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A Whole-Genome Sequencing Study Implicates GRAMD1B in Multiple Sclerosis Susceptibility. Genes (Basel) 2022; 13:genes13122392. [PMID: 36553660 PMCID: PMC9777893 DOI: 10.3390/genes13122392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/13/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
While the role of common genetic variants in multiple sclerosis (MS) has been elucidated in large genome-wide association studies, the contribution of rare variants to the disease remains unclear. Herein, a whole-genome sequencing study in four affected and four healthy relatives of a consanguineous Italian family identified a novel missense c.1801T > C (p.S601P) variant in the GRAMD1B gene that is shared within MS cases and resides under a linkage peak (LOD: 2.194). Sequencing GRAMD1B in 91 familial MS cases revealed two additional rare missense and two splice-site variants, two of which (rs755488531 and rs769527838) were not found in 1000 Italian healthy controls. Functional studies demonstrated that GRAMD1B, a gene with unknown function in the central nervous system (CNS), is expressed by several cell types, including astrocytes, microglia and neurons as well as by peripheral monocytes and macrophages. Notably, GRAMD1B was downregulated in vessel-associated astrocytes of active MS lesions in autopsied brains and by inflammatory stimuli in peripheral monocytes, suggesting a possible role in the modulation of inflammatory response and disease pathophysiology.
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Trinh J, Imhoff S, Dulovic-Mahlow M, Kandaswamy KK, Tadic V, Schäfer J, Dobricic V, Nolte A, Werber M, Rolfs A, Münchau A, Klein C, Lohmann K, Brüggemann N. Novel NAXE variants as a cause for neurometabolic disorder: implications for treatment. J Neurol 2019; 267:770-782. [PMID: 31745726 DOI: 10.1007/s00415-019-09640-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 11/08/2019] [Accepted: 11/14/2019] [Indexed: 11/29/2022]
Abstract
Neurometabolic disorders are often inherited and complex disorders that result from abnormalities of enzymes important for development and function of the nervous system. Recently, biallelic mutations in NAXE (APOA1BP) were found in patients with an infantile, lethal, neurometabolic disease. Here, exome sequencing was performed in two affected sisters and their healthy parents. The best candidate, NAXE, was tested for replication in exome sequencing data from 4351 patients with neurodevelopmental disorders. Quantitative RT-PCR, western blot and form factor analysis were performed to assess NAXE expression, protein levels and to analyze mitochondrial morphology in fibroblasts. Vitamin B3 was administered to one patient. Compound heterozygous missense (c.757G>A: p.Gly253Ser) and splicing (c.665-1G>A) variants in NAXE were identified in both affected sisters. In contrast to the previously reported patients with biallelic NAXE variants, our patients showed a milder phenotype with disease onset in early adulthood with psychosis, cognitive impairment, seizures, cerebellar ataxia and spasticity. The symptoms fluctuated. Additional screening of NAXE identified three novel homozygous missense variants (p.Lys245Gln, p.Asp218Asn, p.Ile214Val) in three patients with overlapping phenotype (fluctuating disease course, respiratory insufficiency, movement disorder). Lastly, patients with the c.665-1G>A splicing variant showed a significant reduction of NAXE expression compared to control fibroblasts and undetectable NAXE protein levels compared to control fibroblasts. Based on the metabolic pathway, vitamin B3 and coenzyme Q treatment was introduced in one patient in addition to antiepileptic treatment. This combination and avoidance of triggers was associated with continuous motor and cognitive improvement. The NAXE variants identified in this study suggest a loss-of-function mechanism leading to an insufficient NAD(P)HX repair system. Importantly, symptoms of patients with NAXE variants may improve with vitamin B3/coenzyme Q administration.
