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Casado Gama H, Amorós MA, Andrade de Araújo M, Sha CM, Vieira MP, Torres RG, Souza GF, Junkes JA, Dokholyan NV, Leite Góes Gitaí D, Duzzioni M. Systematic review and meta-analysis of dysregulated microRNAs derived from liquid biopsies as biomarkers for amyotrophic lateral sclerosis. Noncoding RNA Res 2024; 9:523-535. [PMID: 38511059 PMCID: PMC10950706 DOI: 10.1016/j.ncrna.2024.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 01/05/2024] [Accepted: 02/06/2024] [Indexed: 03/22/2024] Open
Abstract
The discovery of disease-specific biomarkers, such as microRNAs (miRNAs), holds the potential to transform the landscape of Amyotrophic Lateral Sclerosis (ALS) by facilitating timely diagnosis, monitoring treatment response, and accelerating drug discovery. Such advancement could ultimately improve the quality of life and survival rates for ALS patients. Despite more than a decade of research, no miRNA biomarker candidate has been translated into clinical practice. We conducted a systematic review and meta-analysis to quantitatively synthesize data from original studies that analyzed miRNA expression from liquid biopsies via PCR and compared them to healthy controls. Our analysis encompasses 807 miRNA observations from 31 studies, stratified according to their source tissue. We identified consistently dysregulated miRNAs in serum (hsa-miR-3665, -4530, -4745-5p, -206); blood (hsa-miR-338-3p, -183-5p); cerebrospinal fluid (hsa-miR-34a-3p); plasma (hsa-miR-206); and neural-enriched extracellular vesicles from plasma (hsa-miR-146a-5p, -151a-5p, -10b-5p, -29b-3p, and -4454). The meta-analyses provided further support for the upregulation of hsa-miR-206, hsa-miR-338-3p, hsa-miR-146a-5p and hsa-miR-151a-5p, and downregulation of hsa-miR-183-5p, hsa-miR-10b-5p, hsa-miR-29b-3p, and hsa-miR-4454 as consistent indicators of ALS across independent studies. Our findings provide valuable insights into the current understanding of miRNAs' dysregulated expression in ALS patients and on the researchers' choices of methodology. This work contributes to the ongoing efforts towards discovering disease-specific biomarkers.
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Affiliation(s)
- Hemerson Casado Gama
- Laboratory of Pharmacological Innovation, Institute of Biological Sciences and Health, Federal University of Alagoas, Maceió, Alagoas -AL, 57072-900, Brazil
| | - Mariana A. Amorós
- Laboratory of Pharmacological Innovation, Institute of Biological Sciences and Health, Federal University of Alagoas, Maceió, Alagoas -AL, 57072-900, Brazil
| | - Mykaella Andrade de Araújo
- Department of Cellular and Molecular Biology, Institute of Biological Sciences and Health, Federal University of Alagoas, Maceió, Alagoas -AL, 57072-900, Brazil
| | - Congzhou M. Sha
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, PA, 17033, United States
| | - Mirella P.S. Vieira
- Laboratory of Pharmacological Innovation, Institute of Biological Sciences and Health, Federal University of Alagoas, Maceió, Alagoas -AL, 57072-900, Brazil
| | - Rayssa G.D. Torres
- Laboratory of Pharmacological Innovation, Institute of Biological Sciences and Health, Federal University of Alagoas, Maceió, Alagoas -AL, 57072-900, Brazil
| | - Gabriela F. Souza
- Laboratory of Pharmacological Innovation, Institute of Biological Sciences and Health, Federal University of Alagoas, Maceió, Alagoas -AL, 57072-900, Brazil
| | - Janaína A. Junkes
- Postgraduate Program in Society, Technologies and Public Policies, Tiradentes University Centre, AL, 57038-000, Brazil
| | - Nikolay V. Dokholyan
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, PA, 17033, United States
- Department of Pharmacology, Penn State College of Medicine, Hershey, PA, 17033, United States
| | - Daniel Leite Góes Gitaí
- Department of Cellular and Molecular Biology, Institute of Biological Sciences and Health, Federal University of Alagoas, Maceió, Alagoas -AL, 57072-900, Brazil
| | - Marcelo Duzzioni
- Laboratory of Pharmacological Innovation, Institute of Biological Sciences and Health, Federal University of Alagoas, Maceió, Alagoas -AL, 57072-900, Brazil
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D'Antona S, Porro D, Gallivanone F, Bertoli G. Characterization of cell cycle, inflammation, and oxidative stress signaling role in non-communicable diseases: Insights into genetic variants, microRNAs and pathways. Comput Biol Med 2024; 174:108346. [PMID: 38581999 DOI: 10.1016/j.compbiomed.2024.108346] [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: 10/09/2023] [Revised: 02/16/2024] [Accepted: 03/17/2024] [Indexed: 04/08/2024]
Abstract
