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Shani S, Gana-Weisz M, Bar-Shira A, Thaler A, Gurevich T, Mirelman A, Giladi N, Alcalay RN, Goldstein O, Orr-Urtreger A. MAPT Locus in Parkinson's Disease Patients of Ashkenazi Origin: A Stratified Analysis. Genes (Basel) 2023; 15:46. [PMID: 38254936 PMCID: PMC10815687 DOI: 10.3390/genes15010046] [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: 11/13/2023] [Revised: 12/24/2023] [Accepted: 12/25/2023] [Indexed: 01/24/2024] Open
Abstract
Introduction: MAPT locus is associated with Parkinson's disease (PD), which is located within a large inversion region of high linkage disequilibrium (LD). We aimed to determine whether the H2-haplotype protective effect and its effect size depends on the GBA1 or LRRK2 risk allele carrier status, and to further characterize genetic alterations that might contribute to its effect. Methods: LD analysis was performed using whole-genome sequencing data of 202 unrelated Ashkenazi Jewish (AJ) PDs. A haplotype-divergent variant was genotyped in a cohort of 1200 consecutively recruited AJ-PDs. The odd ratios were calculated using AJ-non-neuro cases from the gnomAD database as the controls in an un-stratified and a stratified manner according to the mutation carrier status, and the effect on the Age at Motor Symptom Onset (AMSO) was examined. Expression and splicing quantitative trait locus (eQTL and sQTL) analyses were carried out using brain tissues from a database. Results: The H2 haplotype exhibited significant association with PD protection, with a similar effect size in GBA1 carriers, LRRK2-G2019S carriers, and non-carriers (OR = 0.77, 0.69, and 0.82, respectively), and there was no effect on AMSO. The LD interval was narrowed to approximately 1.2 Mb. The H2 haplotype carried potential variants in candidate genes (MAPT and SPPL2C); structural deletions and segmental duplication (KANSL1); and variants affecting gene expression and intron excision ratio in brain tissues (LRRC37A/2). Conclusions: Our results demonstrate that H2 is associated with PD and its protective effect is not influenced by the GBA1/LRRK2 risk allele carrier status. This effect may be genetically complex, resulting from different levels of variations such as missense mutations in relevant genes, structural variations, epigenetic modifications, and RNA expression changes, which may operate independently or in synergy.
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Affiliation(s)
- Shachar Shani
- Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel; (S.S.); (A.T.); (T.G.); (A.M.); (N.G.); (A.O.-U.)
- The Laboratory of Biomarkers and Genomics of Neurodegeneration, Neurological Institute, Tel Aviv Sourasky Medical Center, Tel Aviv 6423906, Israel; (M.G.-W.); (A.B.-S.); (R.N.A.)
| | - Mali Gana-Weisz
- The Laboratory of Biomarkers and Genomics of Neurodegeneration, Neurological Institute, Tel Aviv Sourasky Medical Center, Tel Aviv 6423906, Israel; (M.G.-W.); (A.B.-S.); (R.N.A.)
| | - Anat Bar-Shira
- The Laboratory of Biomarkers and Genomics of Neurodegeneration, Neurological Institute, Tel Aviv Sourasky Medical Center, Tel Aviv 6423906, Israel; (M.G.-W.); (A.B.-S.); (R.N.A.)
| | - Avner Thaler
- Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel; (S.S.); (A.T.); (T.G.); (A.M.); (N.G.); (A.O.-U.)
- Movement Disorders Division, Neurological Institute, Tel Aviv Sourasky Medical Center, Tel Aviv 6423906, Israel
- Laboratory for Early Markers of Neurodegeneration, Neurological Institute, Tel Aviv Sourasky Medical Center, Tel Aviv 6423906, Israel
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Tanya Gurevich
- Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel; (S.S.); (A.T.); (T.G.); (A.M.); (N.G.); (A.O.-U.)
- Movement Disorders Division, Neurological Institute, Tel Aviv Sourasky Medical Center, Tel Aviv 6423906, Israel
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Anat Mirelman
- Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel; (S.S.); (A.T.); (T.G.); (A.M.); (N.G.); (A.O.-U.)
- Movement Disorders Division, Neurological Institute, Tel Aviv Sourasky Medical Center, Tel Aviv 6423906, Israel
- Laboratory for Early Markers of Neurodegeneration, Neurological Institute, Tel Aviv Sourasky Medical Center, Tel Aviv 6423906, Israel
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Nir Giladi
- Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel; (S.S.); (A.T.); (T.G.); (A.M.); (N.G.); (A.O.-U.)
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
- Brain Institute, Tel Aviv Sourasky Medical Center, Tel Aviv 6423906, Israel
| | - Roy N. Alcalay
- The Laboratory of Biomarkers and Genomics of Neurodegeneration, Neurological Institute, Tel Aviv Sourasky Medical Center, Tel Aviv 6423906, Israel; (M.G.-W.); (A.B.-S.); (R.N.A.)
