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Divi SN, Markova DZ, D'Antonio ND, Lambrechts MJ, Levy HA, Heard JC, Yalla GR, Chang M, Hilibrand AS, Vaccaro AR, Kepler CK. Circulating microRNAs May Be Predictive of Degenerative Cervical Myelopathy. Spine (Phila Pa 1976) 2024; 49:1393-1400. [PMID: 38711175 DOI: 10.1097/brs.0000000000005025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 04/04/2024] [Indexed: 05/08/2024]
Abstract
STUDY DESIGN Basic Science. OBJECTIVE The objective of this study was to identify a unique serum profile of circulating miRNAs and inflammatory markers in patients with degenerative cervical myelopathy (DCM) compared with healthy controls (HC). SUMMARY OF BACKGROUND DATA Currently, DCM is diagnosed with a combination of history, physical examination, and close correlation to advanced imaging. To date, no serum marker has been identified to be diagnostic of this condition. METHODS Whole venous blood was collected from patients with DCM as well as healthy age-matched and gender-matched controls. miRNA was extracted from venous blood, and a screening analysis was initially conducted to identify miRNA dysregulation in DCM patients. RT-qPCR was used to analyze the expression of 2 specific miRNAs based on screening analysis and literature review. Bioinformatics analysis was used to identify gene networks and potential targets of the miRNA. In addition, the serum inflammatory profile of DCM and HC groups was differentiated using a pro-inflammatory panel. RESULTS Thirty-six patients were enrolled in the DCM group (36.1% male, 61.5±9.5 y), while 35 patients were enrolled in the HC group (31.4% male, 57.5±8.9 y). Of the 15 total miRNAs differentially expressed between DCM and HC groups, two were selected for further analysis: miR-223-3p (upregulated) and miR-451a (downregulated). Functional gene network analysis revealed the highest-ranking gene network was involved in neurological disease, while the most overexpressed miRNA in this network (miR-233-3p) was noted to have over 100 targets, including CDKN1B and the insulin receptor. Serum cytokine analysis showed significant upregulation of several pro-inflammatory cytokines in the DCM cohort compared with the HC group. CONCLUSION DCM patients demonstrated a set of unique circulating miRNAs in addition to a different serum inflammatory profile compared with HC. These miRNAs may potentially serve as targets for future therapeutic intervention or diagnostic/prognostic testing.
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Affiliation(s)
- Srikanth N Divi
- Department of Orthopaedic Surgery, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Dessislava Z Markova
- Department of Orthopaedic Surgery, Sidney Kimmel School of Medicine, Thomas Jefferson University, Philadelphia, PA
| | - Nicholas D D'Antonio
- Department of Orthopaedic Surgery, Sidney Kimmel School of Medicine, Thomas Jefferson University, Philadelphia, PA
| | - Mark J Lambrechts
- Department of Orthopaedic Surgery, Sidney Kimmel School of Medicine, Thomas Jefferson University, Philadelphia, PA
- Rothman Institute, Philadelphia, PA
| | - Hannah A Levy
- Department of Orthopaedic Surgery, Sidney Kimmel School of Medicine, Thomas Jefferson University, Philadelphia, PA
| | - Jeremy C Heard
- Department of Orthopaedic Surgery, Sidney Kimmel School of Medicine, Thomas Jefferson University, Philadelphia, PA
| | - Goutham R Yalla
- Department of Orthopaedic Surgery, Sidney Kimmel School of Medicine, Thomas Jefferson University, Philadelphia, PA
| | - Michael Chang
- Department of Orthopaedic Surgery, Sidney Kimmel School of Medicine, Thomas Jefferson University, Philadelphia, PA
- Rothman Institute, Philadelphia, PA
| | - Alan S Hilibrand
- Department of Orthopaedic Surgery, Sidney Kimmel School of Medicine, Thomas Jefferson University, Philadelphia, PA
- Rothman Institute, Philadelphia, PA
| | - Alexander R Vaccaro
- Department of Orthopaedic Surgery, Sidney Kimmel School of Medicine, Thomas Jefferson University, Philadelphia, PA
- Rothman Institute, Philadelphia, PA
| | - Christopher K Kepler
- Department of Orthopaedic Surgery, Sidney Kimmel School of Medicine, Thomas Jefferson University, Philadelphia, PA
- Rothman Institute, Philadelphia, PA
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Pawar P, Akolkar K, Saxena V. An integrated bioinformatics approach reveals the potential role of microRNA-30b-5p and let-7a-5p during SARS CoV-2 spike-1 mediated neuroinflammation. Int J Biol Macromol 2024; 277:134329. [PMID: 39098684 DOI: 10.1016/j.ijbiomac.2024.134329] [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: 04/01/2024] [Revised: 07/16/2024] [Accepted: 07/23/2024] [Indexed: 08/06/2024]
Abstract
SARS-CoV-2 induced neuroinflammation contributing to neurological sequelae is one of the critical outcomes of long-COVID, however underlying regulatory mechanisms involved therein are poorly understood. We deciphered the profile of dysregulated microRNAs, their targets, associated pathways, protein-protein interactions (PPI), transcription factor-hub genes interaction networks, hub genes-microRNA co-regulatory networks in SARS-CoV-2 Spike-1 (S1) stimulated microglial cells along with candidate drug prediction using RNA-sequencing and multiple bioinformatics approaches. We identified 11 dysregulated microRNAs in the S1-stimulated microglial cells (p < 0.05). KEGG analysis revealed involvement of important neuroinflammatory pathways such as MAPK signalling, PI3K-AKT signalling, Ras signalling and axon guidance. PPI analysis further identified 11 hub genes involved in these pathways. Real time PCR validation confirmed a significant upregulation of microRNA-30b-5p and let-7a-5p; proinflammatory cytokines- IL-6, TNF-α, IL-1β, GM-CSF; and inflammatory genes- PIK3CA and AKT in the S1-stimulated microglial cells, while PTEN and SHIP1 expression was decreased as compared to the non-stimulated cells. Drug prediction analysis further indicated resveratrol, diclofenac and rapamycin as the potential drugs based on their degree of interaction with hub genes. Thus, targeting of these microRNAs and/or their intermediate signalling molecules would be a prospective immunotherapeutic approach in alleviating SARS-CoV-2-S1 mediated neuroinflammation; and needs further investigations.
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Affiliation(s)
- Puja Pawar
- Division of Immunology and Serology, ICMR-National Institute of Translational Virology & AIDS Research (NITVAR), MIDC, Bhosari, Pune, Maharashtra, India
| | - Kadambari Akolkar
- Division of Immunology and Serology, ICMR-National Institute of Translational Virology & AIDS Research (NITVAR), MIDC, Bhosari, Pune, Maharashtra, India
| | - Vandana Saxena
- Division of Immunology and Serology, ICMR-National Institute of Translational Virology & AIDS Research (NITVAR), MIDC, Bhosari, Pune, Maharashtra, India.
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3
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Liguori M, Bianco A, Introna A, Consiglio A, Milella G, Abbatangelo E, D'Errico E, Licciulli F, Grillo G, Simone IL. An early Transcriptomic Investigation in Adult Patients with Spinal Muscular Atrophy Under Treatment with Nusinersen. J Mol Neurosci 2024; 74:89. [PMID: 39325116 PMCID: PMC11427494 DOI: 10.1007/s12031-024-02251-1] [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: 04/27/2024] [Accepted: 07/17/2024] [Indexed: 09/27/2024]
Abstract
Spinal muscular atrophy (SMA) is a rare degenerative disorder with loss of motor neurons caused by mutations in the SMN1 gene. Nusinersen, an antisense oligonucleotide, was approved for SMA treatment to compensate the deficit of the encoded protein SMN by modulating the pre-mRNA splicing of SMN2, the centromeric homologous of SMN1, thus inducing the production of a greater amount of biologically active protein. Here, we reported a 10-month transcriptomics investigation in 10 adult SMA who received nusinersen to search for early genetic markers for clinical monitoring. By comparing their profiles with age-matched healthy controls (HC), we also analyzed the changes in miRNA/mRNAs expression and miRNA-target gene interactions possibly associated with SMA. A multidisciplinary approach of HT-NGS followed by bioinformatics/biostatistics analysis was applied. Within the study interval, those SMA patients who showed some clinical improvements were characterized by having the SMN2/SMN1 ratio slightly increased over the time, while in the stable ones the ratio decreased, suggesting that the estimation of SMN2/SMN1 expression may be an early indicator of nusinersen efficacy. On the other hand, the expression of 38/147 genes/genetic regions DE at T0 between SMA and HC like TRADD and JUND resulted "restored" at T10. We also confirmed the dysregulation of miR-146a(-5p), miR-324-5p and miR-423-5p in SMA subjects. Of interest, miR-146a-5p targeted SMN1, in line with experimental evidence showing the key role of astrocyte-produced miR-146a in SMA motor neuron loss. Molecular pathways such as NOTCH, NF-kappa B, and Toll-like receptor signalings seem to be involved in the SMA pathogenesis.
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Grants
- D.U.P. n.246/2019, D.D. n. 3 of 13 January 2021 Apulian Regional Council
- D.U.P. n.246/2019, D.D. n. 3 of 13 January 2021 Apulian Regional Council
- D.U.P. n.246/2019, D.D. n. 3 of 13 January 2021 Apulian Regional Council
- D.U.P. n.246/2019, D.D. n. 3 of 13 January 2021 Apulian Regional Council
- D.U.P. n.246/2019, D.D. n. 3 of 13 January 2021 Apulian Regional Council
- D.U.P. n.246/2019, D.D. n. 3 of 13 January 2021 Apulian Regional Council
- D.U.P. n.246/2019, D.D. n. 3 of 13 January 2021 Apulian Regional Council
- D.U.P. n.246/2019, D.D. n. 3 of 13 January 2021 Apulian Regional Council
- D.U.P. n.246/2019, D.D. n. 3 of 13 January 2021 Apulian Regional Council
- D.U.P. n.246/2019, D.D. n. 3 of 13 January 2021 Apulian Regional Council
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Affiliation(s)
- Maria Liguori
- National Research Council, Department of Biomedicine, Institute of Biomedical Technologies - Bari Unit, 70125, Bari, Italy.
| | - Annalisa Bianco
- National Research Council, Department of Biomedicine, Institute of Biomedical Technologies - Bari Unit, 70125, Bari, Italy
| | - Alessandro Introna
- Neurology Unit, Department of Translational Biomedicine and Neuroscience, University of Bari "Aldo Moro", 70124, Bari, Italy
| | - Arianna Consiglio
- National Research Council, Department of Biomedicine, Institute of Biomedical Technologies - Bari Unit, 70125, Bari, Italy
| | - Giammarco Milella
- Neurology Unit, Department of Translational Biomedicine and Neuroscience, University of Bari "Aldo Moro", 70124, Bari, Italy
| | - Elena Abbatangelo
- National Research Council, Department of Biomedicine, Institute of Biomedical Technologies - Bari Unit, 70125, Bari, Italy
| | - Eustachio D'Errico
- Neurology Unit, Department of Translational Biomedicine and Neuroscience, University of Bari "Aldo Moro", 70124, Bari, Italy
| | - Flavio Licciulli
- National Research Council, Department of Biomedicine, Institute of Biomedical Technologies - Bari Unit, 70125, Bari, Italy
| | - Giorgio Grillo
- National Research Council, Department of Biomedicine, Institute of Biomedical Technologies - Bari Unit, 70125, Bari, Italy
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Noches V, Campos-Melo D, Droppelmann CA, Strong MJ. Epigenetics in the formation of pathological aggregates in amyotrophic lateral sclerosis. Front Mol Neurosci 2024; 17:1417961. [PMID: 39290830 PMCID: PMC11405384 DOI: 10.3389/fnmol.2024.1417961] [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: 04/15/2024] [Accepted: 08/23/2024] [Indexed: 09/19/2024] Open
Abstract
The progressive degeneration of motor neurons in amyotrophic lateral sclerosis (ALS) is accompanied by the formation of a broad array of cytoplasmic and nuclear neuronal inclusions (protein aggregates) largely containing RNA-binding proteins such as TAR DNA-binding protein 43 (TDP-43) or fused in sarcoma/translocated in liposarcoma (FUS/TLS). This process is driven by a liquid-to-solid phase separation generally from proteins in membrane-less organelles giving rise to pathological biomolecular condensates. The formation of these protein aggregates suggests a fundamental alteration in the mRNA expression or the levels of the proteins involved. Considering the role of the epigenome in gene expression, alterations in DNA methylation, histone modifications, chromatin remodeling, non-coding RNAs, and RNA modifications become highly relevant to understanding how this pathological process takes effect. In this review, we explore the evidence that links epigenetic mechanisms with the formation of protein aggregates in ALS. We propose that a greater understanding of the role of the epigenome and how this inter-relates with the formation of pathological LLPS in ALS will provide an attractive therapeutic target.
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Affiliation(s)
- Veronica Noches
- Molecular Medicine Group, Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Danae Campos-Melo
- Molecular Medicine Group, Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Cristian A Droppelmann
- Molecular Medicine Group, Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Michael J Strong
- Molecular Medicine Group, Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
- Department of Clinical Neurological Sciences, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
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5
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Vassileff N, Spiers JG, Lee JD, Woodruff TM, Ebrahimie E, Mohammadi Dehcheshmeh M, Hill AF, Cheng L. A Panel of miRNA Biomarkers Common to Serum and Brain-Derived Extracellular Vesicles Identified in Mouse Model of Amyotrophic Lateral Sclerosis. Mol Neurobiol 2024; 61:5901-5915. [PMID: 38252383 PMCID: PMC11249427 DOI: 10.1007/s12035-023-03857-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 12/05/2023] [Indexed: 01/23/2024]
Abstract
Amyotrophic lateral sclerosis (ALS) is a progressive motor neuron disease characterised by the deposition of aggregated proteins including TAR DNA-binding protein 43 (TDP-43) in vulnerable motor neurons and the brain. Extracellular vesicles (EVs) facilitate the spread of neurodegenerative diseases and can be easily accessed in the bloodstream. This study aimed to identify a panel of EV miRNAs that can capture the pathology occurring in the brain and peripheral circulation. EVs were isolated from the cortex (BDEVs) and serum (serum EVs) of 3 month-old and 6-month-old TDP-43*Q331K and TDP-43*WT mice. Following characterisation and miRNA isolation, the EVs underwent next-generation sequencing where 24 differentially packaged miRNAs were identified in the TDP-43*Q331K BDEVs and 7 in the TDP-43*Q331K serum EVs. Several miRNAs, including miR-183-5p, were linked to ALS. Additionally, miR-122-5p and miR-486b-5p were identified in both panels, demonstrating the ability of the serum EVs to capture the dysregulation occurring in the brain. This is the first study to identify miRNAs common to both the serum EVs and BDEVs in a mouse model of ALS.
