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Hu R, Wang R, Yuan J, Lin Z, Hutchins E, Landin B, Liao Z, Liu G, Scherzer CR, Dong X. Transcriptional pathobiology and multi-omics predictors for Parkinson's disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.18.599639. [PMID: 38948706 PMCID: PMC11212969 DOI: 10.1101/2024.06.18.599639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Early diagnosis and biomarker discovery to bolster the therapeutic pipeline for Parkinson's disease (PD) are urgently needed. In this study, we leverage the large-scale whole-blood total RNA-seq dataset from the Accelerating Medicine Partnership in Parkinson's Disease (AMP PD) program to identify PD-associated RNAs, including both known genes and novel circular RNAs (circRNA) and enhancer RNAs (eRNAs). There were 1,111 significant marker RNAs, including 491 genes, 599 eRNAs, and 21 circRNAs, that were first discovered in the PPMI cohort (FDR < 0.05) and confirmed in the PDBP/BioFIND cohorts (nominal p < 0.05). Functional enrichment analysis showed that the PD-associated genes are involved in neutrophil activation and degranulation, as well as the TNF-alpha signaling pathway. We further compare the PD-associated genes in blood with those in post-mortem brain dopamine neurons in our BRAINcode cohort. 44 genes show significant changes with the same direction in both PD brain neurons and PD blood, including neuroinflammation-associated genes IKBIP , CXCR2 , and NFKBIB . Finally, we built a novel multi-omics machine learning model to predict PD diagnosis with high performance (AUC = 0.89), which was superior to previous studies and might aid the decision-making for PD diagnosis in clinical practice. In summary, this study delineates a wide spectrum of the known and novel RNAs linked to PD and are detectable in circulating blood cells in a harmonized, large-scale dataset. It provides a generally useful computational framework for further biomarker development and early disease prediction. Significance statement Early and accurate diagnosis of Parkinson's disease (PD) is urgently needed. However, biomarkers for early detection of PD are still lacking. Also, the limit of sample size remains one of the main pitfalls of current PD biomarker studies. We employed an analysis of large-scale whole-blood RNA-seq data. By identifying 1,111 significant marker RNAs, we establish a robust foundation for early PD detection, which implicated in neutrophil activation, degranulation, and TNF-alpha signaling, offer unprecedented insights into PD pathogenesis. Our multi-omics machine learning model, boasting an AUC of 0.89, outperforms previous studies, promising a transformative tool for precise PD diagnosis in clinical settings. This study marks a pivotal step toward enhanced biomarker development and early disease prediction.
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Qin Y, Shirakawa J, Xu C, Chen R, Ng C, Nakano S, Elguindy M, Deng Z, Prasanth KV, Eissmann MF, Nakagawa S, Ricci WM, Zhao B. Malat1 fine-tunes bone homeostasis by orchestrating cellular crosstalk and the β-catenin-OPG/Jagged1 pathway. RESEARCH SQUARE 2024:rs.3.rs-3793919. [PMID: 38234849 PMCID: PMC10793491 DOI: 10.21203/rs.3.rs-3793919/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
The IncRNA Malat1 was initially believed to be dispensable for physiology due to the lack of observable phenotypes in Malat1 knockout (KO) mice. However, our study challenges this conclusion. We found that both Malat1 KO and conditional KO mice in the osteoblast lineage exhibit significant osteoporosis. Mechanistically, Malat1 acts as an intrinsic regulator in osteoblasts to promote osteogenesis. Interestingly, Malat1 does not directly affect osteoclastogenesis but inhibits osteoclastogenesis in a non-autonomous manner in vivo via integrating crosstalk between multiple cell types, including osteoblasts, osteoclasts and chondrocytes. Our findings substantiate the existence of a novel remodeling network in which Malat1 serves as a central regulator by binding to β-catenin and functioning through the β-catenin-OPG/Jagged1 pathway in osteoblasts and chondrocytes. In pathological conditions, Malat1 significantly promotes bone regeneration in fracture healing. Bone homeostasis and regeneration are crucial to well-being. Our discoveries establish a previous unrecognized paradigm model of Malat1 function in the skeletal system, providing novel mechanistic insights into how a lncRNA integrates cellular crosstalk and molecular networks to fine tune tissue homeostasis, remodeling and repair.
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Affiliation(s)
- Yongli Qin
- Arthritis and Tissue Degeneration Program and David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, New York, USA
- Department of Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Jumpei Shirakawa
- Arthritis and Tissue Degeneration Program and David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, New York, USA
| | - Cheng Xu
- Arthritis and Tissue Degeneration Program and David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, New York, USA
| | - Ruge Chen
- Arthritis and Tissue Degeneration Program and David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, New York, USA
| | - Courtney Ng
- Arthritis and Tissue Degeneration Program and David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, New York, USA
| | - Shinichi Nakano
- Arthritis and Tissue Degeneration Program and David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, New York, USA
| | - Mahmoud Elguindy
- Arthritis and Tissue Degeneration Program and David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, New York, USA
| | - Zhonghao Deng
- Arthritis and Tissue Degeneration Program and David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, New York, USA
| | - Kannanganattu V Prasanth
- Department of Cell and Developmental Biology, Cancer center at Illinois, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Moritz F. Eissmann
- Institute for Tumor Biology and Experimental Therapy, Paul-Ehrlich-Strasse 42-44, 60596 Frankfurt, Germany
| | - Shinichi Nakagawa
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - William M. Ricci
- Orthopaedic Trauma Service, Hospital for Special Surgery & NewYork-Presbyterian Hospital, USA
| | - Baohong Zhao
- Arthritis and Tissue Degeneration Program and David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, New York, USA
- Department of Medicine, Weill Cornell Medical College, New York, New York, USA
- Graduate Program in Cell and Development Biology, Weill Cornell Graduate School of Medical Sciences, New York, New York, USA
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Beaulieu-Jones BK, Frau F, Bozzi S, Chandross KJ, Peterschmitt MJ, Cohen C, Coulovrat C, Kumar D, Kruger MJ, Lipnick SL, Fitzsimmons L, Kohane IS, Scherzer CR. Disease progression strikingly differs in research and real-world Parkinson's populations. NPJ Parkinsons Dis 2024; 10:58. [PMID: 38480700 PMCID: PMC10937726 DOI: 10.1038/s41531-024-00667-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Accepted: 02/23/2024] [Indexed: 03/17/2024] Open
Abstract
Characterization of Parkinson's disease (PD) progression using real-world evidence could guide clinical trial design and identify subpopulations. Efforts to curate research populations, the increasing availability of real-world data, and advances in natural language processing, particularly large language models, allow for a more granular comparison of populations than previously possible. This study includes two research populations and two real-world data-derived (RWD) populations. The research populations are the Harvard Biomarkers Study (HBS, N = 935), a longitudinal biomarkers cohort study with in-person structured study visits; and Fox Insights (N = 36,660), an online self-survey-based research study of the Michael J. Fox Foundation. Real-world cohorts are the Optum Integrated Claims-electronic health records (N = 157,475), representing wide-scale linked medical and claims data and de-identified data from Mass General Brigham (MGB, N = 22,949), an academic hospital system. Structured, de-identified electronic health records data at MGB are supplemented using a manually validated natural language processing with a large language model to extract measurements of PD progression. Motor and cognitive progression scores change more rapidly in MGB than HBS (median survival until H&Y 3: 5.6 years vs. >10, p < 0.001; mini-mental state exam median decline 0.28 vs. 0.11, p < 0.001; and clinically recognized cognitive decline, p = 0.001). In real-world populations, patients are diagnosed more than eleven years later (RWD mean of 72.2 vs. research mean of 60.4, p < 0.001). After diagnosis, in real-world cohorts, treatment with PD medications has initiated an average of 2.3 years later (95% CI: [2.1-2.4]; p < 0.001). This study provides a detailed characterization of Parkinson's progression in diverse populations. It delineates systemic divergences in the patient populations enrolled in research settings vs. patients in the real-world. These divergences are likely due to a combination of selection bias and real population differences, but exact attribution of the causes is challenging. This study emphasizes a need to utilize multiple data sources and to diligently consider potential biases when planning, choosing data sources, and performing downstream tasks and analyses.
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Affiliation(s)
- Brett K Beaulieu-Jones
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA.
- APDA Center for Advanced Parkinson Research of Harvard Medical School and Brigham and Women's Hospital, Boston, MA, 02115, USA.
- Precision Neurology Program of Brigham & Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
- Department of Medicine, University of Chicago, Chicago, IL, 60615, USA.
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA.
| | | | - Sylvie Bozzi
- Sanofi Health Economics and Value Assessment, Sanofi, Paris, France
| | | | | | | | | | - Dinesh Kumar
- Sanofi Translational Sciences, Framingham, MA, 01701, USA
| | - Mark J Kruger
- Sanofi Genzyme, Clinical Development Neurology, Cambridge, MA, USA
| | - Scott L Lipnick
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
| | - Lane Fitzsimmons
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
| | - Isaac S Kohane
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
| | - Clemens R Scherzer
- APDA Center for Advanced Parkinson Research of Harvard Medical School and Brigham and Women's Hospital, Boston, MA, 02115, USA.
- Precision Neurology Program of Brigham & Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA.
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Beaulieu-Jones BK, Frau F, Bozzi S, Chandross KJ, Peterschmitt MJ, Cohen C, Coulovrat C, Kumar D, Kruger MJ, Lipnick SL, Fitzsimmons L, Kohane IS, Scherzer CR. Disease progression strikingly differs in research and real-world Parkinson's populations. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.02.17.24302981. [PMID: 38405736 PMCID: PMC10889035 DOI: 10.1101/2024.02.17.24302981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Characterization of Parkinson's disease (PD) progression using real-world evidence could guide clinical trial design and identify subpopulations. Efforts to curate research populations, the increasing availability of real-world data and recent advances in natural language processing, particularly large language models, allow for a more granular comparison of populations and the methods of data collection describing these populations than previously possible. This study includes two research populations and two real-world data derived (RWD) populations. The research populations are the Harvard Biomarkers Study (HBS, N = 935), a longitudinal biomarkers cohort study with in-person structured study visits; and Fox Insights (N = 36,660), an online self-survey-based research study of the Michael J. Fox Foundation. Real-world cohorts are the Optum Integrated Claims-electronic health records (N = 157,475), representing wide-scale linked medical and claims data and de-identified data from Mass General Brigham (MGB, N = 22,949), an academic hospital system. Structured, de-identified electronic health records data at MGB are supplemented using natural language processing with a large language model to extract measurements of PD progression. This extraction process is manually validated for accuracy. Motor and cognitive progression scores change more rapidly in MGB than HBS (median survival until H&Y 3: 5.6 years vs. >10, p<0.001; mini-mental state exam median decline 0.28 vs. 0.11, p<0.001; and clinically recognized cognitive decline, p=0.001). In the real-world populations, patients are diagnosed more than eleven years later (RWD mean of 72.2 vs. research mean of 60.4, p<0.001). After diagnosis, in real-world cohorts, treatment with PD medications is initiated 2.3 years later on average (95% CI: [2.1-2.4]; p<0.001). This study provides a detailed characterization of Parkinson's progression in diverse populations. It delineates systemic divergences in the patient populations enrolled in research settings vs. patients in the real world. These divergences are likely due to a combination of selection bias and real population differences, but exact attribution of the causes is challenging using existing data. This study emphasizes a need to utilize multiple data sources and to diligently consider potential biases when planning, choosing data sources, and performing downstream tasks and analyses.
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Affiliation(s)
- Brett K Beaulieu-Jones
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
- APDA Center for Advanced Parkinson Research of Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA
- Precision Neurology Program of Brigham & Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
- Department of Medicine, University of Chicago, Chicago, IL 60615 USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase MD, 20815
| | | | - Sylvie Bozzi
- Sanofi Health Economics and Value Assessment, Sanofi, Paris, France
| | | | | | | | | | - Dinesh Kumar
- Sanofi Translational Sciences, Framingham, 01701 USA
| | - Mark J Kruger
- Sanofi Genzyme, Clinical Development Neurology, Cambridge, MA, United States
| | - Scott L Lipnick
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Lane Fitzsimmons
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Isaac S Kohane
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Clemens R Scherzer
- APDA Center for Advanced Parkinson Research of Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA
- Precision Neurology Program of Brigham & Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase MD, 20815
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Li W, Wu H, Li J, Wang Z, Cai M, Liu X, Liu G. Transcriptomic analysis reveals associations of blood-based A-to-I editing with Parkinson's disease. J Neurol 2024; 271:976-985. [PMID: 37902879 DOI: 10.1007/s00415-023-12053-x] [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: 04/17/2023] [Revised: 10/07/2023] [Accepted: 10/09/2023] [Indexed: 11/01/2023]
Abstract
BACKGROUND Adenosine-to-inosine (A-to-I) editing is the most common type of RNA editing in humans and the role of A-to-I RNA editing remains unclear in Parkinson's disease (PD). OBJECTIVE We aimed to explore the potential causal association between A-to-I editing and PD, and to assess whether changes in A-to-I editing were associated with cognitive progression in PD. METHODS The RNA-seq data from 380 PD patients and 178 healthy controls in the Parkinson's Progression Marker Initiative cohort was used to quantify A-to-I editing sites. We performed cis-RNA editing quantitative trait loci analysis and a two-sample Mendelian Randomization (MR) study by integrating genome-wide association studies to infer the potential causality between A-to-I editing and PD pathogenesis. The potential causal A-to-I editing sites were further confirmed by Summary-data-based MR analysis. Spearman's correlation analysis was performed to characterize the association between longitudinal A-to-I editing and cognitive progression in patients with PD. RESULTS We identified 17 potential causal A-to-I editing sites for PD and indicated that genetic risk variants may contribute to the risk of PD through A-to-I editing. These A-to-I editing sites were located in genes NCOR1, KANSL1 and BST1. Moreover, we observed 57 sites whose longitudinal A-to-I editing levels correlated with cognitive progression in PD. CONCLUSIONS We found potential causal A-to-I editing sites for PD onset and longitudinal changes of A-to-I editing were associated with cognitive progression in PD. We anticipate this study will provide new biological insights and drive the discovery of the epitranscriptomic role underlying Parkinson's disease.
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Affiliation(s)
- Weimin Li
- Shenzhen Key Laboratory of Systems Medicine in Inflammatory Diseases, School of Medicine, Shenzhen Campus of Sun Yat-Sen University, No.66, Gongchang Road, Guangming District, Shenzhen, 518107, Guangdong, People's Republic of China
- Neurobiology Research Center, School of Medicine, Shenzhen Campus of Sun Yat-Sen University, No.66, Gongchang Road, Guangming District, Shenzhen, 518107, Guangdong, People's Republic of China
| | - Hao Wu
- Shenzhen Key Laboratory of Systems Medicine in Inflammatory Diseases, School of Medicine, Shenzhen Campus of Sun Yat-Sen University, No.66, Gongchang Road, Guangming District, Shenzhen, 518107, Guangdong, People's Republic of China
- Neurobiology Research Center, School of Medicine, Shenzhen Campus of Sun Yat-Sen University, No.66, Gongchang Road, Guangming District, Shenzhen, 518107, Guangdong, People's Republic of China
| | - Jinxia Li
- Shenzhen Key Laboratory of Systems Medicine in Inflammatory Diseases, School of Medicine, Shenzhen Campus of Sun Yat-Sen University, No.66, Gongchang Road, Guangming District, Shenzhen, 518107, Guangdong, People's Republic of China
- Neurobiology Research Center, School of Medicine, Shenzhen Campus of Sun Yat-Sen University, No.66, Gongchang Road, Guangming District, Shenzhen, 518107, Guangdong, People's Republic of China
| | - Zhuo Wang
- Warshel Institute for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen, 518172, Guangdong, People's Republic of China
| | - Miao Cai
- Neurology Department, Zhejiang Hospital, Hangzhou, 310013, People's Republic of China
| | - Xiaoli Liu
- Neurology Department, Zhejiang Hospital, Hangzhou, 310013, People's Republic of China
| | - Ganqiang Liu
- Shenzhen Key Laboratory of Systems Medicine in Inflammatory Diseases, School of Medicine, Shenzhen Campus of Sun Yat-Sen University, No.66, Gongchang Road, Guangming District, Shenzhen, 518107, Guangdong, People's Republic of China.
- Neurobiology Research Center, School of Medicine, Shenzhen Campus of Sun Yat-Sen University, No.66, Gongchang Road, Guangming District, Shenzhen, 518107, Guangdong, People's Republic of China.
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Kattan FG, Koukouraki P, Anagnostopoulos AK, Tsangaris GT, Doxakis E. RNA binding protein AUF1/HNRNPD regulates nuclear export, stability and translation of SNCA transcripts. Open Biol 2023; 13:230158. [PMID: 37989221 PMCID: PMC10688287 DOI: 10.1098/rsob.230158] [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: 05/25/2023] [Accepted: 10/11/2023] [Indexed: 11/23/2023] Open
Abstract
Alpha-synuclein (SNCA) accumulation plays a central role in the pathogenesis of Parkinson's disease. Determining and interfering with the mechanisms that control SNCA expression is one approach to limiting disease progression. Currently, most of our understanding of SNCA regulation is protein-based. Post-transcriptional mechanisms directly regulating SNCA mRNA expression via its 3' untranslated region (3'UTR) were investigated here. Mass spectrometry of proteins pulled down from murine brain lysates using a biotinylated SNCA 3'UTR revealed multiple RNA-binding proteins, of which HNRNPD/AUF1 was chosen for further analysis. AUF1 bound both proximal and distal regions of the SNCA 3'UTR, but not the 5'UTR or CDS. In the nucleus, AUF1 attenuated SNCA pre-mRNA maturation and was indispensable for the export of SNCA transcripts. AUF1 destabilized SNCA transcripts in the cytosol, primarily those with shorter 3'UTRs, independently of microRNAs by recruiting the CNOT1-CNOT7 deadenylase complex to trim the polyA tail. Furthermore, AUF1 inhibited SNCA mRNA binding to ribosomes. These data identify AUF1 as a multi-tasking protein regulating maturation, nucleocytoplasmic shuttling, stability and translation of SNCA transcripts.