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Affiliation(s)
- Joanne Trinh
- Institute of Neurogenetics, University of Lübeck, 23538, Lübeck, Germany
| | - Sophie Imhoff
- Institute of Neurogenetics, University of Lübeck, 23538, Lübeck, Germany
| | | | | | - Vera Tadic
- Institute of Neurogenetics, University of Lübeck, 23538, Lübeck, Germany.,Department of Neurology, University of Lübeck, Lübeck, Germany
| | - Jochen Schäfer
- Department of Neurology, University Hospital Dresden, Dresden, Germany
| | - Valerija Dobricic
- Institute of Neurogenetics, University of Lübeck, 23538, Lübeck, Germany
| | - Achim Nolte
- Department of Neurology, Helios Clinic, Geesthacht, Germany
| | | | | | - Alexander Münchau
- Institute of Neurogenetics, University of Lübeck, 23538, Lübeck, Germany
| | - Christine Klein
- Institute of Neurogenetics, University of Lübeck, 23538, Lübeck, Germany.
| | - Katja Lohmann
- Institute of Neurogenetics, University of Lübeck, 23538, Lübeck, Germany
| | - Norbert Brüggemann
- Institute of Neurogenetics, University of Lübeck, 23538, Lübeck, Germany.,Department of Neurology, University of Lübeck, Lübeck, Germany
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3
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Gharagozloo M, Mahmoud S, Simard C, Yamamoto K, Bobbala D, Ilangumaran S, Smith MD, Lamontagne A, Jarjoura S, Denault JB, Blais V, Gendron L, Vilariño-Güell C, Sadovnick AD, Ting JP, Calabresi PA, Amrani A, Gris D. NLRX1 inhibits the early stages of CNS inflammation and prevents the onset of spontaneous autoimmunity. PLoS Biol 2019; 17:e3000451. [PMID: 31525189 PMCID: PMC6762215 DOI: 10.1371/journal.pbio.3000451] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 09/26/2019] [Accepted: 08/28/2019] [Indexed: 12/20/2022] Open
Abstract
Nucleotide-binding, leucine-rich repeat containing X1 (NLRX1) is a mitochondria-located innate immune sensor that inhibits major pro-inflammatory pathways such as type I interferon and nuclear factor-κB signaling. We generated a novel, spontaneous, and rapidly progressing mouse model of multiple sclerosis (MS) by crossing myelin-specific T-cell receptor (TCR) transgenic mice with Nlrx1−/− mice. About half of the resulting progeny developed spontaneous experimental autoimmune encephalomyelitis (spEAE), which was associated with severe demyelination and inflammation in the central nervous system (CNS). Using lymphocyte-deficient mice and a series of adoptive transfer experiments, we demonstrate that genetic susceptibility to EAE lies within the innate immune compartment. We show that NLRX1 inhibits the subclinical stages of microglial activation and prevents the generation of neurotoxic astrocytes that induce neuronal and oligodendrocyte death in vitro. Moreover, we discovered several mutations within NLRX1 that run in MS-affected families. In summary, our findings highlight the importance of NLRX1 in controlling the early stages of CNS inflammation and preventing the onset of spontaneous autoimmunity. NLRX1 is a guardian protein that inhibits the inflammatory response of glial cells within the central nervous system and prevents the onset of a spontaneous multiple sclerosis–like disease in mice. This study uses a novel mouse model to provide mechanistic insights into the neurodegenerative origin of multiple sclerosis.
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Affiliation(s)
- Marjan Gharagozloo
- Department of Pharmacology and Physiology, Faculty of Medicine, Université de Sherbrooke, Sherbrooke, Quebec, Canada
- Department of Neurology, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Shaimaa Mahmoud
- Department of Pharmacology and Physiology, Faculty of Medicine, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Camille Simard
- Department of Pharmacology and Physiology, Faculty of Medicine, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Kenzo Yamamoto
- Department of Chemical Engineering and Biotechnological Engineering, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Diwakar Bobbala
- Department of Anatomy and Cell Biology, Faculty of Medicine, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Subburaj Ilangumaran
- Department of Anatomy and Cell Biology, Faculty of Medicine, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Matthew D. Smith
- Department of Neurology, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Albert Lamontagne
- Department of Neurology, Faculty of Medicine, MS Clinic, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Samir Jarjoura
- Department of Neurology, Faculty of Medicine, MS Clinic, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Jean-Bernard Denault
- Department of Pharmacology and Physiology, Faculty of Medicine, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Véronique Blais
