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Murthy M, Fodder K, Miki Y, Rambarack N, De Pablo Fernandez E, Pihlstrøm L, Mill J, Warner TT, Lashley T, Bettencourt C. DNA methylation patterns in the frontal lobe white matter of multiple system atrophy, Parkinson's disease, and progressive supranuclear palsy: a cross-comparative investigation. Acta Neuropathol 2024; 148:4. [PMID: 38995454 PMCID: PMC11245434 DOI: 10.1007/s00401-024-02764-4] [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: 04/22/2024] [Revised: 07/04/2024] [Accepted: 07/04/2024] [Indexed: 07/13/2024]
Abstract
Multiple system atrophy (MSA) is a rare neurodegenerative disease characterized by neuronal loss and gliosis, with oligodendroglial cytoplasmic inclusions (GCIs) containing α-synuclein being the primary pathological hallmark. Clinical presentations of MSA overlap with other parkinsonian disorders, such as Parkinson's disease (PD), dementia with Lewy bodies (DLB), and progressive supranuclear palsy (PSP), posing challenges in early diagnosis. Numerous studies have reported alterations in DNA methylation in neurodegenerative diseases, with candidate loci being identified in various parkinsonian disorders including MSA, PD, and PSP. Although MSA and PSP present with substantial white matter pathology, alterations in white matter have also been reported in PD. However, studies comparing the DNA methylation architectures of white matter in these diseases are lacking. We therefore aimed to investigate genome-wide DNA methylation patterns in the frontal lobe white matter of individuals with MSA (n = 17), PD (n = 17), and PSP (n = 16) along with controls (n = 15) using the Illumina EPIC array, to identify shared and disease-specific DNA methylation alterations. Genome-wide DNA methylation profiling of frontal lobe white matter in the three parkinsonian disorders revealed substantial commonalities in DNA methylation alterations in MSA, PD, and PSP. We further used weighted gene correlation network analysis to identify disease-associated co-methylation signatures and identified dysregulation in processes relating to Wnt signaling, signal transduction, endoplasmic reticulum stress, mitochondrial processes, RNA interference, and endosomal transport to be shared between these parkinsonian disorders. Our overall analysis points toward more similarities in DNA methylation patterns between MSA and PD, both synucleinopathies, compared to that between MSA and PD with PSP, which is a tauopathy. Our results also highlight several shared DNA methylation changes and pathways indicative of converging molecular mechanisms in the white matter contributing toward neurodegeneration in all three parkinsonian disorders.
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Affiliation(s)
- Megha Murthy
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, London, UK
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
| | - Katherine Fodder
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, London, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
| | - Yasuo Miki
- Department of Neuropathology, Institute of Brain Science, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Naiomi Rambarack
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, London, UK
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
| | - Eduardo De Pablo Fernandez
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, London, UK
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
- Reta Lila Weston Institute, UCL Queen Square Institute of Neurology, London, UK
| | - Lasse Pihlstrøm
- Department of Neurology, Oslo University Hospital, Oslo, Norway
| | - Jonathan Mill
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Thomas T Warner
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, London, UK
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
- Reta Lila Weston Institute, UCL Queen Square Institute of Neurology, London, UK
| | - Tammaryn Lashley
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
| | - Conceição Bettencourt
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, London, UK.
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK.
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2
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Nicholson L, Piras IS, DeBoth MD, Siniard A, Heras-Garvin A, Stefanova N, Huentelman MJ. Transcriptomic insights into multiple system atrophy from a PLP-α-synuclein transgenic mouse model. Brain Res 2024; 1834:148912. [PMID: 38575106 DOI: 10.1016/j.brainres.2024.148912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 03/24/2024] [Accepted: 04/02/2024] [Indexed: 04/06/2024]
Abstract
Multiple system atrophy (MSA) is a rare, neurodegenerative disorder with rapid motor and non-motor symptom progression. MSA is characterized by protein aggregations of α-synuclein found in the cytoplasm of oligodendrocytes. Despite this pathological hallmark, there is still little known about the cause of this disease, resulting in poor treatment options and quality of life post-diagnosis. In this study, we investigated differentially expressed genes (DEGs) via RNA-sequencing of brain samples from a validated PLP-α-synuclein transgenic mouse model, identifying a total of 40 DEGs in the PLP group compared to wild-type (WT), with top detected genes being Gm15446, Mcm6, Aldh7a1 and Gm3435. We observed a significant enrichment of immune pathways and endothelial cell genes among the upregulated genes, whereas downregulated genes were significantly enriched for oligodendrocyte and neuronal genes. We then calculated possible overlap of these DEGs with previously profiled human MSA RNA, resulting in the identification of significant downregulation of the Tsr2 gene. Identifying key gene expression profiles specific to MSA patients is crucial to further understanding the cause, and possible prevention, of this rapidly progressive neurodegenerative disorder.
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Affiliation(s)
- L Nicholson
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - I S Piras
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - M D DeBoth
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - A Siniard
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - A Heras-Garvin
- Laboratory for Translational Neurodegeneration Research, Department of Neurology, Medical University of Innsbruck, Austria
| | - N Stefanova
- Laboratory for Translational Neurodegeneration Research, Department of Neurology, Medical University of Innsbruck, Austria.
| | - M J Huentelman
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, USA.
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Wan L, Zhu S, Chen Z, Qiu R, Tang B, Jiang H. Multidimensional biomarkers for multiple system atrophy: an update and future directions. Transl Neurodegener 2023; 12:38. [PMID: 37501056 PMCID: PMC10375766 DOI: 10.1186/s40035-023-00370-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 07/11/2023] [Indexed: 07/29/2023] Open
Abstract
Multiple system atrophy (MSA) is a fatal progressive neurodegenerative disease. Biomarkers are urgently required for MSA to improve the diagnostic and prognostic accuracy in clinic and facilitate the development and monitoring of disease-modifying therapies. In recent years, significant research efforts have been made in exploring multidimensional biomarkers for MSA. However, currently few biomarkers are available in clinic. In this review, we systematically summarize the latest advances in multidimensional biomarkers for MSA, including biomarkers in fluids, tissues and gut microbiota as well as imaging biomarkers. Future directions for exploration of novel biomarkers and promotion of implementation in clinic are also discussed.
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Affiliation(s)
- Linlin Wan
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, China
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, China
- Department of Radiology, Xiangya Hospital, Central South University, Changsha, 410008, China
- National International Collaborative Research Center for Medical Metabolomics, Central South University, Changsha, 410008, China
| | - Sudan Zhu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Zhao Chen
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, China
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, China
- Hunan International Scientific and Technological Cooperation Base of Neurodegenerative and Neurogenetic Diseases, Changsha, 410008, China
| | - Rong Qiu
- School of Computer Science and Engineering, Central South University, Changsha, 410083, China
| | - Beisha Tang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, China
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, China
- Hunan International Scientific and Technological Cooperation Base of Neurodegenerative and Neurogenetic Diseases, Changsha, 410008, China
| | - Hong Jiang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, China.
- Department of Neurology, The Third Xiangya Hospital, Central South University, Changsha, 410013, China.
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, 410008, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, China.
- Hunan International Scientific and Technological Cooperation Base of Neurodegenerative and Neurogenetic Diseases, Changsha, 410008, China.
- National International Collaborative Research Center for Medical Metabolomics, Central South University, Changsha, 410008, China.
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Santulli C, Bon C, De Cecco E, Codrich M, Narkiewicz J, Parisse P, Perissinotto F, Santoro C, Persichetti F, Legname G, Espinoza S, Gustincich S. Neuronal haemoglobin induces loss of dopaminergic neurons in mouse Substantia nigra, cognitive deficits and cleavage of endogenous α-synuclein. Cell Death Dis 2022; 13:1048. [PMID: 36526614 PMCID: PMC9758156 DOI: 10.1038/s41419-022-05489-y] [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: 05/10/2022] [Revised: 11/30/2022] [Accepted: 12/01/2022] [Indexed: 12/23/2022]
Abstract
Parkinson's disease (PD) presents the selective loss of A9 dopaminergic (DA) neurons of Substantia Nigra pars compacta (SNpc) and the presence of intracellular aggregates called Lewy bodies. α-synuclein (α-syn) species truncated at the carboxy-terminal (C-terminal) accumulate in pathological inclusions and promote α-syn aggregation and toxicity. Haemoglobin (Hb) is the major oxygen carrier protein in erythrocytes. In addition, Hb is expressed in A9 DA neurons where it influences mitochondrial activity. Hb overexpression increases cells' vulnerability in a neurochemical model of PD in vitro and forms cytoplasmic and nucleolar aggregates upon short-term overexpression in mouse SNpc. In this study, α and β-globin chains were co-expressed in DA cells of SNpc in vivo upon stereotaxic injections of an Adeno-Associated Virus isotype 9 (AAV9) and in DA iMN9D cells in vitro. Long-term Hb over-expression in SNpc induced the loss of about 50% of DA neurons, mild motor impairments, and deficits in recognition and spatial working memory. Hb triggered the formation of endogenous α-syn C-terminal truncated species. Similar α-syn fragments were found in vitro in DA iMN9D cells over-expressing α and β- globins when treated with pre-formed α-syn fibrils. Our study positions Hb as a relevant player in PD pathogenesis for its ability to trigger DA cells' loss in vivo and the formation of C-terminal α-syn fragments.