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Affiliation(s)
- Fedon-Giasin Kattan
- Center of Basic Research, Biomedical Research Foundation of the Academy of Athens (BRFAA), Soranou Efesiou 4, Athens 11527, Greece
- Department of Biological Applications and Technology, Faculty of Health Sciences, University of Ioannina, 45110 Ioannina, Greece
| | - Pelagia Koukouraki
- Center of Basic Research, Biomedical Research Foundation of the Academy of Athens (BRFAA), Soranou Efesiou 4, Athens 11527, Greece
| | - Athanasios K. Anagnostopoulos
- Center of Basic Research, Biomedical Research Foundation of the Academy of Athens (BRFAA), Soranou Efesiou 4, Athens 11527, Greece
| | - George T. Tsangaris
- Center of Basic Research, Biomedical Research Foundation of the Academy of Athens (BRFAA), Soranou Efesiou 4, Athens 11527, Greece
| | - Epaminondas Doxakis
- Center of Basic Research, Biomedical Research Foundation of the Academy of Athens (BRFAA), Soranou Efesiou 4, Athens 11527, Greece
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Arnaldo L, Urbizu A, Serradell M, Gaig C, Anillo A, Gea M, Vilas D, Ispierto L, Muñoz-Lopetegi A, Mayà G, Pastor P, Álvarez R, Santamaria J, Iranzo A, Beyer K. Peripheral α-synuclein isoforms are potential biomarkers for diagnosis and prognosis of isolated REM sleep behavior disorder. Parkinsonism Relat Disord 2023; 115:105832. [PMID: 37678102 DOI: 10.1016/j.parkreldis.2023.105832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 08/07/2023] [Accepted: 08/25/2023] [Indexed: 09/09/2023]
Abstract
INTRODUCTION Isolated REM sleep behavior disorder (IRBD) represents an early manifestation of the synucleinopathies Parkinson's disease (PD) and dementia with Lewy bodies (DLB). Aggregation of abnormal α-synuclein and its increased expression in the brain is crucial in the development of the synucleinopathies. Whereas α-synuclein gene (SNCA) transcripts are overexpressed in brain, a concomitant reduction occurs in blood of DLB patients. We assessed whether this decrease is also detectable in IRBD. METHODS 108 IRBD patients and 149 controls were included of which 29 IRBD and 32 control cases were available for expression studies. Expression of SNCAtv1, SNCAtv2, SNCAtv3 and SNCA126 isoforms, and GBA were determined by real-time PCR. Genotype distribution of SNCA SNPs, rs356219 and rs2736990, and correlation with SNCA expression was analyzed. RESULTS Expression of all SNCA transcripts was reduced in IRBD blood whereas GBA expression did not change. SNCAtv3 expression correlated inversely with IRBD duration, being lower in patients with longer follow-up. Rs356219-AA genotype frequency was increased in IRBD patients who later developed PD and DLB. Rs2736990-CC frequency was increased among IRBD cases who remained disease-free. No correlation was observed between rs356219 and rs2736990 genotypes and SNCA transcript levels. CONCLUSION SNCA transcript expression is decreased in blood in IRBD, and levels decrease with IRBD duration. Our findings indicate that changes in SNCA expression occur in the earliest stages of the synucleinopathies before motor and cognitive symptoms become apparent.
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Affiliation(s)
- Laura Arnaldo
- Department of Pathology, Hospital Universitari and Health Sciences Research Institute Germans Trias i Pujol, Badalona, Spain; Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Aintzane Urbizu
- Department of Pathology, Hospital Universitari and Health Sciences Research Institute Germans Trias i Pujol, Badalona, Spain
| | - Mònica Serradell
- IDIBAPS, CIBERNED, Neurology Service, Sleep Disorders Center, Hospital Clínic de Barcelona, Barcelona, Spain
| | - Carles Gaig
- IDIBAPS, CIBERNED, Neurology Service, Sleep Disorders Center, Hospital Clínic de Barcelona, Barcelona, Spain
| | - Ana Anillo
- Department of Pathology, Hospital Universitari and Health Sciences Research Institute Germans Trias i Pujol, Badalona, Spain
| | - Mireia Gea
- Unit of Neurodegenerative Diseases, Department of Neurology, University Hospital Germans Trias i Pujol and the Germans Trias I Pujol Research Institute (IGTP) Badalona, Barcelona, Spain
| | - Dolores Vilas
- Unit of Neurodegenerative Diseases, Department of Neurology, University Hospital Germans Trias i Pujol and the Germans Trias I Pujol Research Institute (IGTP) Badalona, Barcelona, Spain
| | - Lourdes Ispierto
- Unit of Neurodegenerative Diseases, Department of Neurology, University Hospital Germans Trias i Pujol and the Germans Trias I Pujol Research Institute (IGTP) Badalona, Barcelona, Spain
| | - Amaia Muñoz-Lopetegi
- IDIBAPS, CIBERNED, Neurology Service, Sleep Disorders Center, Hospital Clínic de Barcelona, Barcelona, Spain
| | - Gerard Mayà
- IDIBAPS, CIBERNED, Neurology Service, Sleep Disorders Center, Hospital Clínic de Barcelona, Barcelona, Spain
| | - Pau Pastor
- Unit of Neurodegenerative Diseases, Department of Neurology, University Hospital Germans Trias i Pujol and the Germans Trias I Pujol Research Institute (IGTP) Badalona, Barcelona, Spain
| | - Ramiro Álvarez
- Unit of Neurodegenerative Diseases, Department of Neurology, University Hospital Germans Trias i Pujol and the Germans Trias I Pujol Research Institute (IGTP) Badalona, Barcelona, Spain
| | - Joan Santamaria
- IDIBAPS, CIBERNED, Neurology Service, Sleep Disorders Center, Hospital Clínic de Barcelona, Barcelona, Spain
| | - Alex Iranzo
- IDIBAPS, CIBERNED, Neurology Service, Sleep Disorders Center, Hospital Clínic de Barcelona, Barcelona, Spain.
| | - Katrin Beyer
- Department of Pathology, Hospital Universitari and Health Sciences Research Institute Germans Trias i Pujol, Badalona, Spain; Universitat Autònoma de Barcelona, Barcelona, Spain.
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Bhandari N, Walambe R, Kotecha K, Kaliya M. Integrative gene expression analysis for the diagnosis of Parkinson's disease using machine learning and explainable AI. Comput Biol Med 2023; 163:107140. [PMID: 37315380 DOI: 10.1016/j.compbiomed.2023.107140] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 05/29/2023] [Accepted: 06/04/2023] [Indexed: 06/16/2023]
Abstract
Parkinson's disease (PD) is a progressive neurodegenerative disorder. Various symptoms and diagnostic tests are used in combination for the diagnosis of PD; however, accurate diagnosis at early stages is difficult. Blood-based markers can support physicians in the early diagnosis and treatment of PD. In this study, we used Machine Learning (ML) based methods for the diagnosis of PD by integrating gene expression data from different sources and applying explainable artificial intelligence (XAI) techniques to find the significant set of gene features contributing to diagnosis. We utilized the Least Absolute Shrinkage and Selection Operator (LASSO), and Ridge regression for the feature selection process. We utilized state-of-the-art ML techniques for the classification of PD cases and healthy controls. Logistic regression and Support Vector Machine showed the highest diagnostic accuracy. SHapley Additive exPlanations (SHAP) based global interpretable model-agnostic XAI method was utilized for the interpretation of the Support Vector Machine model. A set of significant biomarkers that contributed to the diagnosis of PD were identified. Some of these genes are associated with other neurodegenerative diseases. Our results suggest that the utilization of XAI can be useful in making early therapeutic decisions for the treatment of PD. The integration of datasets from different sources made this model robust. We believe that this research article will be of interest to clinicians as well as computational biologists in translational research.
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Affiliation(s)
- Nikita Bhandari
- Computer Science Department, Symbiosis Institute of Technology, Symbiosis International (Deemed University), Pune, MH, India; Symbiosis Center for Applied Artificial Intelligence (SCAAI), Symbiosis International Deemed University, Pune, Maharashtra, India
| | - Rahee Walambe
- Electronics and Telecommunication Department, Symbiosis Institute of Technology, Symbiosis International (Deemed University), Pune, Maharashtra, India; Symbiosis Center for Applied Artificial Intelligence (SCAAI), Symbiosis International Deemed University, Pune, Maharashtra, India.
| | - Ketan Kotecha
- Computer Science Department, Symbiosis Institute of Technology, Symbiosis International (Deemed University), Pune, MH, India; Electronics and Telecommunication Department, Symbiosis Institute of Technology, Symbiosis International (Deemed University), Pune, Maharashtra, India.
| | - Mehul Kaliya
- Department of General Medicine, AIIMS, Rajkot, Gujrat, India
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Irmady K, Hale CR, Qadri R, Fak J, Simelane S, Carroll T, Przedborski S, Darnell RB. Blood transcriptomic signatures associated with molecular changes in the brain and clinical outcomes in Parkinson's disease. Nat Commun 2023; 14:3956. [PMID: 37407548 DOI: 10.1038/s41467-023-39652-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 06/23/2023] [Indexed: 07/07/2023] Open
Abstract
The ability to use blood to predict the outcomes of Parkinson's disease, including disease progression and cognitive and motor complications, would be of significant clinical value. We undertook bulk RNA sequencing from the caudate and putamen of postmortem Parkinson's disease (n = 35) and control (n = 40) striatum, and compared molecular profiles with clinical features and bulk RNA sequencing data obtained from antemortem peripheral blood. Cognitive and motor complications of Parkinson's disease were associated with molecular changes in the caudate (stress response) and putamen (endothelial pathways) respectively. Later and earlier-onset Parkinson's disease were molecularly distinct, and disease duration was associated with changes in caudate (oligodendrocyte development) and putamen (cellular senescence), respectively. Transcriptome patterns in the postmortem Parkinson's disease brain were also evident in antemortem peripheral blood, and correlated with clinical features of the disease. Together, these findings identify molecular signatures in Parkinson's disease patients' brain and blood of potential pathophysiologic and prognostic importance.
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Affiliation(s)
- Krithi Irmady
- Laboratory of Molecular Neuro-oncology, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA.
| | - Caryn R Hale
- Laboratory of Molecular Neuro-oncology, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Rizwana Qadri
- Laboratory of Molecular Neuro-oncology, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - John Fak
- Laboratory of Molecular Neuro-oncology, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Sitsandziwe Simelane
- Laboratory of Molecular Neuro-oncology, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Thomas Carroll
- Bioinformatics Resource Center, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Serge Przedborski
- Department of Neurology, Columbia University, 630 West 168th Street, New York, NY, 10032, USA
- Department of Pathology & Cell Biology, Columbia University, 630 West 168th Street, New York, NY, 10032, USA
- Department of Neuroscience, Columbia University, 630 West 168th Street, New York, NY, 10032, USA
| | - Robert B Darnell
- Laboratory of Molecular Neuro-oncology, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA.
- Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA.
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10
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Reynolds RH, Wagen AZ, Lona-Durazo F, Scholz SW, Shoai M, Hardy J, Gagliano Taliun SA, Ryten M. Local genetic correlations exist among neurodegenerative and neuropsychiatric diseases. NPJ Parkinsons Dis 2023; 9:70. [PMID: 37117178 PMCID: PMC10147945 DOI: 10.1038/s41531-023-00504-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 03/27/2023] [Indexed: 04/30/2023] Open
Abstract
Genetic correlation ([Formula: see text]) between traits can offer valuable insight into underlying shared biological mechanisms. Neurodegenerative diseases overlap neuropathologically and often manifest comorbid neuropsychiatric symptoms. However, global [Formula: see text] analyses show minimal [Formula: see text] among neurodegenerative and neuropsychiatric diseases. Importantly, local [Formula: see text] s can exist in the absence of global relationships. To investigate this possibility, we applied LAVA, a tool for local [Formula: see text] analysis, to genome-wide association studies of 3 neurodegenerative diseases (Alzheimer's disease, Lewy body dementia and Parkinson's disease) and 3 neuropsychiatric disorders (bipolar disorder, major depressive disorder and schizophrenia). We identified several local [Formula: see text] s missed in global analyses, including between (i) all 3 neurodegenerative diseases and schizophrenia and (ii) Alzheimer's and Parkinson's disease. For those local [Formula: see text] s identified in genomic regions containing disease-implicated genes, such as SNCA, CLU and APOE, incorporation of expression quantitative trait loci identified genes that may drive genetic overlaps between diseases. Collectively, we demonstrate that complex genetic relationships exist among neurodegenerative and neuropsychiatric diseases, highlighting putative pleiotropic genomic regions and genes. These findings imply sharing of pathogenic processes and the potential existence of common therapeutic targets.
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Affiliation(s)
- Regina H Reynolds
- Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, UK.
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA.
| | - Aaron Z Wagen
- Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, UK
- Department of Clinical and Movement Neurosciences, Queen Square Institute of Neurology, London, UK
- Neurodegeneration Biology Laboratory, The Francis Crick Institute, London, UK
| | - Frida Lona-Durazo
- Montréal Heart Institute, Montréal, QC, Canada
- Faculty of Medicine, Université de Montréal, Montréal, Canada
| | - Sonja W Scholz
- Neurodegenerative Diseases Research Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
- Department of Neurology, Johns Hopkins University Medical Center, Baltimore, MD, USA
| | - Maryam Shoai
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- Department of Neurodegenerative Diseases, Queen Square Institute of Neurology, University College London, London, UK
- UK Dementia Research Institute, University College London, London, UK
| | - John Hardy
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- Department of Neurodegenerative Diseases, Queen Square Institute of Neurology, University College London, London, UK
- UK Dementia Research Institute, University College London, London, UK
| | - Sarah A Gagliano Taliun
- Montréal Heart Institute, Montréal, QC, Canada
- Department of Medicine & Department of Neurosciences, Université de Montréal, Montréal, QC, Canada
| | - Mina Ryten
- Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, UK.
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA.
- NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, UK.
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11
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Xue J, Li F, Dai P. The Potential of ANK1 to Predict Parkinson's Disease. Genes (Basel) 2023; 14:genes14010226. [PMID: 36672967 PMCID: PMC9859451 DOI: 10.3390/genes14010226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 01/10/2023] [Accepted: 01/12/2023] [Indexed: 01/18/2023] Open
Abstract
The main cause of Parkinson's disease (PD) remains unknown and the pathologic changes in the brain limit rapid diagnosis. Herein, differentially expressed genes (DEGs) in the Gene Expression Omnibus (GEO) database (GSE8397 and GSE22491) were assessed using linear models for microarray analysis (limma). Ankyrin 1 (ANK1) was the only common gene differentially down-regulated in lateral substantia nigra (LSN), medial substantia nigra (MSN) and blood. Additionally, DEGs between high ANK1 and low ANK1 in GSE99039 were picked out and then uploaded to the Database for Annotation, Visualization and Integrated Discovery (DAVID) for gene ontology (GO) functional annotation analysis. GO analysis displayed that these DEGs were mainly enriched in oxygen transport, myeloid cell development and gas transport (biological process (BP)); hemoglobin complex, haptoglobin-hemoglobin complex and cortical cytoskeleton (cellular component (CC)); and oxygen transporter activity, haptoglobin binding and oxygen binding (molecular function (MF)). Receiver operating characteristic (ROC) curve analysis showed ANK1 had good diagnostic accuracy and increased the area under the curve (AUC) value when combined with other biomarkers. Consistently, intraperitoneal injection of 1-methyl-4-phenyl-1,2,3,6-tetrahydropy-ridi-ne (MPTP) in C57BL/6J mice reduced ANK1 mRNA expression in both substantia nigra and blood compared to the control group. Thus, ANK1 may serve as a candidate biomarker for PD diagnosis.
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12
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Huseby CJ, Delvaux E, Brokaw DL, Coleman PD. Blood RNA transcripts reveal similar and differential alterations in fundamental cellular processes in Alzheimer's disease and other neurodegenerative diseases. Alzheimers Dement 2022. [DOI: 10.1002/alz.12880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 09/30/2022] [Accepted: 10/21/2022] [Indexed: 12/24/2022]
Affiliation(s)
- Carol J. Huseby
- ASU‐Banner Neurodegenerative Disease Research Center Arizona State University Tempe Arizona USA
| | - Elaine Delvaux
- ASU‐Banner Neurodegenerative Disease Research Center Arizona State University Tempe Arizona USA
| | - Danielle L. Brokaw
- University of Pennsylvania Perelman School of Medicine Philadelphia Pennsylvania USA
| | - Paul D. Coleman
- ASU‐Banner Neurodegenerative Disease Research Center Arizona State University Tempe Arizona USA
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13
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Luo J, Wu H, Li J, Xian W, Li W, Locascio JJ, Pei Z, Liu G. Joint Modeling Study Identifies Blood-Based Transcripts Link to Cognitive Decline in Parkinson's Disease. Mov Disord 2022; 37:2386-2395. [PMID: 36087011 DOI: 10.1002/mds.29213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 08/05/2022] [Accepted: 08/17/2022] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Cognitive decline in Parkinson's disease (PD) is prevalent, insidious, and burdensome during the progression of the disease. OBJECTIVES We aimed to find transcriptome-wide biomarkers in blood to predict cognitive decline and identify patients at high risk with cognitive impairment in PD. METHODS We carried out joint modeling analysis to characterize transcriptome-wide longitudinal gene expression and its association with the progression of mild cognitive impairment (MCI) in PD patients. The average time-dependent area under the curves (AUCs) were used for evaluating the accuracy of the significant joint models. A cognitive survival score (CogSs) derived from joint model was leveraged to predict the occurrence of MCI. All predicting models were built in a discovery cohort with 272 patients and replicated in an independent cohort with 177 patients. RESULTS We identified five longitudinal varied expression of transcripts that were significantly associated with MCI progression in patients with PD. The most significant transcript IGLC1 joint model accurately predicted the progression of MCI in PD patients in the discovery and replication cohorts (average time-dependent AUCs >0.82). The CogSs derived from the optimal IGLC1 joint model had a high accuracy at early study stage in both cohorts (AUC ≥0.91). CONCLUSIONS Our transcriptome-wide joint modeling analysis uncovered five blood-based transcripts related to cognitive decline in PD. The joint models will serve as a useful resource for clinicians and researchers to screen PD patients with high risk of development of cognitive impairment and pave the path for Parkinson's personalized medicine. © 2022 International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Junfeng Luo
- Neurobiology Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Hao Wu
- Neurobiology Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Jinxia Li
- Neurobiology Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Wenbiao Xian
- Department of Neurology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Weimin Li
- Neurobiology Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Joseph J Locascio
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Zhong Pei
- Department of Neurology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
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14
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Huseby CJ, Delvaux E, Brokaw DL, Coleman PD. Blood Transcript Biomarkers Selected by Machine Learning Algorithm Classify Neurodegenerative Diseases including Alzheimer's Disease. Biomolecules 2022; 12:1592. [PMID: 36358942 PMCID: PMC9687215 DOI: 10.3390/biom12111592] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/22/2022] [Accepted: 10/22/2022] [Indexed: 10/15/2023] Open
Abstract
The clinical diagnosis of neurodegenerative diseases is notoriously inaccurate and current methods are often expensive, time-consuming, or invasive. Simple inexpensive and noninvasive methods of diagnosis could provide valuable support for clinicians when combined with cognitive assessment scores. Biological processes leading to neuropathology progress silently for years and are reflected in both the central nervous system and vascular peripheral system. A blood-based screen to distinguish and classify neurodegenerative diseases is especially interesting having low cost, minimal invasiveness, and accessibility to almost any world clinic. In this study, we set out to discover a small set of blood transcripts that can be used to distinguish healthy individuals from those with Alzheimer's disease, Parkinson's disease, Huntington's disease, amyotrophic lateral sclerosis, Friedreich's ataxia, or frontotemporal dementia. Using existing public datasets, we developed a machine learning algorithm for application on transcripts present in blood and discovered small sets of transcripts that distinguish a number of neurodegenerative diseases with high sensitivity and specificity. We validated the usefulness of blood RNA transcriptomics for the classification of neurodegenerative diseases. Information about features selected for the classification can direct the development of possible treatment strategies.