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Affiliation(s)
- Natasha Vassileff
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, Australia
| | - Jereme G Spiers
- Clear Vision Research, Eccles Institute of Neuroscience, John Curtin School of Medical Research, College of Health and Medicine, The Australian National University, Acton, ACT, Australia
- School of Medicine and Psychology, College of Health and Medicine, The Australian National University, Acton, ACT, Australia
| | - John D Lee
- School of Biomedical Sciences, The University of Queensland, St. Lucia, Australia
| | - Trent M Woodruff
- School of Biomedical Sciences, The University of Queensland, St. Lucia, Australia
| | - Esmaeil Ebrahimie
- Genomics Research Platform, School of Agriculture, Biomedicine and Environment, La Trobe University, Melbourne, VIC, 3000, Australia
- School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide, SA, 5371, Australia
- School of BioSciences, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | | | - Andrew F Hill
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, Australia
- Institute for Health and Sport, Victoria University, Footscray, Victoria, Australia
| | - Lesley Cheng
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, Australia.
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6
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Dash BP, Freischmidt A, Weishaupt JH, Hermann A. An integrative miRNA-mRNA expression analysis identifies miRNA signatures associated with SOD1 and TARDBP patient-derived motor neurons. Hum Mol Genet 2024; 33:1300-1314. [PMID: 38676626 DOI: 10.1093/hmg/ddae072] [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: 01/28/2024] [Revised: 03/27/2024] [Indexed: 04/29/2024] Open
Abstract
MicroRNAs (miRNAs) are a subset of small non-coding single-stranded RNA molecules involved in the regulation of post-transcriptional gene expression of a variety of transcript targets. Therefore altered miRNA expression may result in the dysregulation of key genes and biological pathways that has been reported with the onset and progression of neurodegenerative diseases, such as Amyotrophic lateral sclerosis (ALS). ALS is marked by a progressive degeneration of motor neurons (MNs) present in the spinal cord, brain stem and motor cortex. Although the pathomechanism underlying molecular interactions of ALS remains poorly understood, alterations in RNA metabolism, including dysregulation of miRNA expression in familial as well as sporadic forms are still scarcely studied. In this study, we performed combined transcriptomic data and miRNA profiling in MN samples of the same samples of iPSC-derived MNs from SOD1- and TARDBP (TDP-43 protein)-mutant-ALS patients and healthy controls. We report a global upregulation of mature miRNAs, and suggest that differentially expressed (DE) miRNAs have a significant impact on mRNA-level in SOD1-, but not in TARDBP-linked ALS. Furthermore, in SOD1-ALS we identified dysregulated miRNAs such as miR-124-3p, miR-19b-3p and miR-218 and their potential targets previously implicated in important functional process and pathogenic pathways underlying ALS. These miRNAs may play key roles in the neuronal development and cell survival related functions in SOD1-ALS. Altogether, we provide evidence of miRNA regulated genes expression mainly in SOD1 rather than TDP43-ALS.
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Affiliation(s)
- Banaja P Dash
- Translational Neurodegeneration Section "Albrecht Kossel", Department of Neurology, University Medical Center Rostock, Gehlsheimer Str. 20, Rostock 18147, Germany
| | - Axel Freischmidt
- Department of Neurology, Ulm University, Albert-Einstein-Allee 11, Ulm 89081, Germany
| | - Jochen H Weishaupt
- Division of Neurodegeneration, Department of Neurology, Mannheim Center for Translational Neurosciences, Medical Faculty Mannheim, Heidelberg University, Theodor-Kutzer-Ufer 1-3, Mannheim 68167, Germany
| | - Andreas Hermann
- Translational Neurodegeneration Section "Albrecht Kossel", Department of Neurology, University Medical Center Rostock, Gehlsheimer Str. 20, Rostock 18147, Germany
- Center for Transdisciplinary Neurosciences Rostock, University Medical Center Rostock, Gehlsheimer Str. 20, Rostock 18147, Germany
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) Rostock/Greifswald, Gehlsheimer Str. 20, Rostock 18147, Germany
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7
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Bodai L, Borosta R, Ferencz Á, Kovács M, Zsindely N. The Role of miR-137 in Neurodegenerative Disorders. Int J Mol Sci 2024; 25:7229. [PMID: 39000336 PMCID: PMC11241563 DOI: 10.3390/ijms25137229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Revised: 06/25/2024] [Accepted: 06/27/2024] [Indexed: 07/16/2024] Open
Abstract
Neurodegenerative diseases affect an increasing part of the population of modern societies, burdening healthcare systems and causing immense suffering at the personal level. The pathogenesis of several of these disorders involves dysregulation of gene expression, which depends on several molecular processes ranging from transcription to protein stability. microRNAs (miRNAs) are short non-coding RNA molecules that modulate gene expression by suppressing the translation of partially complementary mRNAs. miR-137 is a conserved, neuronally enriched miRNA that is implicated in neurodegeneration. Here, we review the current body of knowledge about the role that miR-137 plays in five prominent neurodegenerative disorders, including Alzheimer's disease, Parkinson's disease, Huntington's disease, amyotrophic lateral sclerosis, and multiple sclerosis. The presented data indicate that, rather than having a general neuroprotective role, miR-137 modulates the pathology of distinct disorders differently.
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Affiliation(s)
- László Bodai
- Department of Biochemistry and Molecular Biology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary
| | - Roberta Borosta
- Department of Biochemistry and Molecular Biology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary
| | - Ágnes Ferencz
- Department of Biochemistry and Molecular Biology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary
| | - Mercédesz Kovács
- Department of Biochemistry and Molecular Biology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary
- Doctoral School of Biology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary
| | - Nóra Zsindely
- Department of Biochemistry and Molecular Biology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary
- Department of Genetics, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary
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Cihankaya H, Bader V, Winklhofer KF, Vorgerd M, Matschke J, Stahlke S, Theiss C, Matschke V. Elevated NLRP3 Inflammasome Activation Is Associated with Motor Neuron Degeneration in ALS. Cells 2024; 13:995. [PMID: 38920626 PMCID: PMC11202041 DOI: 10.3390/cells13120995] [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: 04/25/2024] [Revised: 06/03/2024] [Accepted: 06/05/2024] [Indexed: 06/27/2024] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease characterized by motor neuron degeneration in the central nervous system. Recent research has increasingly linked the activation of nucleotide oligomerization domain-like receptor protein 3 (NLRP3) inflammasome to ALS pathogenesis. NLRP3 activation triggers Caspase 1 (CASP 1) auto-activation, leading to the cleavage of Gasdermin D (GSDMD) and pore formation on the cellular membrane. This process facilitates cytokine secretion and ultimately results in pyroptotic cell death, highlighting the complex interplay of inflammation and neurodegeneration in ALS. This study aimed to characterize the NLRP3 inflammasome components and their colocalization with cellular markers using the wobbler mouse as an ALS animal model. Firstly, we checked the levels of miR-223-3p because of its association with NLRP3 inflammasome activity. The wobbler mice showed an increased expression of miR-223-3p in the ventral horn, spinal cord, and cerebellum tissues. Next, increased levels of NLRP3, pro-CASP 1, cleaved CASP 1 (c-CASP 1), full-length GSDMD, and cleaved GDSMD revealed NLRP3 inflammasome activation in wobbler spinal cords, but not in the cerebellum. Furthermore, we investigated the colocalization of the aforementioned proteins with neurons, microglia, and astrocyte markers in the spinal cord tissue. Evidently, the wobbler mice displayed microgliosis, astrogliosis, and motor neuron degeneration in this tissue. Additionally, we showed the upregulation of protein levels and the colocalization of NLRP3, c-CASP1, and GSDMD in neurons, as well as in microglia and astrocytes. Overall, this study demonstrated the involvement of NLRP3 inflammasome activation and pyroptotic cell death in the spinal cord tissue of wobbler mice, which could further exacerbate the motor neuron degeneration and neuroinflammation in this ALS mouse model.
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Affiliation(s)
- Hilal Cihankaya
- Department of Cytology, Institute of Anatomy, Ruhr-University Bochum, 44801 Bochum, Germany; (H.C.); (C.T.)
- International Graduate School of Neuroscience (IGSN), Ruhr-University Bochum, 44801 Bochum, Germany;
| | - Verian Bader
- Department of Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Medical Faculty, Ruhr-University Bochum, 44801 Bochum, Germany;
| | - Konstanze F. Winklhofer
- International Graduate School of Neuroscience (IGSN), Ruhr-University Bochum, 44801 Bochum, Germany;
- Department of Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Medical Faculty, Ruhr-University Bochum, 44801 Bochum, Germany;
| | - Matthias Vorgerd
- Department of Neurology, Heimer Institute for Muscle Research, University Hospital Bergmannsheil, Ruhr-University Bochum, Buerkle-de-la-Camp-Platz 1, 44789 Bochum, Germany;
| | - Johann Matschke
- Institute of Cell Biology (Cancer Research), University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany;
| | - Sarah Stahlke
- Department of Cytology, Institute of Anatomy, Ruhr-University Bochum, 44801 Bochum, Germany; (H.C.); (C.T.)
| | - Carsten Theiss
- Department of Cytology, Institute of Anatomy, Ruhr-University Bochum, 44801 Bochum, Germany; (H.C.); (C.T.)
- International Graduate School of Neuroscience (IGSN), Ruhr-University Bochum, 44801 Bochum, Germany;
| | - Veronika Matschke
- Department of Cytology, Institute of Anatomy, Ruhr-University Bochum, 44801 Bochum, Germany; (H.C.); (C.T.)
- International Graduate School of Neuroscience (IGSN), Ruhr-University Bochum, 44801 Bochum, Germany;
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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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10
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Azam HMH, Rößling RI, Geithe C, Khan MM, Dinter F, Hanack K, Prüß H, Husse B, Roggenbuck D, Schierack P, Rödiger S. MicroRNA biomarkers as next-generation diagnostic tools for neurodegenerative diseases: a comprehensive review. Front Mol Neurosci 2024; 17:1386735. [PMID: 38883980 PMCID: PMC11177777 DOI: 10.3389/fnmol.2024.1386735] [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: 02/15/2024] [Accepted: 04/12/2024] [Indexed: 06/18/2024] Open
Abstract
Neurodegenerative diseases (NDs) are characterized by abnormalities within neurons of the brain or spinal cord that gradually lose function, eventually leading to cell death. Upon examination of affected tissue, pathological changes reveal a loss of synapses, misfolded proteins, and activation of immune cells-all indicative of disease progression-before severe clinical symptoms become apparent. Early detection of NDs is crucial for potentially administering targeted medications that may delay disease advancement. Given their complex pathophysiological features and diverse clinical symptoms, there is a pressing need for sensitive and effective diagnostic methods for NDs. Biomarkers such as microRNAs (miRNAs) have been identified as potential tools for detecting these diseases. We explore the pivotal role of miRNAs in the context of NDs, focusing on Alzheimer's disease, Parkinson's disease, Multiple sclerosis, Huntington's disease, and Amyotrophic Lateral Sclerosis. The review delves into the intricate relationship between aging and NDs, highlighting structural and functional alterations in the aging brain and their implications for disease development. It elucidates how miRNAs and RNA-binding proteins are implicated in the pathogenesis of NDs and underscores the importance of investigating their expression and function in aging. Significantly, miRNAs exert substantial influence on post-translational modifications (PTMs), impacting not just the nervous system but a wide array of tissues and cell types as well. Specific miRNAs have been found to target proteins involved in ubiquitination or de-ubiquitination processes, which play a significant role in regulating protein function and stability. We discuss the link between miRNA, PTM, and NDs. Additionally, the review discusses the significance of miRNAs as biomarkers for early disease detection, offering insights into diagnostic strategies.
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Affiliation(s)
- Hafiz Muhammad Husnain Azam
- Institute of Biotechnology, Faculty of Environment and Natural Sciences, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
| | - Rosa Ilse Rößling
- German Center for Neurodegenerative Diseases (DZNE), Berlin, Germany
- Department of Neurology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Christiane Geithe
- Institute of Biotechnology, Faculty of Environment and Natural Sciences, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
- Faculty of Health Sciences, Joint Faculty of the Brandenburg University of Technology Cottbus - Senftenberg, The Brandenburg Medical School Theodor Fontane and the University of Potsdam, Berlin, Germany
| | - Muhammad Moman Khan
- Institute of Biotechnology, Faculty of Environment and Natural Sciences, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
| | - Franziska Dinter
- Institute of Biotechnology, Faculty of Environment and Natural Sciences, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
- PolyAn GmbH, Berlin, Germany
| | - Katja Hanack
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Harald Prüß
- German Center for Neurodegenerative Diseases (DZNE), Berlin, Germany
- Department of Neurology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Britta Husse
- Institute of Biotechnology, Faculty of Environment and Natural Sciences, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
| | - Dirk Roggenbuck
- Institute of Biotechnology, Faculty of Environment and Natural Sciences, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
| | - Peter Schierack
- Institute of Biotechnology, Faculty of Environment and Natural Sciences, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
| | - Stefan Rödiger
- Institute of Biotechnology, Faculty of Environment and Natural Sciences, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
- Faculty of Health Sciences, Joint Faculty of the Brandenburg University of Technology Cottbus - Senftenberg, The Brandenburg Medical School Theodor Fontane and the University of Potsdam, Berlin, Germany
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11
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Christoforidou E, Moody L, Joilin G, Simoes FA, Gordon D, Talbot K, Hafezparast M. An ALS-associated mutation dysregulates microglia-derived extracellular microRNAs in a sex-specific manner. Dis Model Mech 2024; 17:dmm050638. [PMID: 38721655 PMCID: PMC11152562 DOI: 10.1242/dmm.050638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 04/29/2024] [Indexed: 05/30/2024] Open
Abstract
Evidence suggests the presence of microglial activation and microRNA (miRNA) dysregulation in amyotrophic lateral sclerosis (ALS), the most common form of adult motor neuron disease. However, few studies have investigated whether the miRNA dysregulation originates from microglia. Furthermore, TDP-43 (encoded by TARDBP), involved in miRNA biogenesis, aggregates in tissues of ∼98% of ALS cases. Thus, this study aimed to determine whether expression of the ALS-linked TDP-43M337V mutation in a transgenic mouse model dysregulates microglia-derived miRNAs. RNA sequencing identified several dysregulated miRNAs released by transgenic microglia and a differential miRNA release by lipopolysaccharide-stimulated microglia, which was more pronounced in cells from female mice. We validated the downregulation of three candidate miRNAs, namely, miR-16-5p, miR-99a-5p and miR-191-5p, by reverse transcription quantitative polymerase chain reaction (RT-qPCR) and identified their predicted targets, which primarily include genes involved in neuronal development and function. These results suggest that altered TDP-43 function leads to changes in the miRNA population released by microglia, which may in turn be a source of the miRNA dysregulation observed in the disease. This has important implications for the role of neuroinflammation in ALS pathology and could provide potential therapeutic targets.