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Affiliation(s)
- Chiara Santulli
- grid.5970.b0000 0004 1762 9868Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy
| | - Carlotta Bon
- grid.25786.3e0000 0004 1764 2907Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genova, Italy
| | - Elena De Cecco
- grid.5970.b0000 0004 1762 9868Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy
| | - Marta Codrich
- grid.5970.b0000 0004 1762 9868Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy
| | - Joanna Narkiewicz
- grid.5970.b0000 0004 1762 9868Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy
| | - Pietro Parisse
- grid.5942.a0000 0004 1759 508XElettra – Sincrotrone Trieste S.C.p.A., Trieste, Italy ,grid.472635.10000 0004 6476 9521Istituto Officina dei Materiali – Consiglio Nazionale delle Ricerche, Trieste, Italy
| | - Fabio Perissinotto
- grid.5942.a0000 0004 1759 508XElettra – Sincrotrone Trieste S.C.p.A., Trieste, Italy
| | - Claudio Santoro
- grid.16563.370000000121663741Department of Health Sciences and Research Center on Autoimmune and Allergic Diseases (CAAD), University of Piemonte Orientale (UPO), Novara, Italy
| | - Francesca Persichetti
- grid.16563.370000000121663741Department of Health Sciences and Research Center on Autoimmune and Allergic Diseases (CAAD), University of Piemonte Orientale (UPO), Novara, Italy
| | - Giuseppe Legname
- grid.5970.b0000 0004 1762 9868Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy ,grid.5942.a0000 0004 1759 508XElettra – Sincrotrone Trieste S.C.p.A., Trieste, Italy
| | - Stefano Espinoza
- grid.25786.3e0000 0004 1764 2907Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genova, Italy ,grid.16563.370000000121663741Department of Health Sciences and Research Center on Autoimmune and Allergic Diseases (CAAD), University of Piemonte Orientale (UPO), Novara, Italy
| | - Stefano Gustincich
- grid.5970.b0000 0004 1762 9868Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy ,grid.25786.3e0000 0004 1764 2907Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genova, Italy
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Abstract
Multiple system atrophy (MSA) is a rare neurodegenerative disease that is characterized by neuronal loss and gliosis in multiple areas of the central nervous system including striatonigral, olivopontocerebellar and central autonomic structures. Oligodendroglial cytoplasmic inclusions containing misfolded and aggregated α-synuclein are the histopathological hallmark of MSA. A firm clinical diagnosis requires the presence of autonomic dysfunction in combination with parkinsonism that responds poorly to levodopa and/or cerebellar ataxia. Clinical diagnostic accuracy is suboptimal in early disease because of phenotypic overlaps with Parkinson disease or other types of degenerative parkinsonism as well as with other cerebellar disorders. The symptomatic management of MSA requires a complex multimodal approach to compensate for autonomic failure, alleviate parkinsonism and cerebellar ataxia and associated disabilities. None of the available treatments significantly slows the aggressive course of MSA. Despite several failed trials in the past, a robust pipeline of putative disease-modifying agents, along with progress towards early diagnosis and the development of sensitive diagnostic and progression biomarkers for MSA, offer new hope for patients.
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Epigenetic and gene expression changes of neuronal cells from MSA patients are pronounced in enzymes for cell metabolism and calcium-regulated protein kinases. Acta Neuropathol 2021; 142:781-783. [PMID: 34370068 PMCID: PMC8423633 DOI: 10.1007/s00401-021-02357-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 08/03/2021] [Accepted: 08/04/2021] [Indexed: 11/29/2022]
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Sugiyama A, Cooper G, Hirano S, Yokota H, Mori M, Shimizu K, Yakiyama M, Finke C, Brandt AU, Paul F, Kuwabara S. Cognitive Impairment in Multiple System Atrophy Is Related to White Matter Damage Detected by the T1-Weighted/T2-Weighted Ratio. Eur Neurol 2021; 84:435-443. [PMID: 34284398 DOI: 10.1159/000517360] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 05/15/2021] [Indexed: 11/19/2022]
Abstract
INTRODUCTION This study aimed to use a novel MRI contrast, the standardized T1-weighted/T2-weighted (sT1w/T2w) ratio, to assess damage of the white matter and gray matter in multiple system atrophy (MSA). Furthermore, this study investigated whether the sT1w/T2w ratio was associated with cognitive impairment in MSA. METHODS The white matter and gray matter sT1w/T2w ratio of 37 MSA patients and 19 healthy controls were measured. Correlation analyses were used to evaluate the relationship between sT1w/T2w ratio values and clinical variables, and a multivariate analysis was used to identify independent factors associated with cognitive impairment in MSA. RESULTS MSA patients showed a higher white matter sT1w/T2w ratio value than controls (p < 0.001), and the white matter sT1w/T2w ratio value was significantly correlated with the International Cooperative Ataxia Rating Scale score (r = 0.377, p = 0.021) and the Addenbrooke's cognitive examination III score (r = -0.438, p = 0.007). Cognitively impaired MSA patients had a significantly higher white matter sT1w/T2w ratio value than cognitively preserved MSA patients (p = 0.010), and the multiple logistic regression analysis revealed that the median white matter sT1w/T2w ratio value was independently associated with cognitive impairment in MSA. CONCLUSION The sT1w/T2w ratio is sensitive to degenerative changes in the white matter that is associated with cognitive ability in MSA patients.
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Affiliation(s)
- Atsuhiko Sugiyama
- Department of Neurology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Graham Cooper
- Experimental and Clinical Research Center, Max Delbrueck Center for Molecular Medicine and Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany.,NeuroCure Clinical Research Center, Charité - Universitätsmedizin Berlin, Berlin, Germany.,Einstein Center for Neurosciences, Berlin, Germany.,Department of Experimental Neurology and Center for Stroke Research, Berlin, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Shigeki Hirano
- Department of Neurology, Graduate School of Medicine, Chiba University, Chiba, Japan.,Medical Center for Dementia, Chiba University Hospital, Chiba, Japan
| | - Hajime Yokota
- Department of Diagnostic Radiology and Radiation Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Masahiro Mori
- Department of Neurology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Keisuke Shimizu
- Medical Center for Dementia, Chiba University Hospital, Chiba, Japan
| | | | - Carsten Finke
- Einstein Center for Neurosciences, Berlin, Germany.,Department of Neurology, Charité - Universitätsmedizin Berlin, Berlin, Germany.,Berlin School of Mind and Brain, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Alexander U Brandt
- NeuroCure Clinical Research Center, Charité - Universitätsmedizin Berlin, Berlin, Germany.,Department of Neurology, University of California, Irvine, California, USA
| | - Friedemann Paul
- Experimental and Clinical Research Center, Max Delbrueck Center for Molecular Medicine and Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany.,NeuroCure Clinical Research Center, Charité - Universitätsmedizin Berlin, Berlin, Germany.,Einstein Center for Neurosciences, Berlin, Germany.,Department of Neurology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Satoshi Kuwabara
- Department of Neurology, Graduate School of Medicine, Chiba University, Chiba, Japan.,Medical Center for Dementia, Chiba University Hospital, Chiba, Japan
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Pérez-Soriano A, Martí MJ. Mini-Review: The MSA transcriptome. Neurosci Lett 2020; 743:135586. [PMID: 33352281 DOI: 10.1016/j.neulet.2020.135586] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 12/13/2020] [Indexed: 02/07/2023]
Abstract
Multiple system atrophy (MSA) is an atypical parkinsonism that rapidly affects motor ability and autonomic function, leaving patients wheelchair-bound and dependent for daily activities in 3-5 years. Differential diagnosis is challenging as cases may resemble Parkinson's disease or other ataxic syndromes depending on the clinical variant (MSA-P or MSA-C), especially in early stages. There are limited symptomatic treatments and no disease-modifying therapies. Pathologically, alpha-synuclein aggregates are found in glial cytoplasmic inclusions, among other proteins, as well as in neurons. The molecular pathogenesis of the disease, however, is widely unknown. Transcriptomic studies in MSA have tried to unravel the pathological mechanisms involved in the disease. Several biological and molecular processes have been described in the literature that associate disease pathogenesis with inflammation, mitochondrial, and autophagy related dysfunctions, as well as prion disease and Alzheimer disease associated pathways. These reports have also registered several differential diagnostic biomarker candidates. However, cross-validation between studies, in general, is poor, making clinical applicability and data reliability very challenging. This review will go over the main transcriptomic studies done in MSA, reporting on the most significant transcriptive and post-transcriptive changes described, and focusing on the main consensual findings.