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Affiliation(s)
- Carol J. Huseby
- ASU-Banner Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ 85281, USA
| | - Elaine Delvaux
- ASU-Banner Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ 85281, USA
| | - Danielle L. Brokaw
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Paul D. Coleman
- ASU-Banner Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ 85281, USA
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15
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Petricca L, Chiki N, Hanna-El-Daher L, Aeschbach L, Burai R, Stoops E, Fares MB, Lashuel HA. Comparative Analysis of Total Alpha-Synuclein (αSYN) Immunoassays Reveals That They Do Not Capture the Diversity of Modified αSYN Proteoforms. JOURNAL OF PARKINSON'S DISEASE 2022; 12:1449-1462. [PMID: 35527570 PMCID: PMC9398082 DOI: 10.3233/jpd-223285] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Background: The development of therapeutics for Parkinson’s disease (PD) requires the establishment of biomarker assays to enable stratifying patients, monitoring disease progression, and assessing target engagement. Attempts to develop diagnostic assays based on detecting levels of the α-synuclein (αSYN) protein, a central player in the pathogenesis of PD, have yielded inconsistent results. Objective: To determine whether the three commercial kits that have been extensively used for total αSYN quantification in human biological fluids (from Euroimmun, MSD, and Biolegend) are capable of capturing the diversity and complexity of relevant αSYN proteoforms. Methods: We investigated and compared the ability of the different assays to detect the diversity of αSYN proteoforms using a library of αSYN proteins that comprise the majority of disease-relevant αSYN variants and post-translational modifications (PTMs). Results: Our findings showed that none of the three tested immunoassays accurately capture the totality of relevant αSYN species, and that these assays are unable to recognize most disease-associated C-terminally truncated variants of αSYN. Moreover, several N-terminal truncations and phosphorylation/nitration PTMs differentially modify the level of αSYN detection and recovery by different immunoassays, and a CSF matrix effect was observed for most of the αSYN proteoforms analyzed by the three immunoassays. Conclusion: Our results show that the tested immunoassays do not capture the totality of the relevant αSYN species and therefore may not be appropriate tools to provide an accurate measure of total αSYN levels in samples containing modified forms of the protein. This highlights the need for next generation αSYN immunoassays that capture the diversity of αSYN proteoforms.
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Affiliation(s)
| | - Nour Chiki
- ND Biosciences SA, Epalinges, Switzerland
| | - Layane Hanna-El-Daher
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Brain Mind Institute,Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Lorène Aeschbach
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Brain Mind Institute,Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Ritwik Burai
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Brain Mind Institute,Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Erik Stoops
- ADx NeuroSciences NV, Technologiepark 94 - Bio Incubator, Gent, Belgium
| | | | - Hilal A Lashuel
- ND Biosciences SA, Epalinges, Switzerland.,Laboratory of Molecular and Chemical Biology of Neurodegeneration, Brain Mind Institute,Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
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16
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Hallacli E, Kayatekin C, Nazeen S, Wang XH, Sheinkopf Z, Sathyakumar S, Sarkar S, Jiang X, Dong X, Di Maio R, Wang W, Keeney MT, Felsky D, Sandoe J, Vahdatshoar A, Udeshi ND, Mani DR, Carr SA, Lindquist S, De Jager PL, Bartel DP, Myers CL, Greenamyre JT, Feany MB, Sunyaev SR, Chung CY, Khurana V. The Parkinson's disease protein alpha-synuclein is a modulator of processing bodies and mRNA stability. Cell 2022; 185:2035-2056.e33. [PMID: 35688132 DOI: 10.1016/j.cell.2022.05.008] [Citation(s) in RCA: 55] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 04/05/2022] [Accepted: 05/06/2022] [Indexed: 12/13/2022]
Abstract
Alpha-synuclein (αS) is a conformationally plastic protein that reversibly binds to cellular membranes. It aggregates and is genetically linked to Parkinson's disease (PD). Here, we show that αS directly modulates processing bodies (P-bodies), membraneless organelles that function in mRNA turnover and storage. The N terminus of αS, but not other synucleins, dictates mutually exclusive binding either to cellular membranes or to P-bodies in the cytosol. αS associates with multiple decapping proteins in close proximity on the Edc4 scaffold. As αS pathologically accumulates, aberrant interaction with Edc4 occurs at the expense of physiologic decapping-module interactions. mRNA decay kinetics within PD-relevant pathways are correspondingly disrupted in PD patient neurons and brain. Genetic modulation of P-body components alters αS toxicity, and human genetic analysis lends support to the disease-relevance of these interactions. Beyond revealing an unexpected aspect of αS function and pathology, our data highlight the versatility of conformationally plastic proteins with high intrinsic disorder.
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Affiliation(s)
- Erinc Hallacli
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Division of Movement Disorders, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Can Kayatekin
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Sumaiya Nazeen
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Division of Movement Disorders, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA; Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115
| | - Xiou H Wang
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Division of Movement Disorders, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Zoe Sheinkopf
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Division of Movement Disorders, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Shubhangi Sathyakumar
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Division of Movement Disorders, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Souvarish Sarkar
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Xin Jiang
- Yumanity Therapeutics, Boston, MA 02135, USA
| | - Xianjun Dong
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Genomics and Bioinformatics Hub, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Roberto Di Maio
- Pittsburgh Institute for Neurodegenerative Diseases and Department of Neurology, Pittsburgh, PA 15213, USA
| | - Wen Wang
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Matthew T Keeney
- Pittsburgh Institute for Neurodegenerative Diseases and Department of Neurology, Pittsburgh, PA 15213, USA
| | - Daniel Felsky
- Krembil Centre for Neuroinformatics and Department of Psychiatry, University of Toronto, Toronto, ON M5T 1R8, Canada; Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada; Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, 155 College Street, Toronto, ON M5T 3M7, Canada
| | - Jackson Sandoe
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Aazam Vahdatshoar
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Division of Movement Disorders, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | | | - D R Mani
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Steven A Carr
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Susan Lindquist
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Cambridge, MA 02142, USA; Department of Biology, MIT, Cambridge, MA 02139, USA
| | - Philip L De Jager
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - David P Bartel
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Cambridge, MA 02142, USA; Department of Biology, MIT, Cambridge, MA 02139, USA
| | - Chad L Myers
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - J Timothy Greenamyre
- Pittsburgh Institute for Neurodegenerative Diseases and Department of Neurology, Pittsburgh, PA 15213, USA
| | - Mel B Feany
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Shamil R Sunyaev
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA; Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115
| | | | - Vikram Khurana
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Division of Movement Disorders, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA.
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17
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Augustine J, Jereesh AS. Blood-based gene-expression biomarkers identification for the non-invasive diagnosis of Parkinson's disease using two-layer hybrid feature selection. Gene X 2022; 823:146366. [PMID: 35202733 DOI: 10.1016/j.gene.2022.146366] [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: 09/04/2021] [Revised: 02/15/2022] [Accepted: 02/18/2022] [Indexed: 11/19/2022] Open
Abstract
Parkinson's disease (PD) is one of the most prevalent neurodegenerative diseases. Understanding the molecular mechanism and identifying potential biomarkers of PD promote effective treatments to the patients. Due to less invasiveness and easy accessibility, biomarkers from blood support early detection and diagnosis of PD. This study combined three independent PD microarray gene expression data from blood samples applying the early integration approach. Moderated t-statistics was employed to identify differentially expressed genes (DEGs). Relevant genes were selected using a two-layer embedded wrapper feature selection method with gradient boosting machine (GBM) in the first layer followed by an ensemble of wrappers including Recursive Feature Elimination (RFE), Genetic algorithm (GA) and Bi-directional elimination (Stepwise). All three wrappers were based on logistic regression classifier (LR). The PD-predictability of the generated signature was tested using nine supervised classification models, including eight shallow machine learning and one deep learning. On an independent dataset, GSE72267, Support Vector Machine-Radial (SVMR), and Deep Neural Network (DNN) showed the best performance with AUC 0.821 and 0.82, respectively. Comparison with existing blood-based PD signatures and the biological analysis verified the reliability of the proposed signature.
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Affiliation(s)
- Jisha Augustine
- Bioinformatics Lab, Department of Computer Science, Cochin University of Science and Technology, Kerala 682022, India.
| | - A S Jereesh
- Bioinformatics Lab, Department of Computer Science, Cochin University of Science and Technology, Kerala 682022, India.
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18
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Multiple Criteria Optimization (MCO): A gene selection deterministic tool in RStudio. PLoS One 2022; 17:e0262890. [PMID: 35085348 PMCID: PMC8794188 DOI: 10.1371/journal.pone.0262890] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 01/09/2022] [Indexed: 11/19/2022] Open
Abstract
Identifying genes with the largest expression changes (gene selection) to characterize a given condition is a popular first step to drive exploration into molecular mechanisms and is, therefore, paramount for therapeutic development. Reproducibility in the sciences makes it necessary to emphasize objectivity and systematic repeatability in biological and informatics analyses, including gene selection. With these two characteristics in mind, in previous works our research team has proposed using multiple criteria optimization (MCO) in gene selection to analyze microarray datasets. The result of this effort is the MCO algorithm, which selects genes with the largest expression changes without user manipulation of neither informatics nor statistical parameters. Furthermore, the user is not required to choose either a preference structure among multiple measures or a predetermined quantity of genes to be deemed significant a priori. This implies that using the same datasets and performance measures (PMs), the method will converge to the same set of selected differentially expressed genes (repeatability) despite who carries out the analysis (objectivity). The present work describes the development of an open-source tool in RStudio to enable both: (1) individual analysis of single datasets with two or three PMs and (2) meta-analysis with up to five microarray datasets, using one PM from each dataset. The capabilities afforded by the code include license-free portability and the possibility to carry out analyses via modest computer hardware, such as personal laptops. The code provides affordable, repeatable, and objective detection of differentially expressed genes from microarrays. It can be used to analyze other experiments with similar experimental comparative layouts, such as microRNA arrays and protein arrays, among others. As a demonstration of the capabilities of the code, the analysis of four publicly-available microarray datasets related to Parkinson´s Disease (PD) is presented here, treating each dataset individually or as a four-way meta-analysis. These MCO-supported analyses made it possible to identify MMP9 and TUBB2A as potential PD genetic biomarkers based on their persistent appearance across each of the case studies. A literature search confirmed the importance of these genes in PD and indeed as PD biomarkers, which evidences the code´s potential.
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19
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Parkinson's Disease Subtyping Using Clinical Features and Biomarkers: Literature Review and Preliminary Study of Subtype Clustering. Diagnostics (Basel) 2022; 12:diagnostics12010112. [PMID: 35054279 PMCID: PMC8774435 DOI: 10.3390/diagnostics12010112] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/31/2021] [Accepted: 01/03/2022] [Indexed: 12/29/2022] Open
Abstract
The second most common progressive neurodegenerative disorder, Parkinson’s disease (PD), is characterized by a broad spectrum of symptoms that are associated with its progression. Several studies have attempted to classify PD according to its clinical manifestations and establish objective biomarkers for early diagnosis and for predicting the prognosis of the disease. Recent comprehensive research on the classification of PD using clinical phenotypes has included factors such as dominance, severity, and prognosis of motor and non-motor symptoms and biomarkers. Additionally, neuroimaging studies have attempted to reveal the pathological substrate for motor symptoms. Genetic and transcriptomic studies have contributed to our understanding of the underlying molecular pathogenic mechanisms and provided a basis for classifying PD. Moreover, an understanding of the heterogeneity of clinical manifestations in PD is required for a personalized medicine approach. Herein, we discuss the possible subtypes of PD based on clinical features, neuroimaging, and biomarkers for developing personalized medicine for PD. In addition, we conduct a preliminary clustering using gait features for subtyping PD. We believe that subtyping may facilitate the development of therapeutic strategies for PD.
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20
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Blažeković A, Jerčić KG, Borovečki F. SNCA 3' UTR Genetic Variants in Patients with Parkinson's Disease. Biomolecules 2021; 11:1799. [PMID: 34944443 PMCID: PMC8698872 DOI: 10.3390/biom11121799] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 11/15/2021] [Accepted: 11/27/2021] [Indexed: 11/26/2022] Open
Abstract
The SNCA (Synuclein Alpha) gene represents a major risk gene for Parkinson's disease (PD) and SNCA polymorphisms have been associated with the common sporadic form of PD. Numerous Genome-Wide Association Studies showed strong signals located in the SNCA 3' UTR (untranslated region) region indicating that variants in 3' UTRs of PD-associated genes could contribute to neurodegeneration and may regulate the risk for PD. Genetic variants in 3' UTR can affect miRNA activity and consequently change the translation process. The aim of this study was to access the differences in 3' UTR variants of SNCA genes in a cohort of PD patients and control subjects from Croatia. The cohort consisted of 52 PD patients and 23 healthy control subjects. Differences between 3' UTR allele and genotype frequencies were accessed through next generation sequencing approach from whole blood samples. In our study, we identified four previously reported single nucleotide polymorphisms (SNPs) and one insertion in the 3' UTR region of SNCA gene, namely rs1045722, rs3857053, rs577490090, rs356165, and rs777296100, and five variants not reported in the literature, namely rs35270750, rs529553259, rs377356638, rs571454522, and rs750347645. Our results indicate a significantly higher occurrence of the rs571454522 variant in the PD population. To the best of our knowledge, this variant has not been reported until now in the literature. We analyzed our results in the context of previous research, creating a brief overview of the importance of 3' UTR variants of the SNCA gene. Further studies will be needed to gain a more profound insight regarding their role in PD development, which will help to assess the role and impact of post-transcriptional regulation on disease pathology.
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Affiliation(s)
- Antonela Blažeković
- Department for Functional Genomics, Center for Translational and Clinical Research, University of Zagreb School of Medicine, University Hospital Center Zagreb, 10000 Zagreb, Croatia; (K.G.J.); (F.B.)
- Department for Anatomy and Clinical Anatomy, University of Zagreb School of Medicine, 10000 Zagreb, Croatia
| | - Kristina Gotovac Jerčić
- Department for Functional Genomics, Center for Translational and Clinical Research, University of Zagreb School of Medicine, University Hospital Center Zagreb, 10000 Zagreb, Croatia; (K.G.J.); (F.B.)
- Department of Neurology, University Hospital Center Zagreb, 10000 Zagreb, Croatia
| | - Fran Borovečki
- Department for Functional Genomics, Center for Translational and Clinical Research, University of Zagreb School of Medicine, University Hospital Center Zagreb, 10000 Zagreb, Croatia; (K.G.J.); (F.B.)
- Department of Neurology, University Hospital Center Zagreb, 10000 Zagreb, Croatia
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21
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Yalçin M, Malhan D, Basti A, Peralta AR, Ferreira JJ, Relógio A. A Computational Analysis in a Cohort of Parkinson's Disease Patients and Clock-Modified Colorectal Cancer Cells Reveals Common Expression Alterations in Clock-Regulated Genes. Cancers (Basel) 2021; 13:cancers13235978. [PMID: 34885088 PMCID: PMC8657387 DOI: 10.3390/cancers13235978] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 11/18/2021] [Accepted: 11/21/2021] [Indexed: 12/13/2022] Open
Abstract
Simple Summary Cancer and neurodegenerative diseases are two aging-related pathologies with differential developmental characteristics, but they share altered cellular pathways. Interestingly, dysregulations in the biological clock are reported in both diseases, though the extent and potential consequences of such disruption have not been fully elucidated. In this study, we aimed at characterizing global changes on common cellular pathways associated with Parkinson’s disease (PD) and colorectal cancer (CRC). We used gene expression data retrieved from an idiopathic PD (IPD) patient cohort and from CRC cells with unmodified versus genetically altered clocks. Our results highlight common differentially expressed genes between IPD patients and cells with disrupted clocks, suggesting a role for the circadian clock in the regulation of pathways altered in both pathologies. Interestingly, several of these genes are related to cancer hallmarks and may have an impact on the overall survival of colon cancer patients, as suggested by our analysis. Abstract Increasing evidence suggests a role for circadian dysregulation in prompting disease-related phenotypes in mammals. Cancer and neurodegenerative disorders are two aging related diseases reported to be associated with circadian disruption. In this study, we investigated a possible effect of circadian disruption in Parkinson’s disease (PD) and colorectal cancer (CRC). We used high-throughput data sets retrieved from whole blood of idiopathic PD (IPD) patients and time course data sets derived from an in vitro model of CRC including the wildtype and three core-clock knockout (KO) cell lines. Several gene expression alterations in IPD patients resembled the expression profiles in the core-clock KO cells. These include expression changes in DBP, GBA, TEF, SNCA, SERPINA1 and TGFB1. Notably, our results pointed to alterations in the core-clock network in IPD patients when compared to healthy controls and revealed variations in the expression profile of PD-associated genes (e.g., HRAS and GBA) upon disruption of the core-clock genes. Our study characterizes changes at the transcriptomic level following circadian clock disruption on common cellular pathways associated with cancer and neurodegeneration (e.g., immune system, energy metabolism and RNA processing), and it points to a significant influence on the overall survival of colon cancer patients for several genes resulting from our analysis (e.g., TUBB6, PAK6, SLC11A1).
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Affiliation(s)
- Müge Yalçin
- Institute for Theoretical Biology (ITB), Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, 10117 Berlin, Germany; (M.Y.); (D.M.); (A.B.)
- Molecular Cancer Research Center (MKFZ), Medical Department of Hematology, Oncology, and Tumour Immunology, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, 10117 Berlin, Germany
| | - Deeksha Malhan
- Institute for Theoretical Biology (ITB), Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, 10117 Berlin, Germany; (M.Y.); (D.M.); (A.B.)
- Molecular Cancer Research Center (MKFZ), Medical Department of Hematology, Oncology, and Tumour Immunology, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, 10117 Berlin, Germany
- Institute for Systems Medicine and Faculty of Human Medicine, MSH Medical School Hamburg, 20457 Hamburg, Germany
| | - Alireza Basti
- Institute for Theoretical Biology (ITB), Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, 10117 Berlin, Germany; (M.Y.); (D.M.); (A.B.)
- Molecular Cancer Research Center (MKFZ), Medical Department of Hematology, Oncology, and Tumour Immunology, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, 10117 Berlin, Germany
- Institute for Systems Medicine and Faculty of Human Medicine, MSH Medical School Hamburg, 20457 Hamburg, Germany
| | - Ana Rita Peralta
- EEG/Sleep Laboratory, Department Neurosciences and Mental Health, Hospital de Santa Maria—CHULN, 1649-035 Lisbon, Portugal;
- Department of Neurology, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisbon, Portugal
- Instituto de Fisiologia, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisbon, Portugal
- CNS-Campus Neurológico Senior, 2560-280 Torres Vedras, Portugal;
| | - Joaquim J. Ferreira
- CNS-Campus Neurológico Senior, 2560-280 Torres Vedras, Portugal;
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisbon, Portugal
- Laboratory of Clinical Pharmacology and Therapeutics, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisbon, Portugal
| | - Angela Relógio
- Institute for Theoretical Biology (ITB), Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, 10117 Berlin, Germany; (M.Y.); (D.M.); (A.B.)
