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Jiménez-Jiménez FJ, Alonso-Navarro H, García-Martín E, Álvarez I, Pastor P, Agúndez JAG. Genomic Markers for Essential Tremor. Pharmaceuticals (Basel) 2021; 14:ph14060516. [PMID: 34072005 PMCID: PMC8226734 DOI: 10.3390/ph14060516] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 05/23/2021] [Accepted: 05/24/2021] [Indexed: 12/13/2022] Open
Abstract
There are many reports suggesting an important role of genetic factors in the etiopathogenesis of essential tremor (ET), encouraging continuing the research for possible genetic markers. Linkage studies in families with ET have identified 4 genes/loci for familial ET, although the responsible gene(s) have not been identified. Genome-wide association studies (GWAS) described several variants in LINGO1, SLC1A2, STK32B, PPARGC1A, and CTNNA3, related with ET, but none of them have been confirmed in replication studies. In addition, the case-control association studies performed for candidate variants have not convincingly linked any gene with the risk for ET. Exome studies described the association of several genes with familial ET (FUS, HTRA2, TENM4, SORT1, SCN11A, NOTCH2NLC, NOS3, KCNS2, HAPLN4, USP46, CACNA1G, SLIT3, CCDC183, MMP10, and GPR151), but they were found only in singular families and, again, not found in other families or other populations, suggesting that some can be private polymorphisms. The search for responsible genes for ET is still ongoing.
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Affiliation(s)
- Félix Javier Jiménez-Jiménez
- Section of Neurology, Hospital Universitario del Sureste, E28500 Arganda del Rey, Spain;
- Correspondence: ; Tel.: +34-636-96-83-95; Fax: +34-913-28-07-04
| | | | - Elena García-Martín
- ARADyAL Instituto de Salud Carlos III, University Institute of Molecular Pathology Biomarkers, University of Extremadura, E10071 Caceres, Spain; (E.G.-M.); (J.A.G.A.)
| | - Ignacio Álvarez
- Movement Disorders Unit, Department of Neurology, University Hospital Mútua de Terrassa, Fundació Docencia i Recerça Mútua de Terrassa, E08221 Terrassa, Spain; (I.Á.); (P.P.)
| | - Pau Pastor
- Movement Disorders Unit, Department of Neurology, University Hospital Mútua de Terrassa, Fundació Docencia i Recerça Mútua de Terrassa, E08221 Terrassa, Spain; (I.Á.); (P.P.)
| | - José A. G. Agúndez
- ARADyAL Instituto de Salud Carlos III, University Institute of Molecular Pathology Biomarkers, University of Extremadura, E10071 Caceres, Spain; (E.G.-M.); (J.A.G.A.)
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Odgerel Z, Sonti S, Hernandez N, Park J, Ottman R, Louis ED, Clark LN. Whole genome sequencing and rare variant analysis in essential tremor families. PLoS One 2019; 14:e0220512. [PMID: 31404076 PMCID: PMC6690583 DOI: 10.1371/journal.pone.0220512] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 07/17/2019] [Indexed: 11/19/2022] Open
Abstract
Essential tremor (ET) is one of the most common movement disorders. The etiology of ET remains largely unexplained. Whole genome sequencing (WGS) is likely to be of value in understanding a large proportion of ET with Mendelian and complex disease inheritance patterns. In ET families with Mendelian inheritance patterns, WGS may lead to gene identification where WES analysis failed to identify the causative single nucleotide variant (SNV) or indel due to incomplete coverage of the entire coding region of the genome, in addition to accurate detection of larger structural variants (SVs) and copy number variants (CNVs). Alternatively, in ET families with complex disease inheritance patterns with gene x gene and gene x environment interactions enrichment of functional rare coding and non-coding variants may explain the heritability of ET. We performed WGS in eight ET families (n = 40 individuals) enrolled in the Family Study of Essential Tremor. The analysis included filtering WGS data based on allele frequency in population databases, rare SNV and indel classification and association testing using the Mixed-Model Kernel Based Adaptive Cluster (MM-KBAC) test. A separate analysis of rare SV and CNVs segregating within ET families was also performed. Prioritization of candidate genes identified within families was performed using phenolyzer. WGS analysis identified candidate genes for ET in 5/8 (62.5%) of the families analyzed. WES analysis in a subset of these families in our previously published study failed to identify candidate genes. In one family, we identified a deleterious and damaging variant (c.1367G>A, p.(Arg456Gln)) in the candidate gene, CACNA1G, which encodes the pore forming subunit of T-type Ca(2+) channels, CaV3.1, and is expressed in various motor pathways and has been previously implicated in neuronal autorhythmicity and ET. Other candidate genes identified include SLIT3 which encodes an axon guidance molecule and in three families, phenolyzer prioritized genes that are associated with hereditary neuropathies (family A, KARS, family B, KIF5A and family F, NTRK1). Functional studies of CACNA1G and SLIT3 suggest a role for these genes in ET disease pathogenesis.