- Movement Disorders Division, Neurological Institute, Tel Aviv Sourasky Medical Center, Tel Aviv 6423906, Israel
- Department of Neurology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Orly Goldstein
- The Laboratory of Biomarkers and Genomics of Neurodegeneration, Neurological Institute, Tel Aviv Sourasky Medical Center, Tel Aviv 6423906, Israel; (M.G.-W.); (A.B.-S.); (R.N.A.)
| | - Avi Orr-Urtreger
- Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel; (S.S.); (A.T.); (T.G.); (A.M.); (N.G.); (A.O.-U.)
- The Laboratory of Biomarkers and Genomics of Neurodegeneration, Neurological Institute, Tel Aviv Sourasky Medical Center, Tel Aviv 6423906, Israel; (M.G.-W.); (A.B.-S.); (R.N.A.)
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
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Goldstein O, Gana-Weisz M, Banfi S, Nigro V, Bar-Shira A, Thaler A, Gurevich T, Mirelman A, Giladi N, Alcalay RN, Orr-Urtreger A. Novel variants in genes related to vesicle-mediated-transport modify Parkinson's disease risk. Mol Genet Metab 2023; 139:107608. [PMID: 37201419 DOI: 10.1016/j.ymgme.2023.107608] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 05/11/2023] [Accepted: 05/11/2023] [Indexed: 05/20/2023]
Abstract
OBJECTIVES VPS35 and VPS13 have been associated with Parkinson's disease (PD), and their shared phenotype in yeast when reduced in function is abnormal vacuolar transport. We aim to test if additional potentially deleterious variants in other genes that share this phenotype can modify the risk for PD. METHODS 77 VPS and VPS-related genes were analyzed using whole-genome-sequencing data from 202 PD patients of Ashkenazi Jewish (AJ) ancestry. Filtering was done based on quality and functionality scores. Ten variants in nine genes were further genotyped in 1200 consecutively recruited unrelated AJ-PD patients, and allele frequencies and odds ratio calculated compared to gnomAD-AJ-non-neuro database, in un-stratified (n = 1200) and stratified manner (LRRK2-G2019S-PD patients (n = 145), GBA-PD patients (n = 235), and non-carriers of these mutations (NC, n = 787)). RESULTS Five variants in PIK3C3, VPS11, AP1G2, HGS and VPS13D were significantly associated with PD-risk. PIK3C3-R768W showed a significant association in an un-stratified (all PDs) analysis, as well as in stratified (LRRK2, GBA, and NC) analyses (Odds ratios = 2.71, 5.32, 3.26. and 2.19 with p = 0.0015, 0.002, 0.0287, and 0.0447, respectively). AP1G2-R563W was significantly associated in LRRK2-carriers (OR = 3.69, p = 0.006) while VPS13D-D2932N was significantly associated in GBA-carriers (OR = 5.45, p = 0.0027). VPS11-C846G and HGS-S243Y were significantly associated in NC (OR = 2.48 and 2.06, with p = 0.022 and 0.0163, respectively). CONCLUSIONS Variants in genes involved in vesicle-mediated protein transport and recycling pathways, including autophagy and mitophagy, may differentially modify PD-risk in LRRK2-carriers, GBA carriers, or NC. Specifically, PIK3C3-R768W is a PD-risk allele, with the highest effect size in LRRK2-G2019S carriers. These results suggest oligogenic effect that may depends on the genetic background of the patient. An unbiased burden of mutations approach in these genes should be evaluated in additional PD and control groups. The mechanisms by which these novel variants interact and increase PD-risk should be researched in depth for better tailoring therapeutic intervention for PD prevention or slowing disease progression.
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Affiliation(s)
- Orly Goldstein
- Laboratory of Biomarkers and Genomics of Neurodegeneration, Neurological Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Mali Gana-Weisz
- Laboratory of Biomarkers and Genomics of Neurodegeneration, Neurological Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Sandro Banfi
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, NA, Italy; Medical Genetics, Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Vincenzo Nigro
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, NA, Italy; Medical Genetics, Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Anat Bar-Shira
- Laboratory of Biomarkers and Genomics of Neurodegeneration, Neurological Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Avner Thaler
- Movement disorders Division, Neurological Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel; Laboratory for Early Markers of Neurodegeneration, Neurological Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel; Sackler Faculty of Medicine, and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Tanya Gurevich
- Movement disorders Division, Neurological Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel; Sackler Faculty of Medicine, and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Anat Mirelman
- Movement disorders Division, Neurological Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel; Laboratory for Early Markers of Neurodegeneration, Neurological Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel; Sackler Faculty of Medicine, and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Nir Giladi
- Movement disorders Division, Neurological Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel; Laboratory for Early Markers of Neurodegeneration, Neurological Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel; Sackler Faculty of Medicine, and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Roy N Alcalay
- Laboratory of Biomarkers and Genomics of Neurodegeneration, Neurological Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel; Movement disorders Division, Neurological Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel; Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
| | - Avi Orr-Urtreger
- Laboratory of Biomarkers and Genomics of Neurodegeneration, Neurological Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel; Sackler Faculty of Medicine, and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel.