- Molecular Cancer Research Center (MKFZ), Medical Department of Hematology, Oncology, and Tumour Immunology, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, 10117 Berlin, Germany
- Institute for Systems Medicine and Faculty of Human Medicine, MSH Medical School Hamburg, 20457 Hamburg, Germany
- Correspondence: or
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22
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Booms A, Coetzee GA. Functions of Intracellular Alpha-Synuclein in Microglia: Implications for Parkinson's Disease Risk. Front Cell Neurosci 2021; 15:759571. [PMID: 34671245 PMCID: PMC8521067 DOI: 10.3389/fncel.2021.759571] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 09/06/2021] [Indexed: 11/13/2022] Open
Abstract
Alpha-synuclein accumulation in dopaminergic neurons is one of the primary features of Parkinson’s disease (PD). Despite its toxic properties during PD, alpha-synuclein has some important physiological functions. Although the activity of the protein has been extensively studied in neurons, the protein is also expressed in other cell types including immune cells and glia. Genetic studies show that mutations in synuclein alpha (SNCA), the gene that encodes alpha-synuclein, and alterations in its expression levels are a significant risk factor for PD, which likely impact the functions of a broad range of cell types. The consequences of altered SNCA expression in other cell types is beginning to be explored. Microglia, the primary macrophage population in the Central Nervous System (CNS), for example, are affected by variations in alpha-synuclein levels and functions. Studies suggest that deviations of alpha-synuclein’s normal activity influence hematopoiesis, the process that gives rise to microglia, and microglia’s immune functions. Alpha-synuclein levels also dictate the efficiency of SNARE-mediated vesicle formation, which could influence autophagy and cytokine release in microglia. Starting from the time of conception, these effects could impact one’s risk for developing PD. Further studies are needed to determine the physiological role of alpha-synuclein and how the protein is affected during PD in non-neuronal cells such as microglia. In this review we will discuss the known roles of alpha-synuclein in differentiation, immune responses, and vesicle formation, with insights into how abnormal alpha-synuclein expression and activity are linked to altered functions of microglia during PD.
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Affiliation(s)
- Alix Booms
- Coetzee Laboratory, Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI, United States
| | - Gerhard A Coetzee
- Coetzee Laboratory, Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI, United States
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23
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The Impact of SNCA Variations and Its Product Alpha-Synuclein on Non-Motor Features of Parkinson's Disease. Life (Basel) 2021; 11:life11080804. [PMID: 34440548 PMCID: PMC8401994 DOI: 10.3390/life11080804] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/04/2021] [Accepted: 08/06/2021] [Indexed: 12/14/2022] Open
Abstract
Parkinson’s disease (PD) is a common and progressive neurodegenerative disease, caused by the loss of dopaminergic neurons in the substantia nigra pars compacta in the midbrain, which is clinically characterized by a constellation of motor and non-motor manifestations. The latter include hyposmia, constipation, depression, pain and, in later stages, cognitive decline and dysautonomia. The main pathological features of PD are neuronal loss and consequent accumulation of Lewy bodies (LB) in the surviving neurons. Alpha-synuclein (α-syn) is the main component of LB, and α-syn aggregation and accumulation perpetuate neuronal degeneration. Mutations in the α-syn gene (SNCA) were the first genetic cause of PD to be identified. Generally, patients carrying SNCA mutations present early-onset parkinsonism with severe and early non-motor symptoms, including cognitive decline. Several SNCA polymorphisms were also identified, and some of them showed association with non-motor manifestations. The functional role of these polymorphisms is only partially understood. In this review we explore the contribution of SNCA and its product, α-syn, in predisposing to the non-motor manifestations of PD.
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24
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Craig DW, Hutchins E, Violich I, Alsop E, Gibbs JR, Levy S, Robison M, Prasad N, Foroud T, Crawford KL, Toga AW, Whitsett TG, Kim S, Casey B, Reimer A, Hutten SJ, Frasier M, Kern F, Fehlman T, Keller A, Cookson MR, Van Keuren-Jensen K. RNA sequencing of whole blood reveals early alterations in immune cells and gene expression in Parkinson's disease. NATURE AGING 2021; 1:734-747. [PMID: 37117765 DOI: 10.1038/s43587-021-00088-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 06/21/2021] [Indexed: 04/30/2023]
Abstract
Changes in the blood-based RNA transcriptome have the potential to inform biomarkers of Parkinson's disease (PD) progression. Here we sequenced a discovery set of whole-blood RNA species in 4,871 longitudinally collected samples from 1,570 clinically phenotyped individuals from the Parkinson's Progression Marker Initiative (PPMI) cohort. Samples were sequenced to an average of 100 million read pairs to create a high-quality transcriptome. Participants with PD in the PPMI had significantly altered RNA expression (>2,000 differentially expressed genes), including an early and persistent increase in neutrophil gene expression, with a concomitant decrease in lymphocyte cell counts. This was validated in a cohort from the Parkinson's Disease Biomarkers Program (PDBP) consisting of 1,599 participants and by alterations in immune cell subtypes. This publicly available transcriptomic dataset, coupled with available detailed clinical data, provides new insights into PD biological processes impacting whole blood and new paths for developing diagnostic and prognostic PD biomarkers.
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Affiliation(s)
- David W Craig
- Institute of Translational Genomics, University of Southern California, Los Angeles, CA, USA
| | - Elizabeth Hutchins
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ, USA
| | - Ivo Violich
- Institute of Translational Genomics, University of Southern California, Los Angeles, CA, USA
| | - Eric Alsop
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ, USA
| | - J Raphael Gibbs
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Shawn Levy
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Madison Robison
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Nripesh Prasad
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | | | - Karen L Crawford
- Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
| | - Arthur W Toga
- Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
| | - Timothy G Whitsett
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ, USA
| | - Seungchan Kim
- Center for Computational Systems Biology, Department of Electrical and Computer Engineering, Roy G. Perry College of Engineering, Prairie View A&M University, Prairie View, TX, USA
| | - Bradford Casey
- The Michael J. Fox Foundation for Parkinson's Research, New York, NY, USA
| | - Alyssa Reimer
- The Michael J. Fox Foundation for Parkinson's Research, New York, NY, USA
| | - Samantha J Hutten
- The Michael J. Fox Foundation for Parkinson's Research, New York, NY, USA
| | - Mark Frasier
- The Michael J. Fox Foundation for Parkinson's Research, New York, NY, USA
| | - Fabian Kern
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Tobias Fehlman
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Mark R Cookson
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
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25
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Bakshi R, Macklin EA, Hung AY, Hayes MT, Hyman BT, Wills AM, Gomperts SN, Growdon JH, Ascherio A, Scherzer CR, Schwarzschild MA. Associations of Lower Caffeine Intake and Plasma Urate Levels with Idiopathic Parkinson's Disease in the Harvard Biomarkers Study. JOURNAL OF PARKINSONS DISEASE 2021; 10:505-510. [PMID: 32250320 DOI: 10.3233/jpd-191882] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Two purines, caffeine and urate, have been associated with a reduced risk of idiopathic Parkinson's disease (PD) in multiple cohorts and populations. The Harvard Biomarkers Study (HBS) is a longitudinal study designed to accelerate the discovery and validation of molecular diagnostic and progression markers of early-stage PD. To investigate whether these 'reduced risk' factors are associated with PD within this cohort, we conducted a cross-sectional, case-control study in 566 subjects consisting of idiopathic PD patients and healthy controls. Caffeine intake as assessed by a validated questionnaire was significantly lower in idiopathic PD patients compared to healthy controls in males (mean difference -125 mg/day, p < 0.001) but not in females (mean difference -30 mg/day, p = 0.29). A strong inverse association was also observed with plasma urate levels both in males (mean difference -0.46 mg/dL, p = 0.017) and females (mean difference -0.45 mg/dL, p = 0.001). Both analyses stratified for sex and adjusted for age, body mass index, and either urate level or caffeine consumption, respectively. These results highlight the robustness of caffeine intake and urate as factors inversely associated with idiopathic PD.
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Affiliation(s)
- Rachit Bakshi
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Eric A Macklin
- Harvard Medical School, Boston, MA, USA.,Biostatistics Center, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Albert Y Hung
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Michael T Hayes
- Harvard Medical School, Boston, MA, USA.,APDA Center for Advanced Parkinson Research, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Bradley T Hyman
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Anne-Marie Wills
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Stephen N Gomperts
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - John H Growdon
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Alberto Ascherio
- Biostatistics Center, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Clemens R Scherzer
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA.,APDA Center for Advanced Parkinson Research, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.,Precision Neurology Program, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Michael A Schwarzschild
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
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26
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Liu G, Peng J, Liao Z, Locascio JJ, Corvol JC, Zhu F, Dong X, Maple-Grødem J, Campbell MC, Elbaz A, Lesage S, Brice A, Mangone G, Growdon JH, Hung AY, Schwarzschild MA, Hayes MT, Wills AM, Herrington TM, Ravina B, Shoulson I, Taba P, Kõks S, Beach TG, Cormier-Dequaire F, Alves G, Tysnes OB, Perlmutter JS, Heutink P, Amr SS, van Hilten JJ, Kasten M, Mollenhauer B, Trenkwalder C, Klein C, Barker RA, Williams-Gray CH, Marinus J, Scherzer CR. Genome-wide survival study identifies a novel synaptic locus and polygenic score for cognitive progression in Parkinson's disease. Nat Genet 2021; 53:787-793. [PMID: 33958783 PMCID: PMC8459648 DOI: 10.1038/s41588-021-00847-6] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 03/16/2021] [Indexed: 02/02/2023]
Abstract
A key driver of patients' well-being and clinical trials for Parkinson's disease (PD) is the course that the disease takes over time (progression and prognosis). To assess how genetic variation influences the progression of PD over time to dementia, a major determinant for quality of life, we performed a longitudinal genome-wide survival study of 11.2 million variants in 3,821 patients with PD over 31,053 visits. We discover RIMS2 as a progression locus and confirm this in a replicate population (hazard ratio (HR) = 4.77, P = 2.78 × 10-11), identify suggestive evidence for TMEM108 (HR = 2.86, P = 2.09 × 10-8) and WWOX (HR = 2.12, P = 2.37 × 10-8) as progression loci, and confirm associations for GBA (HR = 1.93, P = 0.0002) and APOE (HR = 1.48, P = 0.001). Polygenic progression scores exhibit a substantial aggregate association with dementia risk, while polygenic susceptibility scores are not predictive. This study identifies a novel synaptic locus and polygenic score for cognitive disease progression in PD and proposes diverging genetic architectures of progression and susceptibility.
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Affiliation(s)
- Ganqiang Liu
- Center for Advanced Parkinson Research, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
- Precision Neurology Program of Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- School of Medicine, Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Jiajie Peng
- Center for Advanced Parkinson Research, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
- Precision Neurology Program of Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- School of Computer Science, Northwestern Polytechnical University, Xi'an, Shaanxi, China
| | - Zhixiang Liao
- Center for Advanced Parkinson Research, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
- Precision Neurology Program of Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Joseph J Locascio
- Center for Advanced Parkinson Research, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
- Precision Neurology Program of Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Jean-Christophe Corvol
- Sorbonne Université, Paris Brain Institute - Institut du Cerveau - ICM, Institut National de Santé et en Recherche Médicale, Centre National de Recherche Scientifique, Assistance Publique Hôpitaux de Paris, Département de Neurologie et de Génétique, Centre d'Investigation Clinique Neurosciences, Hôpital Pitié-Salpêtrière, Paris, France
| | - Frank Zhu
- Center for Advanced Parkinson Research, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
- Precision Neurology Program of Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Xianjun Dong
- Center for Advanced Parkinson Research, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
- Precision Neurology Program of Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jodi Maple-Grødem
- The Norwegian Centre for Movement Disorders, Stavanger University Hospital, Stavanger, Norway
- Department of Chemistry, Bioscience and Environmental Engineering, University of Stavanger, Stavanger, Norway
| | - Meghan C Campbell
- Departments of Neurology and Radiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Alexis Elbaz
- Paris-Saclay University, Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Inserm, Gustave Roussy, 'Exposome and heredity' team, Centre de researche en épidémiologie et santé des populations (CESP), Villejuif, France
| | - Suzanne Lesage
- Sorbonne Université, Paris Brain Institute - Institut du Cerveau - ICM, Institut National de Santé et en Recherche Médicale, Centre National de Recherche Scientifique, Assistance Publique Hôpitaux de Paris, Département de Neurologie et de Génétique, Centre d'Investigation Clinique Neurosciences, Hôpital Pitié-Salpêtrière, Paris, France
| | - Alexis Brice
- Sorbonne Université, Paris Brain Institute - Institut du Cerveau - ICM, Institut National de Santé et en Recherche Médicale, Centre National de Recherche Scientifique, Assistance Publique Hôpitaux de Paris, Département de Neurologie et de Génétique, Centre d'Investigation Clinique Neurosciences, Hôpital Pitié-Salpêtrière, Paris, France
| | - Graziella Mangone
- Sorbonne Université, Paris Brain Institute - Institut du Cerveau - ICM, Institut National de Santé et en Recherche Médicale, Centre National de Recherche Scientifique, Assistance Publique Hôpitaux de Paris, Département de Neurologie et de Génétique, Centre d'Investigation Clinique Neurosciences, Hôpital Pitié-Salpêtrière, Paris, France
| | - John H Growdon
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Albert Y Hung
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Michael A Schwarzschild
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Michael T Hayes
- Center for Advanced Parkinson Research, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
- Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA
| | - Anne-Marie Wills
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Todd M Herrington
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Ira Shoulson
- Department of Neurology, Center for Health + Technology, University of Rochester, Rochester, NY, USA
| | - Pille Taba
- Department of Neurology and Neurosurgery, University of Tartu, Tartu, Estonia
| | - Sulev Kõks
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, Western Australia, Australia
- Perron Institute for Neurological and Translational Science, Perth, Western Australia, Australia
| | | | - Florence Cormier-Dequaire
- Sorbonne Université, Paris Brain Institute - Institut du Cerveau - ICM, Institut National de Santé et en Recherche Médicale, Centre National de Recherche Scientifique, Assistance Publique Hôpitaux de Paris, Département de Neurologie et de Génétique, Centre d'Investigation Clinique Neurosciences, Hôpital Pitié-Salpêtrière, Paris, France
| | - Guido Alves
- The Norwegian Centre for Movement Disorders, Stavanger University Hospital, Stavanger, Norway
- Department of Chemistry, Bioscience and Environmental Engineering, University of Stavanger, Stavanger, Norway
- Department of Neurology, Stavanger University Hospital, Stavanger, Norway
| | - Ole-Bjørn Tysnes
- Department of Neurology, Haukeland University Hospital, Bergen, Norway
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Joel S Perlmutter
- Departments of Neurology and Radiology, Washington University School of Medicine, St. Louis, MO, USA
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO, USA
- Program of Physical Therapy and Program of Occupational Therapy, Washington University School of Medicine, St. Louis, MO, USA
| | - Peter Heutink
- German Center for Neurodegenerative diseases (DZNE), Tübingen, Germany
| | - Sami S Amr
- Translational Genomics Core of Partners HealthCare Personalized Medicine, Cambridge, MA, USA
| | - Jacobus J van Hilten
- Department of Neurology, Leiden University Medical Center, Leiden, the Netherlands
| | - Meike Kasten
- Institute of Neurogenetics, University of Lübeck, University Hospital of Schleswig-Holstein, Lübeck, Germany
- Department of Psychiatry and Psychotherapy, University of Lübeck, Lübeck, Germany
| | - Brit Mollenhauer
- Department of Neurology, University Medical Center Göttingen, Göttingen, Germany
- Paracelsus-Elena-Klinik, Kassel, Germany
| | - Claudia Trenkwalder
- Paracelsus-Elena-Klinik, Kassel, Germany
- Department of Neurosurgery, University Medical Center Göttingen, Göttingen, Germany
| | - Christine Klein
- Institute of Neurogenetics, University of Lübeck, University Hospital of Schleswig-Holstein, Lübeck, Germany
| | - Roger A Barker
- John Van Geest Centre for Brain Repair, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
- Wellcome - MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Caroline H Williams-Gray
- John Van Geest Centre for Brain Repair, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Johan Marinus
- Department of Neurology, Leiden University Medical Center, Leiden, the Netherlands
| | - Clemens R Scherzer
- Center for Advanced Parkinson Research, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA.
- Precision Neurology Program of Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
- Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA.
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Salas-Leal AC, Salas-Pacheco SM, Gavilán-Ceniceros JAP, Castellanos-Juárez FX, Méndez-Hernández EM, La Llave-León O, Camacho-Luis A, Quiñones-Canales G, Romero-Gutiérrez E, Arias-Carrión O, Salas-Pacheco JM, Sandoval-Carrillo AA. α-syn and SNP rs356219 as a potential biomarker in blood for Parkinson's disease in Mexican Mestizos. Neurosci Lett 2021; 754:135901. [PMID: 33865938 DOI: 10.1016/j.neulet.2021.135901] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 04/02/2021] [Accepted: 04/12/2021] [Indexed: 10/21/2022]
Abstract
Clinical criteria diagnose Parkinson's disease (PD), therefore, it is crucial to find biological elements that could support diagnosis or even act as prognostic tools of PD. The SNCA gene codifies a protein called α - synuclein; several studies associate genetic and biochemical factors of SNCA with PD, including transcript and plasmatic protein levels, however, contradictory evidence indicates inconclusive results. We aim to compare SNCA mRNA expression, plasmatic α-syn protein and rs356219 SNP between PD cases and a control group, and to identify a potential biomarker in Mexican mestizos', focusing on these three components determined in blood. We included 88 PD patients and 88 age-matched controls. We observed higher α-syn protein and decreased SNCA mRNA levels in PD subjects, compared to control group (p = 0.044 and p < 0.001, respectively). A statistically significant difference was found in allelic and genotypic frequencies of SNP rs356219 between PD patients and normal subjects (p = 0.006 and p = 0.023, respectively). Logistic regression analysis determined as optimal predictors of PD the GG genotype of SNP rs356219 (OR 2.49; p = 0.006) in a recessive model and α-syn protein (OR 1.057; p = 0.033). Furthermore, the G allele of SNP rs356219 was associated with higher plasmatic α-syn and mRNA levels in PD subjects. The receiver operating curves (ROC) distinguished PD from healthy controls with good sensitivity and specificity considering the plasmatic α-syn protein (AUC = 0.693, Sensitivity = 66.7 %, Specificity = 63.9 %) or a predictive probability of plasmatic α-syn protein and SNP rs356219 in a single model (AUC = 0.692, Sensitivity = 62.3 %, Specificity = 62.5 %). The performance of this classifier model in PD at early stage (n = 31) increase the discriminant power in both, plasmatic α-syn protein (AUC = 0.779, Sensitivity = 72.7 %, Specificity = 73.9 %) and predictive probability (AUC = 0.707, Sensitivity = 63.6 %, Specificity = 62.5 %). We propose that α-syn protein and SNP rs356219 together may work as a good signature of PD, and they can be suggested as a non-invasive biomarker of PD risk.
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Affiliation(s)
- Alma Cristina Salas-Leal
- Instituto de Investigación Científica, Universidad Juárez del Estado de Durango, Durango, 34000, Mexico
| | - Sergio M Salas-Pacheco
- Instituto de Investigación Científica, Universidad Juárez del Estado de Durango, Durango, 34000, Mexico
| | | | | | - Edna M Méndez-Hernández
- Instituto de Investigación Científica, Universidad Juárez del Estado de Durango, Durango, 34000, Mexico
| | - Osmel La Llave-León
- Instituto de Investigación Científica, Universidad Juárez del Estado de Durango, Durango, 34000, Mexico
| | - Abelardo Camacho-Luis
- Facultad de Medicina y Nutrición, Universidad Juárez del Estado de Durango, Durango, 34000, Mexico
| | | | - Elizabeth Romero-Gutiérrez
- Unidad de Trastornos del Movimiento y Sueño, Hospital General Dr. Manuel Gea González, Ciudad de México, 14080, Mexico
| | - Oscar Arias-Carrión
- Unidad de Trastornos del Movimiento y Sueño, Hospital General Dr. Manuel Gea González, Ciudad de México, 14080, Mexico
| | - José M Salas-Pacheco
- Instituto de Investigación Científica, Universidad Juárez del Estado de Durango, Durango, 34000, Mexico.
| | - Ada A Sandoval-Carrillo
- Instituto de Investigación Científica, Universidad Juárez del Estado de Durango, Durango, 34000, Mexico.