- Department of Pharmacology and Physiology, Faculty of Medicine, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Louis Gendron
- Department of Pharmacology and Physiology, Faculty of Medicine, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | | | - A. Dessa Sadovnick
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Jenny P. Ting
- Department of Microbiology and Immunology, Lineberger Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Peter A. Calabresi
- Department of Neurology, Johns Hopkins University, Baltimore, Maryland, United States of America
- Department of Neuroscience, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Abdelaziz Amrani
- Department of Pediatrics, Faculty of Medicine, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Denis Gris
- Department of Pharmacology and Physiology, Faculty of Medicine, Université de Sherbrooke, Sherbrooke, Quebec, Canada
- * E-mail:
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Vilariño-Güell C, Zimprich A, Martinelli-Boneschi F, Herculano B, Wang Z, Matesanz F, Urcelay E, Vandenbroeck K, Leyva L, Gris D, Massaad C, Quandt JA, Traboulsee AL, Encarnacion M, Bernales CQ, Follett J, Yee IM, Criscuoli MG, Deutschländer A, Reinthaler EM, Zrzavy T, Mascia E, Zauli A, Esposito F, Alcina A, Izquierdo G, Espino-Paisán L, Mena J, Antigüedad A, Urbaneja-Romero P, Ortega-Pinazo J, Song W, Sadovnick AD. Exome sequencing in multiple sclerosis families identifies 12 candidate genes and nominates biological pathways for the genesis of disease. PLoS Genet 2019; 15:e1008180. [PMID: 31170158 PMCID: PMC6553700 DOI: 10.1371/journal.pgen.1008180] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 05/07/2019] [Indexed: 12/12/2022] Open
Abstract
Multiple sclerosis (MS) is an inflammatory disease of the central nervous system characterized by myelin loss and neuronal dysfunction. Although the majority of patients do not present familial aggregation, Mendelian forms have been described. We performed whole-exome sequencing analysis in 132 patients from 34 multi-incident families, which nominated likely pathogenic variants for MS in 12 genes of the innate immune system that regulate the transcription and activation of inflammatory mediators. Rare missense or nonsense variants were identified in genes of the fibrinolysis and complement pathways (PLAU, MASP1, C2), inflammasome assembly (NLRP12), Wnt signaling (UBR2, CTNNA3, NFATC2, RNF213), nuclear receptor complexes (NCOA3), and cation channels and exchangers (KCNG4, SLC24A6, SLC8B1). These genes suggest a disruption of interconnected immunological and pro-inflammatory pathways as the initial event in the pathophysiology of familial MS, and provide the molecular and biological rationale for the chronic inflammation, demyelination and neurodegeneration observed in MS patients.
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Affiliation(s)
| | | | - Filippo Martinelli-Boneschi
- Laboratory of Human Genetics of Neurological Disorders, CNS Inflammatory Unit, Institute of Experimental Neurology, IRCCS San Raffaele Scientific Institute, Milan, Italy
- MS Unit and Department of Neurology, IRCCS Policlinico San Donato, Milan, Italy
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Bruno Herculano
- Townsend Family Laboratories, Department of Psychiatry, University of British Columbia, Vancouver, Canada
| | - Zhe Wang
- Townsend Family Laboratories, Department of Psychiatry, University of British Columbia, Vancouver, Canada
- National Clinical Research Center for Geriatric Diseases, Xuanwu Hospital of the Capital Medical University, Beijing, China
| | - Fuencisla Matesanz
- Department of Cell Biology and Immunology, Instituto de Parasitología y Biomedicina López Neyra (IPBLN), CSIC, Granada, Spain
| | - Elena Urcelay
- Immunology Dept, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos (IdISSC), Madrid, Spain
- Red Española de Esclerosis Múltiple REEM, Madrid, Spain
| | - Koen Vandenbroeck
- Achucarro Basque Center for Neuroscience, Universidad del País Vasco (UPV/EHU), Leioa, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | - Laura Leyva
- Red Española de Esclerosis Múltiple REEM, Madrid, Spain
- Instituto de Investigación Biomédica de Málaga-IBIMA, Unidad de Gestion Clínica de Neurociencias, Hospital Regional Universitario de Málaga, Málaga, Spain
| | - Denis Gris
- Division of Immunology, Department of Pediatrics, CR-CHUS, Faculty of Medicine and Health Sciences, University of Sherbrooke, Sherbrooke, Canada
| | - Charbel Massaad
- Toxicology, Pharmacology and Cell Signalisation—UMR-S 1124 Université Paris Descartes, Paris, France
| | - Jacqueline A. Quandt
- Department of Pathology, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Anthony L. Traboulsee
- Division of Neurology, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Mary Encarnacion