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Affiliation(s)
- Eleni Christoforidou
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, BN1 9QG, UK
| | - Libby Moody
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, BN1 9QG, UK
| | - Greig Joilin
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, BN1 9QG, UK
| | - Fabio A. Simoes
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, BN1 9QG, UK
| | - David Gordon
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK
| | - Kevin Talbot
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, OX1 3QU, UK
| | - Majid Hafezparast
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, BN1 9QG, UK
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12
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Pandey S, Jain A, Vagha S. Insights Into Colorectal Carcinoma: A Comprehensive Review of MicroRNA Expression Patterns. Cureus 2024; 16:e56739. [PMID: 38650823 PMCID: PMC11033970 DOI: 10.7759/cureus.56739] [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: 03/04/2024] [Accepted: 03/22/2024] [Indexed: 04/25/2024] Open
Abstract
Colorectal carcinoma (CRC) remains a significant contributor to cancer-related morbidity and mortality worldwide. MicroRNAs (miRNAs) have emerged as crucial regulators of gene expression and play critical roles in various biological processes, including carcinogenesis. This comprehensive review aims to elucidate the role of miRNAs in CRC by analyzing their expression patterns and functional implications. An extensive literature review identified dysregulated miRNAs associated with different stages of CRC progression, from initiation to metastasis. These miRNAs modulate key signaling pathways in tumor growth, invasion, and metastasis. Furthermore, we discuss the potential of miRNAs as diagnostic biomarkers and therapeutic targets in CRC management. Future research directions include elucidating the functional significance of dysregulated miRNAs using advanced experimental models and computational approaches and exploring the therapeutic potential of miRNA-based interventions in personalized treatment strategies for CRC patients. Collaboration among researchers, clinicians, and industry partners will be essential to translate these findings into clinically impactful interventions that improve patient outcomes in CRC.
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Affiliation(s)
- Shweta Pandey
- Pathology, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education and Research, Wardha, IND
| | - Akriti Jain
- Pathology, Delhi State Cancer Institute, Delhi, IND
| | - Sunita Vagha
- Pathology, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education and Research, Wardha, IND
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13
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Irwin KE, Sheth U, Wong PC, Gendron TF. Fluid biomarkers for amyotrophic lateral sclerosis: a review. Mol Neurodegener 2024; 19:9. [PMID: 38267984 PMCID: PMC10809579 DOI: 10.1186/s13024-023-00685-6] [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: 08/28/2023] [Accepted: 11/21/2023] [Indexed: 01/26/2024] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease characterized by the loss of upper and lower motor neurons. Presently, three FDA-approved drugs are available to help slow functional decline for patients with ALS, but no cure yet exists. With an average life expectancy of only two to five years after diagnosis, there is a clear need for biomarkers to improve the care of patients with ALS and to expedite ALS treatment development. Here, we provide a review of the efforts made towards identifying diagnostic, prognostic, susceptibility/risk, and response fluid biomarkers with the intent to facilitate a more rapid and accurate ALS diagnosis, to better predict prognosis, to improve clinical trial design, and to inform interpretation of clinical trial results. Over the course of 20 + years, several promising fluid biomarker candidates for ALS have emerged. These will be discussed, as will the exciting new strategies being explored for ALS biomarker discovery and development.
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Affiliation(s)
- Katherine E Irwin
- Department of Pathology, Johns Hopkins Medicine, Baltimore, MD, 21205, USA
- Department of Neuroscience, Johns Hopkins Medicine, Baltimore, MD, 21205, USA
| | - Udit Sheth
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, USA
- Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Philip C Wong
- Department of Pathology, Johns Hopkins Medicine, Baltimore, MD, 21205, USA.
- Department of Neuroscience, Johns Hopkins Medicine, Baltimore, MD, 21205, USA.
| | - Tania F Gendron
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, USA.
- Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Jacksonville, FL, 32224, USA.
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14
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Grima N, Liu S, Southwood D, Henden L, Smith A, Lee A, Rowe DB, D'Silva S, Blair IP, Williams KL. RNA sequencing of peripheral blood in amyotrophic lateral sclerosis reveals distinct molecular subtypes: Considerations for biomarker discovery. Neuropathol Appl Neurobiol 2023; 49:e12943. [PMID: 37818590 PMCID: PMC10946588 DOI: 10.1111/nan.12943] [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: 06/08/2023] [Revised: 10/02/2023] [Accepted: 10/04/2023] [Indexed: 10/12/2023]
Abstract
AIM Amyotrophic lateral sclerosis (ALS) is a heterogeneous neurodegenerative disease with limited therapeutic options. A key factor limiting the development of effective therapeutics is the lack of disease biomarkers. We sought to assess whether biomarkers for diagnosis, prognosis or cohort stratification could be identified by RNA sequencing (RNA-seq) of ALS patient peripheral blood. METHODS Whole blood RNA-seq data were generated for 96 Australian sporadic ALS (sALS) cases and 48 healthy controls (NCBI GEO accession GSE234297). Differences in sALS-control gene expression, transcript usage and predicted leukocyte proportions were assessed, with pathway analysis used to predict the activity state of biological processes. Weighted Gene Co-expression Network Analysis (WGCNA) and machine learning algorithms were applied to search for diagnostic and prognostic gene expression patterns. Unsupervised clustering analysis was employed to determine whether sALS patient subgroups could be detected. RESULTS Two hundred and forty-five differentially expressed genes were identified in sALS patients relative to controls, with enrichment of immune, metabolic and stress-related pathways. sALS patients also demonstrated switches in transcript usage across a small set of genes. We established a classification model that distinguished sALS patients from controls with an accuracy of 78% (sensitivity: 79%, specificity: 75%) using the expression of 20 genes. Clustering analysis identified four patient subgroups with gene expression signatures and immune cell proportions reflective of distinct peripheral effects. CONCLUSIONS Our findings suggest that peripheral blood RNA-seq can identify diagnostic biomarkers and distinguish molecular subtypes of sALS patients however, its prognostic value requires further investigation.
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Affiliation(s)
- Natalie Grima
- Motor Neuron Disease Research CentreMacquarie Medical SchoolFaculty of Medicine, Health and Human SciencesMacquarie UniversitySydneyNSWAustralia
| | - Sidong Liu
- Centre for Health InformaticsFaculty of Medicine, Health and Human SciencesMacquarie UniversitySydneyNSWAustralia
| | - Dean Southwood
- Motor Neuron Disease Research CentreMacquarie Medical SchoolFaculty of Medicine, Health and Human SciencesMacquarie UniversitySydneyNSWAustralia
| | - Lyndal Henden
- Motor Neuron Disease Research CentreMacquarie Medical SchoolFaculty of Medicine, Health and Human SciencesMacquarie UniversitySydneyNSWAustralia
| | - Andrew Smith
- Motor Neuron Disease Research CentreMacquarie Medical SchoolFaculty of Medicine, Health and Human SciencesMacquarie UniversitySydneyNSWAustralia
| | - Albert Lee
- Motor Neuron Disease Research CentreMacquarie Medical SchoolFaculty of Medicine, Health and Human SciencesMacquarie UniversitySydneyNSWAustralia
| | - Dominic B. Rowe
- Motor Neuron Disease Research CentreMacquarie Medical SchoolFaculty of Medicine, Health and Human SciencesMacquarie UniversitySydneyNSWAustralia
| | - Susan D'Silva
- Motor Neuron Disease Research CentreMacquarie Medical SchoolFaculty of Medicine, Health and Human SciencesMacquarie UniversitySydneyNSWAustralia
| | - Ian P. Blair
- Motor Neuron Disease Research CentreMacquarie Medical SchoolFaculty of Medicine, Health and Human SciencesMacquarie UniversitySydneyNSWAustralia
| | - Kelly L. Williams
- Motor Neuron Disease Research CentreMacquarie Medical SchoolFaculty of Medicine, Health and Human SciencesMacquarie UniversitySydneyNSWAustralia
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15
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Rizzuti M, Sali L, Melzi V, Scarcella S, Costamagna G, Ottoboni L, Quetti L, Brambilla L, Papadimitriou D, Verde F, Ratti A, Ticozzi N, Comi GP, Corti S, Gagliardi D. Genomic and transcriptomic advances in amyotrophic lateral sclerosis. Ageing Res Rev 2023; 92:102126. [PMID: 37972860 DOI: 10.1016/j.arr.2023.102126] [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: 06/01/2023] [Revised: 11/09/2023] [Accepted: 11/10/2023] [Indexed: 11/19/2023]
Abstract
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disorder and the most common motor neuron disease. ALS shows substantial clinical and molecular heterogeneity. In vitro and in vivo models coupled with multiomic techniques have provided important contributions to unraveling the pathomechanisms underlying ALS. To date, despite promising results and accumulating knowledge, an effective treatment is still lacking. Here, we provide an overview of the literature on the use of genomics, epigenomics, transcriptomics and microRNAs to deeply investigate the molecular mechanisms developing and sustaining ALS. We report the most relevant genes implicated in ALS pathogenesis, discussing the use of different high-throughput sequencing techniques and the role of epigenomic modifications. Furthermore, we present transcriptomic studies discussing the most recent advances, from microarrays to bulk and single-cell RNA sequencing. Finally, we discuss the use of microRNAs as potential biomarkers and promising tools for molecular intervention. The integration of data from multiple omic approaches may provide new insights into pathogenic pathways in ALS by shedding light on diagnostic and prognostic biomarkers, helping to stratify patients into clinically relevant subgroups, revealing novel therapeutic targets and supporting the development of new effective therapies.
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Affiliation(s)
- Mafalda Rizzuti
- Neurology Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Luca Sali
- Neurology Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Valentina Melzi
- Neurology Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Simone Scarcella
- Department of Pathophysiology and Transplantation, Dino Ferrari Center, Università degli Studi di Milano, Milan, Italy
| | - Gianluca Costamagna
- Department of Pathophysiology and Transplantation, Dino Ferrari Center, Università degli Studi di Milano, Milan, Italy
| | - Linda Ottoboni
- Department of Pathophysiology and Transplantation, Dino Ferrari Center, Università degli Studi di Milano, Milan, Italy
| | - Lorenzo Quetti
- Neurology Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Lorenzo Brambilla
- Neurology Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | | | - Federico Verde
- Department of Pathophysiology and Transplantation, Dino Ferrari Center, Università degli Studi di Milano, Milan, Italy; Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - Antonia Ratti
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy; Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Milan, Italy
| | - Nicola Ticozzi
- Department of Pathophysiology and Transplantation, Dino Ferrari Center, Università degli Studi di Milano, Milan, Italy; Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - Giacomo Pietro Comi
- Neurology Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy; Department of Pathophysiology and Transplantation, Dino Ferrari Center, Università degli Studi di Milano, Milan, Italy; Neuromuscular and Rare Diseases Unit, Department of Neuroscience, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Stefania Corti
- Neurology Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy; Department of Pathophysiology and Transplantation, Dino Ferrari Center, Università degli Studi di Milano, Milan, Italy.
| | - Delia Gagliardi
- Department of Pathophysiology and Transplantation, Dino Ferrari Center, Università degli Studi di Milano, Milan, Italy.
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16
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Zhu Y, Li M, He Z, Pang X, Du R, Yu W, Zhang J, Bai J, Wang J, Huang X. Evaluating the causal association between microRNAs and amyotrophic lateral sclerosis. Neurol Sci 2023; 44:3567-3575. [PMID: 37261630 DOI: 10.1007/s10072-023-06860-3] [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: 03/25/2023] [Accepted: 05/15/2023] [Indexed: 06/02/2023]
Abstract
BACKGROUND Currently, miRNAs are involved in the development of amyotrophic lateral sclerosis (ALS), and identifying circulating miRNAs that are causally associated with ALS risk as biomarkers is imperative. METHODS We performed a two-sample Mendelian randomization study to evaluate the causal relationship between miRNAs and ALS. Our analysis was conducted using summary statistics from miRNA expression quantitative loci (eQTL) data of the Framingham Heart Study and ALS genome-wide association studies data. Another independent miRNA data was used to further validate. RESULTS We identified eight unique miRNAs that were causally associated with ALS risk. Using expression data of miRNAs from an independent study, we validated three high-confidence miRNAs, namely hsa-miR-27b-3p, hsa-miR-139-5p, and hsa-miR-152-3p, which might have a potential causal effect on ALS risk. CONCLUSION We suggested that higher levels of hsa-miR-27b-3p and hsa-miR-139-5p had protective effects on ALS, whereas higher levels of hsa-miR-152-3p might act as a risk factor for ALS. The analytical framework presented in this study helps to understand the role of miRNAs in the development of ALS and to identify the biomarkers for ALS risk.
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Affiliation(s)
- Yahui Zhu
- Medical School of Chinese PLA, Beijing, China
- Department of Neurology, the First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Mao Li
- Department of Neurology, the First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Zhengqing He
- Medical School of Chinese PLA, Beijing, China
- Department of Neurology, the First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Xinyuan Pang
- Department of Neurology, the First Medical Center, Chinese PLA General Hospital, Beijing, China
- College of Medicine, Nankai University, Tianjin, China
| | - Rongrong Du
- Department of Neurology, the First Medical Center, Chinese PLA General Hospital, Beijing, China
- College of Medicine, Nankai University, Tianjin, China
| | - Wenxiu Yu
- Medical School of Chinese PLA, Beijing, China
- Department of Neurology, the First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Jinghong Zhang
- Medical School of Chinese PLA, Beijing, China
- Department of Neurology, the First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Jiongming Bai
- Department of Neurology, the First Medical Center, Chinese PLA General Hospital, Beijing, China
- College of Medicine, Nankai University, Tianjin, China
| | - Jiao Wang
- Medical School of Chinese PLA, Beijing, China
- Department of Neurology, the First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Xusheng Huang
- Department of Neurology, the First Medical Center, Chinese PLA General Hospital, Beijing, China.
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17
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Saikia BJ, Bhardwaj J, Paul S, Sharma S, Neog A, Paul SR, Binukumar BK. Understanding the Roles and Regulation of Mitochondrial microRNAs (MitomiRs) in Neurodegenerative Diseases: Current Status and Advances. Mech Ageing Dev 2023:111838. [PMID: 37329989 DOI: 10.1016/j.mad.2023.111838] [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: 12/27/2022] [Revised: 06/13/2023] [Accepted: 06/13/2023] [Indexed: 06/19/2023]
Abstract
MicroRNAs (miRNA) are a class of small non-coding RNA, roughly 21 - 22 nucleotides in length, which are master gene regulators. These miRNAs bind to the mRNA's 3' - untranslated region and regulate post-transcriptional gene regulation, thereby influencing various physiological and cellular processes. Another class of miRNAs known as mitochondrial miRNA (MitomiRs) has been found to either originate from the mitochondrial genome or be translocated directly into the mitochondria. Although the role of nuclear DNA encoded miRNA in the progression of various neurological diseases such as Parkinson's disease, Alzheimer's disease, Huntington's disease, etc. is well known, accumulating evidence suggests the possible role of deregulated mitomiRs in the progression of various neurodegenerative diseases with unknown mechanism. We have attempted to outline the current state of mitomiRs role in controlling mitochondrial gene expression and function through this review, paying particular attention to their contribution to neurological processes, their etiology, and their potential therapeutic use.