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28
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Fanning S, Selkoe D, Dettmer U. Vesicle trafficking and lipid metabolism in synucleinopathy. Acta Neuropathol 2021; 141:491-510. [PMID: 32607605 DOI: 10.1007/s00401-020-02177-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 06/05/2020] [Accepted: 06/06/2020] [Indexed: 12/12/2022]
Abstract
The neuronal protein α-synuclein (αS) is central to the pathogenesis of Parkinson's disease and other progressive brain diseases such as Lewy body dementia and multiple system atrophy. These diseases, collectively referred to as 'synucleinopathies', have long been considered purely proteinopathies: diseases characterized by the misfolding of a protein into small and large aggregates mainly consisting of that protein (in this case: α-synuclein). However, recent morphological insights into Lewy bodies, the hallmark neuropathology of human synucleinopathies, suggests these lesions are also rich in vesicles and other membranous organelles. Moreover, αS physiology and pathology are both strongly associated with various aspects of intracellular vesicle trafficking and lipid biology. αS physiologically binds to synaptic and other small vesicles, and several functions of αS in regulating vesicle biology have been proposed. Familial PD-linked αS excess and missense mutations have been shown to impair vesicle trafficking and alter lipid homeostasis. On the other hand, vesicle trafficking and lipid-related genes have emerged as Parkinson's risk factors, suggesting a bidirectional relationship. The answer to the question "Does abnormal αS accumulation cause impaired vesicle trafficking and lipid dyshomeostasis or is αS aggregation the consequence of such impairments?" may be "Both". Here, we review current knowledge of the αS-lipid and αS-vesicle trafficking interplay, with a special focus on Parkinson's disease and Lewy body dementia.
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Du T, Wang L, Liu W, Zhu G, Chen Y, Zhang J. Biomarkers and the Role of α-Synuclein in Parkinson's Disease. Front Aging Neurosci 2021; 13:645996. [PMID: 33833675 PMCID: PMC8021696 DOI: 10.3389/fnagi.2021.645996] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 03/05/2021] [Indexed: 12/13/2022] Open
Abstract
Parkinson’s disease (PD) is a progressive neurodegenerative disorder characterized by the presence of α-synuclein (α-Syn)-rich Lewy bodies (LBs) and the preferential loss of dopaminergic (DA) neurons in the substantia nigra (SN) pars compacta (SNpc). However, the widespread involvement of other central nervous systems (CNS) structures and peripheral tissues is now widely documented. The onset of the molecular and cellular neuropathology of PD likely occurs decades before the onset of the motor symptoms characteristic of PD, so early diagnosis of PD and adequate tracking of disease progression could significantly improve outcomes for patients. Because the clinical diagnosis of PD is challenging, misdiagnosis is common, which highlights the need for disease-specific and early-stage biomarkers. This review article aims to summarize useful biomarkers for the diagnosis of PD, as well as the biomarkers used to monitor disease progression. This review article describes the role of α-Syn in PD and how it could potentially be used as a biomarker for PD. Also, preclinical and clinical investigations encompassing genetics, immunology, fluid and tissue, imaging, as well as neurophysiology biomarkers are discussed. Knowledge of the novel biomarkers for preclinical detection and clinical evaluation will contribute to a deeper understanding of the disease mechanism, which should more effectively guide clinical applications.
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Affiliation(s)
- Tingting Du
- Department of Functional Neurosurgery, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Le Wang
- Molecular Biology Laboratory for Neuropsychiatric Diseases, Department of Neurobiology, Beijing Institute of Brain Disorders, Capital Medical University, Beijing, China
| | - Weijin Liu
- Key Laboratory for Neurodegenerative Disease of the Ministry of Education, Key Laboratory of Neural Regeneration and Repair, Beijing Key Laboratory on Parkinson's Disease, Department of Neurobiology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Guanyu Zhu
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yingchuan Chen
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Jianguo Zhang
- Department of Functional Neurosurgery, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Beijing Key Laboratory of Neurostimulation, Beijing Municipal Science and Technology Commission, Beijing, China
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30
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Nasamran CA, Sachan ANS, Mott J, Kuras YI, Scherzer CR, Study HB, Ricciardelli E, Jepsen K, Edland SD, Fisch KM, Desplats P. Differential blood DNA methylation across Lewy body dementias. ALZHEIMER'S & DEMENTIA (AMSTERDAM, NETHERLANDS) 2021; 13:e12156. [PMID: 33665346 PMCID: PMC7896631 DOI: 10.1002/dad2.12156] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 12/29/2020] [Indexed: 12/17/2022]
Abstract
INTRODUCTION Dementia with Lewy bodies (DLB) and Parkinson's disease dementia (PDD) are characterized by cognitive alterations, visual hallucinations, and motor impairment. Diagnosis is based on type and timing of clinical manifestations; however, determination of clinical subtypes is challenging. The utility of blood DNA methylation as a biomarker for Lewy body disorders (LBD) is mostly unexplored. METHODS We performed a cross-sectional analysis of blood methylation in 42 DLB and 50 PDD cases applying linear models to compare groups and logistic least absolute shrinkage and selection operator regression to explore the discriminant power of methylation signals. RESULTS DLB blood shows differential methylation compared to PDD. Some methylation changes associate with core features of LBD. Sets of probes show high predictive value to discriminate between variants. DISCUSSION Our study is the first to explore LBD blood methylation. Despite overlapping clinical presentation, we detected differential epigenetic signatures that, if confirmed in independent cohorts, could be developed into useful biomarkers.
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Affiliation(s)
- Chanond A. Nasamran
- Center for Computational Biology & BioinformaticsDepartment of MedicineUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Anubhav Nikunj Singh Sachan
- Division of Biostatistics, Department of Family Medicine and Public HealthUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Jennifer Mott
- Department of Neurosciences, School of MedicineUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Yuliya I. Kuras
- Center for Advanced Parkinson Research and Precision Neurology Program, Harvard Medical SchoolBrigham & Women's HospitalBostonMassachusettsUSA
| | - Clemens R. Scherzer
- Center for Advanced Parkinson Research and Precision Neurology Program, Harvard Medical SchoolBrigham & Women's HospitalBostonMassachusettsUSA
| | | | - Eugenia Ricciardelli
- Genomics CenterInstitute for Genomics MedicineUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Kristen Jepsen
- Genomics CenterInstitute for Genomics MedicineUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Steven D. Edland
- Department of Neurosciences, School of MedicineUniversity of California San DiegoLa JollaCaliforniaUSA
- Department of Family Medicine and Public HealthUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Kathleen M. Fisch
- Center for Computational Biology & BioinformaticsDepartment of MedicineUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Paula Desplats
- Department of Neurosciences, School of MedicineUniversity of California San DiegoLa JollaCaliforniaUSA
- Department of Pathology, School of MedicineUniversity of California San DiegoLa JollaCaliforniaUSA
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31
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Marsal-García L, Urbizu A, Arnaldo L, Campdelacreu J, Vilas D, Ispierto L, Gascón-Bayarri J, Reñé R, Álvarez R, Beyer K. Expression Levels of an Alpha-Synuclein Transcript in Blood May Distinguish between Early Dementia with Lewy Bodies and Parkinson's Disease. Int J Mol Sci 2021; 22:ijms22020725. [PMID: 33450872 PMCID: PMC7828374 DOI: 10.3390/ijms22020725] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/09/2021] [Accepted: 01/11/2021] [Indexed: 01/30/2023] Open
Abstract
Lewy body diseases (LBD) including dementia with Lewy bodies (DLB) and Parkinson disease (PD) are characterized by alpha-synuclein pathology. DLB is difficult to diagnose and peripheral biomarkers are urgently needed. Therefore, we analyzed the expression of five alpha-synuclein gene (SNCA) transcripts, SNCAtv1, SNCAtv2, SNCAtv3, SNCA126, and SNCA112, in 45 LBD and control temporal cortex samples and in the blood of 72 DLB, 59 PD, and 54 control subjects. The results revealed overexpression of SNCAtv1 and SNCA112 in DLB, and SNCAtv2 in PD temporal cortices. In DLB blood, diminution of all SNCA transcripts was observed. SNCAtv1 and SNCAtv2 were diminished in PD with disease onset before 70 years. SNCAtv3, driven by its own promoter, showed opposite expression in early DLB and PD, suggesting that its amount may be an early, DLB specific biomarker. Correlation between blood transcript levels and disease duration was positive in DLB and negative in PD, possibly reflecting differences in brain alpha-synuclein aggregation rates associated with differences in disease courses. In conclusion, SNCA transcripts showed a disease-specific increase in the brain and were diminished in blood of LBD patients. SNCAtv3 expression was decreased in early DLB and increased in early PD and could be a biomarker for early DLB diagnosis.
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Affiliation(s)
- Laura Marsal-García
- Department of Pathology, Germans Trias i Pujol Research Institute (IGTP), Universitat Autònoma de Barcelona (UAB), 08193 Barcelona, Spain; (L.M.-G.); (A.U.); (L.A.)
| | - Aintzane Urbizu
- Department of Pathology, Germans Trias i Pujol Research Institute (IGTP), Universitat Autònoma de Barcelona (UAB), 08193 Barcelona, Spain; (L.M.-G.); (A.U.); (L.A.)
| | - Laura Arnaldo
- Department of Pathology, Germans Trias i Pujol Research Institute (IGTP), Universitat Autònoma de Barcelona (UAB), 08193 Barcelona, Spain; (L.M.-G.); (A.U.); (L.A.)
| | - Jaume Campdelacreu
- Servei de Neurologia, Hospital Universitari Bellvitge, 08907 L’Hospitalet de Llobregat, Spain; (J.C.); (J.G.-B.); (R.R.)
| | - Dolores Vilas
- Servei de Neurologia, Hospital Universitari Germans Trias i Pujol, 08916 Badalona, Spain; (D.V.); (L.I.); (R.Á.)
| | - Lourdes Ispierto
- Servei de Neurologia, Hospital Universitari Germans Trias i Pujol, 08916 Badalona, Spain; (D.V.); (L.I.); (R.Á.)
| | - Jordi Gascón-Bayarri
- Servei de Neurologia, Hospital Universitari Bellvitge, 08907 L’Hospitalet de Llobregat, Spain; (J.C.); (J.G.-B.); (R.R.)
| | - Ramón Reñé
- Servei de Neurologia, Hospital Universitari Bellvitge, 08907 L’Hospitalet de Llobregat, Spain; (J.C.); (J.G.-B.); (R.R.)
| | - Ramiro Álvarez
- Servei de Neurologia, Hospital Universitari Germans Trias i Pujol, 08916 Badalona, Spain; (D.V.); (L.I.); (R.Á.)
| | - Katrin Beyer
- Department of Pathology, Germans Trias i Pujol Research Institute (IGTP), Universitat Autònoma de Barcelona (UAB), 08193 Barcelona, Spain; (L.M.-G.); (A.U.); (L.A.)
- Correspondence: ; Tel.: +34-93-497-8355
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Identification of Molecular Signatures in Neural Differentiation and Neurological Diseases Using Digital Color-Coded Molecular Barcoding. Stem Cells Int 2020; 2020:8852313. [PMID: 33005195 PMCID: PMC7503121 DOI: 10.1155/2020/8852313] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 08/26/2020] [Accepted: 08/28/2020] [Indexed: 12/04/2022] Open
Abstract
Human pluripotent stem cells (PSCs), including embryonic stem cells and induced pluripotent stem cells, represent powerful tools for disease modeling and for therapeutic applications. PSCs are particularly useful for the study of development and diseases of the nervous system. However, generating in vitro models that recapitulate the architecture and the full variety of subtypes of cells that make the complexity of our brain remains a challenge. In order to fully exploit the potential of PSCs, advanced methods that facilitate the identification of molecular signatures in neural differentiation and neurological diseases are highly demanded. Here, we review the literature on the development and application of digital color-coded molecular barcoding as a potential tool for standardizing PSC research and applications in neuroscience. We will also describe relevant examples of the use of this technique for the characterization of the heterogeneous composition of the brain tumor glioblastoma multiforme.
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Su C, Tong J, Wang F. Mining genetic and transcriptomic data using machine learning approaches in Parkinson's disease. NPJ PARKINSONS DISEASE 2020; 6:24. [PMID: 32964109 PMCID: PMC7481248 DOI: 10.1038/s41531-020-00127-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 08/13/2020] [Indexed: 01/08/2023]
Abstract
High-throughput techniques have generated abundant genetic and transcriptomic data of Parkinson’s disease (PD) patients but data analysis approaches such as traditional statistical methods have not provided much in the way of insightful integrated analysis or interpretation of the data. As an advanced computational approach, machine learning, which enables people to identify complex patterns and insight from data, has consequently been harnessed to analyze and interpret large, highly complex genetic and transcriptomic data toward a better understanding of PD. In particular, machine learning models have been developed to integrate patient genotype data alone or combined with demographic, clinical, neuroimaging, and other information, for PD outcome study. They have also been used to identify biomarkers of PD based on transcriptomic data, e.g., gene expression profiles from microarrays. This study overviews the relevant literature on using machine learning models for genetic and transcriptomic data analysis in PD, points out remaining challenges, and suggests future directions accordingly. Undoubtedly, the use of machine learning is amplifying PD genetic and transcriptomic achievements for accelerating the study of PD. Existing studies have demonstrated the great potential of machine learning in discovering hidden patterns within genetic or transcriptomic information and thus revealing clues underpinning pathology and pathogenesis. Moving forward, by addressing the remaining challenges, machine learning may advance our ability to precisely diagnose, prognose, and treat PD.
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Affiliation(s)
- Chang Su
- Department of Population Health Sciences, Weill Cornell Medical College, Cornell University, New York, NY USA
| | - Jie Tong
- Department of Mechanical and Aerospace Engineering, New York University, New York, NY USA
| | - Fei Wang
- Department of Population Health Sciences, Weill Cornell Medical College, Cornell University, New York, NY USA
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Falchetti M, Prediger RD, Zanotto-Filho A. Classification algorithms applied to blood-based transcriptome meta-analysis to predict idiopathic Parkinson's disease. Comput Biol Med 2020; 124:103925. [PMID: 32889300 DOI: 10.1016/j.compbiomed.2020.103925] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 07/19/2020] [Indexed: 11/18/2022]
Abstract
Diagnosis of Parkinson's disease (PD) remains a challenge in clinical practice, mostly due to lack of peripheral blood markers. Transcriptomic analysis of blood samples has emerged as a potential means to identify biomarkers and gene signatures of PD. In this context, classification algorithms can assist in detecting data patterns such as phenotypes and transcriptional signatures with potential diagnostic application. In this study, we performed gene expression meta-analysis of blood transcriptome from PD and control patients in order to identify a gene-set capable of predicting PD using classification algorithms. We examined microarray data from public repositories and, after systematic review, 4 independent cohorts (GSE6613, GSE57475, GSE72267 and GSE99039) comprising 711 samples (388 idiopathic PD and 323 healthy individuals) were selected. Initially, analysis of differentially expressed genes resulted in minimal overlap among datasets. To circumvent this, we carried out meta-analysis of 17,712 genes across datasets, and calculated weighted mean Hedges' g effect sizes. From the top-100- positive and negative gene effect sizes, algorithms of collinearity recognition and recursive feature elimination were used to generate a 59-gene signature of idiopathic PD. This signature was evaluated by 9 classification algorithms and 4 sample size-adjusted training groups to create 36 models. Of these, 33 showed accuracy higher than the non-information rate, and 2 models built on Support Vector Machine Regression bestowed best accuracy to predict PD and healthy control samples. In summary, the gene meta-analysis followed by machine learning methodology employed herein identified a gene-set capable of accurately predicting idiopathic PD in blood samples.
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Affiliation(s)
- Marcelo Falchetti
- Laboratório Experimental de Doenças Neurodegenerativas, Departamento de Farmacologia, Universidade Federal de Santa Catarina (UFSC), Florianópolis, Santa Catarina, Brazil; Laboratório de Farmacologia Bioquímica e Molecular, Departamento de Farmacologia, Universidade Federal de Santa Catarina (UFSC), Florianópolis, Santa Catarina, Brazil
| | - Rui Daniel Prediger
- Laboratório Experimental de Doenças Neurodegenerativas, Departamento de Farmacologia, Universidade Federal de Santa Catarina (UFSC), Florianópolis, Santa Catarina, Brazil
| | - Alfeu Zanotto-Filho
- Laboratório de Farmacologia Bioquímica e Molecular, Departamento de Farmacologia, Universidade Federal de Santa Catarina (UFSC), Florianópolis, Santa Catarina, Brazil.
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Iron-responsive-like elements and neurodegenerative ferroptosis. ACTA ACUST UNITED AC 2020; 27:395-413. [PMID: 32817306 PMCID: PMC7433652 DOI: 10.1101/lm.052282.120] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 07/02/2020] [Indexed: 12/26/2022]
Abstract
A set of common-acting iron-responsive 5′untranslated region (5′UTR) motifs can fold into RNA stem loops that appear significant to the biology of cognitive declines of Parkinson's disease dementia (PDD), Lewy body dementia (LDD), and Alzheimer's disease (AD). Neurodegenerative diseases exhibit perturbations of iron homeostasis in defined brain subregions over characteristic time intervals of progression. While misfolding of Aβ from the amyloid-precursor-protein (APP), alpha-synuclein, prion protein (PrP) each cause neuropathic protein inclusions in the brain subregions, iron-responsive-like element (IRE-like) RNA stem–loops reside in their transcripts. APP and αsyn have a role in iron transport while gene duplications elevate the expression of their products to cause rare familial cases of AD and PDD. Of note, IRE-like sequences are responsive to excesses of brain iron in a potential feedback loop to accelerate neuronal ferroptosis and cognitive declines as well as amyloidosis. This pathogenic feedback is consistent with the translational control of the iron storage protein ferritin. We discuss how the IRE-like RNA motifs in the 5′UTRs of APP, alpha-synuclein and PrP mRNAs represent uniquely folded drug targets for therapies to prevent perturbed iron homeostasis that accelerates AD, PD, PD dementia (PDD) and Lewy body dementia, thus preventing cognitive deficits. Inhibition of alpha-synuclein translation is an option to block manganese toxicity associated with early childhood cognitive problems and manganism while Pb toxicity is epigenetically associated with attention deficit and later-stage AD. Pathologies of heavy metal toxicity centered on an embargo of iron export may be treated with activators of APP and ferritin and inhibitors of alpha-synuclein translation.