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Cecily Q. Bernales
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Jordan Follett
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Irene M. Yee
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Maria G. Criscuoli
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Angela Deutschländer
- Department of Neurology, Mayo Clinic Florida, Jacksonville, FL, United States of America
- Department of Clinical Genomics, Mayo Clinic Florida, Jacksonville, FL, United States of America
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, United States of America
| | - Eva M. Reinthaler
- Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Tobias Zrzavy
- Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Elisabetta Mascia
- Laboratory of Human Genetics of Neurological Disorders, CNS Inflammatory Unit, Institute of Experimental Neurology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Andrea Zauli
- Laboratory of Human Genetics of Neurological Disorders, CNS Inflammatory Unit, Institute of Experimental Neurology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Federica Esposito
- Laboratory of Human Genetics of Neurological Disorders, CNS Inflammatory Unit, Institute of Experimental Neurology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Antonio Alcina
- Department of Cell Biology and Immunology, Instituto de Parasitología y Biomedicina López Neyra (IPBLN), CSIC, Granada, Spain
| | | | - Laura Espino-Paisán
- Immunology Dept, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos (IdISSC), Madrid, Spain
- Red Española de Esclerosis Múltiple REEM, Madrid, Spain
| | - Jorge Mena
- Achucarro Basque Center for Neuroscience, Universidad del País Vasco (UPV/EHU), Leioa, Spain
| | - Alfredo Antigüedad
- Neurology Department, Hospital Universitario de Cruces, S/N, Baracaldo, Spain
| | - Patricia Urbaneja-Romero
- Red Española de Esclerosis Múltiple REEM, Madrid, Spain
- Instituto de Investigación Biomédica de Málaga-IBIMA, Unidad de Gestion Clínica de Neurociencias, Hospital Regional Universitario de Málaga, Málaga, Spain
| | - Jesús Ortega-Pinazo
- Instituto de Investigación Biomédica de Málaga-IBIMA, Unidad de Gestion Clínica de Neurociencias, Hospital Regional Universitario de Málaga, Málaga, Spain
| | - Weihong Song
- Townsend Family Laboratories, Department of Psychiatry, University of British Columbia, Vancouver, Canada
| | - A. Dessa Sadovnick
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
- Division of Neurology, Faculty of Medicine, University of British Columbia, Vancouver, Canada
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5
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Trinh J, Lohmann K, Baumann H, Balck A, Borsche M, Brüggemann N, Dure L, Dean M, Volkmann J, Tunc S, Prasuhn J, Pawlack H, Imhoff S, Lill CM, Kasten M, Bauer P, Rolfs A, Klein C. Utility and implications of exome sequencing in early‐onset Parkinson's disease. Mov Disord 2018; 34:133-137. [DOI: 10.1002/mds.27559] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 10/10/2018] [Accepted: 10/10/2018] [Indexed: 01/12/2023] Open
Affiliation(s)
- Joanne Trinh
- Institute of Neurogenetics University of Lübeck Lübeck Germany
| | - Katja Lohmann
- Institute of Neurogenetics University of Lübeck Lübeck Germany
| | - Hauke Baumann
- Institute of Neurogenetics University of Lübeck Lübeck Germany
| | - Alexander Balck
- Institute of Neurogenetics University of Lübeck Lübeck Germany
- Department of Neurology University of Lübeck Lübeck Germany
| | - Max Borsche
- Institute of Neurogenetics University of Lübeck Lübeck Germany
- Department of Neurology University of Lübeck Lübeck Germany
| | - Norbert Brüggemann
- Institute of Neurogenetics University of Lübeck Lübeck Germany
- Department of Neurology University of Lübeck Lübeck Germany
| | - Leon Dure
- Department of Neurology University of Alabama at Birmingham Birmingham Alabama USA
| | - Marissa Dean
- Department of Neurology University of Alabama at Birmingham Birmingham Alabama USA
| | - Jens Volkmann
- Departement of Neurology Universitatsklinikum Würzburg Würzburg Germany
| | - Sinem Tunc
- Institute of Neurogenetics University of Lübeck Lübeck Germany
- Department of Neurology University of Lübeck Lübeck Germany
| | - Jannik Prasuhn
- Institute of Neurogenetics University of Lübeck Lübeck Germany
- Department of Neurology University of Lübeck Lübeck Germany
| | - Heike Pawlack
- Institute of Neurogenetics University of Lübeck Lübeck Germany
| | - Sophie Imhoff
- Institute of Neurogenetics University of Lübeck Lübeck Germany
| | | | - Meike Kasten
- Institute of Neurogenetics University of Lübeck Lübeck Germany
- Psychiatry University of Lübeck Lübeck Germany
| | - Peter Bauer