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Affiliation(s)
- Bhaskar Jyoti Saikia
- CSIR Institute of Genomics and Integrative Biology, Mall Road, New Delhi - 110007; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Juhi Bhardwaj
- CSIR Institute of Genomics and Integrative Biology, Mall Road, New Delhi - 110007; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Sangita Paul
- CSIR Institute of Genomics and Integrative Biology, Mall Road, New Delhi - 110007; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Srishti Sharma
- CSIR Institute of Genomics and Integrative Biology, Mall Road, New Delhi - 110007; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Anindita Neog
- CSIR Institute of Genomics and Integrative Biology, Mall Road, New Delhi - 110007
| | - Swaraj Ranjan Paul
- CSIR Institute of Genomics and Integrative Biology, Mall Road, New Delhi - 110007
| | - B K Binukumar
- CSIR Institute of Genomics and Integrative Biology, Mall Road, New Delhi - 110007; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India.
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18
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Liu Y, Ding M, Pan S, Zhou R, Yao J, Fu R, Yu H, Lu Z. MicroRNA-23a-3p is upregulated in plasma exosomes of bulbar-onset ALS patients and targets ERBB4. Neuroscience 2023:S0306-4522(23)00250-6. [PMID: 37290686 DOI: 10.1016/j.neuroscience.2023.05.030] [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: 01/09/2023] [Revised: 05/24/2023] [Accepted: 05/27/2023] [Indexed: 06/10/2023]
Abstract
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease related to the progressive death of motor neurons. Understanding the pathogenesis of ALS continues to provide considerable challenges. Bulbar-onset ALS involves faster functional loss and shorter survival time than spinal cord-onset ALS. However, debate is ongoing regarding typical plasma miRNA changes in ALS patients with bulbar onset. Exosomal miRNAs have not yet been described as a tool for bulbar-onset ALS diagnosis or prognosis prediction. In this study, candidate exosomal miRNAs were identified by small RNA sequencing using samples from patients with bulbar-onset ALS and healthy controls. Potential pathogenic mechanisms were identified through enrichment analysis of target genes for differential miRNAs. Expression of miR-16-5p, miR-23a-3p, miR-22-3p, and miR-93-5p was significantly up-regulated in plasma exosomes from bulbar-onset ALS patients compared with healthy control subjects. Among them, miR-16-5p and miR-23a-3p were significantly lower in spinal-onset ALS patients than those with bulbar-onset. Furthermore, up-regulation of miR-23a-3p in motor neuron-like NSC-34 cells promoted apoptosis and inhibited cell viability. This miRNA was found to directly target ERBB4 and regulate the AKT/GSK3β pathway. Collectively, the above miRNAs and their targets are related to the development of bulbar-onset ALS. Our research indicates that miR-23a-3p might have an effect on motor neuron loss observed in bulbar-onset ALS and may be a novel target for the therapy of ALS in the future.
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Affiliation(s)
- Yue Liu
- Department of Neurology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Man Ding
- Department of Neurology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Sijia Pan
- Department of Neurology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Rumeng Zhou
- Department of Neurology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Jiajia Yao
- Department of Neurology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Rong Fu
- Department of Neurology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Hang Yu
- Department of Neurology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Zuneng Lu
- Department of Neurology, Renmin Hospital of Wuhan University, Wuhan, China.
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Feng H, Hu P, Chen Y, Sun H, Cai J, He X, Cao Q, Yin M, Zhang Y, Li Q, Gao J, Marshall C, Sheng C, Shi J, Xiao M. Decreased miR-451a in cerebrospinal fluid, a marker for both cognitive impairment and depressive symptoms in Alzheimer's disease. Theranostics 2023; 13:3021-3040. [PMID: 37284450 PMCID: PMC10240826 DOI: 10.7150/thno.81826] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 04/06/2023] [Indexed: 06/08/2023] Open
Abstract
Background: Alzheimer's disease (AD) patients are often accompanied by depressive symptoms, but its underlying mechanism remains unclear. The present study aimed to explore the potential role of microRNAs in the comorbidity of AD and depression. Methods: The miRNAs associated with AD and depression were screened from databases and literature and then confirmed in the cerebrospinal fluid (CSF) of AD patients and different ages of transgenic APP/PS1 mice. AAV9-miR-451a-GFP was injected into the medial prefrontal cortex (mPFC) of APP/PS1 mice at seven months, and four weeks later, a series of behavioral and pathological analyses were performed. Results: AD patients had low CSF levels of miR-451a, which was positively correlated with the cognitive assessment score, but negatively with their depression scale. In the mPFC of APP/PS1 transgenic mice, the miR-451a levels also decreased significantly in the neurons and microglia. Specific virus vector-induced overexpression of miR-451a in the mPFC of APP/PS1 mice ameliorated AD-related behavior deficits and pathologies, including long-term memory defects, depression-like phenotype, β-amyloid load, and neuroinflammation. Mechanistically, miR-451a decreased the expression of neuronal β-secretase 1 of neurons through inhibiting Toll-like receptor 4/Inhibitor of kappa B Kinase β/ Nuclear factor kappa-B signaling pathway and microglial activation by inhibiting activation of NOD-like receptor protein 3, respectively. Conclusion: This finding highlighted miR-451a as a potential target for diagnosing and treating AD, especially for those with coexisting symptoms of depression.
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Affiliation(s)
- Hu Feng
- Jiangsu Key Laboratory of Neurodegeneration, Nanjing Medical University, Nanjing, 211166, China
- Brain Institute, Nanjing Brain Hospital, Nanjing Medical University, Nanjing, 210029, China
| | - Panpan Hu
- Jiangsu Key Laboratory of Neurodegeneration, Nanjing Medical University, Nanjing, 211166, China
- Department of Anesthetic Pharmacology, Faculty of Anesthesiology, Naval Medical University, Shanghai, 200082, China
| | - Yan Chen
- Jiangsu Key Laboratory of Neurodegeneration, Nanjing Medical University, Nanjing, 211166, China
- Brain Institute, Nanjing Brain Hospital, Nanjing Medical University, Nanjing, 210029, China
| | - Huaiqing Sun
- Jiangsu Key Laboratory of Neurodegeneration, Nanjing Medical University, Nanjing, 211166, China
- Department of Neurology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Jiachen Cai
- Jiangsu Key Laboratory of Neurodegeneration, Nanjing Medical University, Nanjing, 211166, China
- Brain Institute, Nanjing Brain Hospital, Nanjing Medical University, Nanjing, 210029, China
| | - Xiaoxin He
- Jiangsu Key Laboratory of Neurodegeneration, Nanjing Medical University, Nanjing, 211166, China
- Brain Institute, Nanjing Brain Hospital, Nanjing Medical University, Nanjing, 210029, China
| | - Qiuchen Cao
- Jiangsu Key Laboratory of Neurodegeneration, Nanjing Medical University, Nanjing, 211166, China
| | - Mengmei Yin
- Jiangsu Key Laboratory of Neurodegeneration, Nanjing Medical University, Nanjing, 211166, China
- Department of Neurology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Yanli Zhang
- Jiangsu Key Laboratory of Neurodegeneration, Nanjing Medical University, Nanjing, 211166, China
- Brain Institute, Nanjing Brain Hospital, Nanjing Medical University, Nanjing, 210029, China
| | - Qian Li
- Jiangsu Key Laboratory of Neurodegeneration, Nanjing Medical University, Nanjing, 211166, China
- Brain Institute, Nanjing Brain Hospital, Nanjing Medical University, Nanjing, 210029, China
| | - Junying Gao
- Jiangsu Key Laboratory of Neurodegeneration, Nanjing Medical University, Nanjing, 211166, China
- Brain Institute, Nanjing Brain Hospital, Nanjing Medical University, Nanjing, 210029, China
| | | | - Chengyu Sheng
- Jiangsu Key Laboratory of Neurodegeneration, Nanjing Medical University, Nanjing, 211166, China
- Brain Institute, Nanjing Brain Hospital, Nanjing Medical University, Nanjing, 210029, China
| | - Jingping Shi
- Brain Institute, Nanjing Brain Hospital, Nanjing Medical University, Nanjing, 210029, China
- Department of Neurology, the Affiliated Nanjing Brain Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Ming Xiao
- Jiangsu Key Laboratory of Neurodegeneration, Nanjing Medical University, Nanjing, 211166, China
- Brain Institute, Nanjing Brain Hospital, Nanjing Medical University, Nanjing, 210029, China
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20
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Brown JS. Comparison of Oncogenes, Tumor Suppressors, and MicroRNAs Between Schizophrenia and Glioma: The Balance of Power. Neurosci Biobehav Rev 2023; 151:105206. [PMID: 37178944 DOI: 10.1016/j.neubiorev.2023.105206] [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: 11/29/2022] [Revised: 04/25/2023] [Accepted: 04/30/2023] [Indexed: 05/15/2023]
Abstract
The risk of cancer in schizophrenia has been controversial. Confounders of the issue are cigarette smoking in schizophrenia, and antiproliferative effects of antipsychotic medications. The author has previously suggested comparison of a specific cancer like glioma to schizophrenia might help determine a more accurate relationship between cancer and schizophrenia. To accomplish this goal, the author performed three comparisons of data; the first a comparison of conventional tumor suppressors and oncogenes between schizophrenia and cancer including glioma. This comparison determined schizophrenia has both tumor-suppressive and tumor-promoting characteristics. A second, larger comparison between brain-expressed microRNAs in schizophrenia with their expression in glioma was then performed. This identified a core carcinogenic group of miRNAs in schizophrenia offset by a larger group of tumor-suppressive miRNAs. This proposed "balance of power" between oncogenes and tumor suppressors could cause neuroinflammation. This was assessed by a third comparison between schizophrenia, glioma and inflammation in asbestos-related lung cancer and mesothelioma (ALRCM). This revealed that schizophrenia shares more oncogenic similarity to ALRCM than glioma.
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Redenšek Trampuž S, Vogrinc D, Goričar K, Dolžan V. Shared miRNA landscapes of COVID-19 and neurodegeneration confirm neuroinflammation as an important overlapping feature. Front Mol Neurosci 2023; 16:1123955. [PMID: 37008787 PMCID: PMC10064073 DOI: 10.3389/fnmol.2023.1123955] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 02/20/2023] [Indexed: 03/19/2023] Open
Abstract
Introduction Development and worsening of most common neurodegenerative diseases, such as Alzheimer's disease, Parkinson's disease, and multiple sclerosis, have been associated with COVID-19 However, the mechanisms associated with neurological symptoms in COVID-19 patients and neurodegenerative sequelae are not clear. The interplay between gene expression and metabolite production in CNS is driven by miRNAs. These small non-coding molecules are dysregulated in most common neurodegenerative diseases and COVID-19. Methods We have performed a thorough literature screening and database mining to search for shared miRNA landscapes of SARS-CoV-2 infection and neurodegeneration. Differentially expressed miRNAs in COVID-19 patients were searched using PubMed, while differentially expressed miRNAs in patients with five most common neurodegenerative diseases (Alzheimer's disease, Parkinson's disease, Huntington's disease, amyotrophic lateral sclerosis, and multiple sclerosis) were searched using the Human microRNA Disease Database. Target genes of the overlapping miRNAs, identified with the miRTarBase, were used for the pathway enrichment analysis performed with Kyoto Encyclopedia of Genes and Genomes and Reactome. Results In total, 98 common miRNAs were found. Additionally, two of them (hsa-miR-34a and hsa-miR-132) were highlighted as promising biomarkers of neurodegeneration, as they are dysregulated in all five most common neurodegenerative diseases and COVID-19. Additionally, hsa-miR-155 was upregulated in four COVID-19 studies and found to be dysregulated in neurodegeneration processes as well. Screening for miRNA targets identified 746 unique genes with strong evidence for interaction. Target enrichment analysis highlighted most significant KEGG and Reactome pathways being involved in signaling, cancer, transcription and infection. However, the more specific identified pathways confirmed neuroinflammation as being the most important shared feature. Discussion Our pathway based approach has identified overlapping miRNAs in COVID-19 and neurodegenerative diseases that may have a valuable potential for neurodegeneration prediction in COVID-19 patients. Additionally, identified miRNAs can be further explored as potential drug targets or agents to modify signaling in shared pathways. Graphical AbstractShared miRNA molecules among the five investigated neurodegenerative diseases and COVID-19 were identified. The two overlapping miRNAs, hsa-miR-34a and has-miR-132, present potential biomarkers of neurodegenerative sequelae after COVID-19. Furthermore, 98 common miRNAs between all five neurodegenerative diseases together and COVID-19 were identified. A KEGG and Reactome pathway enrichment analyses was performed on the list of shared miRNA target genes and finally top 20 pathways were evaluated for their potential for identification of new drug targets. A common feature of identified overlapping miRNAs and pathways is neuroinflammation. AD, Alzheimer's disease; ALS, amyotrophic lateral sclerosis; COVID-19, coronavirus disease 2019; HD, Huntington's disease; KEGG, Kyoto Encyclopedia of Genes and Genomes; MS, multiple sclerosis; PD, Parkinson's disease.
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Affiliation(s)
| | | | | | - Vita Dolžan
- Pharmacogenetics Laboratory, Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
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22
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Hur J, Paez-Colasante X, Figueroa-Romero C, Lo TW, Barmada SJ, Paulsen MT, Ljungman M, Alakwaa FM, Savelieff MG, Goutman SA, Feldman EL. miRNA analysis reveals novel dysregulated pathways in amyotrophic lateral sclerosis. Hum Mol Genet 2023; 32:934-947. [PMID: 36219176 PMCID: PMC9990999 DOI: 10.1093/hmg/ddac250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 10/01/2022] [Accepted: 10/03/2022] [Indexed: 11/14/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease. Its complex pathogenesis and phenotypic heterogeneity hinder therapeutic development and early diagnosis. Altered RNA metabolism is a recurrent pathophysiologic theme, including distinct microRNA (miRNA) profiles in ALS tissues. We profiled miRNAs in accessible biosamples, including skin fibroblasts and whole blood and compared them in age- and sex-matched healthy controls versus ALS participants with and without repeat expansions to chromosome 9 open reading frame 72 (C9orf72; C9-ALS and nonC9-ALS), the most frequent ALS mutation. We identified unique and shared profiles of differential miRNA (DmiRNA) levels in each C9-ALS and nonC9-ALS tissues versus controls. Fibroblast DmiRNAs were validated by quantitative real-time PCR and their target mRNAs by 5-bromouridine and 5-bromouridine-chase sequencing. We also performed pathway analysis to infer biological meaning, revealing anticipated, tissue-specific pathways and pathways previously linked to ALS, as well as novel pathways that could inform future research directions. Overall, we report a comprehensive study of a miRNA profile dataset from C9-ALS and nonC9-ALS participants across two accessible biosamples, providing evidence of dysregulated miRNAs in ALS and possible targets of interest. Distinct miRNA patterns in accessible tissues may also be leveraged to distinguish ALS participants from healthy controls for earlier diagnosis. Future directions may look at potential correlations of miRNA profiles with clinical parameters.