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Huh YE, Chiang MSR, Locascio JJ, Liao Z, Liu G, Choudhury K, Kuras YI, Tuncali I, Videnovic A, Hunt AL, Schwarzschild MA, Hung AY, Herrington TM, Hayes MT, Hyman BT, Wills AM, Gomperts SN, Growdon JH, Sardi SP, Scherzer CR. β-Glucocerebrosidase activity in GBA-linked Parkinson disease: The type of mutation matters. Neurology 2020; 95:e685-e696. [PMID: 32540937 PMCID: PMC7455354 DOI: 10.1212/wnl.0000000000009989] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 01/26/2020] [Indexed: 02/01/2023] Open
Abstract
OBJECTIVE To test the relationship between clinically relevant types of GBA mutations (none, risk variants, mild mutations, severe mutations) and β-glucocerebrosidase activity in patients with Parkinson disease (PD) in cross-sectional and longitudinal case-control studies. METHODS A total of 481 participants from the Harvard Biomarkers Study (HBS) and the NIH Parkinson's Disease Biomarkers Program (PDBP) were analyzed, including 47 patients with PD carrying GBA variants (GBA-PD), 247 without a GBA variant (idiopathic PD), and 187 healthy controls. Longitudinal analysis comprised 195 participants with 548 longitudinal measurements over a median follow-up period of 2.0 years (interquartile range, 1-2 years). RESULTS β-Glucocerebrosidase activity was low in blood of patients with GBA-PD compared to healthy controls and patients with idiopathic PD, respectively, in HBS (p < 0.001) and PDBP (p < 0.05) in multivariate analyses adjusting for age, sex, blood storage time, and batch. Enzyme activity in patients with idiopathic PD was unchanged. Innovative enzymatic quantitative trait locus (xQTL) analysis revealed a negative linear association between residual β-glucocerebrosidase activity and mutation type with p < 0.0001. For each increment in the severity of mutation type, a reduction of mean β-glucocerebrosidase activity by 0.85 μmol/L/h (95% confidence interval, -1.17, -0.54) was predicted. In a first longitudinal analysis, increasing mutation severity types were prospectively associated with steeper declines in β-glucocerebrosidase activity during a median 2 years of follow-up (p = 0.02). CONCLUSIONS Residual activity of the β-glucocerebrosidase enzyme measured in blood inversely correlates with clinical severity types of GBA mutations in PD. β-Glucocerebrosidase activity is a quantitative endophenotype that can be monitored noninvasively and targeted therapeutically.
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Affiliation(s)
- Young Eun Huh
- From the APDA Center for Advanced Parkinson Research (Y.E.H., J.J.L., Z.L., G.L., K.C., Y.I.K., I.T., M.T.H., C.R.S.) and Precision Neurology Program (Y.E.H., Z.L., G.L., Y.I.K., C.R.S.), Harvard Medical School, and Department of Neurology (Y.E.H., G.L., C.R.S.), Brigham and Women's Hospital, Boston, MA; Department of Neurology (Y.E.H.), CHA Bundang Medical Center, CHA University, Seongnam, Korea; Rare and Neurological Diseases Therapeutic Area (M.S.R.C., S.P.S.), Sanofi, Framingham, MA; School of Medicine (G.L.), Sun Yat-Sen University, Guangzhou, Guangdong, China; and Department of Neurology (J.J.L., A.V., A.L.H., M.A.S., A.Y.H., T.M.H., B.T.H., A.-M.W., S.N.G., J.H.G., C.R.S.), Massachusetts General Hospital, Boston
| | - Ming Sum Ruby Chiang
- From the APDA Center for Advanced Parkinson Research (Y.E.H., J.J.L., Z.L., G.L., K.C., Y.I.K., I.T., M.T.H., C.R.S.) and Precision Neurology Program (Y.E.H., Z.L., G.L., Y.I.K., C.R.S.), Harvard Medical School, and Department of Neurology (Y.E.H., G.L., C.R.S.), Brigham and Women's Hospital, Boston, MA; Department of Neurology (Y.E.H.), CHA Bundang Medical Center, CHA University, Seongnam, Korea; Rare and Neurological Diseases Therapeutic Area (M.S.R.C., S.P.S.), Sanofi, Framingham, MA; School of Medicine (G.L.), Sun Yat-Sen University, Guangzhou, Guangdong, China; and Department of Neurology (J.J.L., A.V., A.L.H., M.A.S., A.Y.H., T.M.H., B.T.H., A.-M.W., S.N.G., J.H.G., C.R.S.), Massachusetts General Hospital, Boston
| | - Joseph J Locascio
- From the APDA Center for Advanced Parkinson Research (Y.E.H., J.J.L., Z.L., G.L., K.C., Y.I.K., I.T., M.T.H., C.R.S.) and Precision Neurology Program (Y.E.H., Z.L., G.L., Y.I.K., C.R.S.), Harvard Medical School, and Department of Neurology (Y.E.H., G.L., C.R.S.), Brigham and Women's Hospital, Boston, MA; Department of Neurology (Y.E.H.), CHA Bundang Medical Center, CHA University, Seongnam, Korea; Rare and Neurological Diseases Therapeutic Area (M.S.R.C., S.P.S.), Sanofi, Framingham, MA; School of Medicine (G.L.), Sun Yat-Sen University, Guangzhou, Guangdong, China; and Department of Neurology (J.J.L., A.V., A.L.H., M.A.S., A.Y.H., T.M.H., B.T.H., A.-M.W., S.N.G., J.H.G., C.R.S.), Massachusetts General Hospital, Boston
| | - Zhixiang Liao
- From the APDA Center for Advanced Parkinson Research (Y.E.H., J.J.L., Z.L., G.L., K.C., Y.I.K., I.T., M.T.H., C.R.S.) and Precision Neurology Program (Y.E.H., Z.L., G.L., Y.I.K., C.R.S.), Harvard Medical School, and Department of Neurology (Y.E.H., G.L., C.R.S.), Brigham and Women's Hospital, Boston, MA; Department of Neurology (Y.E.H.), CHA Bundang Medical Center, CHA University, Seongnam, Korea; Rare and Neurological Diseases Therapeutic Area (M.S.R.C., S.P.S.), Sanofi, Framingham, MA; School of Medicine (G.L.), Sun Yat-Sen University, Guangzhou, Guangdong, China; and Department of Neurology (J.J.L., A.V., A.L.H., M.A.S., A.Y.H., T.M.H., B.T.H., A.-M.W., S.N.G., J.H.G., C.R.S.), Massachusetts General Hospital, Boston
| | - Ganqiang Liu
- From the APDA Center for Advanced Parkinson Research (Y.E.H., J.J.L., Z.L., G.L., K.C., Y.I.K., I.T., M.T.H., C.R.S.) and Precision Neurology Program (Y.E.H., Z.L., G.L., Y.I.K., C.R.S.), Harvard Medical School, and Department of Neurology (Y.E.H., G.L., C.R.S.), Brigham and Women's Hospital, Boston, MA; Department of Neurology (Y.E.H.), CHA Bundang Medical Center, CHA University, Seongnam, Korea; Rare and Neurological Diseases Therapeutic Area (M.S.R.C., S.P.S.), Sanofi, Framingham, MA; School of Medicine (G.L.), Sun Yat-Sen University, Guangzhou, Guangdong, China; and Department of Neurology (J.J.L., A.V., A.L.H., M.A.S., A.Y.H., T.M.H., B.T.H., A.-M.W., S.N.G., J.H.G., C.R.S.), Massachusetts General Hospital, Boston
| | - Karbi Choudhury
- From the APDA Center for Advanced Parkinson Research (Y.E.H., J.J.L., Z.L., G.L., K.C., Y.I.K., I.T., M.T.H., C.R.S.) and Precision Neurology Program (Y.E.H., Z.L., G.L., Y.I.K., C.R.S.), Harvard Medical School, and Department of Neurology (Y.E.H., G.L., C.R.S.), Brigham and Women's Hospital, Boston, MA; Department of Neurology (Y.E.H.), CHA Bundang Medical Center, CHA University, Seongnam, Korea; Rare and Neurological Diseases Therapeutic Area (M.S.R.C., S.P.S.), Sanofi, Framingham, MA; School of Medicine (G.L.), Sun Yat-Sen University, Guangzhou, Guangdong, China; and Department of Neurology (J.J.L., A.V., A.L.H., M.A.S., A.Y.H., T.M.H., B.T.H., A.-M.W., S.N.G., J.H.G., C.R.S.), Massachusetts General Hospital, Boston
| | - Yuliya I Kuras
- From the APDA Center for Advanced Parkinson Research (Y.E.H., J.J.L., Z.L., G.L., K.C., Y.I.K., I.T., M.T.H., C.R.S.) and Precision Neurology Program (Y.E.H., Z.L., G.L., Y.I.K., C.R.S.), Harvard Medical School, and Department of Neurology (Y.E.H., G.L., C.R.S.), Brigham and Women's Hospital, Boston, MA; Department of Neurology (Y.E.H.), CHA Bundang Medical Center, CHA University, Seongnam, Korea; Rare and Neurological Diseases Therapeutic Area (M.S.R.C., S.P.S.), Sanofi, Framingham, MA; School of Medicine (G.L.), Sun Yat-Sen University, Guangzhou, Guangdong, China; and Department of Neurology (J.J.L., A.V., A.L.H., M.A.S., A.Y.H., T.M.H., B.T.H., A.-M.W., S.N.G., J.H.G., C.R.S.), Massachusetts General Hospital, Boston
| | - Idil Tuncali
- From the APDA Center for Advanced Parkinson Research (Y.E.H., J.J.L., Z.L., G.L., K.C., Y.I.K., I.T., M.T.H., C.R.S.) and Precision Neurology Program (Y.E.H., Z.L., G.L., Y.I.K., C.R.S.), Harvard Medical School, and Department of Neurology (Y.E.H., G.L., C.R.S.), Brigham and Women's Hospital, Boston, MA; Department of Neurology (Y.E.H.), CHA Bundang Medical Center, CHA University, Seongnam, Korea; Rare and Neurological Diseases Therapeutic Area (M.S.R.C., S.P.S.), Sanofi, Framingham, MA; School of Medicine (G.L.), Sun Yat-Sen University, Guangzhou, Guangdong, China; and Department of Neurology (J.J.L., A.V., A.L.H., M.A.S., A.Y.H., T.M.H., B.T.H., A.-M.W., S.N.G., J.H.G., C.R.S.), Massachusetts General Hospital, Boston
| | - Aleksandar Videnovic
- From the APDA Center for Advanced Parkinson Research (Y.E.H., J.J.L., Z.L., G.L., K.C., Y.I.K., I.T., M.T.H., C.R.S.) and Precision Neurology Program (Y.E.H., Z.L., G.L., Y.I.K., C.R.S.), Harvard Medical School, and Department of Neurology (Y.E.H., G.L., C.R.S.), Brigham and Women's Hospital, Boston, MA; Department of Neurology (Y.E.H.), CHA Bundang Medical Center, CHA University, Seongnam, Korea; Rare and Neurological Diseases Therapeutic Area (M.S.R.C., S.P.S.), Sanofi, Framingham, MA; School of Medicine (G.L.), Sun Yat-Sen University, Guangzhou, Guangdong, China; and Department of Neurology (J.J.L., A.V., A.L.H., M.A.S., A.Y.H., T.M.H., B.T.H., A.-M.W., S.N.G., J.H.G., C.R.S.), Massachusetts General Hospital, Boston
| | - Ann L Hunt
- From the APDA Center for Advanced Parkinson Research (Y.E.H., J.J.L., Z.L., G.L., K.C., Y.I.K., I.T., M.T.H., C.R.S.) and Precision Neurology Program (Y.E.H., Z.L., G.L., Y.I.K., C.R.S.), Harvard Medical School, and Department of Neurology (Y.E.H., G.L., C.R.S.), Brigham and Women's Hospital, Boston, MA; Department of Neurology (Y.E.H.), CHA Bundang Medical Center, CHA University, Seongnam, Korea; Rare and Neurological Diseases Therapeutic Area (M.S.R.C., S.P.S.), Sanofi, Framingham, MA; School of Medicine (G.L.), Sun Yat-Sen University, Guangzhou, Guangdong, China; and Department of Neurology (J.J.L., A.V., A.L.H., M.A.S., A.Y.H., T.M.H., B.T.H., A.-M.W., S.N.G., J.H.G., C.R.S.), Massachusetts General Hospital, Boston
| | - Michael A Schwarzschild
- From the APDA Center for Advanced Parkinson Research (Y.E.H., J.J.L., Z.L., G.L., K.C., Y.I.K., I.T., M.T.H., C.R.S.) and Precision Neurology Program (Y.E.H., Z.L., G.L., Y.I.K., C.R.S.), Harvard Medical School, and Department of Neurology (Y.E.H., G.L., C.R.S.), Brigham and Women's Hospital, Boston, MA; Department of Neurology (Y.E.H.), CHA Bundang Medical Center, CHA University, Seongnam, Korea; Rare and Neurological Diseases Therapeutic Area (M.S.R.C., S.P.S.), Sanofi, Framingham, MA; School of Medicine (G.L.), Sun Yat-Sen University, Guangzhou, Guangdong, China; and Department of Neurology (J.J.L., A.V., A.L.H., M.A.S., A.Y.H., T.M.H., B.T.H., A.-M.W., S.N.G., J.H.G., C.R.S.), Massachusetts General Hospital, Boston
| | - Albert Y Hung
- From the APDA Center for Advanced Parkinson Research (Y.E.H., J.J.L., Z.L., G.L., K.C., Y.I.K., I.T., M.T.H., C.R.S.) and Precision Neurology Program (Y.E.H., Z.L., G.L., Y.I.K., C.R.S.), Harvard Medical School, and Department of Neurology (Y.E.H., G.L., C.R.S.), Brigham and Women's Hospital, Boston, MA; Department of Neurology (Y.E.H.), CHA Bundang Medical Center, CHA University, Seongnam, Korea; Rare and Neurological Diseases Therapeutic Area (M.S.R.C., S.P.S.), Sanofi, Framingham, MA; School of Medicine (G.L.), Sun Yat-Sen University, Guangzhou, Guangdong, China; and Department of Neurology (J.J.L., A.V., A.L.H., M.A.S., A.Y.H., T.M.H., B.T.H., A.-M.W., S.N.G., J.H.G., C.R.S.), Massachusetts General Hospital, Boston
| | - Todd M Herrington
- From the APDA Center for Advanced Parkinson Research (Y.E.H., J.J.L., Z.L., G.L., K.C., Y.I.K., I.T., M.T.H., C.R.S.) and Precision Neurology Program (Y.E.H., Z.L., G.L., Y.I.K., C.R.S.), Harvard Medical School, and Department of Neurology (Y.E.H., G.L., C.R.S.), Brigham and Women's Hospital, Boston, MA; Department of Neurology (Y.E.H.), CHA Bundang Medical Center, CHA University, Seongnam, Korea; Rare and Neurological Diseases Therapeutic Area (M.S.R.C., S.P.S.), Sanofi, Framingham, MA; School of Medicine (G.L.), Sun Yat-Sen University, Guangzhou, Guangdong, China; and Department of Neurology (J.J.L., A.V., A.L.H., M.A.S., A.Y.H., T.M.H., B.T.H., A.-M.W., S.N.G., J.H.G., C.R.S.), Massachusetts General Hospital, Boston
| | - Michael T Hayes
- From the APDA Center for Advanced Parkinson Research (Y.E.H., J.J.L., Z.L., G.L., K.C., Y.I.K., I.T., M.T.H., C.R.S.) and Precision Neurology Program (Y.E.H., Z.L., G.L., Y.I.K., C.R.S.), Harvard Medical School, and Department of Neurology (Y.E.H., G.L., C.R.S.), Brigham and Women's Hospital, Boston, MA; Department of Neurology (Y.E.H.), CHA Bundang Medical Center, CHA University, Seongnam, Korea; Rare and Neurological Diseases Therapeutic Area (M.S.R.C., S.P.S.), Sanofi, Framingham, MA; School of Medicine (G.L.), Sun Yat-Sen University, Guangzhou, Guangdong, China; and Department of Neurology (J.J.L., A.V., A.L.H., M.A.S., A.Y.H., T.M.H., B.T.H., A.-M.W., S.N.G., J.H.G., C.R.S.), Massachusetts General Hospital, Boston
| | - Bradley T Hyman
- From the APDA Center for Advanced Parkinson Research (Y.E.H., J.J.L., Z.L., G.L., K.C., Y.I.K., I.T., M.T.H., C.R.S.) and Precision Neurology Program (Y.E.H., Z.L., G.L., Y.I.K., C.R.S.), Harvard Medical School, and Department of Neurology (Y.E.H., G.L., C.R.S.), Brigham and Women's Hospital, Boston, MA; Department of Neurology (Y.E.H.), CHA Bundang Medical Center, CHA University, Seongnam, Korea; Rare and Neurological Diseases Therapeutic Area (M.S.R.C., S.P.S.), Sanofi, Framingham, MA; School of Medicine (G.L.), Sun Yat-Sen University, Guangzhou, Guangdong, China; and Department of Neurology (J.J.L., A.V., A.L.H., M.A.S., A.Y.H., T.M.H., B.T.H., A.-M.W., S.N.G., J.H.G., C.R.S.), Massachusetts General Hospital, Boston
| | - Anne-Marie Wills
- From the APDA Center for Advanced Parkinson Research (Y.E.H., J.J.L., Z.L., G.L., K.C., Y.I.K., I.T., M.T.H., C.R.S.) and Precision Neurology Program (Y.E.H., Z.L., G.L., Y.I.K., C.R.S.), Harvard Medical School, and Department of Neurology (Y.E.H., G.L., C.R.S.), Brigham and Women's Hospital, Boston, MA; Department of Neurology (Y.E.H.), CHA Bundang Medical Center, CHA University, Seongnam, Korea; Rare and Neurological Diseases Therapeutic Area (M.S.R.C., S.P.S.), Sanofi, Framingham, MA; School of Medicine (G.L.), Sun Yat-Sen University, Guangzhou, Guangdong, China; and Department of Neurology (J.J.L., A.V., A.L.H., M.A.S., A.Y.H., T.M.H., B.T.H., A.-M.W., S.N.G., J.H.G., C.R.S.), Massachusetts General Hospital, Boston
| | - Stephen N Gomperts
- From the APDA Center for Advanced Parkinson Research (Y.E.H., J.J.L., Z.L., G.L., K.C., Y.I.K., I.T., M.T.H., C.R.S.) and Precision Neurology Program (Y.E.H., Z.L., G.L., Y.I.K., C.R.S.), Harvard Medical School, and Department of Neurology (Y.E.H., G.L., C.R.S.), Brigham and Women's Hospital, Boston, MA; Department of Neurology (Y.E.H.), CHA Bundang Medical Center, CHA University, Seongnam, Korea; Rare and Neurological Diseases Therapeutic Area (M.S.R.C., S.P.S.), Sanofi, Framingham, MA; School of Medicine (G.L.), Sun Yat-Sen University, Guangzhou, Guangdong, China; and Department of Neurology (J.J.L., A.V., A.L.H., M.A.S., A.Y.H., T.M.H., B.T.H., A.-M.W., S.N.G., J.H.G., C.R.S.), Massachusetts General Hospital, Boston
| | - John H Growdon
- From the APDA Center for Advanced Parkinson Research (Y.E.H., J.J.L., Z.L., G.L., K.C., Y.I.K., I.T., M.T.H., C.R.S.) and Precision Neurology Program (Y.E.H., Z.L., G.L., Y.I.K., C.R.S.), Harvard Medical School, and Department of Neurology (Y.E.H., G.L., C.R.S.), Brigham and Women's Hospital, Boston, MA; Department of Neurology (Y.E.H.), CHA Bundang Medical Center, CHA University, Seongnam, Korea; Rare and Neurological Diseases Therapeutic Area (M.S.R.C., S.P.S.), Sanofi, Framingham, MA; School of Medicine (G.L.), Sun Yat-Sen University, Guangzhou, Guangdong, China; and Department of Neurology (J.J.L., A.V., A.L.H., M.A.S., A.Y.H., T.M.H., B.T.H., A.-M.W., S.N.G., J.H.G., C.R.S.), Massachusetts General Hospital, Boston
| | - Sergio Pablo Sardi
- From the APDA Center for Advanced Parkinson Research (Y.E.H., J.J.L., Z.L., G.L., K.C., Y.I.K., I.T., M.T.H., C.R.S.) and Precision Neurology Program (Y.E.H., Z.L., G.L., Y.I.K., C.R.S.), Harvard Medical School, and Department of Neurology (Y.E.H., G.L., C.R.S.), Brigham and Women's Hospital, Boston, MA; Department of Neurology (Y.E.H.), CHA Bundang Medical Center, CHA University, Seongnam, Korea; Rare and Neurological Diseases Therapeutic Area (M.S.R.C., S.P.S.), Sanofi, Framingham, MA; School of Medicine (G.L.), Sun Yat-Sen University, Guangzhou, Guangdong, China; and Department of Neurology (J.J.L., A.V., A.L.H., M.A.S., A.Y.H., T.M.H., B.T.H., A.-M.W., S.N.G., J.H.G., C.R.S.), Massachusetts General Hospital, Boston
| | - Clemens R Scherzer
- From the APDA Center for Advanced Parkinson Research (Y.E.H., J.J.L., Z.L., G.L., K.C., Y.I.K., I.T., M.T.H., C.R.S.) and Precision Neurology Program (Y.E.H., Z.L., G.L., Y.I.K., C.R.S.), Harvard Medical School, and Department of Neurology (Y.E.H., G.L., C.R.S.), Brigham and Women's Hospital, Boston, MA; Department of Neurology (Y.E.H.), CHA Bundang Medical Center, CHA University, Seongnam, Korea; Rare and Neurological Diseases Therapeutic Area (M.S.R.C., S.P.S.), Sanofi, Framingham, MA; School of Medicine (G.L.), Sun Yat-Sen University, Guangzhou, Guangdong, China; and Department of Neurology (J.J.L., A.V., A.L.H., M.A.S., A.Y.H., T.M.H., B.T.H., A.-M.W., S.N.G., J.H.G., C.R.S.), Massachusetts General Hospital, Boston.