- Centogene AG, Institute for Rare Diseases Rostock Germany
| | - Arndt Rolfs
- Centogene AG, Institute for Rare Diseases Rostock Germany
- Albrecht Kossel Institute for Neuroregeneration University Hospital Rostock Rostock Germany
| | - Christine Klein
- Institute of Neurogenetics University of Lübeck Lübeck Germany
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Bernales CQ, Encarnacion M, Criscuoli MG, Yee IM, Traboulsee AL, Sadovnick AD, Vilariño-Güell C. Analysis of NOD-like receptor NLRP1 in multiple sclerosis families. Immunogenetics 2017; 70:205-207. [PMID: 28988323 DOI: 10.1007/s00251-017-1034-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 09/29/2017] [Indexed: 11/24/2022]
Abstract
The implementation of exome sequencing technologies has started to unravel the genetic etiology of familial multiple sclerosis (MS). A homozygote p.G587S mutation in NLRP1 has been suggested as potentially causative for the onset of MS in an affected sibling pair, who later developed malignant melanoma. To validate the proposed role of recessive NLRP1 mutations in the pathological mechanisms of MS, we examined exome sequencing data from 326 MS patients from Canada for the identification of NLRP1 missense and nonsense variants. This analysis did not identify the previously described p.G587S mutation; however, three patients with potential NLRP1 compound heterozygote mutations were observed. Haplotype and segregation analyses indicate that the variants observed in these patients were inherited in cis, and do not segregate with disease within families. Thus, the analysis of MS patients from Canada failed to identify potentially pathogenic mutations in NLRP1, including the previously described p.G587S mutation. Further studies are necessary to confirm a role of NLRP1 in the pathophysiology of MS.
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Affiliation(s)
- Cecily Q Bernales
- Department of Medical Genetics, University of British Columbia, 5639-2215 Wesbrook Mall, Vancouver, BC, V6T 1Z3, Canada
| | - Mary Encarnacion
- Department of Medical Genetics, University of British Columbia, 5639-2215 Wesbrook Mall, Vancouver, BC, V6T 1Z3, Canada
| | - Maria G Criscuoli
- Department of Medical Genetics, University of British Columbia, 5639-2215 Wesbrook Mall, Vancouver, BC, V6T 1Z3, Canada
| | - Irene M Yee
- Department of Medical Genetics, University of British Columbia, 5639-2215 Wesbrook Mall, Vancouver, BC, V6T 1Z3, Canada
| | - Anthony L Traboulsee
- Division of Neurology, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - A Dessa Sadovnick
- Department of Medical Genetics, University of British Columbia, 5639-2215 Wesbrook Mall, Vancouver, BC, V6T 1Z3, Canada.,Division of Neurology, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Carles Vilariño-Güell
- Department of Medical Genetics, University of British Columbia, 5639-2215 Wesbrook Mall, Vancouver, BC, V6T 1Z3, Canada.
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7
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Sadovnick AD, Gu BJ, Traboulsee AL, Bernales CQ, Encarnacion M, Yee IM, Criscuoli MG, Huang X, Ou A, Milligan CJ, Petrou S, Wiley JS, Vilariño-Güell C. Purinergic receptors P2RX4 and P2RX7 in familial multiple sclerosis. Hum Mutat 2017; 38:736-744. [PMID: 28326637 DOI: 10.1002/humu.23218] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 03/08/2017] [Accepted: 03/16/2017] [Indexed: 12/11/2022]
Abstract
Genetic variants in the purinergic receptors P2RX4 and P2RX7 have been shown to affect susceptibility to multiple sclerosis (MS). In this study, we set out to evaluate whether rare coding variants of major effect could also be identified in these purinergic receptors. Sequencing analysis of P2RX4 and P2RX7 in 193 MS patients and 100 controls led to the identification of a rare three variant haplotype (P2RX7 rs140915863:C>T [p.T205M], P2RX7 rs201921967:A>G [p.N361S], and P2RX4 rs765866317:G>A [p.G135S]) segregating with disease in a multi-incident family with six family members diagnosed with MS (logarithm of odds = 3.07). Functional analysis of this haplotype in HEK293 cells revealed impaired P2X7 surface expression (P < 0.01), resulting in over 95% inhibition of adenosine triphosphate (ATP)-induced pore function (P < 0.001) and a marked reduction in phagocytic ability (P < 0.05). In addition, transfected cells showed 40% increased peak ATP-induced inward current (P < 0.01), and a greater Ca2+ response to the P2X4 135S variant compared with wild type (P < 0.0001). Our study nominates rare genetic variants in P2RX4 and P2RX7 as major genetic contributors to disease, further supporting a role for these purinergic receptors in MS and the disruption of transmembrane cation channels leading to impairment of phagocytosis as the pathological mechanisms of disease.