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Affiliation(s)
- Alexandra Pérez-Soriano
- Parkinson's Disease & Movement Disorders Unit, Hospital Clínic / IDIBAPS / CIBERNED CB06/05/0018/ European Reference Network for Rare NeurologicalDiseases (ERN-RND Project ID: 739510) / Institut de Neurociències, University of Barcelona, Catalonia, Spain
| | - María J Martí
- Parkinson's Disease & Movement Disorders Unit, Hospital Clínic / IDIBAPS / CIBERNED CB06/05/0018/ European Reference Network for Rare NeurologicalDiseases (ERN-RND Project ID: 739510) / Institut de Neurociències, University of Barcelona, Catalonia, Spain.
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Pérez-Soriano A, Arnal Segura M, Botta-Orfila T, Giraldo D, Fernández M, Compta Y, Fernández-Santiago R, Ezquerra M, Tartaglia GG, Martí MJ. Transcriptomic differences in MSA clinical variants. Sci Rep 2020; 10:10310. [PMID: 32587362 PMCID: PMC7316739 DOI: 10.1038/s41598-020-66221-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 05/15/2020] [Indexed: 11/09/2022] Open
Abstract
Background: Multiple system atrophy (MSA) is a rare oligodendroglial synucleinopathy of unknown etiopathogenesis including two major clinical variants with predominant parkinsonism (MSA-P) or cerebellar dysfunction (MSA-C). Objective: To identify novel disease mechanisms we performed a blood transcriptomic study investigating differential gene expression changes and biological process alterations in MSA and its clinical subtypes. Methods: We compared the transcriptome from rigorously gender and age-balanced groups of 10 probable MSA-P, 10 probable MSA-C cases, 10 controls from the Catalan MSA Registry (CMSAR), and 10 Parkinson Disease (PD) patients. Results: Gene set enrichment analyses showed prominent positive enrichment in processes related to immunity and inflammation in all groups, and a negative enrichment in cell differentiation and development of the nervous system in both MSA-P and PD, in contrast to protein translation and processing in MSA-C. Gene set enrichment analysis using expression patterns in different brain regions as a reference also showed distinct results between the different synucleinopathies. Conclusions: In line with the two major phenotypes described in the clinic, our data suggest that gene expression and biological processes might be differentially affected in MSA-P and MSA-C. Future studies using larger sample sizes are warranted to confirm these results.
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Affiliation(s)
- Alexandra Pérez-Soriano
- Parkinson's Disease & Movement Disorders Unit, Hospital Clínic/IDIBAPS/CIBERNED/European Reference Network for Rare Neurological Diseases (ERN-RND)/Institut de Neurociències, University of Barcelona, Catalonia, Spain.,Laboratory of Parkinson Disease and Other Neurodegenerative Movement Disorders, IDIBAPS, Barcelona, Catalonia, Spain.,Gene Function and Evolution Group, Centre for Genomic Regulation (CRG), Parc de Recerca Biomédica de Barcelona (PRBB), Barcelona, Catalonia, Spain
| | - Magdalena Arnal Segura
- Gene Function and Evolution Group, Centre for Genomic Regulation (CRG), Parc de Recerca Biomédica de Barcelona (PRBB), Barcelona, Catalonia, Spain.,Human Computational Biology Group, Hospital del Mar Medical Research Institute (IMIM), Parc de Recerca Biomédica de Barcelona (PRBB), Barcelona, Catalonia, Spain
| | - Teresa Botta-Orfila
- Gene Function and Evolution Group, Centre for Genomic Regulation (CRG), Parc de Recerca Biomédica de Barcelona (PRBB), Barcelona, Catalonia, Spain.,Biological Fluids Biobank; IDIBAPS-Hospital Clinic of Barcelona, Barcelona, Catalonia, Spain
| | - Darly Giraldo
- Parkinson's Disease & Movement Disorders Unit, Hospital Clínic/IDIBAPS/CIBERNED/European Reference Network for Rare Neurological Diseases (ERN-RND)/Institut de Neurociències, University of Barcelona, Catalonia, Spain
| | - Manel Fernández
- Laboratory of Parkinson Disease and Other Neurodegenerative Movement Disorders, IDIBAPS, Barcelona, Catalonia, Spain.,María de Maeztu Unit of Excellence (Institute of Neurosciences, University of Barcelona), Ministry of Science, Innovation and Universities, Barcelona, Catalonia, Spain
| | - Yaroslau Compta
- Parkinson's Disease & Movement Disorders Unit, Hospital Clínic/IDIBAPS/CIBERNED/European Reference Network for Rare Neurological Diseases (ERN-RND)/Institut de Neurociències, University of Barcelona, Catalonia, Spain
| | - Rubén Fernández-Santiago
- Laboratory of Parkinson Disease and Other Neurodegenerative Movement Disorders, IDIBAPS, Barcelona, Catalonia, Spain
| | - Mario Ezquerra
- Laboratory of Parkinson Disease and Other Neurodegenerative Movement Disorders, IDIBAPS, Barcelona, Catalonia, Spain
| | - Gian G Tartaglia
- Gene Function and Evolution Group, Centre for Genomic Regulation (CRG), Parc de Recerca Biomédica de Barcelona (PRBB), Barcelona, Catalonia, Spain.,María de Maeztu Unit of Excellence (Institute of Neurosciences, University of Barcelona), Ministry of Science, Innovation and Universities, Barcelona, Catalonia, Spain.,Institució Catalana de Recerca I Estudis Avançats (ICREA), Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - M J Martí
- Parkinson's Disease & Movement Disorders Unit, Hospital Clínic/IDIBAPS/CIBERNED/European Reference Network for Rare Neurological Diseases (ERN-RND)/Institut de Neurociències, University of Barcelona, Catalonia, Spain.
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10
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Piras IS, Bleul C, Schrauwen I, Talboom J, Llaci L, De Both MD, Naymik MA, Halliday G, Bettencourt C, Holton JL, Serrano GE, Sue LI, Beach TG, Stefanova N, Huentelman MJ. Transcriptional profiling of multiple system atrophy cerebellar tissue highlights differences between the parkinsonian and cerebellar sub-types of the disease. Acta Neuropathol Commun 2020; 8:76. [PMID: 32493431 PMCID: PMC7268362 DOI: 10.1186/s40478-020-00950-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 05/19/2020] [Indexed: 01/04/2023] Open
Abstract
Multiple system atrophy (MSA) is a rare adult-onset neurodegenerative disease of unknown cause, with no effective therapeutic options, and no cure. Limited work to date has attempted to characterize the transcriptional changes associated with the disease, which presents as either predominating parkinsonian (MSA-P) or cerebellar (MSC-C) symptoms. We report here the results of RNA expression profiling of cerebellar white matter (CWM) tissue from two independent cohorts of MSA patients (n = 66) and healthy controls (HC; n = 66). RNA samples from bulk brain tissue and from oligodendrocytes obtained by laser capture microdissection (LCM) were sequenced. Differentially expressed genes (DEGs) were obtained and were examined before and after stratifying by MSA clinical sub-type.We detected the highest number of DEGs in the MSA-C group (n = 747) while only one gene was noted in MSA-P, highlighting the larger dysregulation of the transcriptome in the MSA-C CWM. Results from both bulk tissue and LCM analysis showed a downregulation of oligodendrocyte genes and an enrichment for myelination processes with a key role noted for the QKI gene. Additionally, we observed a significant upregulation of neuron-specific gene expression in MSA-C and enrichment for synaptic processes. A third cluster of genes was associated with the upregulation of astrocyte and endothelial genes, two cell types with a key role in inflammation processes. Finally, network analysis in MSA-C showed enrichment for β-amyloid related functional classes, including the known Alzheimer's disease (AD) genes, APP and PSEN1.This is the largest RNA profiling study ever conducted on post-mortem brain tissue from MSA patients. We were able to define specific gene expression signatures for MSA-C highlighting the different stages of the complex neurodegenerative cascade of the disease that included alterations in several cell-specific transcriptional programs. Finally, several results suggest a common transcriptional dysregulation between MSA and AD-related genes despite the clinical and neuropathological distinctions between the two diseases.