Non-Communicable Diseases (NCDs) significantly impact global health, contributing to over 70% of premature deaths, as reported by the World Health Organization (WHO). These diseases have complex and multifactorial origins, involving genetic, epigenetic, environmental and lifestyle factors. While Genome-Wide Association Study (GWAS) is widely recognized as a valuable tool for identifying variants associated with complex phenotypes; the multifactorial nature of NCDs necessitates a more comprehensive exploration, encompassing not only the genetic but also the epigenetic aspect. For this purpose, we employed a bioinformatics-multiomics approach to examine the genetic and epigenetic characteristics of NCDs (i.e. colorectal cancer, coronary atherosclerosis, squamous cell lung cancer, psoriasis, type 2 diabetes, and multiple sclerosis), aiming to identify novel biomarkers for diagnosis and prognosis. Leveraging GWAS summary statistics, we pinpointed Single Nucleotide Polymorphisms (SNPs) independently associated with each NCD. Subsequently, we identified genes linked to cell cycle, inflammation and oxidative stress mechanisms, revealing shared genes across multiple diseases, suggesting common functional pathways. From an epigenetic perspective, we identified microRNAs (miRNAs) with regulatory functions targeting these genes of interest. Our findings underscore critical genetic pathways implicated in these diseases. In colorectal cancer, the dysregulation of the "Cytokine Signaling in Immune System" pathway, involving LAMA5 and SMAD7, regulated by Hsa-miR-21-5p, Hsa-miR-103a-3p, and Hsa-miR-195-5p, emerged as pivotal. In coronary atherosclerosis, the pathway associated with "binding of TCF/LEF:CTNNB1 to target gene promoters" displayed noteworthy implications, with the MYC factor controlled by Hsa-miR-16-5p as a potential regulatory factor. Squamous cell lung carcinoma analysis revealed significant pathways such as "PTK6 promotes HIF1A stabilization," regulated by Hsa-let-7b-5p. In psoriasis, the "Endosomal/Vacuolar pathway," involving HLA-C and Hsa-miR-148a-3p and Hsa-miR-148b-3p, was identified as crucial. Type 2 Diabetes implicated the "Regulation of TP53 Expression" pathway, controlled by Hsa-miR-106a-5p and Hsa-miR-106b-5p. In conclusion, our study elucidates the genetic framework and molecular mechanisms underlying NCDs, offering crucial insights into potential genetic/epigenetic biomarkers for diagnosis and prognosis. The specificity of pathways and related miRNAs in different pathologies highlights promising candidates for further clinical validation, with the potential to advance personalized treatments and alleviate the global burden of NCDs.
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Affiliation(s)
- Salvatore D'Antona
- Institute of Bioimaging and Molecular Physiology, National Research Council, Via F.lli Cervi 93, 20054, Milan, Italy
| | - Danilo Porro
- Institute of Bioimaging and Molecular Physiology, National Research Council, Via F.lli Cervi 93, 20054, Milan, Italy; National Biodiversity Future Center (NBFC), Palermo, Italy
| | - Francesca Gallivanone
- Institute of Bioimaging and Molecular Physiology, National Research Council, Via F.lli Cervi 93, 20054, Milan, Italy
| | - Gloria Bertoli
- Institute of Bioimaging and Molecular Physiology, National Research Council, Via F.lli Cervi 93, 20054, Milan, Italy; National Biodiversity Future Center (NBFC), Palermo, Italy.
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3
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Meng C, Chen G, Liu Y, Wen D, Cui J, Dong L, Yang Z, Meng H, Gao Y, Feng J, Cui X, Wu C. miR-4687-5p Affects Intracellular Survival of Mycobacterium tuberculosis through Its Regulation of NRAMP1 Expression in A549 Cells. Microorganisms 2024; 12:227. [PMID: 38276212 PMCID: PMC10818500 DOI: 10.3390/microorganisms12010227] [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: 12/04/2023] [Revised: 01/18/2024] [Accepted: 01/20/2024] [Indexed: 01/27/2024] Open
Abstract
Tuberculosis (TB), as one of the leading causes of death, poses a serious predicament to the world. MicroRNAs (miRNAs) play a role in the post-transcriptional regulation of gene expression. It has been reported that the expression of miRNAs changes upon mycobacterial infection; the screening and identification of miRNAs regulating the expression of genes could benefit our understanding of TB pathogenesis and generate effective strategies for its control and prevention. In this study, luciferase assays showed that miR-4687-5p is bound to the 3'-untranslated region of natural resistance-associated macrophage protein 1 (NRAMP1). Additionally, we found a significant increase in miR-4687-5p expression in Mycobacterium tuberculosis (Mtb)-infected A549 cells. Concomitantly, we detected a reduced level of NRAMP1 expression, suggesting that NRAMP1 is one of the targets of miR-4687-5p. Infection experiments evidenced that the transfection of miR-4687-5p induced a decrease in NRAMP1 expression and increased intracellular Mtb loads post-infection, indicating that miR-4687-5p promotes the intracellular survival of Mtb through its downregulation of the NRAMP1 protein level. We also found that the transfection of miR-4687-5p induced increased apoptosis and decreased cell proliferation post-infection with Mtb. The results presented in our study suggest that miR-4687-5p may be indicative of the susceptibility of Mtb infection to humans and could act as a potential therapeutic target for tuberculosis treatment.