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Relationship between Nutrition, Lifestyle, and Neurodegenerative Disease: Lessons from ADH1B, CYP1A2 and MTHFR. Genes (Basel) 2022; 13:genes13081498. [PMID: 36011409 PMCID: PMC9408177 DOI: 10.3390/genes13081498] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/18/2022] [Accepted: 08/19/2022] [Indexed: 11/17/2022] Open
Abstract
In the present review, the main features involved in the susceptibility and progression of neurodegenerative disorders (NDDs) have been discussed, with the purpose of highlighting their potential application for promoting the management and treatment of patients with NDDs. In particular, the impact of genetic and epigenetic factors, nutrients, and lifestyle will be presented, with particular emphasis on Alzheimer’s disease (AD) and Parkinson’s disease (PD). Metabolism, dietary habits, physical exercise and microbiota are part of a complex network that is crucial for brain function and preservation. This complex equilibrium can be disrupted by genetic, epigenetic, and environmental factors causing perturbations in central nervous system homeostasis, contributing thereby to neuroinflammation and neurodegeneration. Diet and physical activity can directly act on epigenetic modifications, which, in turn, alter the expression of specific genes involved in NDDs onset and progression. On this subject, the introduction of nutrigenomics shed light on the main molecular players involved in the modulation of health and disease status. In particular, the review presents data concerning the impact of ADH1B, CYP1A2, and MTHFR on the susceptibility and progression of NDDs (especially AD and PD) and how they may be exploited for developing precision medicine strategies for the disease treatment and management.
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Goldstein O, Gana-Weisz M, Attar R, Bar-Shira A, Lederkremer M, Shiner T, Thaler A, Mirelman A, Giladi N, Orr-Urtreger A. The GBA-370Rec Parkinson's disease risk haplotype harbors a potentially pathogenic variant in the mitochondrial gene SLC25A44. Mol Genet Metab 2021; 133:109-112. [PMID: 33762134 DOI: 10.1016/j.ymgme.2021.03.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 03/14/2021] [Accepted: 03/14/2021] [Indexed: 11/24/2022]
Abstract
GBA variations are common risk factors for Parkinson's disease (PD), and are found in 21.7% of Ashkenazi PD patients (AJ-PD), 4.23% of them carry an allele, 370Rec, which is different from the common GBA-N370S allele. Using whole-genome-sequencing of 370Rec carriers, N370S carriers, and non-carriers, we characterize the unique 370Rec haplotype in AJ-PDs, and show that it harbors a missense variant replacing the highly conserved methionine-27 with valine in the transmembrane domain of the mitochondrial SLC25A44.
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Affiliation(s)
- Orly Goldstein
- The Genomic Research Laboratory for Neurodegeneration, Neurological Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Mali Gana-Weisz
- The Genomic Research Laboratory for Neurodegeneration, Neurological Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Reut Attar
- The Genomic Research Laboratory for Neurodegeneration, Neurological Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Anat Bar-Shira
- The Genomic Research Laboratory for Neurodegeneration, Neurological Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | | | - Tamara Shiner
- Cognitive Neurology Unit, Neurological Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel; Movement disorders Unit, Neurological Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel; Sackler Faculty of Medicine, and Sagol School of Neuroscience, Tel Aviv University, Israel
| | - Avner Thaler
- Movement disorders Unit, Neurological Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel; Laboratory for Early Markers of Neurodegeneration, Neurological Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel; Sackler Faculty of Medicine, and Sagol School of Neuroscience, Tel Aviv University, Israel
| | - Anat Mirelman
- Movement disorders Unit, Neurological Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel; Laboratory for Early Markers of Neurodegeneration, Neurological Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel; Sackler Faculty of Medicine, and Sagol School of Neuroscience, Tel Aviv University, Israel
| | - Nir Giladi
- Movement disorders Unit, Neurological Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel; Laboratory for Early Markers of Neurodegeneration, Neurological Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel; Sackler Faculty of Medicine, and Sagol School of Neuroscience, Tel Aviv University, Israel
| | - Avi Orr-Urtreger
- The Genomic Research Laboratory for Neurodegeneration, Neurological Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel; Sackler Faculty of Medicine, and Sagol School of Neuroscience, Tel Aviv University, Israel.
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