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El Haddad S, Serrano A, Moal F, Normand T, Robin C, Charpentier S, Valery A, Brulé-Morabito F, Auzou P, Mollet L, Ozsancak C, Legrand A. Disturbed expression of autophagy genes in blood of Parkinson’s disease patients. Gene 2020; 738:144454. [DOI: 10.1016/j.gene.2020.144454] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 01/17/2020] [Accepted: 02/04/2020] [Indexed: 12/26/2022]
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Abd Elhadi S, Grigoletto J, Poli M, Arosio P, Arkadir D, Sharon R. α-Synuclein in blood cells differentiates Parkinson's disease from healthy controls. Ann Clin Transl Neurol 2019; 6:2426-2436. [PMID: 31742923 PMCID: PMC6917335 DOI: 10.1002/acn3.50944] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 10/05/2019] [Accepted: 10/09/2019] [Indexed: 11/09/2022] Open
Abstract
OBJECTIVE To determine whether blood cells expressed α-Syn can differentiate Parkinson's disease (PD) from healthy controls (HC). METHODS The concentrations of α-Syn were determined in samples of blood cell pellets using a quantitative Lipid-ELISA assay. In addition, the levels of total protein, hemoglobin, iron and H-ferritin were determined. The study includes samples from the Biofind cohort (n = 46 PD and 45 HC) and results were validated with an additional cohort (n = 35 PD and 28 HC). RESULTS A composite biomarker consisting of the concentrations of total α-Syn, proteinase-K resistant (PKres ) α-Syn and phospho-Serine 129 α-Syn (PSer 129), is designed based on the analysis of the discovery BioFIND cohort. This composite biomarker differentiates a PD subgroup, presenting motor symptoms without dementia from a HC group, with a convincing accuracy, represented by an AUC = 0.81 (95% CI, 0.71 to 0.92). Closely similar results were obtained for the validation cohort, that is, AUC = 0.81, (95% CI, 0.70 to 0.94). INTERPRETATION Our results demonstrate the potential usefulness of blood cells expressed α-Syn as a biomarker for PD.
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Affiliation(s)
- Suaad Abd Elhadi
- Department of Biochemistry and Molecular BiologyIMRICThe Hebrew University‐Hadassah Medical SchoolEin Kerem9112001JerusalemIsrael
| | - Jessica Grigoletto
- Department of Biochemistry and Molecular BiologyIMRICThe Hebrew University‐Hadassah Medical SchoolEin Kerem9112001JerusalemIsrael
| | - Maura Poli
- Laboratory of Molecular BiologyDepartment of Molecular and Translational MedicineUniversity of BresciaBresciaItaly
| | - Paolo Arosio
- Laboratory of Molecular BiologyDepartment of Molecular and Translational MedicineUniversity of BresciaBresciaItaly
| | - David Arkadir
- Department of NeurologyHadassah‐Hebrew University Medical CenterJerusalemIsrael
| | - Ronit Sharon
- Department of Biochemistry and Molecular BiologyIMRICThe Hebrew University‐Hadassah Medical SchoolEin Kerem9112001JerusalemIsrael
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Fornasiero EF, Rizzoli SO. Pathological changes are associated with shifts in the employment of synonymous codons at the transcriptome level. BMC Genomics 2019; 20:566. [PMID: 31288782 PMCID: PMC6617700 DOI: 10.1186/s12864-019-5921-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 06/20/2019] [Indexed: 01/07/2023] Open
Abstract
Background The usage of different synonymous codons reflects the genome organization and has been connected to parameters such as mRNA abundance and protein folding. It is also been established that mutations targeting specific synonymous codons can trigger disease. Results We performed a systematic meta-analysis of transcriptome results from 75 datasets representing 40 pathologies. We found that a subset of codons was preferentially employed in abundant transcripts, while other codons were preferentially found in low-abundance transcripts. By comparing control and pathological transcriptomes, we observed a shift in the employment of synonymous codons for every analyzed disease. For example, cancerous tissue employed preferentially A- or U-ending codons, shifting from G- or C-ending codons, which were preferred by control tissues. This analysis was able to discriminate patients and controls with high specificity and sensitivity. Conclusions Here we show that the employment of specific synonymous codons, quantified at the whole transcriptome level, changes profoundly in many diseases. We propose that the changes in codon employment offer a novel perspective for disease studies, and could be used to design new diagnostic tools. Electronic supplementary material The online version of this article (10.1186/s12864-019-5921-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Eugenio F Fornasiero
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, 37073, Göttingen, Germany. .,Center for Biostructural Imaging of Neurodegeneration (BIN), 37075, Göttingen, Germany.
| | - Silvio O Rizzoli
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, 37073, Göttingen, Germany. .,Center for Biostructural Imaging of Neurodegeneration (BIN), 37075, Göttingen, Germany.
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Dal Ben M, Bongiovanni R, Tuniz S, Fioriti E, Tiribelli C, Moretti R, Gazzin S. Earliest Mechanisms of Dopaminergic Neurons Sufferance in a Novel Slow Progressing Ex Vivo Model of Parkinson Disease in Rat Organotypic Cultures of Substantia Nigra. Int J Mol Sci 2019; 20:E2224. [PMID: 31064126 PMCID: PMC6539377 DOI: 10.3390/ijms20092224] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 04/30/2019] [Accepted: 05/03/2019] [Indexed: 12/17/2022] Open
Abstract
The current treatments of Parkinson disease (PD) are ineffective mainly due to the poor understanding of the early events causing the decline of dopaminergic neurons (DOPAn). To overcome this problem, slow progressively degenerating models of PD allowing the study of the pre-clinical phase are crucial. We recreated in a short ex vivo time scale (96 h) all the features of human PD (needing dozens of years) by challenging organotypic culture of rat substantia nigra with low doses of rotenone. Thus, taking advantage of the existent knowledge, the model was used to perform a time-dependent comparative study of the principal possible causative molecular mechanisms undergoing DOPAn demise. Alteration in the redox state and inflammation started at 3 h, preceding the reduction in DOPAn number (pre-diagnosis phase). The number of DOPAn declined to levels compatible with diagnosis only at 12 h. The decline was accompanied by a persistent inflammation and redox imbalance. Significant microglia activation, apoptosis, a reduction in dopamine vesicle transporters, and the ubiquitination of misfolded protein clearance pathways were late (96 h, consequential) events. The work suggests inflammation and redox imbalance as simultaneous early mechanisms undergoing DOPAn sufferance, to be targeted for a causative treatment aimed to stop/delay PD.
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Affiliation(s)
- Matteo Dal Ben
- Department of Medical, Surgical, and Health Sciences, University of Trieste, 34100 Trieste, Italy.
- Fondazione Italiana Fegato, AREA Science Park, 34149 Trieste, Italy.
| | | | - Simone Tuniz
- Fondazione Italiana Fegato, AREA Science Park, 34149 Trieste, Italy.
| | - Emanuela Fioriti
- Fondazione Italiana Fegato, AREA Science Park, 34149 Trieste, Italy.
| | - Claudio Tiribelli
- Fondazione Italiana Fegato, AREA Science Park, 34149 Trieste, Italy.
| | - Rita Moretti
- Neurology Clinic, Department of Medical, Surgical, and Health Sciences, University of Trieste, 34100 Trieste, Italy.
| | - Silvia Gazzin
- Fondazione Italiana Fegato, AREA Science Park, 34149 Trieste, Italy.
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41
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O'Bryant SE, Edwards M, Zhang F, Johnson LA, Hall J, Kuras Y, Scherzer CR. Potential two-step proteomic signature for Parkinson's disease: Pilot analysis in the Harvard Biomarkers Study. ALZHEIMER'S & DEMENTIA: DIAGNOSIS, ASSESSMENT & DISEASE MONITORING 2019; 11:374-382. [PMID: 31080873 PMCID: PMC6502745 DOI: 10.1016/j.dadm.2019.03.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Introduction We sought to determine if our previously validated proteomic profile for detecting Alzheimer's disease would detect Parkinson's disease (PD) and distinguish PD from other neurodegenerative diseases. Methods Plasma samples were assayed from 150 patients of the Harvard Biomarkers Study (PD, n = 50; other neurodegenerative diseases, n = 50; healthy controls, n = 50) using electrochemiluminescence and Simoa platforms. Results The first step proteomic profile distinguished neurodegenerative diseases from controls with a diagnostic accuracy of 0.94. The second step profile distinguished PD cases from other neurodegenerative diseases with a diagnostic accuracy of 0.98. The proteomic profile differed in step 1 versus step 2, suggesting that a multistep proteomic profile algorithm to detecting and distinguishing between neurodegenerative diseases may be optimal. Discussion These data provide evidence of the potential use of a multitiered blood-based proteomic screening method for detecting individuals with neurodegenerative disease and then distinguishing PD from other neurodegenerative diseases.
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Affiliation(s)
- Sid E O'Bryant
- Institute for Translational Research, Department of Pharmacology & Neuroscience, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - Melissa Edwards
- Department of Neuro-Oncology, MD Anderson Cancer Center, Houston, TX, USA
| | - Fan Zhang
- Vermont Genetics Network, University of Vermont, Burlington, VT, USA
| | - Leigh A Johnson
- Institute for Translational Research, Department of Pharmacology & Neuroscience, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - James Hall
- Institute for Translational Research, Department of Pharmacology & Neuroscience, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - Yuliya Kuras
- Advanced Center for Parkinson's Disease Research of Brigham & Women's Hospital, and Harvard Medical School, Boston, MA, USA.,Precision Neurology Program, Harvard Medical School, Brigham & Women's Hospital, Boston, MA, USA
| | - Clemens R Scherzer
- Advanced Center for Parkinson's Disease Research of Brigham & Women's Hospital, and Harvard Medical School, Boston, MA, USA.,Precision Neurology Program, Harvard Medical School, Brigham & Women's Hospital, Boston, MA, USA.,Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
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42
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Henderson-Smith A, Fisch KM, Hua J, Liu G, Ricciardelli E, Jepsen K, Huentelman M, Stalberg G, Edland SD, Scherzer CR, Dunckley T, Desplats P. DNA methylation changes associated with Parkinson's disease progression: outcomes from the first longitudinal genome-wide methylation analysis in blood. Epigenetics 2019; 14:365-382. [PMID: 30871403 DOI: 10.1080/15592294.2019.1588682] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Parkinson's Disease (PD) is a common neurodegenerative disorder currently diagnosed based on the presentation of characteristic movement symptoms. Unfortunately, patients exhibiting these symptoms have already undergone significant dopaminergic neuronal loss. Earlier diagnosis, aided by molecular biomarkers specific to PD, would improve overall patient care. Epigenetic mechanisms, which are modified by both environment and disease pathophysiology, are emerging as important components of neurodegeneration. Alterations to the PD methylome have been reported in epigenome-wide association studies. However, the extent to which methylation changes correlate with disease progression has not yet been reported; nor the degree to which methylation is affected by PD medication. We performed a longitudinal genome-wide methylation study surveying ~850,000 CpG sites in whole blood from 189 well-characterized PD patients and 191 control individuals obtained at baseline and at a follow-up visit ~2 y later. We identified distinct patterns of methylation in PD cases versus controls. Importantly, we identified genomic sites where methylation changes longitudinally as the disease progresses. Moreover, we identified methylation changes associated with PD pathology through the analysis of PD cases that were not exposed to anti-parkinsonian therapy. In addition, we identified methylation sites modulated by exposure to dopamine replacement drugs. These results indicate that DNA methylation is dynamic in PD and changes over time during disease progression. To the best of our knowledge, this is the first longitudinal epigenome-wide methylation analysis for Parkinson's disease and reveals changes associated with disease progression and in response to dopaminergic medications in the blood methylome.
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Affiliation(s)
- Adrienne Henderson-Smith
- a Biodesign Institute , Arizona State University , Tempe , AZ , USA.,b Neurogenomics Division , Translational Genomics Research Institute , Phoenix , AZ , USA
| | - Kathleen M Fisch
- c Center for Computational Biology & Bioinformatics, Department of Medicine , University of California San Diego , La Jolla , CA , USA
| | - Jianping Hua
- d Center for Bioinformatics and Genomics Systems Engineering, Texas A&M Engineering Experiment Station , Texas A&M University , College Station , TX , USA
| | - Ganqiang Liu
- e Advanced Center for Parkinson's Disease Research and Precision Neurology Program, Harvard Medical School , Brigham & Women's Hospital , Boston , MA , USA
| | - Eugenia Ricciardelli
- f Genomics Center, Institute for Genomics Medicine , University of California San Diego , La Jolla , CA , USA
| | - Kristen Jepsen
- f Genomics Center, Institute for Genomics Medicine , University of California San Diego , La Jolla , CA , USA
| | - Mathew Huentelman
- b Neurogenomics Division , Translational Genomics Research Institute , Phoenix , AZ , USA
| | - Gabriel Stalberg
- e Advanced Center for Parkinson's Disease Research and Precision Neurology Program, Harvard Medical School , Brigham & Women's Hospital , Boston , MA , USA.,g Harvard Biomarkers Study investigators are listed in the Acknowledgement section
| | - Steven D Edland
- h Department of Neurosciences , University of California San Diego , La Jolla , CA , USA
| | - Clemens R Scherzer
- e Advanced Center for Parkinson's Disease Research and Precision Neurology Program, Harvard Medical School , Brigham & Women's Hospital , Boston , MA , USA
| | - Travis Dunckley
- a Biodesign Institute , Arizona State University , Tempe , AZ , USA
| | - Paula Desplats
- h Department of Neurosciences , University of California San Diego , La Jolla , CA , USA.,i Department of Pathology , University of California San Diego , La Jolla , CA , USA
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Seo Y, Pak K, Nam HY, Seok JW, Lee MJ, Kim EJ, Lee JM, Kim SJ, Kim IJ. Effect of rs3910105 in the Synuclein Gene on Dopamine Transporter Availability in Healthy Subjects. Yonsei Med J 2018; 59:787-792. [PMID: 29978616 PMCID: PMC6037603 DOI: 10.3349/ymj.2018.59.6.787] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 06/01/2018] [Accepted: 06/15/2018] [Indexed: 12/03/2022] Open
Abstract
PURPOSE The present study investigated associations between dopamine transporter (DAT) availability and α-synuclein levels in cerebrospinal fluid, as well as synuclein gene (SNCA) transcripts, and the effect of single nucleotide polymorphism of SNCA on DAT availability in healthy subjects. MATERIALS AND METHODS The study population comprised healthy controls who underwent ¹²³I-FP-CIT single-photon emission computed tomography screening. Five SNCA probes were used to target the boundaries of exon 3 and exon 4 (SNCA-E3E4), transcripts with a long 3'UTR region (SNCA-3UTR-1, SNCA-3UTR-2), transcripts that skip exon 5 (SNCA-E4E6), and the rare short transcript isoforms that comprise exons 1-4 (SNCA-007). RESULTS In total, 123 healthy subjects (male 75, female 48) were included in this study. DAT availability in the caudate nucleus (p=0.0661) and putamen (p=0.0739) tended to differ according to rs3910105 genotype. In post-hoc analysis, DAT availability in the putamen was lower in subjects of TT genotype than those of CC/CT (p=0.0317). DAT availability in the caudate nucleus also showed a trend similar to that in the putamen (p=0.0597). Subjects of CT genotype with rs3910105 showed negative correlations with DAT availability in the putamen with SNCA-E3E4 (p=0.037, rho=-0.277), and SNCA-E4E6 (p=0.042, rho=-0.270), but not those of CC/TT genotypes. CONCLUSION This is the first study to investigate the association of rs3910105 in SNCA with DAT availability. rs3910105 had an effect on DAT availability, and the correlation between DAT availability and SNCA transcripts were significant in CT genotypes of rs3910105.