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Affiliation(s)
- A Dessa Sadovnick
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada.,Division of Neurology, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Ben J Gu
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, Victoria, Australia
| | - Anthony L Traboulsee
- Division of Neurology, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Cecily Q Bernales
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Mary Encarnacion
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Irene M Yee
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Maria G Criscuoli
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Xin Huang
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, Victoria, Australia
| | - Amber Ou
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, Victoria, Australia
| | - Carol J Milligan
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, Victoria, Australia
| | - Steven Petrou
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, Victoria, Australia
| | - James S Wiley
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, Victoria, Australia
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8
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Common genetic etiology between “multiple sclerosis-like” single-gene disorders and familial multiple sclerosis. Hum Genet 2017; 136:705-714. [DOI: 10.1007/s00439-017-1784-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 03/18/2017] [Indexed: 12/24/2022]
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9
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Zhou H, Skolnick J. A knowledge-based approach for predicting gene-disease associations. Bioinformatics 2016; 32:2831-8. [PMID: 27283949 DOI: 10.1093/bioinformatics/btw358] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 05/31/2016] [Indexed: 01/20/2023] Open
Abstract
MOTIVATION Recent advances of next-generation sequence technologies have made it possible to rapidly and inexpensively identify gene variations. Knowing the disease association of these gene variations is important for early intervention to treat deadly diseases and provide possible targets to cure these diseases. Genome-wide association studies (GWAS) have identified many individual genes associated with common diseases. To exploit the large amount of data obtained from GWAS studies and leverage our understanding of common as well as rare diseases, we have developed a knowledge-based approach to predict gene-disease associations. We first derive gene-gene mutual information by utilizing the cooccurrence of genes in known gene-disease association data. Subsequently, the mutual information is combined with known protein-protein interaction networks by a boosted tree regression method. RESULTS The method called Know-GENE is compared with the method of random walking on the heterogeneous network using the same input data. For a set of 960 diseases, using the same training data in testing in 3-fold cross-validation, the average recall rate within the top ranked 100 genes by Know-GENE is 65.0% compared with 37.9% by the state of the art random walking on heterogeneous network. This significant improvement is mostly due to the inclusion of knowledge-based mutual information. AVAILABILITY AND IMPLEMENTATION Predictions for genes associated with the 960 diseases are available at http://cssb2.biology.gatech.edu/knowgene CONTACT : skolnick@gatech.edu.
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Affiliation(s)
- Hongyi Zhou
- School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Jeffrey Skolnick
- School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
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10
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DCTN1 p.K56R in progressive supranuclear palsy. Parkinsonism Relat Disord 2016; 28:56-61. [PMID: 27132499 DOI: 10.1016/j.parkreldis.2016.04.025] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Revised: 04/05/2016] [Accepted: 04/22/2016] [Indexed: 11/20/2022]
Abstract
INTRODUCTION Mutations in dynactin DCTN1 (p150(glued)) have previously been linked to familial motor neuron disease or Perry syndrome (PS) consisting of depression, parkinsonism and hypoventilation. METHODS We sequenced DCTN1 in 636 Caucasian patients with parkinsonism (Parkinson's disease and Parkinson-plus syndromes) and 508 healthy controls. Variants (MAF < 0.01) were subsequently genotyped in Caucasian (1360 cases and 1009 controls) and Asian cohorts (1046 cases and 830 controls), and the functional implications of pathogenic variants were assessed. RESULTS We identified 17 rare variants leading to non-synonymous amino-acid substitutions. Four of the variants were only observed in control subjects, four in both cases and controls and the remaining nine in cases only. One of the variants, DCTN1 p.K56R, was present in two patients with progressive supranuclear palsy (PSP) with a shared minimal 2.2 Mb haplotype. Both subjects have parkinsonism as the most prominent symptom with abnormal ocular movements, moderate cognitive impairment and little to no l-dopa response. Neither subject presents with depression, central hypoventilation or weight loss. For one of the subjects MRI shows symmetrical atrophy of temporal and frontoparietal lobes. In HEK293 cells mutant p150(glued) (p.K56R) shows less affinity for microtubules than wild-type, with a more diffuse cytoplasmic distribution. CONCLUSIONS We have identified DCTN1 p.K56R in patients with PSP. This variant is immediately adjacent to the N-terminal p150(glued) 'CAP-Gly' domain, affects a highly conserved amino acid and alters the protein's affinity to microtubules and its cytoplasmic distribution.