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Affiliation(s)
- Chaoqun Meng
- The Key Laboratory of Medical Molecular Cell Biology of Shanxi Province, Institute of Biomedical Sciences, Shanxi University, 92 Wucheng Road, Taiyuan 030006, China; (C.M.); (G.C.); (Y.L.); (D.W.); (J.C.); (L.D.); (Z.Y.); (H.M.); (Y.G.); (J.F.)
- The Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education of China, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China
- The Key Laboratory of the Prevention and Control of Major Infectious Disease of Shanxi Province, Shanxi University, Taiyuan 030006, China
| | - Guangxin Chen
- The Key Laboratory of Medical Molecular Cell Biology of Shanxi Province, Institute of Biomedical Sciences, Shanxi University, 92 Wucheng Road, Taiyuan 030006, China; (C.M.); (G.C.); (Y.L.); (D.W.); (J.C.); (L.D.); (Z.Y.); (H.M.); (Y.G.); (J.F.)
- The Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education of China, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China
| | - Yue Liu
- The Key Laboratory of Medical Molecular Cell Biology of Shanxi Province, Institute of Biomedical Sciences, Shanxi University, 92 Wucheng Road, Taiyuan 030006, China; (C.M.); (G.C.); (Y.L.); (D.W.); (J.C.); (L.D.); (Z.Y.); (H.M.); (Y.G.); (J.F.)
- The Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education of China, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China
| | - Da Wen
- The Key Laboratory of Medical Molecular Cell Biology of Shanxi Province, Institute of Biomedical Sciences, Shanxi University, 92 Wucheng Road, Taiyuan 030006, China; (C.M.); (G.C.); (Y.L.); (D.W.); (J.C.); (L.D.); (Z.Y.); (H.M.); (Y.G.); (J.F.)
- The Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education of China, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China
| | - Jia Cui
- The Key Laboratory of Medical Molecular Cell Biology of Shanxi Province, Institute of Biomedical Sciences, Shanxi University, 92 Wucheng Road, Taiyuan 030006, China; (C.M.); (G.C.); (Y.L.); (D.W.); (J.C.); (L.D.); (Z.Y.); (H.M.); (Y.G.); (J.F.)
- The Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education of China, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China
- The Key Laboratory of the Prevention and Control of Major Infectious Disease of Shanxi Province, Shanxi University, Taiyuan 030006, China
| | - Li Dong
- The Key Laboratory of Medical Molecular Cell Biology of Shanxi Province, Institute of Biomedical Sciences, Shanxi University, 92 Wucheng Road, Taiyuan 030006, China; (C.M.); (G.C.); (Y.L.); (D.W.); (J.C.); (L.D.); (Z.Y.); (H.M.); (Y.G.); (J.F.)
- The Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education of China, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China
| | - Zhiqiang Yang
- The Key Laboratory of Medical Molecular Cell Biology of Shanxi Province, Institute of Biomedical Sciences, Shanxi University, 92 Wucheng Road, Taiyuan 030006, China; (C.M.); (G.C.); (Y.L.); (D.W.); (J.C.); (L.D.); (Z.Y.); (H.M.); (Y.G.); (J.F.)
- The Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education of China, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China
| | - Hangting Meng
- The Key Laboratory of Medical Molecular Cell Biology of Shanxi Province, Institute of Biomedical Sciences, Shanxi University, 92 Wucheng Road, Taiyuan 030006, China; (C.M.); (G.C.); (Y.L.); (D.W.); (J.C.); (L.D.); (Z.Y.); (H.M.); (Y.G.); (J.F.)
- The Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education of China, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China
| | - Yuanting Gao
- The Key Laboratory of Medical Molecular Cell Biology of Shanxi Province, Institute of Biomedical Sciences, Shanxi University, 92 Wucheng Road, Taiyuan 030006, China; (C.M.); (G.C.); (Y.L.); (D.W.); (J.C.); (L.D.); (Z.Y.); (H.M.); (Y.G.); (J.F.)
- The Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education of China, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China
| | - Jiao Feng
- The Key Laboratory of Medical Molecular Cell Biology of Shanxi Province, Institute of Biomedical Sciences, Shanxi University, 92 Wucheng Road, Taiyuan 030006, China; (C.M.); (G.C.); (Y.L.); (D.W.); (J.C.); (L.D.); (Z.Y.); (H.M.); (Y.G.); (J.F.)
- The Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education of China, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China
| | - Xiaogang Cui
- The Key Laboratory of Medical Molecular Cell Biology of Shanxi Province, Institute of Biomedical Sciences, Shanxi University, 92 Wucheng Road, Taiyuan 030006, China; (C.M.); (G.C.); (Y.L.); (D.W.); (J.C.); (L.D.); (Z.Y.); (H.M.); (Y.G.); (J.F.)