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Affiliation(s)
- Junguk Hur
- Department of Biomedical Sciences, University of North Dakota, Grand Forks, ND 58202, USA
| | | | - Claudia Figueroa-Romero
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA
- NeuroNetwork for Emerging Therapies, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ting-wen Lo
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sami J Barmada
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Michelle T Paulsen
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Mats Ljungman
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Internal Medicine, Division of Nephrology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Fadhl M Alakwaa
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Masha G Savelieff
- NeuroNetwork for Emerging Therapies, University of Michigan, Ann Arbor, MI 48109, USA
| | - Stephen A Goutman
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA
- NeuroNetwork for Emerging Therapies, University of Michigan, Ann Arbor, MI 48109, USA
| | - Eva L Feldman
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA
- NeuroNetwork for Emerging Therapies, University of Michigan, Ann Arbor, MI 48109, USA
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23
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Founta K, Dafou D, Kanata E, Sklaviadis T, Zanos TP, Gounaris A, Xanthopoulos K. Gene targeting in amyotrophic lateral sclerosis using causality-based feature selection and machine learning. Mol Med 2023; 29:12. [PMID: 36694130 PMCID: PMC9872307 DOI: 10.1186/s10020-023-00603-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 01/06/2023] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Amyotrophic lateral sclerosis (ALS) is a rare progressive neurodegenerative disease that affects upper and lower motor neurons. As the molecular basis of the disease is still elusive, the development of high-throughput sequencing technologies, combined with data mining techniques and machine learning methods, could provide remarkable results in identifying pathogenetic mechanisms. High dimensionality is a major problem when applying machine learning techniques in biomedical data analysis, since a huge number of features is available for a limited number of samples. The aim of this study was to develop a methodology for training interpretable machine learning models in the classification of ALS and ALS-subtypes samples, using gene expression datasets. METHODS We performed dimensionality reduction in gene expression data using a semi-automated preprocessing systematic gene selection procedure using Statistically Equivalent Signature (SES), a causality-based feature selection algorithm, followed by Boosted Regression Trees (XGBoost) and Random Forest to train the machine learning classifiers. The SHapley Additive exPlanations (SHAP values) were used for interpretation of the machine learning classifiers. The methodology was developed and tested using two distinct publicly available ALS RNA-seq datasets. We evaluated the performance of SES as a dimensionality reduction method against: (a) Least Absolute Shrinkage and Selection Operator (LASSO), and (b) Local Outlier Factor (LOF). RESULTS The proposed methodology achieved 85.18% accuracy for the classification of cerebellum or frontal cortex samples as C9orf72-related familial ALS, sporadic ALS or healthy samples. Importantly, the genes identified as the most determinative have also been reported as disease-associated in ALS literature. When tested in the evaluation dataset, the methodology achieved 88.89% accuracy for the classification of sporadic ALS motor neuron samples. When LASSO was used as feature selection method instead of SES, the accuracy of the machine learning classifiers ranged from 74.07 to 96.30%, depending on tissue assessed, while LOF underperformed significantly (77.78% accuracy for the classification of pooled cerebellum and frontal cortex samples). CONCLUSIONS Using SES, we addressed the challenge of high dimensionality in gene expression data analysis, and we trained accurate machine learning ALS classifiers, specific for the gene expression patterns of different disease subtypes and tissue samples, while identifying disease-associated genes.
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Affiliation(s)
- Kyriaki Founta
- Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Northwell Health, Hempstead, NY, 11549, USA
- Institute of Molecular Medicine, Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY, 11030, USA
- Laboratory of Pharmacology, School of Pharmacy, School of Health Sciences, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Dimitra Dafou
- Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Eirini Kanata
- Laboratory of Pharmacology, School of Pharmacy, School of Health Sciences, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Theodoros Sklaviadis
- Laboratory of Pharmacology, School of Pharmacy, School of Health Sciences, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Theodoros P Zanos
- Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Northwell Health, Hempstead, NY, 11549, USA
- Feinstein Institutes for Medical Research, Institute of Health Systems Science, Northwell Health, Manhasset, NY, 11030, USA
- Institute of Bioelectronic Medicine, Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY, 11030, USA
| | - Anastasios Gounaris
- School of Informatics, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Konstantinos Xanthopoulos
- Laboratory of Pharmacology, School of Pharmacy, School of Health Sciences, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece.
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, 57001, Thermi, Greece.
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24
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Fenoglio C, Serpente M, Visconte C, Arcaro M, Sorrentino F, D’Anca M, Arighi A, Rotondo E, Vimercati R, Rossi G, Scarpini E, Galimberti D. Circulating Non-Coding RNA Levels Are Altered in Autosomal Dominant Frontotemporal Dementia. Int J Mol Sci 2022; 23:14723. [PMID: 36499048 PMCID: PMC9737170 DOI: 10.3390/ijms232314723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/14/2022] [Accepted: 11/21/2022] [Indexed: 11/27/2022] Open
Abstract
Frontotemporal Dementia (FTD) represents a highly heritable neurodegenerative disorder. Most of the heritability is caused by autosomal dominant mutations in the Microtubule-Associated Protein Tau (MAPT), Progranulin (GRN), and the pathologic exanucleotide expansion of C9ORF72 genes. At the pathological level, either the tau or the TAR DNA-binding protein (TDP-43) account for almost all cases of FTD. Pathogenic mechanisms are just arising, and the emerging role of non-coding RNAs (ncRNAs), such as microRNAs (miRNA) and long non-coding RNAs (lncRNAs), have become increasingly evident. Using specific arrays, an exploratory analysis testing the expression levels of 84 miRNAs and 84 lncRNAs has been performed in a population consisting of 24 genetic FTD patients (eight GRN, eight C9ORF72, and eight MAPT mutation carriers), eight sporadic FTD patients, and eight healthy controls. The results showed a generalized ncRNA downregulation in patients carrying GRN and C9ORF72 when compared with the controls, with statistically significant results for the following miRNAs: miR-155-5p (Fold Change FC: 0.45, p = 0.037 FDR = 0.52), miR-15a-5p (FC: 0.13, p = 0.027, FDR = 1), miR-222-3p (FC: 0.13, p = 0.027, FDR = 0.778), miR-140-3p (FC: 0.096, p = 0.034, FRD = 0.593), miR-106b-5p (FC: 0.13, p = 0.02, FDR = 0.584) and an upregulation solely for miR-124-3p (FC: 2.1, p = 0.01, FDR = 0.893). Conversely, MAPT mutation carriers showed a generalized robust upregulation in several ncRNAs, specifically for miR-222-3p (FC: 22.3, p = 7 × 10-6, FDR = 0.117), miR-15a-5p (FC: 30.2, p = 0.008, FDR = 0.145), miR-27a-3p (FC: 27.8, p = 6 × 10-6, FDR = 0.0005), miR-223-3p (FC: 18.9, p = 0.005, FDR = 0.117), and miR-16-5p (FC: 10.9, p = 5.26 × 10-5, FDR = 0.001). These results suggest a clear, distinctive pattern of dysregulation among ncRNAs and specific enrichment gene pathways between mutations associated with the TDP-43 and tau pathologies. Nevertheless, these preliminary results need to be confirmed in a larger independent cohort.
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Affiliation(s)
- Chiara Fenoglio
- Department of Pathophysiology and Transplantation, Dino Ferrari Center, University of Milan, 20122 Milan, Italy
| | - Maria Serpente
- Fondazione, IRCCS Ca’ Granda, Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Caterina Visconte
- Department of Biomedical, Surgical and Dental Sciences, Dino Ferrari Center, University of Milan, 20122 Milan, Italy
| | - Marina Arcaro
- Fondazione, IRCCS Ca’ Granda, Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Federica Sorrentino
- Department of Biomedical, Surgical and Dental Sciences, Dino Ferrari Center, University of Milan, 20122 Milan, Italy
| | - Marianna D’Anca
- Fondazione, IRCCS Ca’ Granda, Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Andrea Arighi
- Fondazione, IRCCS Ca’ Granda, Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Emanuela Rotondo
- Fondazione, IRCCS Ca’ Granda, Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Roberto Vimercati
- Fondazione, IRCCS Ca’ Granda, Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Giacomina Rossi
- Unit of Neurology V—Neuropathology, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133 Milan, Italy
| | - Elio Scarpini
- Fondazione, IRCCS Ca’ Granda, Ospedale Maggiore Policlinico, 20122 Milan, Italy
- Department of Biomedical, Surgical and Dental Sciences, Dino Ferrari Center, University of Milan, 20122 Milan, Italy
| | - Daniela Galimberti
- Fondazione, IRCCS Ca’ Granda, Ospedale Maggiore Policlinico, 20122 Milan, Italy
- Department of Biomedical, Surgical and Dental Sciences, Dino Ferrari Center, University of Milan, 20122 Milan, Italy
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25
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Zhang J, Chen Z, Chen H, Deng Y, Li S, Jin L. Recent Advances in the Roles of MicroRNA and MicroRNA-Based Diagnosis in Neurodegenerative Diseases. BIOSENSORS 2022; 12:1074. [PMID: 36551041 PMCID: PMC9776063 DOI: 10.3390/bios12121074] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 11/17/2022] [Accepted: 11/23/2022] [Indexed: 06/17/2023]
Abstract
Neurodegenerative diseases manifest as progressive loss of neuronal structures and their myelin sheaths and lead to substantial morbidity and mortality, especially in the elderly. Despite extensive research, there are few effective treatment options for the diseases. MicroRNAs have been shown to be involved in the developmental processes of the central nervous system. Mounting evidence suggest they play an important role in the development of neurodegenerative diseases such as Alzheimer's disease and Parkinson's disease. However, there are few reviews regarding the roles of miRNAs in neurodegenerative diseases. This review summarizes the recent developments in the roles of microRNAs in neurodegenerative diseases and presents the application of microRNA-based methods in the early diagnosis of these diseases.
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26
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Banack SA, Dunlop RA, Stommel EW, Mehta P, Cox PA. miRNA extracted from extracellular vesicles is a robust biomarker of amyotrophic lateral sclerosis. J Neurol Sci 2022; 442:120396. [PMID: 36081303 DOI: 10.1016/j.jns.2022.120396] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 08/18/2022] [Accepted: 08/24/2022] [Indexed: 10/31/2022]
Abstract
BACKGROUND AND OBJECTIVES We examined miRNA biomarkers for ALS extracted from extracellular vesicles in blood samples using a large and diverse patient and control population. Different blood collection and storage protocols by different investigators could impact repeatability of miRNA analysis. We tested the hypotheses that miRNA extracted from extracellular vesicles using immunoaffinity purification techniques are robust and repeatable across investigators, laboratories and in a broad ALS population. METHODS De-identified patient blood plasma samples obtained from the U.S. National ALS Biorepository were compared with plasma from non-ALS controls. Extracellular vesicles were extracted and isolated using L1CAM immunoaffinity purification. Total RNA was extracted, and miRNA quantified using qPCR following careful quality control measures. Gene fold expressions of eight miRNAs were compared using a Mann-Whitney two-tailed test. RESULTS One hundred blinded, blood plasma samples were analyzed. Thirty-five men and 15 women with ALS were compared with controls consisting of 30 men and 20 women. None of the ALS patient cohort reported family members with ALS suggesting sporadic ALS. Five of the eight biomarkers previously published were found to significantly discriminate ALS patient samples from control samples. DISCUSSION The methods used in this study provide a repeatable measure of miRNA biomarkers that statistically differentiate ALS patient samples from control samples. The broad inclusion criteria for both the ALS patient cohort and controls along with the collection of blood samples by different investigators suggest that these methods are robust and represent good candidates for further research and development aimed at clinical application.
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Affiliation(s)
| | | | - Elijah W Stommel
- Department of Neurology, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
| | - Paul Mehta
- Centers for Disease Control and Prevention/Agency for Toxic Substances and Disease Registry, National ALS Registry (CDC/ATSDR), Atlanta, GA, USA
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López-Cepeda L, Castro JD, Aristizábal-Pachón AF, González-Giraldo Y, Pinzón A, Puentes-Rozo PJ, González J. Modulation of Small RNA Signatures by Astrocytes on Early Neurodegeneration Stages; Implications for Biomarker Discovery. Life (Basel) 2022; 12:1720. [PMID: 36362875 PMCID: PMC9696502 DOI: 10.3390/life12111720] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/01/2022] [Accepted: 10/12/2022] [Indexed: 04/04/2024] Open
Abstract
Diagnosis of neurodegenerative disease (NDD) is complex, therefore simpler, less invasive, more accurate biomarkers are needed. small non-coding RNA (sncRNA) dysregulates in NDDs and sncRNA signatures have been explored for the diagnosis of NDDs, however, the performance of previous biomarkers is still better. Astrocyte dysfunction promotes neurodegeneration and thus derived scnRNA signatures could provide a more precise way to identify of changes related to NDD course and pathogenesis, and it could be useful for the dissection of mechanistic insights operating in NDD. Often sncRNA are transported outside the cell by the action of secreted particles such as extracellular vesicles (EV), which protect sncRNA from degradation. Furthermore, EV associated sncRNA can cross the BBB to be found in easier to obtain peripheral samples, EVs also inherit cell-specific surface markers that can be used for the identification of Astrocyte Derived Extracellular Vesicles (ADEVs) in a peripheral sample. By the study of the sncRNA transported in ADEVs it is possible to identify astrocyte specific sncRNA signatures that could show astrocyte dysfunction in a more simpler manner than previous methods. However, sncRNA signatures in ADEV are not a copy of intracellular transcriptome and methodological aspects such as the yield of sncRNA produced in ADEV or the variable amount of ADEV captured after separation protocols must be considered. Here we review the role as signaling molecules of ADEV derived sncRNA dysregulated in conditions associated with risk of neurodegeneration, providing an explanation of why to choose ADEV for the identification of astrocyte-specific transcriptome. Finally, we discuss possible limitations of this approach and the need to improve the detection limits of sncRNA for the use of ADEV derived sncRNA signatures.