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Affiliation(s)
- Ignazio S Piras
- Neurogenomics Division, The Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Christiane Bleul
- Neurogenomics Division, The Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Isabelle Schrauwen
- Neurogenomics Division, The Translational Genomics Research Institute, Phoenix, AZ, USA
- Present Address: Department of Neurology, Center for Statistical Genetics, Gertrude H. Sergievsky Center, Columbia University Medical Center, 630 W 168th St, New York, NY, 10032, USA
| | - Joshua Talboom
- Neurogenomics Division, The Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Lorida Llaci
- Neurogenomics Division, The Translational Genomics Research Institute, Phoenix, AZ, USA
- Present address: Division of Biology and Biomedical Sciences, Molecular Genetics and Genomics Program, Washington University in St. Louis, St. Louis, MO, 63110, USA
| | - Matthew D De Both
- Neurogenomics Division, The Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Marcus A Naymik
- Neurogenomics Division, The Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Glenda Halliday
- The University of Sydney Brain and Mind Centre and Faculty of Medicine and Health, School of Medical Science, and Neuroscience Research Australia, Sydney, Australia
| | - Conceicao Bettencourt
- Queen Square Brain Bank for Neurological Disorders and Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
| | - Janice L Holton
- Queen Square Brain Bank for Neurological Disorders and Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
| | - Geidy E Serrano
- Civin Laboratory of Neuropathology at Banner Sun Health Research Institute, Sun City, AZ, 85351, USA
| | - Lucia I Sue
- Civin Laboratory of Neuropathology at Banner Sun Health Research Institute, Sun City, AZ, 85351, USA
| | - Thomas G Beach
- Civin Laboratory of Neuropathology at Banner Sun Health Research Institute, Sun City, AZ, 85351, USA
| | - Nadia Stefanova
- Department of Neurology, Division of Neurobiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Matthew J Huentelman
- Neurogenomics Division, The Translational Genomics Research Institute, Phoenix, AZ, USA.
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11
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Sugiyama A, Cooper G, Hirano S, Yokota H, Mori M, Shimizu K, Yakiyama M, Finke C, Brandt AU, Paul F, Kuwabara S. WITHDRAWN: Cognitive impairment in multiple system atrophy is related to white matter damage detected by the T1w/T2w ratio. Parkinsonism Relat Disord 2020. [DOI: 10.1016/j.parkreldis.2020.05.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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12
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Altinoz MA, Guloksuz S, Schmidt-Kastner R, Kenis G, Ince B, Rutten BPF. Involvement of hemoglobins in the pathophysiology of Alzheimer's disease. Exp Gerontol 2019; 126:110680. [PMID: 31382012 DOI: 10.1016/j.exger.2019.110680] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 07/03/2019] [Accepted: 08/01/2019] [Indexed: 12/11/2022]
Abstract
Hemoglobins (Hbs) are heme-containing proteins binding oxygen, carbon monoxide, and nitric oxide. While erythrocytes are the most well-known location of Hbs, Hbs also exist in neurons, glia and oligodendroglia and they are primarily localized in the inner mitochondrial membrane of neurons with likely roles in cellular respiration and buffering protons. Recently, studies have suggested links between hypoxia and neurodegenerative disorders such as Alzheimer Disease (AD) and furthermore suggested involvement of Hbs in the pathogenesis of AD. While cellular immunohistochemical studies on AD brains have observed reduced levels of Hb in the cytoplasm of pre-tangle and tangle-bearing neurons, other studies on homogenates of AD brain samples observed increased Hb levels. This potential discrepancy may result from differential presence and function of intracellular versus extracellular Hbs. Intracellular Hbs may protect neurons against hypoxia and hyperoxia. On the other hand, extracellular free Hb and its degradation products may trigger inflammatory immune and oxidative reactions against neural macromolecules and/or damage the blood-brain barrier. Therefore, biological processes leading to reduction of Hb transcription (including clinically silent Hb mutations) may influence intra-erythrocytic and neural Hbs, and reduce the transport of oxygen, carbon monoxide and nitric oxide which may be involved in the (patho)physiology of neurodegenerative disorders such as AD. Agents such as erythropoietin, which stimulate both erythropoiesis, reduce eryptosis and induce intracellular neural Hbs may exert multiple beneficial effects on the onset and course of AD. Thus, evidence accumulates for a role of Hbs in the central nervous system while Hbs deserve more attention as possible candidate molecules involved in AD.
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Affiliation(s)
- Meric A Altinoz
- Department of Psychiatry and Psychology, School for Mental Health and Neuroscience, Maastricht University Medical Centre, Maastricht, the Netherlands.
| | - Sinan Guloksuz
- Department of Psychiatry and Psychology, School for Mental Health and Neuroscience, Maastricht University Medical Centre, Maastricht, the Netherlands; Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
| | - Rainald Schmidt-Kastner
- Integrated Medical Science Department, Charles E. Schmidt College of Medicine, Florida Atlantic University (FAU), Boca Raton, FL, USA
| | - Gunter Kenis
- Department of Psychiatry and Psychology, School for Mental Health and Neuroscience, Maastricht University Medical Centre, Maastricht, the Netherlands
| | - Bahri Ince
- Department of Psychiatry, Mazhar Osman Bakirkoy Mental Diseases Research and Education Hospital, Istanbul, Turkey
| | - Bart P F Rutten
- Department of Psychiatry and Psychology, School for Mental Health and Neuroscience, Maastricht University Medical Centre, Maastricht, the Netherlands
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13
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Non-cell-autonomous actions of α-synuclein: Implications in glial synucleinopathies. Prog Neurobiol 2018; 169:158-171. [DOI: 10.1016/j.pneurobio.2018.06.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 07/24/2017] [Accepted: 06/30/2018] [Indexed: 01/11/2023]
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14
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Vanni S, Zattoni M, Moda F, Giaccone G, Tagliavini F, Haïk S, Deslys JP, Zanusso G, Ironside JW, Carmona M, Ferrer I, Kovacs GG, Legname G. Hemoglobin mRNA Changes in the Frontal Cortex of Patients with Neurodegenerative Diseases. Front Neurosci 2018; 12:8. [PMID: 29403351 PMCID: PMC5786544 DOI: 10.3389/fnins.2018.00008] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Accepted: 01/05/2018] [Indexed: 01/06/2023] Open
Abstract
Background: Hemoglobin is the major protein found in erythrocytes, where it acts as an oxygen carrier molecule. In recent years, its expression has been reported also in neurons and glial cells, although its role in brain tissue remains still unknown. Altered hemoglobin expression has been associated with various neurodegenerative disorders. Here, we investigated hemoglobin mRNA levels in brains of patients affected by variant, iatrogenic, and sporadic forms of Creutzfeldt-Jakob disease (vCJD, iCJD, sCJD, respectively) and in different genetic forms of prion diseases (gPrD) in comparison to Alzheimer's disease (AD) subjects and age-matched controls. Methods: Total RNA was obtained from the frontal cortex of vCJD (n = 20), iCJD (n = 11), sCJD (n = 23), gPrD (n = 30), and AD (n = 14) patients and age-matched controls (n = 30). RT-qPCR was performed for hemoglobin transcripts HBB and HBA1/2 using four reference genes for normalization. In addition, expression analysis of the specific erythrocyte marker ALAS2 was performed in order to account for blood contamination of the tissue samples. Hba1/2 and Hbb protein expression was then investigated with immunofluorescence and confocal microscope analysis. Results: We observed a significant up-regulation of HBA1/2 in vCJD brains together with a significant down-regulation of HBB in iCJD. In addition, while in sporadic and genetic forms of prion disease hemoglobin transcripts did not shown any alterations, both chains display a strong down-regulation in AD brains. These results were confirmed also at a protein level. Conclusions: These data indicate distinct hemoglobin transcriptional responses depending on the specific alterations occurring in different neurodegenerative diseases. In particular, the initial site of misfolding event (central nervous system vs. peripheral tissue)-together with specific molecular and conformational features of the pathological agent of the disease-seem to dictate the peculiar hemoglobin dysregulation found in prion and non-prion neurodegenerative disorders. In addition, these results suggest that gene expression of HBB and HBA1/2 in brain tissue is differentially affected by distinct prion and prion-like aggregating protein strains. Validation of these results in more accessible tissues could prompt the development of novel diagnostic tests for neurodegenerative disorders.
