EOAD, p value = 0.03, OR = 2.21 95% CI 1.05-4.82) and frontotemporal dementia (FTD, p = 0.006, OR = 2.59, 95% CI 1.28-5.49) patient cohorts. DPP6 is a type II transmembrane protein with a highly structured extracellular domain and is mainly expressed in brain, where it binds to the potassium channel Kv4.2 enhancing its expression, regulating its gating properties and controlling the dendritic excitability of hippocampal neurons. Using in vitro modeling, we showed that the missense variants found in patients destabilize DPP6 and reduce its membrane expression (p < 0.001 and p < 0.0001) leading to a loss of protein. Reduced DPP6 and/or Kv4.2 expression was also detected in brain tissue of missense variant carriers. Loss of DPP6 is known to cause neuronal hyperexcitability and behavioral alterations in Dpp6-KO mice. Taken together, the results of our genomic, genetic, expression and modeling analyses, provided direct evidence supporting the involvement of DPP6 loss in dementia. We propose that loss of function variants have a higher penetrance and disease impact, whereas the missense variants have a variable risk contribution to disease that can vary from high to low penetrance. Our findings of DPP6, as novel gene in dementia, strengthen the involvement of neuronal hyperexcitability and alteration in the homeostasis of neuronal firing as a disease mechanism to further investigate.
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Affiliation(s)
- Rita Cacace
- Center for Molecular Neurology, VIB, Antwerp, Belgium
- Institute Born-Bunge, Antwerp, Belgium
- University of Antwerp, Antwerp, Belgium
| | - Bavo Heeman
- Center for Molecular Neurology, VIB, Antwerp, Belgium
- Institute Born-Bunge, Antwerp, Belgium
- University of Antwerp, Antwerp, Belgium
| | - Sara Van Mossevelde
- Center for Molecular Neurology, VIB, Antwerp, Belgium
- Institute Born-Bunge, Antwerp, Belgium
- University of Antwerp, Antwerp, Belgium
- Department of Neurology, Antwerp University Hospital, Edegem, Belgium
- Department of Neurology and Memory Clinic, Hospital Network Antwerp (ZNA), Middelheim and Hoge Beuken, Antwerp, Belgium
| | - Arne De Roeck
- Center for Molecular Neurology, VIB, Antwerp, Belgium
- Institute Born-Bunge, Antwerp, Belgium
- University of Antwerp, Antwerp, Belgium
| | - Julie Hoogmartens
- Center for Molecular Neurology, VIB, Antwerp, Belgium
- Institute Born-Bunge, Antwerp, Belgium
- University of Antwerp, Antwerp, Belgium
| | - Peter De Rijk
- Center for Molecular Neurology, VIB, Antwerp, Belgium
- University of Antwerp, Antwerp, Belgium
| | - Helena Gossye
- Center for Molecular Neurology, VIB, Antwerp, Belgium
- Institute Born-Bunge, Antwerp, Belgium
- University of Antwerp, Antwerp, Belgium
- Department of Neurology, Antwerp University Hospital, Edegem, Belgium
- Department of Neurology and Memory Clinic, Hospital Network Antwerp (ZNA), Middelheim and Hoge Beuken, Antwerp, Belgium
| | - Kristof De Vos
- Center for Molecular Neurology, VIB, Antwerp, Belgium
- Institute Born-Bunge, Antwerp, Belgium
- University of Antwerp, Antwerp, Belgium
| | - Wouter De Coster
- Center for Molecular Neurology, VIB, Antwerp, Belgium
- University of Antwerp, Antwerp, Belgium
| | - Mojca Strazisar
- Center for Molecular Neurology, VIB, Antwerp, Belgium
- University of Antwerp, Antwerp, Belgium
| | - Greet De Baets
- Switch Laboratory, VIB-KU Leuven Centre for Brain and Disease Research, Louvain, Belgium
- Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Louvain, Belgium
| | - Joost Schymkowitz
- Switch Laboratory, VIB-KU Leuven Centre for Brain and Disease Research, Louvain, Belgium
- Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Louvain, Belgium
| | - Frederic Rousseau
- Switch Laboratory, VIB-KU Leuven Centre for Brain and Disease Research, Louvain, Belgium
- Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Louvain, Belgium
| | - Nathalie Geerts
- Center for Molecular Neurology, VIB, Antwerp, Belgium
- Institute Born-Bunge, Antwerp, Belgium
- University of Antwerp, Antwerp, Belgium
| | - Tim De Pooter
- Center for Molecular Neurology, VIB, Antwerp, Belgium
- University of Antwerp, Antwerp, Belgium
| | - Karin Peeters
- Center for Molecular Neurology, VIB, Antwerp, Belgium
- Institute Born-Bunge, Antwerp, Belgium
- University of Antwerp, Antwerp, Belgium
| | - Anne Sieben
- Center for Molecular Neurology, VIB, Antwerp, Belgium
- Institute Born-Bunge, Antwerp, Belgium
- Department of Neurology, University Hospital Ghent and University of Ghent, Ghent, Belgium
| | | | - Sebastiaan Engelborghs
- Institute Born-Bunge, Antwerp, Belgium
- University of Antwerp, Antwerp, Belgium
- Department of Neurology and Memory Clinic, Hospital Network Antwerp (ZNA), Middelheim and Hoge Beuken, Antwerp, Belgium
| | - Eric Salmon
- Department of Neurology, Centre Hospitalier Universitaire de Liège and University of Liège, Liège, Belgium
| | - Patrick Santens
- Department of Neurology, University Hospital Ghent and University of Ghent, Ghent, Belgium
| | - Rik Vandenberghe
- Department of Neurosciences, Faculty of Medicine, KU Leuven, Louvain, Belgium
- Laboratory of Cognitive Neurology, Department of Neurology, University Hospitals Leuven, Louvain, Belgium
| | - Patrick Cras
- Institute Born-Bunge, Antwerp, Belgium
- University of Antwerp, Antwerp, Belgium
- Department of Neurology, Antwerp University Hospital, Edegem, Belgium
| | - Peter P. De Deyn
- Institute Born-Bunge, Antwerp, Belgium
- University of Antwerp, Antwerp, Belgium
- Department of Neurology and Memory Clinic, Hospital Network Antwerp (ZNA), Middelheim and Hoge Beuken, Antwerp, Belgium
| | - John C. van Swieten
- Department of Neurology, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Cornelia M. van Duijn
- Department of Epidemiology, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Julie van der Zee
- Center for Molecular Neurology, VIB, Antwerp, Belgium
- Institute Born-Bunge, Antwerp, Belgium
- University of Antwerp, Antwerp, Belgium
| | - Kristel Sleegers
- Center for Molecular Neurology, VIB, Antwerp, Belgium
- Institute Born-Bunge, Antwerp, Belgium
- University of Antwerp, Antwerp, Belgium
| | - Christine Van Broeckhoven
- Center for Molecular Neurology, VIB, Antwerp, Belgium
- Institute Born-Bunge, Antwerp, Belgium
- University of Antwerp, Antwerp, Belgium
- Neurodegenerative Brain Diseases Group, VIB Center for Molecular Neurology, University of Antwerp, CDE, Universiteitsplein 1, 2610 Antwerp, Belgium
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