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Affiliation(s)
- Leonardo López-Cepeda
- Departamento de Nutrición y Bioquímica, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá 110231, Colombia
| | - Juan David Castro
- Departamento de Nutrición y Bioquímica, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá 110231, Colombia
| | | | - Yeimy González-Giraldo
- Departamento de Nutrición y Bioquímica, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá 110231, Colombia
| | - Andrés Pinzón
- Laboratorio de Bioinformática y Biología de Sistemas, Universidad Nacional de Colombia, Bogotá 111321, Colombia
| | - Pedro J. Puentes-Rozo
- Grupo de Neurociencias del Caribe, Unidad de Neurociencias Cognitivas, Universidad Simón Bolívar, Barranquilla 080002, Colombia
- Grupo de Neurociencias del Caribe, Universidad del Atlántico, Barranquilla 080007, Colombia
| | - Janneth González
- Departamento de Nutrición y Bioquímica, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá 110231, Colombia
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Epigenetic Changes in Prion and Prion-like Neurodegenerative Diseases: Recent Advances, Potential as Biomarkers, and Future Perspectives. Int J Mol Sci 2022; 23:ijms232012609. [PMID: 36293477 PMCID: PMC9604074 DOI: 10.3390/ijms232012609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 10/09/2022] [Accepted: 10/18/2022] [Indexed: 12/01/2022] Open
Abstract
Prion diseases are transmissible spongiform encephalopathies (TSEs) caused by a conformational conversion of the native cellular prion protein (PrPC) to an abnormal, infectious isoform called PrPSc. Amyotrophic lateral sclerosis, Alzheimer’s, Parkinson’s, and Huntington’s diseases are also known as prion-like diseases because they share common features with prion diseases, including protein misfolding and aggregation, as well as the spread of these misfolded proteins into different brain regions. Increasing evidence proposes the involvement of epigenetic mechanisms, namely DNA methylation, post-translational modifications of histones, and microRNA-mediated post-transcriptional gene regulation in the pathogenesis of prion-like diseases. Little is known about the role of epigenetic modifications in prion diseases, but recent findings also point to a potential regulatory role of epigenetic mechanisms in the pathology of these diseases. This review highlights recent findings on epigenetic modifications in TSEs and prion-like diseases and discusses the potential role of such mechanisms in disease pathology and their use as potential biomarkers.
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Saghazadeh A, Rezaei N. MicroRNA expression profiles of peripheral blood and mononuclear cells in myasthenia gravis: A systematic review. Int Immunopharmacol 2022; 112:109205. [PMID: 36087508 DOI: 10.1016/j.intimp.2022.109205] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 07/21/2022] [Accepted: 08/26/2022] [Indexed: 11/05/2022]
Abstract
BACKGROUND Studies have described the role of microRNAs (miRNAs) in thymic function, along with directly observing the altered expression of miRNAs in thymuses of myasthenia gravis (MG) patients; so, miRNAs became a core component in the pathophysiology of MG. However, because the miRNA analysis results are contradictory, the identification of MG-related miRNAs is daunting. OBJECTIVE We did a systematic review of studies analyzing the miRNA expression profile of peripheral blood and mononuclear cells for patients with MG. METHODS We ran a database search in PubMed, Scopus, and Web of Science on August 17, 2021. Original articles that analyzed miRNA profiles in peripheral blood (serum, plasma, and whole blood) and peripheral blood mononuclear cells (PBMCs) for patients with MG in comparison with a non-MG or healthy control (HC) group were eligible. The quality of studies was assessed using the Quality Assessment of Diagnostic Accuracy Studies 2 (QUADAS-2). RESULTS 26 studies were included. The quality of studies was fair (median score, 5). Among 226 different miRNAs that were deregulated in at least one study (range, 1-87), ten miRNAs were significantly deregulated in three or more studies. Five miRNAs (50%) showed the same deregulation: miR-106b-3p and miR-21-5p were consistently upregulated, and miR-20b, miR-15b, and miR-16 were consistently downregulated. Also, there were five miRNAs that were mostly upregulated, miR-150-5p, miR-146a, miR-30e-5p, and miR-338-3p, or downregulated, miR-324-3p, across studies. CONCLUSION These miRNAs contribute to different pathways, importantly neural apoptosis and autophagy, inflammation, T regulatory cell development, and T helper cell balance. Prior to being used for diagnostic and therapeutic purposes, it is required to pursue molecular mechanisms these consistently and mostly dysregulated miRNAs specifically use in the context of MG.
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Affiliation(s)
- Amene Saghazadeh
- Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran; Systematic Review and Meta-analysis Expert Group (SRMEG), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Nima Rezaei
- Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran; Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran; Network of Immunity in Infection, Malignancy, and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Tehran, Iran.
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30
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Yang Y, Huang H, Li Y. Roles of exosomes and exosome-derived miRNAs in pulmonary fibrosis. Front Pharmacol 2022; 13:928933. [PMID: 36034858 PMCID: PMC9403513 DOI: 10.3389/fphar.2022.928933] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 07/15/2022] [Indexed: 11/13/2022] Open
Abstract
Pulmonary fibrosis is a chronic, progressive fibrosing interstitial lung disease of unknown etiology that leads rapidly to death. It is characterized by the replacement of healthy tissue through an altered extracellular matrix and damage to the alveolar structure. New pharmacological treatments and biomarkers are needed for pulmonary fibrosis to ensure better outcomes and earlier diagnosis of patients. Exosomes are nanoscale vesicles released by nearly all cell types that play a central role as mediators of cell-to-cell communication. Moreover, exosomes are emerging as a crucial factor in antigen presentation, immune response, immunomodulation, inflammation, and cellular phenotypic transformation and have also shown promising therapeutic potential in pulmonary fibrosis. This review summarizes current knowledge of exosomes that may promote pulmonary fibrosis and be utilized for diagnostics and prognostics. In addition, the utilization of exosomes and their cargo miRNAs as novel therapeutics and their potential mechanisms are also discussed. This review aims to elucidate the role of exosomes in the pathogenesis of pulmonary fibrosis and paves the way for developing novel therapeutics for pulmonary fibrosis. Further in-depth research and clinical trials on this topic are encouraged in the future.
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Affiliation(s)
- Yongfeng Yang
- Precision Medicine Key Laboratory, Institute of Respiratory Health, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Hong Huang
- Precision Medicine Key Laboratory, Institute of Respiratory Health, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Transplantation Engineering and Immunology, Institute of Clinical Pathology, Ministry of Health, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yi Li
- Precision Medicine Key Laboratory, Institute of Respiratory Health, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- *Correspondence: Yi Li,
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31
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Peng LS, Xu Y, Wang QS. YY1 PROMOTES MICROGLIA M2 POLARIZATION THROUGH THE MIR-130A-3P/TREM-2 AXIS TO ALLEVIATE SEPSIS-ASSOCIATED ENCEPHALOPATHY. Shock 2022; 58:128-136. [PMID: 35234205 DOI: 10.1097/shk.0000000000001914] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
ABSTRACT Purpose: Sepsis-associated encephalopathy (SAE) induces cognitive dysfunction via mechanisms that commonly involve neuroinflammation. Yin Yang 1 (YY1) is an important transcription factor that acts as a key role in sepsis and neuroepithelium development. However, the function of YY1 in SAE remains unclear. Our study aimed to probe the intrinsic and concrete molecular mechanism of YY1 in SAE. Methods: SAE cell model and SAE animal model were constructed by lipopolysaccharide (LPS) treatment and cecal ligation and puncture surgery, respectively. Behavioral tests were performed to analyze the cognitive function. The polarization state of mouse microglia (BV-2 cells) was assessed by flow cytometry assay. The mRNA and protein expressions were assessed by qRT-PCR and western blot. Finally, the binding relationships between YY1, miR-130a-3p, andTREM-2were verified by dual luciferase reporter gene assay and/or ChIP assay. Results: Here our results described that YY1 and TREM-2 were downregulated and miR-130a-3p was upregulated in SAE. YY1 overexpression could promote M2 polarization of microglia, and alleviate neuroinflammation and behavioral deficits in vitro and in vivo. YY1 could inhibit miR-130a-3p promoter activity. As expected, miR-130a-3p overexpression abolished the effects of YY1 overexpression on LPS-treated BV-2 cells. Besides, TREM-2 was identified as the target of miR-130a-3p. TREM-2 silencing could reverse the effects of miR-130a-3p inhibition on LPS-treated BV-2 cells. Conclusion: Taken together, YY1 promoted microglia M2 polarization via upregulating TREM-2 by interacting with miR-130a-3p promoter, suggesting YY1 overexpression might be a novel therapeutic strategy of SAE.
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Affiliation(s)
- Liang-Shan Peng
- The First Affiliated Hospital, Department of Critical Care Medicine, Hengyang Medical School, University of South China, Hengyang, Hunan, China
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32
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Kim G, Chen X, Yang Y. Pathogenic Extracellular Vesicle (EV) Signaling in Amyotrophic Lateral Sclerosis (ALS). Neurotherapeutics 2022; 19:1119-1132. [PMID: 35426061 PMCID: PMC9587178 DOI: 10.1007/s13311-022-01232-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/03/2022] [Indexed: 02/06/2023] Open
Abstract
Extracellular vesicles (EVs), once considered a pathway for cells to remove waste, have now emerged as an important mechanism for intercellular communication. EVs are particularly appealing in understanding the central nervous system (CNS) communication, given that there are very diverse cell types in the CNS and constant communications among various cells to respond to the frequently changing environment. While they are heterogeneous and new vesicles are continuously to be discovered, EVs are primarily classified as plasma membrane-derived microvesicles (MVs) and endosome-derived exosomes. Secretion of EVs has been shown from all CNS cell types in vitro and intercellular EV signaling has been implicated in neural development, axon integrity, neuron to glia communication, and propagation of protein aggregates formed by disease pathogenic proteins. However, significant hurdles remain to be tackled in understanding their physiological and pathological roles as well as how they can be developed as biomarkers or new therapeutics. Here we provide our summary on the known cell biology of EVs and discuss opportunities and challenges in understanding EV biology in the CNS and particularly their involvement in ALS pathogenesis.
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Affiliation(s)
- Gloria Kim
- Department of Neuroscience, Tufts University School of Medicine, 136 Harrison Ave, Boston, MA, 02111, USA
| | - Xuan Chen
- Department of Neuroscience, Tufts University School of Medicine, 136 Harrison Ave, Boston, MA, 02111, USA
| | - Yongjie Yang
- Department of Neuroscience, Tufts University School of Medicine, 136 Harrison Ave, Boston, MA, 02111, USA.
- Graduate School of Biomedical Sciences, Tufts University, 136 Harrison Ave, Boston, MA, 02111, USA.
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33
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Alvia M, Aytan N, Spencer KR, Foster ZW, Rauf NA, Guilderson L, Robey I, Averill JG, Walker SE, Alvarez VE, Huber BR, Mathais R, Cormier KA, Nicks R, Pothast M, Labadorf A, Agus F, Alosco ML, Mez J, Kowall NW, McKee AC, Brady CB, Stein TD. MicroRNA Alterations in Chronic Traumatic Encephalopathy and Amyotrophic Lateral Sclerosis. Front Neurosci 2022; 16:855096. [PMID: 35663558 PMCID: PMC9160996 DOI: 10.3389/fnins.2022.855096] [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] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 03/09/2022] [Indexed: 11/13/2022] Open
Abstract
Repetitive head impacts (RHI) and traumatic brain injuries are risk factors for the neurodegenerative diseases chronic traumatic encephalopathy (CTE) and amyotrophic lateral sclerosis (ALS). ALS and CTE are distinct disorders, yet in some instances, share pathology, affect similar brain regions, and occur together. The pathways involved and biomarkers for diagnosis of both diseases are largely unknown. MicroRNAs (miRNAs) involved in gene regulation may be altered in neurodegeneration and be useful as stable biomarkers. Thus, we set out to determine associations between miRNA levels and disease state within the prefrontal cortex in a group of brain donors with CTE, ALS, CTE + ALS and controls. Of 47 miRNAs previously implicated in neurological disease and tested here, 28 (60%) were significantly different between pathology groups. Of these, 21 (75%) were upregulated in both ALS and CTE, including miRNAs involved in inflammatory, apoptotic, and cell growth/differentiation pathways. The most significant change occurred in miR-10b, which was significantly increased in ALS, but not CTE or CTE + ALS. Overall, we found patterns of miRNA expression that are common and unique to CTE and ALS and that suggest shared and distinct mechanisms of pathogenesis.
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Affiliation(s)
- Marcela Alvia
- Boston University Alzheimer’s Disease Research Center, Boston University CTE Center, Boston University School of Medicine, Boston, MA, United States
| | - Nurgul Aytan
- Boston University Alzheimer’s Disease Research Center, Boston University CTE Center, Boston University School of Medicine, Boston, MA, United States
- Department of Neurology, Boston University School of Medicine, Boston, MA, United States
| | | | | | | | | | - Ian Robey
- Southern Arizona VA Healthcare System, Tucson, AZ, United States
| | - James G. Averill
- Southern Arizona VA Healthcare System, Tucson, AZ, United States
| | - Sean E. Walker
- Southern Arizona VA Healthcare System, Tucson, AZ, United States
| | - Victor E. Alvarez
- Boston University Alzheimer’s Disease Research Center, Boston University CTE Center, Boston University School of Medicine, Boston, MA, United States
- Department of Neurology, Boston University School of Medicine, Boston, MA, United States
- VA Boston Healthcare System, Boston, MA, United States
- Department of Veterans Affairs Medical Center, Bedford, MA, United States
| | - Bertrand R. Huber
- Boston University Alzheimer’s Disease Research Center, Boston University CTE Center, Boston University School of Medicine, Boston, MA, United States
- Department of Neurology, Boston University School of Medicine, Boston, MA, United States
- VA Boston Healthcare System, Boston, MA, United States
| | - Rebecca Mathais
- Boston University Alzheimer’s Disease Research Center, Boston University CTE Center, Boston University School of Medicine, Boston, MA, United States
| | - Kerry A. Cormier
- Boston University Alzheimer’s Disease Research Center, Boston University CTE Center, Boston University School of Medicine, Boston, MA, United States
- VA Boston Healthcare System, Boston, MA, United States
- Department of Veterans Affairs Medical Center, Bedford, MA, United States
| | - Raymond Nicks
- Boston University Alzheimer’s Disease Research Center, Boston University CTE Center, Boston University School of Medicine, Boston, MA, United States
| | - Morgan Pothast
- Boston University Alzheimer’s Disease Research Center, Boston University CTE Center, Boston University School of Medicine, Boston, MA, United States
| | - Adam Labadorf
- Department of Neurology, Boston University School of Medicine, Boston, MA, United States
- VA Boston Healthcare System, Boston, MA, United States
| | - Filisia Agus
- Department of Neurology, Boston University School of Medicine, Boston, MA, United States
| | - Michael L. Alosco
- Boston University Alzheimer’s Disease Research Center, Boston University CTE Center, Boston University School of Medicine, Boston, MA, United States
- Department of Neurology, Boston University School of Medicine, Boston, MA, United States
| | - Jesse Mez
- Boston University Alzheimer’s Disease Research Center, Boston University CTE Center, Boston University School of Medicine, Boston, MA, United States
- Department of Neurology, Boston University School of Medicine, Boston, MA, United States
| | - Neil W. Kowall
- Boston University Alzheimer’s Disease Research Center, Boston University CTE Center, Boston University School of Medicine, Boston, MA, United States
- Department of Neurology, Boston University School of Medicine, Boston, MA, United States
- VA Boston Healthcare System, Boston, MA, United States
| | - Ann C. McKee
- Boston University Alzheimer’s Disease Research Center, Boston University CTE Center, Boston University School of Medicine, Boston, MA, United States
- Department of Neurology, Boston University School of Medicine, Boston, MA, United States
- VA Boston Healthcare System, Boston, MA, United States
- Department of Veterans Affairs Medical Center, Bedford, MA, United States
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, MA, United States
| | - Christopher B. Brady
- Department of Neurology, Boston University School of Medicine, Boston, MA, United States
- VA Boston Healthcare System, Boston, MA, United States
- Department of Veterans Affairs Medical Center, Bedford, MA, United States
| | - Thor D. Stein
- Boston University Alzheimer’s Disease Research Center, Boston University CTE Center, Boston University School of Medicine, Boston, MA, United States
- VA Boston Healthcare System, Boston, MA, United States
- Department of Veterans Affairs Medical Center, Bedford, MA, United States
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, MA, United States
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Wu Z, Cai Z, Shi H, Huang X, Cai M, Yuan K, Huang P, Shi G, Yan T, Li Z. Effective biomarkers and therapeutic targets of nerve-immunity interaction in the treatment of depression: an integrated investigation of the miRNA-mRNA regulatory networks. Aging (Albany NY) 2022; 14:3569-3596. [PMID: 35468096 PMCID: PMC9085226 DOI: 10.18632/aging.204030] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 04/11/2022] [Indexed: 11/25/2022]
Abstract
Background: Major depressive disorder (MDD) is an emotional condition that interferes with sufferers’ work and daily life. Numerous studies have found that miRNAs play a significant role in the development of MDD and can be utilized as a biomarker for its diagnosis and therapy. However, there have been few studies on nerve-immunity interaction treatment for the brains of MMD patients. Methods: The work is performed on microarray data. We analyzed the differences of miRNAs (GSE58105, GSE81152, GSE152267, and GSE182194) and mRNA (GSE19738, GSE32280, GSE44593, GSE53987, and GSE98793) in MDD and healthy samples from GEO datasets. FunRich was used to predict the transcription factors and target genes of the miRNAs, and TF and GO enrichment analyses were performed. Then, by comparing the differential expression of the anticipated target genes and five mRNAs, intersecting mRNAs were discovered. The intersecting genes were submitted to GO and KEGG analyses to determine their functions. These intersecting potential genes and pathways that linked to MDD in neurological and immunological aspects have been identified for future investigation. Results: We discovered five hub genes: KCND2, MYT1L, GJA1, CHL1, and SNAP25, which were all up-regulated genes. However, in MMD, the equivalent miRNAs, hsa-miR-206 and hsa-miR-338-3p, were both down-regulated. These miRNAs can activate or inhibit the T cell receptor signal pathway, JAK-STAT and other signal pathways, govern immune-inflammatory response, neuronal remodeling, and mediate the onset and development of MMD Conclusions: The results of a thorough bioinformatics investigation of miRNAs and mRNAs in MDD showed that miR-338-3P and miR-206 might be effective biomarkers and possible therapeutic targets for the treatment of MDD via nerve-immunity interaction.