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Affiliation(s)
- Silvia Vanni
- Laboratory of Prion Biology, Department of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati, Trieste, Italy
| | - Marco Zattoni
- Laboratory of Prion Biology, Department of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati, Trieste, Italy
| | - Fabio Moda
- Neurology and Neuropathology Unit, Istituto di Ricovero e Cura a Carattere Scientifico Foundation Carlo Besta Neurological Institute, Milan, Italy
| | - Giorgio Giaccone
- Neurology and Neuropathology Unit, Istituto di Ricovero e Cura a Carattere Scientifico Foundation Carlo Besta Neurological Institute, Milan, Italy
| | - Fabrizio Tagliavini
- Neurology and Neuropathology Unit, Istituto di Ricovero e Cura a Carattere Scientifico Foundation Carlo Besta Neurological Institute, Milan, Italy
| | - Stéphane Haïk
- UPMC Univ Paris 06 UMR S 1127 and Centre National de la Recherche Scientifique UMR 7225, ICM, Sorbonne Universités, Paris, France
| | | | - Gianluigi Zanusso
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - James W Ironside
- National CJD Research and Surveillance Unit, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Margarita Carmona
- Department of Pathology and Experimental Therapeutics, University of Barcelona, Barcelona, Spain
| | - Isidre Ferrer
- Institut d'Investigació Biomédica de Bellvitge (IDIBELL), Bellvitge University Hospital (CIBERNED), Hospitalet de LLobregat, Spain
| | - Gabor G Kovacs
- Institute of Neurology, Medical University of Vienna, Vienna, Austria
| | - Giuseppe Legname
- Laboratory of Prion Biology, Department of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati, Trieste, Italy
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15
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Abstract
Multiple system atrophy (MSA) is an orphan, fatal, adult-onset neurodegenerative disorder of uncertain etiology that is clinically characterized by various combinations of parkinsonism, cerebellar, autonomic, and motor dysfunction. MSA is an α-synucleinopathy with specific glioneuronal degeneration involving striatonigral, olivopontocerebellar, and autonomic nervous systems but also other parts of the central and peripheral nervous systems. The major clinical variants correlate with the morphologic phenotypes of striatonigral degeneration (MSA-P) and olivopontocerebellar atrophy (MSA-C). While our knowledge of the molecular pathogenesis of this devastating disease is still incomplete, updated consensus criteria and combined fluid and imaging biomarkers have increased its diagnostic accuracy. The neuropathologic hallmark of this unique proteinopathy is the deposition of aberrant α-synuclein in both glia (mainly oligodendroglia) and neurons forming glial and neuronal cytoplasmic inclusions that cause cell dysfunction and demise. In addition, there is widespread demyelination, the pathogenesis of which is not fully understood. The pathogenesis of MSA is characterized by propagation of misfolded α-synuclein from neurons to oligodendroglia and cell-to-cell spreading in a "prion-like" manner, oxidative stress, proteasomal and mitochondrial dysfunction, dysregulation of myelin lipids, decreased neurotrophic factors, neuroinflammation, and energy failure. The combination of these mechanisms finally results in a system-specific pattern of neurodegeneration and a multisystem involvement that are specific for MSA. Despite several pharmacological approaches in MSA models, addressing these pathogenic mechanisms, no effective neuroprotective nor disease-modifying therapeutic strategies are currently available. Multidisciplinary research to elucidate the genetic and molecular background of the deleterious cycle of noxious processes, to develop reliable biomarkers and targets for effective treatment of this hitherto incurable disorder is urgently needed.
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16
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Overk C, Rockenstein E, Valera E, Stefanova N, Wenning G, Masliah E. Multiple system atrophy: experimental models and reality. Acta Neuropathol 2018; 135:33-47. [PMID: 29058121 PMCID: PMC6156777 DOI: 10.1007/s00401-017-1772-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 09/29/2017] [Accepted: 09/29/2017] [Indexed: 01/08/2023]
Abstract
Multiple system atrophy (MSA) is a rapidly progressing fatal synucleinopathy of the aging population characterized by parkinsonism, dysautonomia, and in some cases ataxia. Unlike other synucleinopathies, in this disorder the synaptic protein, α-synuclein (α-syn), predominantly accumulates in oligodendroglial cells (and to some extent in neurons), leading to maturation defects of oligodendrocytes, demyelination, and neurodegeneration. The mechanisms through which α-syn deposits occur in oligodendrocytes and neurons in MSA are not completely clear. While some studies suggest that α-syn might transfer from neurons to glial cells, others propose that α-syn might be aberrantly overexpressed by oligodendroglial cells. A number of in vivo models have been developed, including transgenic mice overexpressing α-syn under oligodendroglial promoters (e.g.: MBP, PLP, and CNP). Other models have been recently developed either by injecting synthetic α-syn fibrils or brain homogenates from patients with MSA into wild-type mice or by using viral vectors expressing α-syn under the MBP promoter in rats and non-human primates. Each of these models reproduces some of the neuropathological and functional aspects of MSA; however, none of them fully replicate the spectrum of MSA. Understanding better the mechanisms of how α-syn accumulates in oligodendrocytes and neurons will help in developing better models that recapitulate various pathogenic aspects of MSA in combination with translatable biomarkers of early stages of the disease that are necessary to devise disease-modifying therapeutics for MSA.
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Affiliation(s)
- Cassia Overk
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, 92093-0624, USA
| | - Edward Rockenstein
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, 92093-0624, USA
| | - Elvira Valera
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, 92093-0624, USA
| | - Nadia Stefanova
- Division of Clinical Neurobiology, Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria
| | - Gregor Wenning
- Division of Clinical Neurobiology, Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria
| | - Eliezer Masliah
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, 92093-0624, USA.
- Molecular Neuropathology Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, 20892, USA.
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17
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Szkop KJ, Cooke PIC, Humphries JA, Kalna V, Moss DS, Schuster EF, Nobeli I. Dysregulation of Alternative Poly-adenylation as a Potential Player in Autism Spectrum Disorder. Front Mol Neurosci 2017; 10:279. [PMID: 28955198 PMCID: PMC5601403 DOI: 10.3389/fnmol.2017.00279] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 08/17/2017] [Indexed: 11/30/2022] Open
Abstract
We present here the hypothesis that alternative poly-adenylation (APA) is dysregulated in the brains of individuals affected by Autism Spectrum Disorder (ASD), due to disruptions in the calcium signaling networks. APA, the process of selecting different poly-adenylation sites on the same gene, yielding transcripts with different-length 3′ untranslated regions (UTRs), has been documented in different tissues, stages of development and pathologic conditions. Differential use of poly-adenylation sites has been shown to regulate the function, stability, localization and translation efficiency of target RNAs. However, the role of APA remains rather unexplored in neurodevelopmental conditions. In the human brain, where transcripts have the longest 3′ UTRs and are thus likely to be under more complex post-transcriptional regulation, erratic APA could be particularly detrimental. In the context of ASD, a condition that affects individuals in markedly different ways and whose symptoms exhibit a spectrum of severity, APA dysregulation could be amplified or dampened depending on the individual and the extent of the effect on specific genes would likely vary with genetic and environmental factors. If this hypothesis is correct, dysregulated APA events might be responsible for certain aspects of the phenotypes associated with ASD. Evidence supporting our hypothesis is derived from standard RNA-seq transcriptomic data but we suggest that future experiments should focus on techniques that probe the actual poly-adenylation site (3′ sequencing). To address issues arising from the use of post-mortem tissue and low numbers of heterogeneous samples affected by confounding factors (such as the age, gender and health of the individuals), carefully controlled in vitro systems will be required to model the effect of calcium signaling dysregulation in the ASD brain.