- The Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education of China, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China
- The Key Laboratory of the Prevention and Control of Major Infectious Disease of Shanxi Province, Shanxi University, Taiyuan 030006, China
| | - Changxin Wu
- The Key Laboratory of Medical Molecular Cell Biology of Shanxi Province, Institute of Biomedical Sciences, Shanxi University, 92 Wucheng Road, Taiyuan 030006, China; (C.M.); (G.C.); (Y.L.); (D.W.); (J.C.); (L.D.); (Z.Y.); (H.M.); (Y.G.); (J.F.)
- The Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education of China, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China
- The Key Laboratory of the Prevention and Control of Major Infectious Disease of Shanxi Province, Shanxi University, Taiyuan 030006, China
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4
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Velikic G, Maric DM, Maric DL, Supic G, Puletic M, Dulic O, Vojvodic D. Harnessing the Stem Cell Niche in Regenerative Medicine: Innovative Avenue to Combat Neurodegenerative Diseases. Int J Mol Sci 2024; 25:993. [PMID: 38256066 PMCID: PMC10816024 DOI: 10.3390/ijms25020993] [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: 08/29/2023] [Revised: 11/30/2023] [Accepted: 12/06/2023] [Indexed: 01/24/2024] Open
Abstract
Regenerative medicine harnesses the body's innate capacity for self-repair to restore malfunctioning tissues and organs. Stem cell therapies represent a key regenerative strategy, but to effectively harness their potential necessitates a nuanced understanding of the stem cell niche. This specialized microenvironment regulates critical stem cell behaviors including quiescence, activation, differentiation, and homing. Emerging research reveals that dysfunction within endogenous neural stem cell niches contributes to neurodegenerative pathologies and impedes regeneration. Strategies such as modifying signaling pathways, or epigenetic interventions to restore niche homeostasis and signaling, hold promise for revitalizing neurogenesis and neural repair in diseases like Alzheimer's and Parkinson's. Comparative studies of highly regenerative species provide evolutionary clues into niche-mediated renewal mechanisms. Leveraging endogenous bioelectric cues and crosstalk between gut, brain, and vascular niches further illuminates promising therapeutic opportunities. Emerging techniques like single-cell transcriptomics, organoids, microfluidics, artificial intelligence, in silico modeling, and transdifferentiation will continue to unravel niche complexity. By providing a comprehensive synthesis integrating diverse views on niche components, developmental transitions, and dynamics, this review unveils new layers of complexity integral to niche behavior and function, which unveil novel prospects to modulate niche function and provide revolutionary treatments for neurodegenerative diseases.
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Affiliation(s)
- Gordana Velikic
- Department for Research and Development, Clinic Orto MD-Parks Dr. Dragi Hospital, 21000 Novi Sad, Serbia
- Hajim School of Engineering, University of Rochester, Rochester, NY 14627, USA
| | - Dusan M. Maric
- Department for Research and Development, Clinic Orto MD-Parks Dr. Dragi Hospital, 21000 Novi Sad, Serbia
- Faculty of Stomatology Pancevo, University Business Academy, 26000 Pancevo, Serbia;
| | - Dusica L. Maric
- Department of Anatomy, Faculty of Medicine, University of Novi Sad, 21000 Novi Sad, Serbia
| | - Gordana Supic
- Institute for Medical Research, Military Medical Academy, 11000 Belgrade, Serbia; (G.S.); (D.V.)
- Medical Faculty of Military Medical Academy, University of Defense, 11000 Belgrade, Serbia
| | - Miljan Puletic
- Faculty of Stomatology Pancevo, University Business Academy, 26000 Pancevo, Serbia;
| | - Oliver Dulic
- Department of Surgery, Faculty of Medicine, University of Novi Sad, 21000 Novi Sad, Serbia;
| | - Danilo Vojvodic
- Institute for Medical Research, Military Medical Academy, 11000 Belgrade, Serbia; (G.S.); (D.V.)
- Medical Faculty of Military Medical Academy, University of Defense, 11000 Belgrade, Serbia
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5
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Lauria G, Curcio R, Tucci P. A Machine Learning Approach for Highlighting microRNAs as Biomarkers Linked to Amyotrophic Lateral Sclerosis Diagnosis and Progression. Biomolecules 2023; 14:47. [PMID: 38254647 PMCID: PMC10813207 DOI: 10.3390/biom14010047] [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: 10/30/2023] [Revised: 12/04/2023] [Accepted: 12/20/2023] [Indexed: 01/24/2024] Open
Abstract
Amyotrophic Lateral Sclerosis (ALS) is a fatal neurodegenerative disease characterized by the progressive loss of motor neurons in the brain and spinal cord. The early diagnosis of ALS can be challenging, as it usually depends on clinical examination and the exclusion of other possible causes. In this regard, the analysis of miRNA expression profiles in biofluids makes miRNAs promising non-invasive clinical biomarkers. Due to the increasing amount of scientific literature that often provides controversial results, this work aims to deepen the understanding of the current state of the art on this topic using a machine-learning-based approach. A systematic literature search was conducted to analyze a set of 308 scientific articles using the MySLR digital platform and the Latent Dirichlet Allocation (LDA) algorithm. Two relevant topics were identified, and the articles clustered in each of them were analyzed and discussed in terms of biomolecular mechanisms, as well as in translational and clinical settings. Several miRNAs detected in the tissues and biofluids of ALS patients, including blood and cerebrospinal fluid (CSF), have been linked to ALS diagnosis and progression. Some of them may represent promising non-invasive clinical biomarkers. In this context, future scientific priorities and goals have been proposed.