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Affiliation(s)
- Zixuan Wu
- Guangzhou University of Chinese Medicine, Guangzhou 510006, Guangdong Province, China
| | - Zhixiang Cai
- Guangzhou University of Chinese Medicine, Guangzhou 510006, Guangdong Province, China
| | - Hongshuo Shi
- Shandong University of Traditional Chinese Medicine, Jinan 250355, Shandong Province, China
| | - Xuyan Huang
- Guangzhou University of Chinese Medicine, Guangzhou 510006, Guangdong Province, China
| | - Minjie Cai
- Guangzhou University of Chinese Medicine, Guangzhou 510006, Guangdong Province, China.,Shantou Health School, Shantou 515061, Guangdong Province, China
| | - Kai Yuan
- Yunnan University of Chinese Medicine, Kunming 650500, Yunnan Province, China
| | - Peidong Huang
- Yunnan University of Chinese Medicine, Kunming 650500, Yunnan Province, China
| | - Guoqi Shi
- Guangzhou University of Chinese Medicine, Guangzhou 510006, Guangdong Province, China
| | - Tao Yan
- Guangzhou University of Chinese Medicine, Guangzhou 510006, Guangdong Province, China.,Department of Cardiovascular Surgery, General Hospital of Southern Theater Command, PLA 510010, Guangdong Province, China
| | - Zhichao Li
- The Second Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan 250355, Shandong Province, China
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35
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Nguyen TPN, Kumar M, Fedele E, Bonanno G, Bonifacino T. MicroRNA Alteration, Application as Biomarkers, and Therapeutic Approaches in Neurodegenerative Diseases. Int J Mol Sci 2022; 23:ijms23094718. [PMID: 35563107 PMCID: PMC9104163 DOI: 10.3390/ijms23094718] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/20/2022] [Accepted: 04/21/2022] [Indexed: 01/27/2023] Open
Abstract
MicroRNAs (miRNAs) are essential post-transcriptional gene regulators involved in various neuronal and non-neuronal cell functions and play a key role in pathological conditions. Numerous studies have demonstrated that miRNAs are dysregulated in major neurodegenerative diseases, such as Alzheimer’s disease, Parkinson’s disease, multiple sclerosis, amyotrophic lateral sclerosis, or Huntington’s disease. Hence, in the present work, we constructed a comprehensive overview of individual microRNA alterations in various models of the above neurodegenerative diseases. We also provided evidence of miRNAs as promising biomarkers for prognostic and diagnostic approaches. In addition, we summarized data from the literature about miRNA-based therapeutic applications via inhibiting or promoting miRNA expression. We finally identified the overlapping miRNA signature across the diseases, including miR-128, miR-140-5p, miR-206, miR-326, and miR-155, associated with multiple etiological cellular mechanisms. However, it remains to be established whether and to what extent miRNA-based therapies could be safely exploited in the future as effective symptomatic or disease-modifying approaches in the different human neurodegenerative disorders.
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Affiliation(s)
- T. P. Nhung Nguyen
- Pharmacology and Toxicology Unit, Department of Pharmacy, University of Genoa, Viale Cembrano 4, 16148 Genoa, Italy; (T.P.N.N.); (M.K.); (G.B.); (T.B.)
| | - Mandeep Kumar
- Pharmacology and Toxicology Unit, Department of Pharmacy, University of Genoa, Viale Cembrano 4, 16148 Genoa, Italy; (T.P.N.N.); (M.K.); (G.B.); (T.B.)
| | - Ernesto Fedele
- Pharmacology and Toxicology Unit, Department of Pharmacy, University of Genoa, Viale Cembrano 4, 16148 Genoa, Italy; (T.P.N.N.); (M.K.); (G.B.); (T.B.)
- IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
- Correspondence:
| | - Giambattista Bonanno
- Pharmacology and Toxicology Unit, Department of Pharmacy, University of Genoa, Viale Cembrano 4, 16148 Genoa, Italy; (T.P.N.N.); (M.K.); (G.B.); (T.B.)
- IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
| | - Tiziana Bonifacino
- Pharmacology and Toxicology Unit, Department of Pharmacy, University of Genoa, Viale Cembrano 4, 16148 Genoa, Italy; (T.P.N.N.); (M.K.); (G.B.); (T.B.)
- Inter-University Center for the Promotion of the 3Rs Principles in Teaching & Research (Centro 3R), 56122 Genoa, Italy
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36
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Kos MZ, Puppala S, Cruz D, Neary JL, Kumar A, Dalan E, Li C, Nathanielsz P, Carless MA. Blood-Based miRNA Biomarkers as Correlates of Brain-Based miRNA Expression. Front Mol Neurosci 2022; 15:817290. [PMID: 35392269 PMCID: PMC8981579 DOI: 10.3389/fnmol.2022.817290] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 02/18/2022] [Indexed: 01/08/2023] Open
Abstract
The use of easily accessible peripheral samples, such as blood or saliva, to investigate neurological and neuropsychiatric disorders is well-established in genetic and epigenetic research, but the pathological implications of such biomarkers are not easily discerned. To better understand the relationship between peripheral blood- and brain-based epigenetic activity, we conducted a pilot study on captive baboons (Papio hamadryas) to investigate correlations between miRNA expression in peripheral blood mononuclear cells (PBMCs) and 14 different cortical and subcortical brain regions, represented by two study groups comprised of 4 and 6 animals. Using next-generation sequencing, we identified 362 miRNAs expressed at ≥ 10 read counts in 80% or more of the brain samples analyzed. Nominally significant pairwise correlations (one-sided P < 0.05) between peripheral blood and mean brain expression levels of individual miRNAs were observed for 39 and 44 miRNAs in each group. When miRNA expression levels were averaged for tissue type across animals within the groups, Spearman's rank correlations between PBMCs and the brain regions are all highly significant (r s = 0.47-0.57; P < 2.2 × 10-16), although pairwise correlations among the brain regions are markedly stronger (r s = 0.86-0.99). Principal component analysis revealed differentiation in miRNA expression between peripheral blood and the brain regions for the first component (accounting for ∼75% of variance). Linear mixed effects modeling attributed most of the variance in expression to differences between miRNAs (>70%), with non-significant 7.5% and 13.1% assigned to differences between blood and brain-based samples in the two study groups. Hierarchical UPGMA clustering revealed a major co-expression branch in both study groups, comprised of miRNAs globally upregulated in blood relative to the brain samples, exhibiting an enrichment of miRNAs expressed in immune cells (CD14+, CD15+, CD19+, CD3+, and CD56 + leukocytes) among the top blood-brain correlates, with the gene MYC, encoding a master transcription factor that regulates angiogenesis and neural stem cell activation, representing the most prevalent miRNA target. Although some differentiation was observed between tissue types, these preliminary findings reveal wider correlated patterns between blood- and brain-expressed miRNAs, suggesting the potential utility of blood-based miRNA profiling for investigating by proxy certain miRNA activity in the brain, with implications for neuroinflammatory and c-Myc-mediated processes.
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Affiliation(s)
- Mark Z. Kos
- Department of Human Genetics, South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Edinburg, TX, United States
| | - Sobha Puppala
- Department of Internal Medicine-Section of Molecular Medicine, Wake Forest Baptist Medical Center, Winston-Salem, NC, United States
| | - Dianne Cruz
- Duke University School of Medicine, Durham, NC, United States
| | - Jennifer L. Neary
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN, United States
| | - Ashish Kumar
- Department of Internal Medicine-Section of Molecular Medicine, Wake Forest Baptist Medical Center, Winston-Salem, NC, United States
| | - Emma Dalan
- Department of Biology, University of Texas at San Antonio, San Antonio, TX, United States
| | - Cun Li
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, United States,Department of Animal Science, University of Wyoming, Laramie, WY, United States
| | - Peter Nathanielsz
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, United States,Department of Animal Science, University of Wyoming, Laramie, WY, United States
| | - Melanie A. Carless
- Department of Biology, University of Texas at San Antonio, San Antonio, TX, United States,Population Health, Texas Biomedical Research Institute, San Antonio, TX, United States,*Correspondence: Melanie A. Carless,
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Gene expression and epigenetic markers of prion diseases. Cell Tissue Res 2022; 392:285-294. [PMID: 35307791 PMCID: PMC10113299 DOI: 10.1007/s00441-022-03603-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 02/24/2022] [Indexed: 12/19/2022]
Abstract
Epigenetics, meaning the variety of mechanisms underpinning gene regulation and chromatin states, plays a key role in normal development as well as in disease initiation and progression. Epigenetic mechanisms like alteration of DNA methylation, histone modifications, and non-coding RNAs, have been proposed as biomarkers for diagnosis, classification, or monitoring of responsiveness to treatment in many diseases. In prion diseases, the profound associations with human aging, the effects of cell type and differentiation on in vitro susceptibility, and recently identified human risk factors, all implicate causal epigenetic mechanisms. Here, we review the current state of the art of epigenetics in prion diseases and its interaction with genetic determinants. In particular, we will review recent advances made by several groups in the field profiling DNA methylation and microRNA expression in mammalian prion diseases and the potential for these discoveries to be exploited as biomarkers.
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38
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Bottero V, Santiago JA, Quinn JP, Potashkin JA. Key Disease Mechanisms Linked to Amyotrophic Lateral Sclerosis in Spinal Cord Motor Neurons. Front Mol Neurosci 2022; 15:825031. [PMID: 35370543 PMCID: PMC8965442 DOI: 10.3389/fnmol.2022.825031] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 02/15/2022] [Indexed: 12/11/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease with no modifying treatments available. The molecular mechanisms underpinning disease pathogenesis are not fully understood. Recent studies have employed co-expression networks to identify key genes, known as “switch genes”, responsible for dramatic transcriptional changes in the blood of ALS patients. In this study, we directly investigate the root cause of ALS by examining the changes in gene expression in motor neurons that degenerate in patients. Co-expression networks identified in ALS patients’ spinal cord motor neurons revealed 610 switch genes in seven independent microarrays. Switch genes were enriched in several pathways, including viral carcinogenesis, PI3K-Akt, focal adhesion, proteoglycans in cancer, colorectal cancer, and thyroid hormone signaling. Transcription factors ELK1 and GATA2 were identified as key master regulators of the switch genes. Protein-chemical network analysis identified valproic acid, cyclosporine, estradiol, acetaminophen, quercetin, and carbamazepine as potential therapeutics for ALS. Furthermore, the chemical analysis identified metals and organic compounds including, arsenic, copper, nickel, and benzo(a)pyrene as possible mediators of neurodegeneration. The identification of switch genes provides insights into previously unknown biological pathways associated with ALS.
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Affiliation(s)
- Virginie Bottero
- Chicago Medical School, Rosalind Franklin University of Medicine and Science, Center for Neurodegenerative Diseases and Therapeutics, Discipline of Cellular and Molecular Pharmacology, North Chicago, IL, United States
| | | | | | - Judith A. Potashkin
- Chicago Medical School, Rosalind Franklin University of Medicine and Science, Center for Neurodegenerative Diseases and Therapeutics, Discipline of Cellular and Molecular Pharmacology, North Chicago, IL, United States
- *Correspondence: Judy A. Potashkin
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Biomarkers in Human Peripheral Blood Mononuclear Cells: The State of the Art in Amyotrophic Lateral Sclerosis. Int J Mol Sci 2022; 23:ijms23052580. [PMID: 35269723 PMCID: PMC8910056 DOI: 10.3390/ijms23052580] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 02/21/2022] [Accepted: 02/25/2022] [Indexed: 12/11/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a devastating neurodegenerative disease, characterized by the progressive loss of lower motor neurons, weakness and muscle atrophy. ALS lacks an effective cure and diagnosis is often made by exclusion. Thus, it is imperative to search for biomarkers. Biomarkers can help in understanding ALS pathomechanisms, identification of targets for treatment and development of effective therapies. Peripheral blood mononuclear cells (PBMCs) represent a valid source for biomarkers compared to cerebrospinal fluid, as they are simple to collect, and to plasma, because of the possibility of detecting lower expressed proteins. They are a reliable model for patients’ stratification. This review provides an overview on PBMCs as a potential source of biomarkers in ALS. We focused on altered RNA metabolism (coding/non-coding RNA), including RNA processing, mRNA stabilization, transport and translation regulation. We addressed protein abnormalities (aggregation, misfolding and modifications); specifically, we highlighted that SOD1 appears to be the most characterizing protein in ALS. Finally, we emphasized the correlation between biological parameters and disease phenotypes, as regards prognosis, severity and clinical features. In conclusion, even though further studies are needed to standardize the use of PBMCs as a tool for biomarker investigation, they represent a promising approach in ALS research.