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Affiliation(s)
- Krzysztof J Szkop
- Department of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck, University of LondonLondon, United Kingdom
| | - Peter I C Cooke
- Department of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck, University of LondonLondon, United Kingdom
| | - Joanne A Humphries
- Department of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck, University of LondonLondon, United Kingdom
| | - Viktoria Kalna
- Department of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck, University of LondonLondon, United Kingdom
| | - David S Moss
- Department of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck, University of LondonLondon, United Kingdom
| | | | - Irene Nobeli
- Department of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck, University of LondonLondon, United Kingdom
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18
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Curry-Hyde A, Chen BJ, Ueberham U, Arendt T, Janitz M. Multiple System Atrophy: Many Lessons from the Transcriptome. Neuroscientist 2017; 24:294-307. [PMID: 28770651 DOI: 10.1177/1073858417723915] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Multiple system atrophy (MSA) is a complex, multifactorial, debilitating neurodegenerative disease that is often misdiagnosed and misunderstood. MSA has two subclasses, MSA-P and MSA-C, defined by the dominance of parkinsonism or cerebellar dysfunction in the earlier stages of disease, coupled with dysautonomia. This distinction between subclasses becomes largely redundant as the disease progresses. Aggregation of α-synuclein is a clinical marker used to confirm MSA diagnoses, which can only be performed postmortem. Transcriptome profiling provides in-depth information about the diseased state and can contribute to further understanding of MSA, enabling easier and more rapid diagnosis as well as contributing to improving the quality of life of people with MSA. Currently, there is no method of diagnosing MSA with certainty, and there is no cure for this disease. This review provides an update on current advances in investigations of molecular pathology of MSA with particular focus on perturbation of individual gene expression and MSA transcriptome.
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Affiliation(s)
- Ashton Curry-Hyde
- 1 School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Bei Jun Chen
- 1 School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Uwe Ueberham
- 2 Paul Flechsig Institute for Brain Research, University of Leipzig, Leipzig, Germany
| | - Thomas Arendt
- 2 Paul Flechsig Institute for Brain Research, University of Leipzig, Leipzig, Germany
| | - Michael Janitz
- 1 School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia.,2 Paul Flechsig Institute for Brain Research, University of Leipzig, Leipzig, Germany
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19
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Chen BJ, Ueberham U, Mills JD, Kirazov L, Kirazov E, Knobloch M, Bochmann J, Jendrek R, Takenaka K, Bliim N, Arendt T, Janitz M. RNA sequencing reveals pronounced changes in the noncoding transcriptome of aging synaptosomes. Neurobiol Aging 2017; 56:67-77. [PMID: 28499146 DOI: 10.1016/j.neurobiolaging.2017.04.005] [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: 01/15/2017] [Revised: 03/31/2017] [Accepted: 04/08/2017] [Indexed: 12/12/2022]
Abstract
Normal aging is associated with impairments in cognitive functions. These alterations are caused by diminutive changes in the biology of synapses, and ineffective neurotransmission, rather than loss of neurons. Hitherto, only a few studies, exploring molecular mechanisms of healthy brain aging in higher vertebrates, utilized synaptosomal fractions to survey local changes in aging-related transcriptome dynamics. Here we present, for the first time, a comparative analysis of the synaptosomes transcriptome in the aging mouse brain using RNA sequencing. Our results show changes in the expression of genes contributing to biological pathways related to neurite guidance, synaptosomal physiology, and RNA splicing. More intriguingly, we also discovered alterations in the expression of thousands of novel, unannotated lincRNAs during aging. Further, detailed characterization of the cleavage and polyadenylation factor I subunit 1 (Clp1) mRNA and protein expression indicates its increased expression in neuronal processes of hippocampal stratum radiatum in aging mice. Together, our study uncovers a new layer of transcriptional regulation which is targeted by aging within the local environment of interconnecting neuronal cells.
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Affiliation(s)
- Bei Jun Chen
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Uwe Ueberham
- Paul-Flechsig-Institute for Brain Research, University of Leipzig, School of Medicine, Leipzig, Germany
| | - James D Mills
- Department of (Neuro)Pathology, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Ludmil Kirazov
- Paul-Flechsig-Institute for Brain Research, University of Leipzig, School of Medicine, Leipzig, Germany; Institute of Experimental Morphology, Pathology and Anthropology with Museum, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Evgeni Kirazov
- Paul-Flechsig-Institute for Brain Research, University of Leipzig, School of Medicine, Leipzig, Germany; Institute of Experimental Morphology, Pathology and Anthropology with Museum, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Mara Knobloch
- Paul-Flechsig-Institute for Brain Research, University of Leipzig, School of Medicine, Leipzig, Germany
| | - Jana Bochmann
- Paul-Flechsig-Institute for Brain Research, University of Leipzig, School of Medicine, Leipzig, Germany
| | - Renate Jendrek
- Paul-Flechsig-Institute for Brain Research, University of Leipzig, School of Medicine, Leipzig, Germany
| | - Konii Takenaka
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Nicola Bliim
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Thomas Arendt
- Paul-Flechsig-Institute for Brain Research, University of Leipzig, School of Medicine, Leipzig, Germany
| | - Michael Janitz
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia.
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20
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Abstract
Multiple system atrophy (MSA) is a devastating and fatal neurodegenerative disorder. The clinical presentation of this disease is highly variable, with parkinsonism, cerebellar ataxia and autonomic failure being the most common - and often debilitating - symptoms. These symptoms progress rapidly, and patients die from MSA-related complications after 9 years of symptom duration on average. Unfortunately, the course of the disease cannot be improved by drug or surgical treatment. In addition, symptomatic treatment options are currently limited, and therapeutic benefits are often only transient. Thus, further interventional studies of candidate disease-modifying and symptomatic therapies are essential to improve patient care. In the past 15 years, the understanding of MSA-specific requirements in trial methodology has improved, resulting in a substantial increase in high-quality interventional studies. In this Review, we discuss MSA risk factors, clinical presentation and neuropathology, and we provide a hypothesis on key pathophysiological events, a summary of recent randomized controlled trials, and an overview of ongoing international collaborations.
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21
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Codrich M, Bertuzzi M, Russo R, Francescatto M, Espinoza S, Zentilin L, Giacca M, Cesselli D, Beltrami AP, Ascenzi P, Zucchelli S, Persichetti F, Leanza G, Gustincich S. Neuronal hemoglobin affects dopaminergic cells' response to stress. Cell Death Dis 2017; 8:e2538. [PMID: 28055011 PMCID: PMC5386368 DOI: 10.1038/cddis.2016.458] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 11/21/2016] [Accepted: 12/05/2016] [Indexed: 11/14/2022]
Abstract
Hemoglobin (Hb) is the major protein in erythrocytes and carries oxygen (O2) throughout the body. Recently, Hb has been found synthesized in atypical sites, including the brain. Hb is highly expressed in A9 dopaminergic (DA) neurons of the substantia nigra (SN), whose selective degeneration leads to Parkinson's disease (PD). Here we show that Hb confers DA cells' susceptibility to 1-methyl-4-phenylpyridinium (MPP+) and rotenone, neurochemical cellular models of PD. The toxic property of Hb does not depend on O2 binding and is associated with insoluble aggregate formation in the nucleolus. Neurochemical stress induces epigenetic modifications, nucleolar alterations and autophagy inhibition that depend on Hb expression. When adeno-associated viruses carrying α- and β-chains of Hb are stereotaxically injected into mouse SN, Hb forms aggregates and causes motor learning impairment. These results position Hb as a potential player in DA cells' homeostasis and dysfunction in PD.