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Forwell AL, Bernales CQ, Ross JP, Yee IM, Encarnacion M, Lee JD, Sadovnick AD, Traboulsee AL, Vilariño-Güell C. Analysis of CH25H in multiple sclerosis and neuromyelitis optica. J Neuroimmunol 2015; 291:70-2. [PMID: 26857497 DOI: 10.1016/j.jneuroim.2015.12.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 12/28/2015] [Indexed: 11/28/2022]
Abstract
Oxysterols produced by CH25H during cholesterol metabolism have been shown to play an important role in the immune response. In this study we report the genetic characterization of CH25H in patients diagnosed with multiples sclerosis (MS) or neuromyelitis optica (NMO), for the identification of genetic variants affecting disease susceptibility and course. Exome analysis in 212 MS and 14 NMO patients identified a rare CH25H p.Q17H mutation in two NMO patients of Asian ancestry. In addition, association analysis of common CH25H variants identified a nominally significant association with MS patients presenting a clinical course consistent with primary progressive disease.
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Affiliation(s)
- Amanda L Forwell
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Cecily Q Bernales
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Jay P Ross
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Irene M Yee
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Mary Encarnacion
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Joshua D Lee
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - A Dessa Sadovnick
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada; Division of Neurology, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Anthony L Traboulsee
- Division of Neurology, Faculty of Medicine, University of British Columbia, Vancouver, Canada
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VPS35 and DNAJC13 disease-causing variants in essential tremor. Eur J Hum Genet 2014; 23:887-8. [PMID: 25118025 DOI: 10.1038/ejhg.2014.164] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 07/01/2014] [Accepted: 07/09/2014] [Indexed: 11/08/2022] Open
Abstract
Exome-sequencing analyses have identified vacuolar protein sorting 35 homolog (VPS35) and DnaJ (Hsp40) homolog, subfamily C, member 13 (DNAJC13) harboring disease-causing variants for Parkinson disease (PD). Owing to the suggested clinical, pathological and genetic overlap between PD and essential tremor (ET) we assessed the presence of two VPS35 and DNAJC13 disease-causing variants in ET patients. TaqMan probes were used to genotype VPS35 c.1858G>A (p.(D620N)) (rs188286943) and DNAJC13 c.2564A>G (p.(N855S)) (rs387907571) in 571 ET patients of European descent, and microsatellite markers were used to define the disease haplotype in variant carriers. Genotyping of DNAJC13 identified two ET patients harboring the c.2564A>G (p.(N855S)) variant previously identified in PD patients. Both patients appear to share the disease haplotype previously reported. ET patients with the VPS35 c.1858G>A (p.(D620N)) variants were not observed. Although a genetic link between PD and ET has been suggested, DNAJC13 c.2564A>G (p.(N855S)) represents the first disease-causing variant identified in both, and suggests the regulation of clathrin dynamics and endosomal trafficking in the pathophysiology of a subset of ET patients.