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Affiliation(s)
| | - Rosita Curcio
- Correspondence: (R.C.); (P.T.); Tel.: +39-0984493046 (R.C.); +39-0984493185 (P.T.)
| | - Paola Tucci
- Correspondence: (R.C.); (P.T.); Tel.: +39-0984493046 (R.C.); +39-0984493185 (P.T.)
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6
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Gomes BC, Peixinho N, Pisco R, Gromicho M, Pronto-Laborinho AC, Rueff J, de Carvalho M, Rodrigues AS. Differential Expression of miRNAs in Amyotrophic Lateral Sclerosis Patients. Mol Neurobiol 2023; 60:7104-7117. [PMID: 37531027 PMCID: PMC10657797 DOI: 10.1007/s12035-023-03520-7] [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: 04/28/2023] [Accepted: 07/14/2023] [Indexed: 08/03/2023]
Abstract
Amyotrophic lateral sclerosis (ALS) is a progressive motor neuron disease that affects nerve cells in the brain and spinal cord, causing loss of muscle control, muscle atrophy and in later stages, death. Diagnosis has an average delay of 1 year after symptoms onset, which impairs early management. The identification of a specific disease biomarker could help decrease the diagnostic delay. MicroRNA (miRNA) expression levels have been proposed as ALS biomarkers, and altered function has been reported in ALS pathogenesis. The aim of this study was to assess the differential expression of plasma miRNAs in ALS patients and two control populations (healthy controls and ALS-mimic disorders). For that, 16 samples from each group were pooled, and then 1008 miRNAs were assessed through reverse transcription-quantitative polymerase chain reaction (RT-qPCR). From these, ten candidate miRNAs were selected and validated in 35 ALS patients, 16 ALS-mimic disorders controls and 15 healthy controls. We also assessed the same miRNAs in two different time points of disease progression. Although we were unable to determine a miRNA signature to use as disease or condition marker, we found that miR-7-2-3p, miR-26a-1-3p, miR-224-5p and miR-206 are good study candidates to understand the pathophysiology of ALS.
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Affiliation(s)
- Bruno Costa Gomes
- Instituto de Fisiologia, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal.
- ToxOmics, NOVA Medical School, Faculdade de Ciências Médicas, NMS, FCM, Universidade NOVA de Lisboa, Lisboa, Portugal.
| | - Nuno Peixinho
- ToxOmics, NOVA Medical School, Faculdade de Ciências Médicas, NMS, FCM, Universidade NOVA de Lisboa, Lisboa, Portugal
| | - Rita Pisco
- ToxOmics, NOVA Medical School, Faculdade de Ciências Médicas, NMS, FCM, Universidade NOVA de Lisboa, Lisboa, Portugal
| | - Marta Gromicho
- Instituto de Fisiologia, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Ana Catarina Pronto-Laborinho
- Instituto de Fisiologia, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - José Rueff
- ToxOmics, NOVA Medical School, Faculdade de Ciências Médicas, NMS, FCM, Universidade NOVA de Lisboa, Lisboa, Portugal
| | - Mamede de Carvalho
- Instituto de Fisiologia, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
- Department of Neurosciences and Mental Health, Hospital de Santa Maria CHULN, Lisboa, Portugal
| | - António Sebastião Rodrigues
- ToxOmics, NOVA Medical School, Faculdade de Ciências Médicas, NMS, FCM, Universidade NOVA de Lisboa, Lisboa, Portugal
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7
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Wang R, Zhong J, Pan X, Su Z, Xu Y, Zhang M, Chen X, Chen N, Yu T, Zhou Q. A novel intronic circular RNA circFGFR1 int2 up-regulates FGFR1 by recruiting transcriptional activators P65/FUS and suppressing miR-4687-5p to promote prostate cancer progression. J Transl Med 2023; 21:840. [PMID: 37993879 PMCID: PMC10664560 DOI: 10.1186/s12967-023-04718-y] [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: 08/25/2023] [Accepted: 11/10/2023] [Indexed: 11/24/2023] Open
Abstract
Fibroblast growth factor receptor 1 (FGFR1) is a core component of the FGFs/FGFR pathway that activates multiple signalling pathways, including ERK1/2, PI3K/AKT, PLCγ, and NF-κB. Aberrant expression of FGFR1 due to gene amplification, chromosome rearrangement, point mutation, and epigenetic deregulations, have been reported in various cancers. FGFR1 overexpression has also been reported in prostate cancer (PCa), but the underlining mechanisms are not clear. Here we report a novel circular RNA, circFGFR1int2, derived from intron 2 of FGFR1 gene, which is overexpressed in PCa and associated with tumor progression. Importantly, we show that circFGFR1int2 facilitates FGFR1 transcription by recruiting transcription activators P65/FUS and by interacting with FGFR1 promoter. Moreover, we show that circFGFR1int2 suppresses post-transcriptional inhibitory effects of miR-4687-5p on FGFR1 mRNA. These mechanisms synergistically promote PCa cell growth, migration, and invasion. Overexpression of circFGFR1int2 is significantly correlated with higher tumor grade, Gleason score, and PSA level, and is a significant unfavorable prognosticator for CRPC-free survival (CFS) (RR = 3.277, 95% confidence interval: 1.192-9.009; P = 0.021). These findings unravelled novel mechanisms controlling FGFR1 gene expression by intronic circRNA and its potential clinicopathological utility as a diagnostic or therapeutic target.