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Affiliation(s)
- Zagaa Odgerel
- Department of Pathology and Cell Biology, College of Physicians and Surgeons, Columbia University, New York, NY, United States of America
| | - Shilpa Sonti
- Department of Pathology and Cell Biology, College of Physicians and Surgeons, Columbia University, New York, NY, United States of America
| | - Nora Hernandez
- Department of Neurology, Yale School of Medicine, Yale University, New Haven, CT, United States of America
| | - Jemin Park
- Department of Neurology, Yale School of Medicine, Yale University, New Haven, CT, United States of America
| | - Ruth Ottman
- G.H Sergievsky Center, Columbia University, New York, NY, United States of America
- Department of Neurology, College of Physicians and Surgeons, Columbia University New York, NY, United States of America
- Department of Epidemiology, Mailman School of Public Health, Columbia University, NY, United States of America
- Division of Epidemiology, New York State Psychiatric Institute, New York, NY, United States of America
| | - Elan D. Louis
- Department of Neurology, Yale School of Medicine, Yale University, New Haven, CT, United States of America
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, CT, United States of America
| | - Lorraine N. Clark
- Department of Pathology and Cell Biology, College of Physicians and Surgeons, Columbia University, New York, NY, United States of America
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, New York, NY, United States of America
- * E-mail:
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Figueroa KP, Paul S, Calì T, Lopreiato R, Karan S, Frizzarin M, Ames D, Zanni G, Brini M, Dansithong W, Milash B, Scoles DR, Carafoli E, Pulst SM. Spontaneous shaker rat mutant - a new model for X-linked tremor/ataxia. Dis Model Mech 2016; 9:553-62. [PMID: 27013529 PMCID: PMC4892658 DOI: 10.1242/dmm.022848] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 02/29/2016] [Indexed: 12/18/2022] Open
Abstract
The shaker rat is an X-linked recessive spontaneous model of progressive Purkinje cell (PC) degeneration exhibiting a shaking ataxia and wide stance. Generation of Wistar Furth (WF)/Brown Norwegian (BN) F1 hybrids and genetic mapping of F2 sib-sib offspring using polymorphic markers narrowed the candidate gene region to 26 Mbp denoted by the last recombinant genetic marker DXRat21 at 133 Mbp to qter (the end of the long arm). In the WF background, the shaker mutation has complete penetrance, results in a stereotypic phenotype and there is a narrow window for age of disease onset; by contrast, the F2 hybrid phenotype was more varied, with a later age of onset and likely non-penetrance of the mutation. By deep RNA-sequencing, five variants were found in the candidate region; four were novel without known annotation. One of the variants caused an arginine (R) to cysteine (C) change at codon 35 of the ATPase, Ca2+ transporting, plasma membrane 3 (Atp2b3) gene encoding PMCA3 that has high expression in the cerebellum. The variant was well supported by hundreds of overlapping reads, and was found in 100% of all affected replicas and 0% of the wild-type (WT) replicas. The mutation segregated with disease in all affected animals and the amino acid change was found in an evolutionarily conserved region of PMCA3. Despite strong genetic evidence for pathogenicity, in vitro analyses of PMCA3R35C function did not show any differences to WT PMCA3. Because Atp2b3 mutation leads to congenital ataxia in humans, the identified Atp2b3 missense change in the shaker rat presents a good candidate for the shaker rat phenotype based on genetic criteria, but cannot yet be considered a definite pathogenic variant owing to lack of functional changes. Summary: The shaker rat mutant: a new model for essential tremors and ataxia characterized by Purkinje cell degeneration.
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Affiliation(s)
- Karla P Figueroa
- Department of Neurology, University of Utah, Salt Lake City, UT 84112, USA
| | - Sharan Paul
- Department of Neurology, University of Utah, Salt Lake City, UT 84112, USA
| | - Tito Calì
- Department of Biomedical Sciences, University of Padova, Padova, Italy
| | | | - Sukanya Karan
- Department of Neurology, University of Utah, Salt Lake City, UT 84112, USA
| | - Martina Frizzarin
- Department of Biomedical Sciences, University of Padova, Padova, Italy
| | - Darren Ames
- Bioinformatics Shared Resource, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
| | - Ginevra Zanni
- Unit of Molecular Medicine for Neuromuscular and Neurodegenerative Disorders, Department of Neurosciences, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Marisa Brini
- Department of Biology, University of Padova, Padova, Italy
| | - Warunee Dansithong
- Department of Neurology, University of Utah, Salt Lake City, UT 84112, USA
| | - Brett Milash
- Bioinformatics Shared Resource, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
| | - Daniel R Scoles
- Department of Neurology, University of Utah, Salt Lake City, UT 84112, USA
| | | | - Stefan M Pulst
- Department of Neurology, University of Utah, Salt Lake City, UT 84112, USA
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