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Affiliation(s)
- Marta Codrich
- Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), via Bonomea 265, Trieste 34136, Italy
- Department of Health Sciences, University of Eastern Piedmont ‘A. Avogadro', via Solaroli 17, 28100 Novara, Italy
| | - Maria Bertuzzi
- Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), via Bonomea 265, Trieste 34136, Italy
| | - Roberta Russo
- Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), via Bonomea 265, Trieste 34136, Italy
| | - Margherita Francescatto
- Department of Neuroscience and Brain Technologies, Istituto Italiano di Tecnologia (IIT), via Morego 30, Genova 16163, Italy
| | - Stefano Espinoza
- Department of Neuroscience and Brain Technologies, Istituto Italiano di Tecnologia (IIT), via Morego 30, Genova 16163, Italy
| | | | | | - Daniela Cesselli
- Department of Medical and Biological Sciences, University of Udine, Piazzale Kolbe 4, Udine, 33100, Italy
| | - Antonio Paolo Beltrami
- Department of Medical and Biological Sciences, University of Udine, Piazzale Kolbe 4, Udine, 33100, Italy
| | - Paolo Ascenzi
- Department of Sciences, University of Roma Tre, viale G. Marconi 446, Roma 00146, Italy
| | - Silvia Zucchelli
- Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), via Bonomea 265, Trieste 34136, Italy
- Department of Health Sciences, University of Eastern Piedmont ‘A. Avogadro', via Solaroli 17, 28100 Novara, Italy
| | - Francesca Persichetti
- Department of Health Sciences, University of Eastern Piedmont ‘A. Avogadro', via Solaroli 17, 28100 Novara, Italy
| | - Giampiero Leanza
- Department of Life Sciences, University of Trieste, via Fleming 22, Trieste 34127, Italy
| | - Stefano Gustincich
- Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), via Bonomea 265, Trieste 34136, Italy
- Department of Neuroscience and Brain Technologies, Istituto Italiano di Tecnologia (IIT), via Morego 30, Genova 16163, Italy
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22
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Chen BJ, Mills JD, Takenaka K, Bliim N, Halliday GM, Janitz M. Characterization of circular RNAs landscape in multiple system atrophy brain. J Neurochem 2016; 139:485-496. [DOI: 10.1111/jnc.13752] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 07/24/2016] [Accepted: 07/26/2016] [Indexed: 12/26/2022]
Affiliation(s)
- Bei Jun Chen
- School of Biotechnology and Biomolecular Sciences; University of New South Wales; Sydney New South Wales Australia
| | - James D. Mills
- Deptartment of (Neuro) Pathology; Academic Medical Center and Swammerdam Institute for Life Sciences; Centre for Neuroscience; University of Amsterdam; Amsterdam The Netherlands
| | - Konii Takenaka
- School of Biotechnology and Biomolecular Sciences; University of New South Wales; Sydney New South Wales Australia
| | - Nicola Bliim
- School of Biotechnology and Biomolecular Sciences; University of New South Wales; Sydney New South Wales Australia
| | - Glenda M. Halliday
- Neuroscience Research Australia; Sydney New South Wales Australia
- School of Medical Sciences; University of New South Wales; Sydney New South Wales Australia
| | - Michael Janitz
- School of Biotechnology and Biomolecular Sciences; University of New South Wales; Sydney New South Wales Australia
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23
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Jellinger KA, Wenning GK. Multiple system atrophy: pathogenic mechanisms and biomarkers. J Neural Transm (Vienna) 2016; 123:555-72. [PMID: 27098666 DOI: 10.1007/s00702-016-1545-2] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 03/31/2016] [Indexed: 12/13/2022]
Abstract
Multiple system atrophy (MSA) is a unique proteinopathy that differs from other α-synucleinopathies since the pathological process resulting from accumulation of aberrant α-synuclein (αSyn) involves the oligodendroglia rather than neurons, although both pathologies affect multiple parts of the brain, spinal cord, autonomic and peripheral nervous system. Both the etiology and pathogenesis of MSA are unknown, although animal models have provided insight into the basic molecular changes of this disorder. Accumulation of aberrant αSyn in oligodendroglial cells and preceded by relocation of p25α protein from myelin to oligodendroglia results in the formation of insoluble glial cytoplasmic inclusions that cause cell dysfunction and demise. These changes are associated with proteasomal, mitochondrial and lipid transport dysfunction, oxidative stress, reduced trophic transport, neuroinflammation and other noxious factors. Their complex interaction induces dysfunction of the oligodendroglial-myelin-axon-neuron complex, resulting in the system-specific pattern of neurodegeneration characterizing MSA as a synucleinopathy with oligodendroglio-neuronopathy. Propagation of modified toxic αSyn species from neurons to oligodendroglia by "prion-like" transfer and its spreading associated with neuronal pathways result in a multi-system involvement. No reliable biomarkers are currently available for the clinical diagnosis and prognosis of MSA. Multidisciplinary research to elucidate the genetic and molecular background of the deleterious cycle of noxious processes, to develop reliable diagnostic biomarkers and to deliver targets for effective treatment of this hitherto incurable disorder is urgently needed.
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Affiliation(s)
- Kurt A Jellinger
- Institute of Clinical Neurobiology, Alberichgasse 5/13, 1150, Vienna, Austria.
| | - Gregor K Wenning
- Division of Clinical Neurobiology, Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria
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24
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Schafferer S, Khurana R, Refolo V, Venezia S, Sturm E, Piatti P, Hechenberger C, Hackl H, Kessler R, Willi M, Gstir R, Krogsdam A, Lusser A, Poewe W, Wenning GK, Hüttenhofer A, Stefanova N. Changes in the miRNA-mRNA Regulatory Network Precede Motor Symptoms in a Mouse Model of Multiple System Atrophy: Clinical Implications. PLoS One 2016; 11:e0150705. [PMID: 26962858 PMCID: PMC4786272 DOI: 10.1371/journal.pone.0150705] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 02/18/2016] [Indexed: 12/31/2022] Open
Abstract
Multiple system atrophy (MSA) is a fatal rapidly progressive α-synucleinopathy, characterized by α-synuclein accumulation in oligodendrocytes. It is accepted that the pathological α-synuclein accumulation in the brain of MSA patients plays a leading role in the disease process, but little is known about the events in the early stages of the disease. In this study we aimed to define potential roles of the miRNA-mRNA regulatory network in the early pre-motor stages of the disease, i.e., downstream of α-synuclein accumulation in oligodendroglia, as assessed in a transgenic mouse model of MSA. We investigated the expression patterns of miRNAs and their mRNA targets in substantia nigra (SN) and striatum, two brain regions that undergo neurodegeneration at a later stage in the MSA model, by microarray and RNA-seq analysis, respectively. Analysis was performed at a time point when α-synuclein accumulation was already present in oligodendrocytes at neuropathological examination, but no neuronal loss nor deficits of motor function had yet occurred. Our data provide a first evidence for the leading role of gene dysregulation associated with deficits in immune and inflammatory responses in the very early, non-symptomatic disease stages of MSA. While dysfunctional homeostasis and oxidative stress were prominent in SN in the early stages of MSA, in striatum differential gene expression in the non-symptomatic phase was linked to oligodendroglial dysfunction, disturbed protein handling, lipid metabolism, transmembrane transport and altered cell death control, respectively. A large number of putative miRNA-mRNAs interaction partners were identified in relation to the control of these processes in the MSA model. Our results support the role of early changes in the miRNA-mRNA regulatory network in the pathogenesis of MSA preceding the clinical onset of the disease. The findings thus contribute to understanding the disease process and are likely to pave the way towards identifying disease biomarkers for early diagnosis of MSA.
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Affiliation(s)
- Simon Schafferer
- Division of Genomics and RNomics, Biocenter, Medical University of Innsbruck, Innrain 80–82, 6020 Innsbruck, Austria
| | - Rimpi Khurana
- Division of Genomics and RNomics, Biocenter, Medical University of Innsbruck, Innrain 80–82, 6020 Innsbruck, Austria
| | - Violetta Refolo
- Division of Neurobiology, Department of Neurology, Medical University of Innsbruck, Innrain 66/G2, 6020 Innsbruck, Austria
| | - Serena Venezia
- Division of Neurobiology, Department of Neurology, Medical University of Innsbruck, Innrain 66/G2, 6020 Innsbruck, Austria
| | - Edith Sturm
- Division of Neurobiology, Department of Neurology, Medical University of Innsbruck, Innrain 66/G2, 6020 Innsbruck, Austria
| | - Paolo Piatti
- Division of Molecular Biology, Biocenter, Medical University of Innsbruck, Innrain 80–82, 6020 Innsbruck, Austria
| | - Clara Hechenberger
- Division of Molecular Biology, Biocenter, Medical University of Innsbruck, Innrain 80–82, 6020 Innsbruck, Austria
| | - Hubert Hackl
- Division of Bioinformatics, Biocenter, Medical University of Innsbruck, Innrain 80–82, 6020 Innsbruck, Austria
| | - Roman Kessler
- Division of Genomics and RNomics, Biocenter, Medical University of Innsbruck, Innrain 80–82, 6020 Innsbruck, Austria
| | - Michaela Willi
- Division of Bioinformatics, Biocenter, Medical University of Innsbruck, Innrain 80–82, 6020 Innsbruck, Austria
| | - Ronald Gstir
- Division of Genomics and RNomics, Biocenter, Medical University of Innsbruck, Innrain 80–82, 6020 Innsbruck, Austria
| | - Anne Krogsdam
- Division of Bioinformatics, Biocenter, Medical University of Innsbruck, Innrain 80–82, 6020 Innsbruck, Austria
| | - Alexandra Lusser
- Division of Molecular Biology, Biocenter, Medical University of Innsbruck, Innrain 80–82, 6020 Innsbruck, Austria
| | - Werner Poewe
- Department of Neurology, Medical University of Innsbruck, Anichstr. 35, 6020 Innsbruck, Austria
| | - Gregor K. Wenning
- Division of Neurobiology, Department of Neurology, Medical University of Innsbruck, Innrain 66/G2, 6020 Innsbruck, Austria
| | - Alexander Hüttenhofer
- Division of Genomics and RNomics, Biocenter, Medical University of Innsbruck, Innrain 80–82, 6020 Innsbruck, Austria
- * E-mail: (NS); (AH)
| | - Nadia Stefanova
- Division of Neurobiology, Department of Neurology, Medical University of Innsbruck, Innrain 66/G2, 6020 Innsbruck, Austria
- * E-mail: (NS); (AH)
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25
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Bleasel JM, Halliday GM, Kim WS. Animal modeling an oligodendrogliopathy--multiple system atrophy. Acta Neuropathol Commun 2016; 4:12. [PMID: 26860328 PMCID: PMC4748629 DOI: 10.1186/s40478-016-0279-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 01/23/2016] [Indexed: 12/21/2022] Open
Abstract
Multiple system atrophy (MSA) is a rare, yet rapidly-progressive neurodegenerative disease that presents clinically with autonomic failure in combination with parkinsonism or cerebellar ataxia. The definitive neuropathology differentiating MSA from Lewy body diseases is the presence of α-synuclein aggregates in oligodendrocytes (called glial cytoplasmic inclusion or GCI) rather than the fibrillar aggregates in neurons (called Lewy bodies). This makes the pathological pathway(s) in MSA unique in that oligodendrocytes are involved rather than predominantly neurons, as is most other neurodegenerative disorders. MSA is therefore regarded as an oligodendrogliopathy. The etiology of MSA is unknown. No definitive risk factors have been identified, although α-synuclein and other genes have been variably linked to MSA risk. Utilization of postmortem brain tissues has greatly advanced our understanding of GCI pathology and the subsequent neurodegeneration. However, extrapolating the early pathogenesis of MSA from such resource has been difficult and limiting. In recent years, cell and animal models developed for MSA have been instrumental in delineating unique MSA pathological pathways, as well as aiding in clinical phenotyping. The purpose of this review is to bring together and discuss various animal models that have been developed for MSA and how they have advanced our understanding of MSA pathogenesis, particularly the dynamics of α-synuclein aggregation. This review will also discuss how animal models have been used to explore potential therapeutic avenues for MSA, and future directions of MSA modeling.