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Affiliation(s)
- Ruyue Wang
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Jinjing Zhong
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xiuyi Pan
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Zhengzheng Su
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yunyi Xu
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Mengni Zhang
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xueqin Chen
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Ni Chen
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Ting Yu
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, 610041, China.
| | - Qiao Zhou
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, 610041, China.
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8
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Ruffo P, Catalano S, La Bella V, Conforti FL. Deregulation of Plasma microRNA Expression in a TARDBP-ALS Family. Biomolecules 2023; 13:biom13040706. [PMID: 37189452 DOI: 10.3390/biom13040706] [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: 03/14/2023] [Revised: 04/06/2023] [Accepted: 04/19/2023] [Indexed: 05/17/2023] Open
Abstract
TDP-43 intracellular aggregates are a pathogenic sign of most amyotrophic lateral sclerosis (ALS) cases. Familial ALS, brought on by TARDBP gene mutations, emphasizes the relevance of this altered protein in pathophysiology. Growing evidence suggests a role for dysregulated microRNA (miRNA) in ALS disease. Furthermore, several studies showed that miRNAs are highly stable in various biological fluids (CSF, blood, plasma, and serum), and they are expressed differentially by comparing ALS patients and controls. In 2011, our research group discovered a rare mutation in a TARDBP gene (G376D) in a large ALS Apulian family with affected members exhibiting a rapidly progressing disease. To identify potential non-invasive biomarkers of preclinical and clinical progression in the TARDBP-ALS family, we assessed the expression levels of plasma microRNAs in affected patients (n = 7) and asymptomatic mutation carriers (n = 7) compared with healthy controls (n = 13). Applying qPCR, we investigate 10 miRNAs that bind TDP-43 in vitro during their biogenesis or in their mature form, and the other nine are known to be deregulated in the disease. We highlight the potential of miR-132-5p, miR-132-3p, miR-124-3p, and miR-133a-3p expression levels in plasma as biomarkers of preclinical progression for G376D-TARDBP-associated ALS. Our research strongly supports the potential of plasma miRNAs as biomarkers for performing predictive diagnostics and identifying new therapeutic targets.
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Affiliation(s)
- Paola Ruffo
- Medical Genetics Laboratory, Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Rende, Italy
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA
| | - Stefania Catalano
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Rende, Italy
| | - Vincenzo La Bella
- ALS Clinical Research Centre and Laboratory of Neurochemistry, Department of Experimental Biomedicine and Clinical Neurosciences, University of Palermo, 90133 Palermo, Italy
| | - Francesca Luisa Conforti
- Medical Genetics Laboratory, Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Rende, Italy
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Sanchez-Tejerina D, Llaurado A, Sotoca J, Lopez-Diego V, Vidal Taboada JM, Salvado M, Juntas-Morales R. Biofluid Biomarkers in the Prognosis of Amyotrophic Lateral Sclerosis: Recent Developments and Therapeutic Applications. Cells 2023; 12:cells12081180. [PMID: 37190090 DOI: 10.3390/cells12081180] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/15/2023] [Accepted: 04/17/2023] [Indexed: 05/17/2023] Open
Abstract
Amyotrophic lateral sclerosis is a neurodegenerative disease characterized by the degeneration of motor neurons for which effective therapies are lacking. One of the most explored areas of research in ALS is the discovery and validation of biomarkers that can be applied to clinical practice and incorporated into the development of innovative therapies. The study of biomarkers requires an adequate theoretical and operational framework, highlighting the "fit-for-purpose" concept and distinguishing different types of biomarkers based on common terminology. In this review, we aim to discuss the current status of fluid-based prognostic and predictive biomarkers in ALS, with particular emphasis on those that are the most promising ones for clinical trial design and routine clinical practice. Neurofilaments in cerebrospinal fluid and blood are the main prognostic and pharmacodynamic biomarkers. Furthermore, several candidates exist covering various pathological aspects of the disease, such as immune, metabolic and muscle damage markers. Urine has been studied less often and should be explored for its possible advantages. New advances in the knowledge of cryptic exons introduce the possibility of discovering new biomarkers. Collaborative efforts, prospective studies and standardized procedures are needed to validate candidate biomarkers. A combined biomarkers panel can provide a more detailed disease status.