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Genetic variants in IL2RA and IL7R affect multiple sclerosis disease risk and progression. Neurogenetics 2014; 15:165-9. [PMID: 24770783 DOI: 10.1007/s10048-014-0403-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Accepted: 04/09/2014] [Indexed: 12/22/2022]
Abstract
Multiple sclerosis (MS) is a common demyelinating neurodegenerative disease with a strong genetic component. Previous studies have associated genetic variants in IL2RA and IL7R in the pathophysiology of the disease. In this study, we describe the association between IL2RA (rs2104286) and IL7R (rs6897932) in the Canadian population. Genotyping 1,978 MS patients and 830 controls failed to identify any significant association between these variants and disease risk. However, stratified analysis for family history of disease and disease course identified a trend towards association for IL2RA in patients without a family history (p = 0.05; odds ratio = 0.77) and a significant association between IL7R and patients who developed progressive MS (PrMS) (p = 0.002; odds ratio = 0.73). Although not statistically significant, the effect of IL2RA (rs2104286) in patients without a family history of MS indicates that the genetic components for familial and sporadic disease are perhaps distinct. This data suggests that the onset of sporadic disease is likely determined by a large number of variants of small effect, whereas MS in patients with a family history of disease is caused by a few deleterious variants. In addition, the significant association between PrMS and rs6897932 indicates that IL7R may not be disease-causing but a determinant of disease course. Further characterization of the effect of IL2RA and IL7R genetic variants in defined MS subtypes is warranted to evaluate the effect of these genes on specific clinical outcomes and to further elucidate the mechanisms of disease onset and progression.
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Bernales CQ, Ross JP, Lee JD, Zhao Y, Sadovnick AD, Traboulsee AL, Vilariño-Güell C. Progressive multiple sclerosis does not associate with rs996343 and rs2046748. Mult Scler 2013; 20:766-7. [PMID: 24368757 DOI: 10.1177/1352458513517280] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Cecily Q Bernales
- Department of Medical Genetics, University of British Columbia, Canada
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Trinh J, Amouri R, Duda JE, Morley JF, Read M, Donald A, Vilariño-Güell C, Thompson C, Szu Tu C, Gustavsson EK, Ben Sassi S, Hentati E, Zouari M, Farhat E, Nabli F, Hentati F, Farrer MJ. Comparative study of Parkinson's disease and leucine-rich repeat kinase 2 p.G2019S parkinsonism. Neurobiol Aging 2013; 35:1125-31. [PMID: 24355527 DOI: 10.1016/j.neurobiolaging.2013.11.015] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2013] [Revised: 11/13/2013] [Accepted: 11/15/2013] [Indexed: 11/16/2022]
Abstract
Parkinson disease is a progressive neurodegenerative disease for which leucine-rich repeat kinase 2 (LRRK2 carriers) p.G2019S confers substantial genotypic and population attributable risk. With informed consent, we have recruited clinical data from 778 patients from Tunisia (of which 266 have LRRK2 parkinsonism) and 580 unaffected subjects. Motor, autonomic, and cognitive assessments in idiopathic Parkinson disease and LRRK2 patients were compared with regression models. The age-associated cumulative incidence of LRRK2 parkinsonism was also estimated using case-control and family-based designs. LRRK2 parkinsonism patients had slightly less gastrointestinal dysfunction and rapid eye movement sleep disorder. Overall, disease penetrance in LRRK2 carriers was 80% by 70 years but women become affected a median 5 years younger than men. Idiopathic Parkinson disease patients with younger age at diagnosis have slower disease progression. However, age at diagnoses does not predict progression in LRRK2 parkinsonism. LRRK2 p.G2019S mutation is a useful aid to diagnosis and modifiers of disease in LRRK2 parkinsonism may aid in developing therapeutic targets.
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Affiliation(s)
- Joanne Trinh
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.
| | - Rim Amouri
- Mongi Ben Hamida National Institute of neurology, Tunis, Tunisia
| | - John E Duda
- Department of Neurology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - James F Morley
- Department of Neurology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | | | - Alan Donald
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Carles Vilariño-Güell
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Christina Thompson
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Chelsea Szu Tu
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Emil K Gustavsson
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Samia Ben Sassi
- Mongi Ben Hamida National Institute of neurology, Tunis, Tunisia
| | - Emna Hentati
- Mongi Ben Hamida National Institute of neurology, Tunis, Tunisia
| | - Mourad Zouari
- Mongi Ben Hamida National Institute of neurology, Tunis, Tunisia
| | - Emna Farhat
- Mongi Ben Hamida National Institute of neurology, Tunis, Tunisia
| | - Fatma Nabli
- Mongi Ben Hamida National Institute of neurology, Tunis, Tunisia
| | - Faycel Hentati
- Mongi Ben Hamida National Institute of neurology, Tunis, Tunisia
| | - Matthew J Farrer
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
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