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26
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The Antisense Transcriptome and the Human Brain. J Mol Neurosci 2015; 58:1-15. [PMID: 26697858 DOI: 10.1007/s12031-015-0694-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 11/24/2015] [Indexed: 10/22/2022]
Abstract
The transcriptome of a cell is made up of a varied array of RNA species, including protein-coding RNAs, long non-coding RNAs, short non-coding RNAs, and circular RNAs. The cellular transcriptome is dynamic and can change depending on environmental factors, disease state and cellular context. The human brain has perhaps the most diverse transcriptome profile that is enriched for many species of RNA, including antisense transcripts. Antisense transcripts are produced when both the plus and minus strand of the DNA helix are transcribed at a particular locus. This results in an RNA transcript that has a partial or complete overlap with an intronic or exonic region of the sense transcript. While antisense transcription is known to occur at some level in most organisms, this review focuses specifically on antisense transcription in the brain and how regulation of genes by antisense transcripts can contribute to functional aspects of the healthy and diseased brain. First, we discuss different techniques that can be used in the identification and quantification of antisense transcripts. This is followed by examples of antisense transcription and modes of regulatory function that have been identified in the brain.
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27
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Brudek T, Winge K, Rasmussen NB, Bahl JMC, Tanassi J, Agander TK, Hyde TM, Pakkenberg B. Altered α-synuclein, parkin, and synphilin isoform levels in multiple system atrophy brains. J Neurochem 2015; 136:172-85. [DOI: 10.1111/jnc.13392] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 09/29/2015] [Indexed: 01/16/2023]
Affiliation(s)
- Tomasz Brudek
- Research Laboratory for Stereology and Neuroscience; Bispebjerg-Frederiksberg Hospital; University Hospital of Copenhagen; Copenhagen NV Denmark
- Bispebjerg Movement Disorders Biobank; Bispebjerg-Frederiksberg Hospital; University Hospital of Copenhagen; Copenhagen N Denmark
| | - Kristian Winge
- Department of Neurology; Bispebjerg-Frederiksberg Hospital; University Hospital of Copenhagen; Copenhagen NV Denmark
- Bispebjerg Movement Disorders Biobank; Bispebjerg-Frederiksberg Hospital; University Hospital of Copenhagen; Copenhagen N Denmark
| | - Nadja Bredo Rasmussen
- Research Laboratory for Stereology and Neuroscience; Bispebjerg-Frederiksberg Hospital; University Hospital of Copenhagen; Copenhagen NV Denmark
| | | | - Julia Tanassi
- Department of Autoimmunology and Biomarkers; Statens Serum Institut; Copenhagen S Denmark
| | | | - Thomas M. Hyde
- Lieber Institute for Brain Development; Johns Hopkins Medical Campus; Baltimore Maryland USA
- Department of Psychiatry and Behavioral Sciences; Johns Hopkins University School of Medicine; Baltimore Maryland USA
- Department of Neurology; Johns Hopkins University School of Medicine; Baltimore Maryland USA
| | - Bente Pakkenberg
- Research Laboratory for Stereology and Neuroscience; Bispebjerg-Frederiksberg Hospital; University Hospital of Copenhagen; Copenhagen NV Denmark
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28
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Lourenco GF, Janitz M, Huang Y, Halliday GM. Long noncoding RNAs in TDP-43 and FUS/TLS-related frontotemporal lobar degeneration (FTLD). Neurobiol Dis 2015. [DOI: 10.1016/j.nbd.2015.07.011] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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29
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Ward M, McEwan C, Mills JD, Janitz M. Conservation and tissue-specific transcription patterns of long noncoding RNAs. ACTA ACUST UNITED AC 2015; 1:2-9. [PMID: 27335896 PMCID: PMC4894084 DOI: 10.3109/23324015.2015.1077591] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 07/15/2015] [Indexed: 12/31/2022]
Abstract
Over the past decade, the focus of molecular biology has shifted from being predominately DNA and protein-centric to having a greater appreciation of RNA. It is now accepted that the genome is pervasively transcribed in tissue- and cell-specific manner, to produce not only protein-coding RNAs, but also an array of noncoding RNAs (ncRNAs). Many of these ncRNAs have been found to interact with DNA, protein and other RNA molecules where they exert regulatory functions. Long ncRNAs (lncRNAs) are a subclass of ncRNAs that are particularly interesting due to their cell-specific and species-specific expression patterns and unique conservation patterns. Currently, individual lncRNAs have been classified functionally; however, for the vast majority the functional relevance is unknown. To better categorize lncRNAs, an understanding of their specific expression patterns and evolutionary constraints are needed.
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Affiliation(s)
- Melanie Ward
- School of Biotechnology and Biomolecular Sciences, University of New South Wales , Sydney, NSW 2052, Australia
| | - Callum McEwan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales , Sydney, NSW 2052, Australia
| | - James D Mills
- School of Biotechnology and Biomolecular Sciences, University of New South Wales , Sydney, NSW 2052, Australia
| | - Michael Janitz
- School of Biotechnology and Biomolecular Sciences, University of New South Wales , Sydney, NSW 2052, Australia
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30
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Mills JD, Chen J, Kim WS, Waters PD, Prabowo AS, Aronica E, Halliday GM, Janitz M. Long intervening non-coding RNA 00320 is human brain-specific and highly expressed in the cortical white matter. Neurogenetics 2015; 16:201-13. [PMID: 25819921 DOI: 10.1007/s10048-015-0445-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 03/14/2015] [Indexed: 12/30/2022]
Abstract
Pervasive transcription of the genome produces a diverse array of functional non-coding RNAs (ncRNAs). One particular class of ncRNAs, long intervening non-coding RNAs (lincRNAs) are thought to play a role in regulating gene expression and may be a major contributor to organism and tissue complexity. The human brain with its heterogeneous cellular make-up is a rich source of lincRNAs; however, the functions of the majority of lincRNAs are unknown. Recently, by completing RNA sequencing (RNA-Seq) of the human frontal cortex, we identified linc00320 as being highly expressed in the white matter compared to grey matter in multiple system atrophy (MSA) brain. Here, we further investigate the expression patterns of linc00320 and conclude that it is involved in specific brain regions rather than having involvement in the MSA disease process. We also show that the full-length linc00320 is only expressed in human brain tissue and not in other primates, suggesting that it may be involved in improved functional connectivity for higher human brain cognition.
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Affiliation(s)
- James D Mills
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
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