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Affiliation(s)
- Daniel Sanchez-Tejerina
- Neuromuscular Diseases Unit, Neurology Department, Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain
- Peripheral Nervous System Group, Vall d'Hebron Research Institut (VHIR), Vall d'Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain
- European Reference Network on Rare Neuromuscular Diseases (ERN EURO-NMD), Vall d'Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain
- Medicine Department, Universitat Autónoma de Barcelona, 08035 Barcelon, Spain
| | - Arnau Llaurado
- Neuromuscular Diseases Unit, Neurology Department, Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain
- Peripheral Nervous System Group, Vall d'Hebron Research Institut (VHIR), Vall d'Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain
- European Reference Network on Rare Neuromuscular Diseases (ERN EURO-NMD), Vall d'Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain
| | - Javier Sotoca
- Neuromuscular Diseases Unit, Neurology Department, Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain
- Peripheral Nervous System Group, Vall d'Hebron Research Institut (VHIR), Vall d'Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain
- European Reference Network on Rare Neuromuscular Diseases (ERN EURO-NMD), Vall d'Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain
| | - Veronica Lopez-Diego
- Neuromuscular Diseases Unit, Neurology Department, Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain
- Peripheral Nervous System Group, Vall d'Hebron Research Institut (VHIR), Vall d'Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain
- European Reference Network on Rare Neuromuscular Diseases (ERN EURO-NMD), Vall d'Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain
| | - Jose M Vidal Taboada
- Peripheral Nervous System Group, Vall d'Hebron Research Institut (VHIR), Vall d'Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain
- Medicine Department, Universitat Autónoma de Barcelona, 08035 Barcelon, Spain
| | - Maria Salvado
- Neuromuscular Diseases Unit, Neurology Department, Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain
- Peripheral Nervous System Group, Vall d'Hebron Research Institut (VHIR), Vall d'Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain
- European Reference Network on Rare Neuromuscular Diseases (ERN EURO-NMD), Vall d'Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain
| | - Raul Juntas-Morales
- Neuromuscular Diseases Unit, Neurology Department, Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain
- Peripheral Nervous System Group, Vall d'Hebron Research Institut (VHIR), Vall d'Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain
- European Reference Network on Rare Neuromuscular Diseases (ERN EURO-NMD), Vall d'Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain
- Medicine Department, Universitat Autónoma de Barcelona, 08035 Barcelon, Spain
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10
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Hadjiargyrou M, Salichos L, Kloen P. Identification of the miRNAome in human fracture callus and nonunion tissues. J Orthop Translat 2023; 39:113-123. [PMID: 36909863 PMCID: PMC9996375 DOI: 10.1016/j.jot.2023.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 01/09/2023] [Accepted: 01/31/2023] [Indexed: 03/14/2023] Open
Abstract
Background Nonunions remain a challenging post-traumatic complication that often leads to a financial and health burden that affects the patient's quality of life. Despite a wealth of knowledge about fracture repair, especially gene and more recently miRNA expression, much remains unknown about the molecular differences between normal physiological repair (callus tissue) and a nonunion. To probe this lack of knowledge, we embarked on a study that sought to identify and compare the human miRNAome of normal bone to that present in a normal fracture callus and those from two different classic nonunion types, hypertrophic and oligotrophic. Methods Normal bone and callus tissue samples were harvested during revision surgery from patients with physiological fracture repair and nonunions (hypertrophic and oligotrophic) and analyzed using histology. Also, miRNAs were isolated and screened using microarrays followed by bioinformatic analyses, including, differential expression, pathways and biological processes, as well as elucidation of target genes. Results Out of 30,424 mature miRNAs (from 203 organisms) screened via microarrays, 635 (∼2.1%) miRNAs were found to be upregulated and 855 (∼2.8%) downregulated in the fracture callus and nonunion tissues as compared to intact bone. As our tissue samples were derived from humans, we focused on the human miRNAs and out of the 4223 human miRNAs, 86 miRNAs (∼2.0%) were upregulated and 51 (∼1.2%) were downregulated. Although there were similarities between the three experimental samples, we also found specific miRNAs that were unique to individual samples. We further identified the predicted target genes from these differentially expressed miRNAs as well as the relevant biological processes, including specific signaling pathways that are activated in all three experimental samples. Conclusion Collectively, this is the first comprehensive study reporting on the miRNAome of intact bone as compared to fracture callus and nonunion tissues. Further, we identify specific miRNAs involved in normal physiological fracture repair as well as those of nonunions. The translational potential of this article The data generated from this study further increase our molecular understanding of the roles of miRNAs during normal and aberrant fracture repair and this knowledge can be used in the future in the development of miRNA-based therapeutics for skeletal regeneration.