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Affiliation(s)
- Youngduk Seo
- Department of Nuclear Medicine, Busan Seongso Hospital, Busan, Korea
| | - Kyoungjune Pak
- Department of Nuclear Medicine and Biomedical Research Institute, Pusan National University Hospital, Busan, Korea.
| | - Hyun Yeol Nam
- Department of Nuclear Medicine, Samsung Changwon Hospital, Sungkyunkwan University School of Medicine, Changwon, Korea
| | - Ju Won Seok
- Department of Nuclear Medicine, Chung-Ang University College of Medicine, Seoul, Korea.
| | - Myung Jun Lee
- Department of Neurology and Biomedical Research Institute, Pusan National University Hospital, Busan, Korea
| | - Eun Joo Kim
- Department of Neurology and Biomedical Research Institute, Pusan National University Hospital, Busan, Korea
| | - Jae Meen Lee
- Department of Neurosurgery and Biomedical Research Institute, Pusan National University Hospital, Busan, Korea
| | - Seong Jang Kim
- Department of Nuclear Medicine and Research Institute for Convergence of Biomedical Science and Technology, Pusan National University Yangsan Hospital, Yangsan, Korea
| | - In Joo Kim
- Department of Nuclear Medicine and Biomedical Research Institute, Pusan National University Hospital, Busan, Korea
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Santiago JA, Bottero V, Potashkin JA. Evaluation of RNA Blood Biomarkers in the Parkinson's Disease Biomarkers Program. Front Aging Neurosci 2018; 10:157. [PMID: 29896099 PMCID: PMC5986959 DOI: 10.3389/fnagi.2018.00157] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 05/08/2018] [Indexed: 01/01/2023] Open
Abstract
There is a high misdiagnosis rate between Parkinson’s disease (PD) and atypical parkinsonian disorders (APD), such as progressive supranuclear palsy (PSP), the second most common parkinsonian syndrome. In our earlier studies, we identified and replicated RNA blood biomarkers in several independent cohorts, however, replication in a cohort that includes PSP patients has not yet been performed. To this end, we evaluated the diagnostic potential of nine previously identified RNA biomarkers using quantitative PCR assays in 138 blood samples at baseline from PD, PSP and healthy controls (HCs) nested in the PD Biomarkers Program. Linear discriminant analysis showed that COPZ1 and PTPN1 distinguished PD from PSP patients with 62.5% accuracy. Five biomarkers, PTPN1, COPZ1, FAXDC2, SLC14A1s and NAMPT were useful for distinguishing PSP from controls with 69% accuracy. Several biomarkers correlated with clinical features in PD patients. SLC14A1-s correlated with Unified Parkinson’s Disease Rating Scale total and part III scores. In addition, COPZ1, PTPN1 and MLST8, correlated with Montreal Cognitive Assessment (MoCA). Interestingly, COPZ1, EFTUD2 and PTPN1 were downregulated in cognitively impaired (CI) compared to normal subjects. Linear discriminant analysis showed that age, PTPN1, COPZ1, FAXDC2, EFTUD2 and MLST8 distinguished CI from normal subjects with 65.9% accuracy. These results suggest that COPZ1 and PTPN1 are useful for distinguishing PD from PSP patients. In addition, the combination of PTPN1, COPZ1, FAXDC2, EFTUD2 and MLST8 is a useful signature for cognitive impairment. Evaluation of these biomarkers in a larger study will be a key to advancing these biomarkers into the clinic.
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Affiliation(s)
- Jose A Santiago
- Department of Cellular and Molecular Pharmacology, The Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL, United States
| | - Virginie Bottero
- Department of Cellular and Molecular Pharmacology, The Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL, United States
| | - Judith A Potashkin
- Department of Cellular and Molecular Pharmacology, The Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL, United States
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Perez-Roca L, Adame-Castillo C, Campdelacreu J, Ispierto L, Vilas D, Rene R, Alvarez R, Gascon-Bayarri J, Serrano-Munoz MA, Ariza A, Beyer K. Glucocerebrosidase mRNA is Diminished in Brain of Lewy Body Diseases and Changes with Disease Progression in Blood. Aging Dis 2018; 9:208-219. [PMID: 29896411 PMCID: PMC5963343 DOI: 10.14336/ad.2017.0505] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Accepted: 05/05/2017] [Indexed: 12/16/2022] Open
Abstract
Parkinson disease (PD) and dementia with Lewy bodies (DLB) are Lewy body diseases characterized by abnormal alpha-synuclein deposits and overlapping pathological features in the brain. Several studies have shown that glucocerebrosidase (GBA) deficiency is involved in the development of LB diseases. Here, we aimed to find out if this deficiency starts at the transcriptional level, also involves alternative splicing, and if GBA expression changes in brain are also detectable in blood of patients with LB diseases. The expression of three GBA transcript variants (GBAtv1, GBAtv2 and GBAtv5) was analyzed in samples from 20 DLB, 25 PD and 17 control brains and in blood of 20 DLB, 26 PD patients and 17 unaffected individuals. Relative mRNA expression was determined by real-time PCR. Expression changes were evaluated by the ΔΔCt method. In brain, specific expression profiles were identified in the temporal cortex of DLB and in the caudate nucleus of PD. In blood, significant GBA mRNA diminution was found in both DLB and PD patients. Early PD and early-onset DLB patients showed lowest GBA levels which were normal in PD patients with advanced disease and DLB patients who developed disease after 70 years of age. In conclusion, disease group specific GBA expression profiles were found in mostly affected areas of LBD. In blood, GBA expression was diminished in LB diseases, especially in patients with early onset DLB and in patients with early PD. Age of disease onset exerts an opposite effect on GBA expression in DLB and PD.
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Affiliation(s)
- Laia Perez-Roca
- 1Department of Pathology, Hospital Universitari and Health Sciences Research Institute Germans Trias i Pujol, Universitat Autònoma de Barcelona, Spain
| | - Cristina Adame-Castillo
- 1Department of Pathology, Hospital Universitari and Health Sciences Research Institute Germans Trias i Pujol, Universitat Autònoma de Barcelona, Spain
| | - Jaume Campdelacreu
- 2Department of Neurology, Hospital Universitari de Bellvitge, L'Hospitalet de Llobregat, Spain
| | - Lourdes Ispierto
- 3Department of Neurology, Hospital Universitari Germans Trias i Pujol, Badalona, Barcelona, Spain
| | - Dolores Vilas
- 3Department of Neurology, Hospital Universitari Germans Trias i Pujol, Badalona, Barcelona, Spain
| | - Ramon Rene
- 2Department of Neurology, Hospital Universitari de Bellvitge, L'Hospitalet de Llobregat, Spain
| | - Ramiro Alvarez
- 3Department of Neurology, Hospital Universitari Germans Trias i Pujol, Badalona, Barcelona, Spain
| | - Jordi Gascon-Bayarri
- 2Department of Neurology, Hospital Universitari de Bellvitge, L'Hospitalet de Llobregat, Spain
| | - Maria A Serrano-Munoz
- 1Department of Pathology, Hospital Universitari and Health Sciences Research Institute Germans Trias i Pujol, Universitat Autònoma de Barcelona, Spain
| | - Aurelio Ariza
- 1Department of Pathology, Hospital Universitari and Health Sciences Research Institute Germans Trias i Pujol, Universitat Autònoma de Barcelona, Spain
| | - Katrin Beyer
- 1Department of Pathology, Hospital Universitari and Health Sciences Research Institute Germans Trias i Pujol, Universitat Autònoma de Barcelona, Spain
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Gámez-Valero A, Beyer K. Alternative Splicing of Alpha- and Beta-Synuclein Genes Plays Differential Roles in Synucleinopathies. Genes (Basel) 2018; 9:genes9020063. [PMID: 29370097 PMCID: PMC5852559 DOI: 10.3390/genes9020063] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 01/15/2018] [Accepted: 01/17/2018] [Indexed: 11/16/2022] Open
Abstract
The synuclein family is composed of three members, two of which, α- and β-synuclein, play a major role in the development of synucleinopathies, including Parkinson’s disease (PD) as most important movement disorder, dementia with Lewy bodies (DLB) as the second most frequent cause of dementia after Alzheimer’s disease and multiple system atrophy. Whereas abnormal oligomerization and fibrillation of α-synuclein are now well recognized as initial steps in the development of synucleinopathies, β-synuclein is thought to be a natural α-synuclein anti-aggregant. α-synuclein is encoded by the SNCA gene, and β-synuclein by SNCB. Both genes are homologous and undergo complex splicing events. On one hand, in-frame splicing of coding exons gives rise to at least three shorter transcripts, and the functional properties of the corresponding protein isoforms are different. Another type of alternative splicing is the alternative inclusion of at least four initial exons in the case of SNCA, and two in the case of SNCB. Finally, different lengths of 3’ untranslated regions have been also reported for both genes. SNCB only expresses in the brain, but some of the numerous SNCA transcripts are also brain-specific. With the present article, we aim to provide a systematic review of disease related changes in the differential expression of the various SNCA and SNCB transcript variants in brain, blood, and non-neuronal tissue of synucleinopathies, but especially PD and DLB as major neurodegenerative disorders.
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Affiliation(s)
- Ana Gámez-Valero
- Department of Pathology, Germans Trias i Pujol Research Institute, Badalona, 08916 Barcelona, Spain.
| | - Katrin Beyer
- Department of Pathology, Germans Trias i Pujol Research Institute, Badalona, 08916 Barcelona, Spain.
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Marchese D, Botta-Orfila T, Cirillo D, Rodriguez JA, Livi CM, Fernández-Santiago R, Ezquerra M, Martí MJ, Bechara E, Tartaglia GG. Discovering the 3' UTR-mediated regulation of alpha-synuclein. Nucleic Acids Res 2018; 45:12888-12903. [PMID: 29149290 PMCID: PMC5728410 DOI: 10.1093/nar/gkx1048] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 10/20/2017] [Indexed: 12/24/2022] Open
Abstract
Recent evidence indicates a link between Parkinson's Disease (PD) and the expression of a-synuclein (SNCA) isoforms with different 3′ untranslated regions (3′UTRs). Yet, the post-transcriptional mechanisms regulating SNCA expression are unknown. Using a large-scale in vitro /in silico screening we identified RNA-binding proteins (RBPs) that interact with SNCA 3′ UTRs. We identified two RBPs, ELAVL1 and TIAR, that bind with high affinity to the most abundant and translationally active 3′ UTR isoform (575 nt). Knockdown and overexpression experiments indicate that both ELAVL1 and TIAR positively regulate endogenous SNCA in vivo. The mechanism of regulation implies mRNA stabilization as well as enhancement of translation in the case of TIAR. We observed significant alteration of both TIAR and ELAVL1 expression in motor cortex of post-mortem brain donors and primary cultured fibroblast from patients affected by PD and Multiple System Atrophy (MSA). Moreover, trans expression quantitative trait loci (trans-eQTLs) analysis revealed that a group of single nucleotide polymorphisms (SNPs) in TIAR genomic locus influences SNCA expression in two different brain areas, nucleus accumbens and hippocampus. Our study sheds light on the 3′ UTR-mediated regulation of SNCA and its link with PD pathogenesis, thus opening up new avenues for investigation of post-transcriptional mechanisms in neurodegeneration.
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Affiliation(s)
- Domenica Marchese
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Teresa Botta-Orfila
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Davide Cirillo
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,Barcelona Supercomputing Center (BSC), Torre Girona c/Jordi Girona, 29, 08034 Barcelona, Spain
| | - Juan Antonio Rodriguez
- Universitat Pompeu Fabra (UPF), Barcelona, Spain.,Centro Nacional de Análisis Genómico, c/BaldiriReixac, 4, 08028 Barcelona, Spain
| | - Carmen Maria Livi
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,IFOM, the FIRC Institute of Molecular Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Rubén Fernández-Santiago
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Parkinson's Disease and Movement Disorders Unit, Institut de Neurociències Hospital Clínic, CIBERNED, Barcelona, Spain
| | - Mario Ezquerra
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Parkinson's Disease and Movement Disorders Unit, Institut de Neurociències Hospital Clínic, CIBERNED, Barcelona, Spain
| | - Maria J Martí
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Parkinson's Disease and Movement Disorders Unit, Institut de Neurociències Hospital Clínic, CIBERNED, Barcelona, Spain
| | - Elias Bechara
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Gian Gaetano Tartaglia
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
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48
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Integrated microarray analysis provided a new insight of the pathogenesis of Parkinson’s disease. Neurosci Lett 2018; 662:51-58. [DOI: 10.1016/j.neulet.2017.09.051] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 08/25/2017] [Accepted: 09/25/2017] [Indexed: 12/14/2022]
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Le W, Dong J, Li S, Korczyn AD. Can Biomarkers Help the Early Diagnosis of Parkinson's Disease? Neurosci Bull 2017; 33:535-542. [PMID: 28866850 DOI: 10.1007/s12264-017-0174-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 04/27/2017] [Indexed: 12/11/2022] Open
Abstract
Parkinson's disease (PD) is a complex neurodegenerative disease with progressive loss of dopamine neurons. PD patients usually manifest a series of motor and non-motor symptoms. In order to provide better early diagnosis and subsequent disease-modifying therapies for PD patients, there is an urgent need to identify sensitive and specific biomarkers. Biomarkers can be divided into four categories: clinical, imaging, biochemical, and genetic. Ideal biomarkers not only improve our understanding of PD pathogenesis and progression, but also provide benefits for early risk evaluation and clinical diagnosis of PD. Although many efforts have been made and several biomarkers have been extensively investigated, few if any have been found useful for early diagnosis. Here, we summarize recent developments in the discovered biomarkers of PD and discuss their merits and limitations for the early diagnosis of PD.
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Affiliation(s)
- Weidong Le
- Liaoning Provincial Center for Clinical Research on Neurological Diseases, The First Affiliated Hospital, Dalian Medical University, Dalian, 116021, China. .,Liaoning Provincial Key Laboratory for Research on the Pathogenic Mechanisms of Neurological Diseases, The First Affiliated Hospital, Dalian Medical University, Dalian, 116021, China. .,Collaborative Innovation Center for Brain Science, The First Affiliated Hospital, Dalian Medical University, Dalian, 116021, China.
| | - Jie Dong
- Liaoning Provincial Center for Clinical Research on Neurological Diseases, The First Affiliated Hospital, Dalian Medical University, Dalian, 116021, China.,Liaoning Provincial Key Laboratory for Research on the Pathogenic Mechanisms of Neurological Diseases, The First Affiliated Hospital, Dalian Medical University, Dalian, 116021, China
| | - Song Li
- Liaoning Provincial Center for Clinical Research on Neurological Diseases, The First Affiliated Hospital, Dalian Medical University, Dalian, 116021, China.,Liaoning Provincial Key Laboratory for Research on the Pathogenic Mechanisms of Neurological Diseases, The First Affiliated Hospital, Dalian Medical University, Dalian, 116021, China
| | - Amos D Korczyn
- Department of Neurology, Sackler School of Medicine, Tel Aviv University, 69978, Ramat-Aviv, Israel.
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50
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Eidson LN, Kannarkat GT, Barnum CJ, Chang J, Chung J, Caspell-Garcia C, Taylor P, Mollenhauer B, Schlossmacher MG, Ereshefsky L, Yen M, Kopil C, Frasier M, Marek K, Hertzberg VS, Tansey MG. Candidate inflammatory biomarkers display unique relationships with alpha-synuclein and correlate with measures of disease severity in subjects with Parkinson's disease. J Neuroinflammation 2017; 14:164. [PMID: 28821274 PMCID: PMC5563061 DOI: 10.1186/s12974-017-0935-1] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 08/07/2017] [Indexed: 12/12/2022] Open
Abstract
Background Efforts to identify fluid biomarkers of Parkinson’s disease (PD) have intensified in the last decade. As the role of inflammation in PD pathophysiology becomes increasingly recognized, investigators aim to define inflammatory signatures to help elucidate underlying mechanisms of disease pathogenesis and aid in identification of patients with inflammatory endophenotypes that could benefit from immunomodulatory interventions. However, discordant results in the literature and a lack of information regarding the stability of inflammatory factors over a 24-h period have hampered progress. Methods Here, we measured inflammatory proteins in serum and CSF of a small cohort of PD (n = 12) and age-matched healthy control (HC) subjects (n = 6) at 11 time points across 24 h to (1) identify potential diurnal variation, (2) reveal differences in PD vs HC, and (3) to correlate with CSF levels of amyloid β (Aβ) and α-synuclein in an effort to generate data-driven hypotheses regarding candidate biomarkers of PD. Results Despite significant variability in other factors, a repeated measures two-way analysis of variance by time and disease state for each analyte revealed that serum IFNγ, TNF, and neutrophil gelatinase-associated lipocalin (NGAL) were stable across 24 h and different between HC and PD. Regression analysis revealed that C-reactive protein (CRP) was the only factor with a strong linear relationship between CSF and serum. PD and HC subjects showed significantly different relationships between CSF Aβ proteins and α-synuclein and specific inflammatory factors, and CSF IFNγ and serum IL-8 positively correlated with clinical measures of PD. Finally, linear discriminant analysis revealed that serum TNF and CSF α-synuclein discriminated between PD and HC with a minimum of 82% sensitivity and 83% specificity. Conclusions Our findings identify a panel of inflammatory factors in serum and CSF that can be reliably measured, distinguish between PD and HC, and monitor inflammation as disease progresses or in response to interventional therapies. This panel may aid in generating hypotheses and feasible experimental designs towards identifying biomarkers of neurodegenerative disease by focusing on analytes that remain stable regardless of time of sample collection. Electronic supplementary material The online version of this article (doi:10.1186/s12974-017-0935-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lori N Eidson
- Department of Physiology, Emory University, 615 Michael Street, 605L Whitehead Biomedical Res. Bldg., Atlanta, GA, 30322, USA
| | - George T Kannarkat
- Department of Physiology, Emory University, 615 Michael Street, 605L Whitehead Biomedical Res. Bldg., Atlanta, GA, 30322, USA
| | - Christopher J Barnum
- Department of Physiology, Emory University, 615 Michael Street, 605L Whitehead Biomedical Res. Bldg., Atlanta, GA, 30322, USA
| | - Jianjun Chang
- Department of Physiology, Emory University, 615 Michael Street, 605L Whitehead Biomedical Res. Bldg., Atlanta, GA, 30322, USA
| | - Jaegwon Chung
- Department of Physiology, Emory University, 615 Michael Street, 605L Whitehead Biomedical Res. Bldg., Atlanta, GA, 30322, USA
| | - Chelsea Caspell-Garcia
- Department of Biostatistics, University of Iowa, 145 N. Riverside Drive, 100 CPHB, Iowa City, Iowa, 52242, USA
| | - Peggy Taylor
- BioLegend, Inc., 180 Rustcraft Rd # 140, Dedham, Massachusetts, 02026, USA
| | - Brit Mollenhauer
- Paracelsus-Elena-Klinik, 34128 Kassel, Kassel, Germany.,Georg-August University Medical Center Goettingen, 37075, Goettingen, Germany
| | - Michael G Schlossmacher
- Program in Neuroscience and Division of Neurology, The Ottawa Hospital, University of Ottawa Brain & Mind Institute, 451 Smyth Road, Room 1412, Ottawa, K1H 8M5, Canada
| | - Larry Ereshefsky
- Follow the Molecule, 143 Voyage Mall, Marina del Rey, CA, 90292, USA
| | - Mark Yen
- PAREXEL International, Early Phase Unit, 1560 E. Chevy Chase Drive, Suite 140, Glendale, CA, 91206, USA
| | - Catherine Kopil
- Research Programs, The Michael J. Fox Foundation for Parkinson's Research, 69 7th Avenue, 498, New York, NY, 10018, USA
| | - Mark Frasier
- Research Programs, The Michael J. Fox Foundation for Parkinson's Research, 69 7th Avenue, 498, New York, NY, 10018, USA
| | - Kenneth Marek
- Yale-New Haven Hospital, 20 York Street, New Haven, CT, 06510, USA
| | - Vicki S Hertzberg
- Nell Hodgson Woodruff School of Nursing, Emory University, 1520 Clifton Rd, Atlanta, GA, 30322, USA
| | - Malú G Tansey
- Department of Physiology, Emory University, 615 Michael Street, 605L Whitehead Biomedical Res. Bldg., Atlanta, GA, 30322, USA.
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