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Affiliation(s)
- Michael Hadjiargyrou
- Department of Biological & Chemical Sciences, New York Institute of Technology, Old Westbury, NY, 11568, USA
| | - Leonidas Salichos
- Department of Biological & Chemical Sciences, New York Institute of Technology, Old Westbury, NY, 11568, USA
| | - Peter Kloen
- Department of Orthopedic Surgery and Sports Medicine, Amsterdam UMC Location Meibergdreef, Amsterdam, the Netherlands
- Amsterdam Movement Sciences, (Tissue Function and Regeneration), Amsterdam, the Netherlands
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Biological aspects of nitrogen heterocycles for amyotrophic lateral sclerosis. Appl Microbiol Biotechnol 2022; 107:43-56. [DOI: 10.1007/s00253-022-12317-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 11/24/2022] [Accepted: 11/26/2022] [Indexed: 12/13/2022]
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12
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Brusati A, Ratti A, Pensato V, Peverelli S, Gentilini D, Dalla Bella E, Sorce MN, Meneri M, Gagliardi D, Corti S, Gellera C, Lauria Pinter G, Ticozzi N, Silani V. Analysis of miRNA rare variants in amyotrophic lateral sclerosis and in silico prediction of their biological effects. Front Genet 2022; 13:1055313. [PMID: 36568378 PMCID: PMC9768194 DOI: 10.3389/fgene.2022.1055313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 11/21/2022] [Indexed: 12/13/2022] Open
Abstract
Background: Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease affecting upper and/or lower motor neurons and characterized by complex etiology. Familial cases show high genetic heterogeneity and sporadic cases (90%) are associated with several genetic and environmental risk factors. Among the genetic risk factors, the contribution of non-coding elements, such as microRNAs (miRNAs), to ALS disease susceptibility remains largely unexplored. Aim: This work aims to identify rare variants in miRNA genes in sporadic ALS (sALS) patients which may cause a defective miRNA maturation or altered target gene recognition by changing miRNA secondary structure or seed sequence, respectively. Methods: Rare variants located in miRNA loci with a minor allele frequency (MAF) < 0.01 were extracted from whole genome sequencing (WGS) data of 100 sALS patients. The secondary pre-miRNA structures were predicted using MiRVas to evaluate the impact of the variants on RNA folding process. Human TargetScan was used to retrieve all the potential target genes of miRNAs with variants in the seed region. Over Representation Analysis (ORA) was conducted to compare the lists of target genes for the reference and mutated miRNAs in the seed sequence. Results: Our analysis identified 86 rare variants in 77 distinct miRNAs and distributed in different parts of the miRNA precursors. The presence of these variants changed miRNA secondary structures in ∼70% of MiRVas predictions. By focusing on the 6 rare variants mapping within the seed sequence, the predicted target genes increased in number compared to the reference miRNA and included novel targets in a proportion ranging from 30 to 82%. Interestingly, ORA revealed significant changes in gene set enrichment only for mutated miR-509-1 and miR-941-3 for which the Gene Ontology term related to "nervous system development" was absent and present, respectively, compared to target lists of the reference miRNA. Conclusion: We here developed a workflow to study miRNA rare variants from WGS data and to predict their biological effects on miRNA folding, maturation and target gene recognition. Although this in silico approach certainly needs functional validation in vitro and in vivo, it may help define the role of miRNA variability in ALS and complex diseases.
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Affiliation(s)
- Alberto Brusati
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy,Department Brain and Behavioral Sciences, University of Pavia, Pavia, Italy
| | - Antonia Ratti
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy,Department Medical Biotechnology and Translational Medicine, University of Milan, Milan, Italy,*Correspondence: Antonia Ratti,
| | - Viviana Pensato
- Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano, Italy
| | - Silvia Peverelli
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - Davide Gentilini
- Department Brain and Behavioral Sciences, University of Pavia, Pavia, Italy,Bioinformatics and Statistical Genomics Unit,IRCCS Istituto Auxologico Italiano,Milan,Italy
| | | | - Marta Nice Sorce
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - Megi Meneri
- Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Milano, Italy,Department of Pathophysiology and Transplantation, Dino Ferrari Center, University of Milan, Milan, Italy
| | - Delia Gagliardi
- Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Milano, Italy
| | - Stefania Corti
- Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Milano, Italy,Department of Pathophysiology and Transplantation, Dino Ferrari Center, University of Milan, Milan, Italy
| | - Cinzia Gellera
- Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano, Italy
| | - Giuseppe Lauria Pinter
- Department Medical Biotechnology and Translational Medicine, University of Milan, Milan, Italy,Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano, Italy
| | - Nicola Ticozzi
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy,Department of Pathophysiology and Transplantation, Dino Ferrari Center, University of Milan, Milan, Italy
| | - Vincenzo Silani
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy,Department of Pathophysiology and Transplantation, Dino Ferrari Center, University of Milan, Milan, Italy
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