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Rastegar-moghaddam SH, Ebrahimzadeh-Bideskan A, Shahba S, Malvandi AM, Mohammadipour A. MicroRNA-22: a Novel and Potent Biological Therapeutics in Neurological Disorders. Mol Neurobiol 2022; 59:2694-2701. [DOI: 10.1007/s12035-022-02769-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 02/07/2022] [Indexed: 01/03/2023]
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41
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Dowling L, Duseja A, Vilaca T, Walsh JS, Goljanek-Whysall K. MicroRNAs in obesity, sarcopenia, and commonalities for sarcopenic obesity: a systematic review. J Cachexia Sarcopenia Muscle 2022; 13:68-85. [PMID: 34984856 PMCID: PMC8818592 DOI: 10.1002/jcsm.12878] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 10/24/2021] [Accepted: 10/29/2021] [Indexed: 12/11/2022] Open
Abstract
Sarcopenic obesity is a distinct condition of sarcopenia in the context of obesity, with the cumulative health risks of both phenotypes. Differential expression of microRNAs (miRNAs) has been reported separately in people with obesity and sarcopenia and may play a role in the pathogenesis of sarcopenic obesity. However, this has not been explored to date. This study aimed to identify differentially expressed miRNAs reported in serum, plasma, and skeletal muscle of people with obesity and sarcopenia and whether there are any commonalities between these conditions. We performed a systematic review on Embase and MEDLINE (PROSPERO, CRD42020224486) for differentially expressed miRNAs (fold change >1.5 or P-value <0.05) in (i) sarcopenia or frailty and (ii) obesity or metabolic syndrome. The functions and targets of miRNAs commonly changed in both conditions, in the same direction, were searched using PubMed. Following deduplication, 247 obesity and 42 sarcopenia studies were identified for full-text screening. Screening identified 36 obesity and 6 sarcopenia studies for final inclusion. A total of 351 miRNAs were identified in obesity and 157 in sarcopenia. Fifty-five miRNAs were identified in both obesity and sarcopenia-by sample type, 48 were found in plasma and one each in serum and skeletal muscle. Twenty-four miRNAs were identified from 10 of the included studies as commonly changed in the same direction (22 in plasma and one each in serum and skeletal muscle) in obesity and sarcopenia. The majority of miRNA-validated targets identified in the literature search were members of the phosphoinositide 3-kinase/protein kinase B and transforming growth factor-β signalling pathways. The most common targets identified were insulin-like growth factor 1 (miR-424-5p, miR-483-3p, and miR-18b-5p) and members of the SMAD family (miR-483-3p, miR-92a-3p, and miR-424-5p). The majority of commonly changed miRNAs were involved in protein homeostasis, mitochondrial dynamics, determination of muscle fibre type, insulin resistance, and adipogenesis. Twenty-four miRNAs were identified as commonly dysregulated in obesity and sarcopenia with functions and targets implicated in the pathogenesis of sarcopenic obesity. Given the adverse health outcomes associated with sarcopenic obesity, understanding the pathogenesis underlying this phenotype has the potential to lead to effective screening, monitoring, or treatment strategies. Further research is now required to confirm whether these miRNAs are differentially expressed in older adults with sarcopenic obesity.
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Affiliation(s)
| | | | | | | | - Katarzyna Goljanek-Whysall
- The University of Liverpool, Liverpool, UK.,Department of Physiology, School of Medicine, Nursing and Health Sciences, College of Medicine, National University of Ireland, Galway, Galway, Ireland
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Identification of let-7f and miR-338 as plasma-based biomarkers for sporadic amyotrophic lateral sclerosis using meta-analysis and empirical validation. Sci Rep 2022; 12:1373. [PMID: 35082326 PMCID: PMC8791978 DOI: 10.1038/s41598-022-05067-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 01/06/2022] [Indexed: 12/11/2022] Open
Abstract
AbstractAmyotrophic lateral sclerosis (ALS) is a lethal neurodegenerative disease that in most cases occurs sporadic (sALS). The disease is not curable, and its pathogenesis mechanisms are not well understood yet. Given the intricacy of underlying molecular interactions and heterogeneity of ALS, the discovery of molecules contributing to disease onset and progression will open a new avenue for advancement in early diagnosis and therapeutic intervention. Here we conducted a meta-analysis of 12 circulating miRNA profiling studies using the robust rank aggregation (RRA) method, followed by enrichment analysis and experimental verification. We identified miR-451a and let-7f-5p as meta-signature miRNAs whose targets are involved in critical pathogenic pathways underlying ALS, including ‘FoxO signaling pathway’, ‘MAPK signaling pathway’, and ‘apoptosis’. A systematic review of 7 circulating gene profiling studies elucidated that 241 genes up-regulated in sALS circulation with concomitant being targets of the meta-signature miRNAs. Protein–protein interaction (PPI) network analysis of the candidate targets using MCODE algorithm revealed the main subcluster is involved in multiple cascades eventually leads apoptosis, including ‘positive regulation of neuron apoptosis. Besides, we validated the meta-analysis results using RT-qPCR. Indeed, relative expression analysis verified let-7f-5p and miR-338-3p as significantly down-regulated and up-regulated biomarkers in the plasma of sALS patients, respectively. Receiver operating characteristic (ROC) analysis also highlighted the let-7f-5p and miR-338-3p potential as robustness plasma biomarkers for diagnosis and potential therapeutic targets of sALS disease.
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Staats KA, Borchelt DR, Tansey MG, Wymer J. Blood-based biomarkers of inflammation in amyotrophic lateral sclerosis. Mol Neurodegener 2022; 17:11. [PMID: 35073950 PMCID: PMC8785449 DOI: 10.1186/s13024-022-00515-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Accepted: 12/30/2021] [Indexed: 12/11/2022] Open
Abstract
Amyotrophic Lateral Sclerosis (ALS) is a devastating neurodegenerative disease in which many processes are detected including (neuro)inflammation. Many drugs have been tested for ALS in clinical trials but most have failed to reach their primary endpoints. The development and inclusion of different types of biomarkers in diagnosis and clinical trials can assist in determining target engagement of a drug, in distinguishing between ALS and other diseases, and in predicting disease progression rate, drug responsiveness, or an adverse event. Ideally, among other characteristics, a biomarker in ALS correlates highly with a disease process in the central nervous system or with disease progression and is conveniently obtained in a peripheral tissue. Here, we describe the state of biomarkers of inflammation in ALS by focusing on peripherally detectable and cellular responses from blood cells, and provide new (combinatorial) directions for exploration that are now feasible due to technological advancements.
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Affiliation(s)
- Kim A. Staats
- Staats Life Sciences Consulting, LLC, Los Angeles, CA USA
| | - David R. Borchelt
- Department of Neuroscience, University of Florida College of Medicine, McKnight Brain Institute, Center for Translational Research in Neurodegenerative Disease, University of Florida, Gainesville, Florida USA
| | - Malú Gámez Tansey
- Department of Neuroscience and Center for Translational Research in Neurodegenerative Disease at The University of Florida College of Medicine, Gainesville, Florida USA
| | - James Wymer
- Department of Neurology, University of Florida College of Medicine, Gainesville, Florida USA
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Xu Y, Hu Y, Xu S, Liu F, Gao Y. Exosomal microRNAs as Potential Biomarkers and Therapeutic Agents for Acute Ischemic Stroke: New Expectations. Front Neurol 2022; 12:747380. [PMID: 35173663 PMCID: PMC8842672 DOI: 10.3389/fneur.2021.747380] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 12/10/2021] [Indexed: 12/11/2022] Open
Abstract
The morbidity and mortality rates of ischemic stroke (IS) are very high, and IS constitutes one of the main causes of disability and death worldwide. The pathogenesis of ischemic stroke includes excitotoxicity, calcium overload, oxygen radical injury, inflammatory reactions, necrosis/apoptosis, destruction of the blood-brain barrier (BBB), and other pathologic processes. Recent studies have shown that exosomes are critical to the pathogenesis, diagnosis, and treatment of cerebral infarctions resulting from ischemic stroke; and there is growing interest in the role of exosomes and exosomal miRNAs in the diagnosis and treatment of IS. Exosomes from central nervous system cells can be found in cerebrospinal fluid and peripheral bodily fluids, and exosomal contents have been reported to change with disease occurrence. Exosomes are small membranous extracellular vesicles (EVs), 30–150 nm in diameter, that are released from the cell membrane into the depressions that arise from the membranes of multivesicular bodies. Exosomes carry lipids, proteins, mRNAs, and microRNAs (miRNAs) and transport information to target cells. This exosomal transfer of functional mRNAs/miRNAs and proteins ultimately affects transcription and translation within recipient cells. Exosomes are EVs with a double-membrane structure that protects them from ribonucleases in the blood, allowing exosomal miRNAs to be more stable and to avoid degradation. New evidence shows that exosomes derived from neural cells, endothelial cells, and various stem cells create a fertile environment that supports the proliferation and growth of neural cells and endothelial cells, inhibits apoptosis and inflammatory responses, and promotes angiogenesis. In the present review, we discuss how circulating exosomes—and exosomal miRNAs in particular—may provide novel strategies for the early diagnosis and treatment of ischemic stroke via their potential as non-invasive biomarkers and drug carriers.
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Affiliation(s)
- Yingzhi Xu
- Institute for Brain Disorders, Beijing University of Chinese Medicine, Beijing, China
- Department of Neurology, Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, China
- Key Laboratory of Chinese Internal Medicine of Ministry of Education and Beijing, Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Yue Hu
- School of Integrated Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Shixin Xu
- Medical Experiment Center, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China
- Tianjin Key Laboratory of Translational Research of TCM Prescription and Syndrome, Tianjin, China
| | - Fengzhi Liu
- Key Laboratory of Chinese Internal Medicine of Ministry of Education and Beijing, Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Ying Gao
- Institute for Brain Disorders, Beijing University of Chinese Medicine, Beijing, China
- Department of Neurology, Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, China
- *Correspondence: Ying Gao
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You D, Cohen JD, Pustovalova O, Lewis L, Shen L. OUP accepted manuscript. Toxicol Sci 2022; 186:221-241. [PMID: 35134991 PMCID: PMC8963304 DOI: 10.1093/toxsci/kfac011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
| | - Jennifer D Cohen
- Jennifer D. Cohen, Drug Safety Research & Evaluation, Takeda Development Center Americas, Inc., 9625 Towne Centre Drive, San Diego, CA 92121-1964, USA. E-mail:
| | | | - Lauren Lewis
- Drug Safety Research & Evaluation, Takeda Development Center Americas, Inc., Cambridge, Massachusetts 02139, USA
| | - Lei Shen
- Data Science Institute, Takeda Development Center Americas, Inc., Cambridge, Massachusetts 02139, USA
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Gowda P, Reddy PH, Kumar S. Deregulated mitochondrial microRNAs in Alzheimer's disease: Focus on synapse and mitochondria. Ageing Res Rev 2022; 73:101529. [PMID: 34813976 PMCID: PMC8692431 DOI: 10.1016/j.arr.2021.101529] [Citation(s) in RCA: 61] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 10/17/2021] [Accepted: 11/16/2021] [Indexed: 01/03/2023]
Abstract
Alzheimer's disease (AD) is the most common cause of dementia and is currently one of the biggest public health concerns in the world. Mitochondrial dysfunction in neurons is one of the major hallmarks of AD. Emerging evidence suggests that mitochondrial miRNAs potentially play important roles in the mitochondrial dysfunctions, focusing on synapse in AD progression. In this meta-analysis paper, a comprehensive literature review was conducted to identify and discuss the (1) role of mitochondrial miRNAs that regulate mitochondrial and synaptic functions; (2) the role of various factors such as mitochondrial dynamics, biogenesis, calcium signaling, biological sex, and aging on synapse and mitochondrial function; (3) how synapse damage and mitochondrial dysfunctions contribute to AD; (4) the structure and function of synapse and mitochondria in the disease process; (5) latest research developments in synapse and mitochondria in healthy and disease states; and (6) therapeutic strategies that improve synaptic and mitochondrial functions in AD. Specifically, we discussed how differences in the expression of mitochondrial miRNAs affect ATP production, oxidative stress, mitophagy, bioenergetics, mitochondrial dynamics, synaptic activity, synaptic plasticity, neurotransmission, and synaptotoxicity in neurons observed during AD. However, more research is needed to confirm the locations and roles of individual mitochondrial miRNAs in the development of AD.
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Affiliation(s)
- Prashanth Gowda
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, USA; Neuroscience & Pharmacology, Texas Tech University Health Sciences Center, Lubbock, TX, USA; Neurology, Departments of School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, USA; Public Health Department of Graduate School of Biomedical Sciences, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - P Hemachandra Reddy
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, USA; Neuroscience & Pharmacology, Texas Tech University Health Sciences Center, Lubbock, TX, USA; Neurology, Departments of School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, USA; Public Health Department of Graduate School of Biomedical Sciences, Texas Tech University Health Sciences Center, Lubbock, TX, USA; Department of Speech, Language and Hearing Sciences, School Health Professions, Texas Tech University Health Sciences Center, Lubbock, TX, USA.
| | - Subodh Kumar
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, USA.
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Belkozhayev AM, Al-Yozbaki M, George A, Niyazova RY, Sharipov KO, Byrne LJ, Wilson CM. Extracellular Vesicles, Stem Cells and the Role of miRNAs in Neurodegeneration. Curr Neuropharmacol 2022; 20:1450-1478. [PMID: 34414870 PMCID: PMC9881087 DOI: 10.2174/1570159x19666210817150141] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 05/16/2021] [Accepted: 06/14/2021] [Indexed: 11/22/2022] Open
Abstract
There are different modalities of intercellular communication governed by cellular homeostasis. In this review, we will explore one of these forms of communication called extracellular vesicles (EVs). These vesicles are released by all cells in the body and are heterogeneous in nature. The primary function of EVs is to share information through their cargo consisting of proteins, lipids and nucleic acids (mRNA, miRNA, dsDNA etc.) with other cells, which have a direct consequence on their microenvironment. We will focus on the role of EVs of mesenchymal stem cells (MSCs) in the nervous system and how these participate in intercellular communication to maintain physiological function and provide neuroprotection. However, deregulation of this same communication system could play a role in several neurodegenerative diseases, such as Alzheimer's disease, Parkinson's disease, Amyotrophic lateral sclerosis, multiple sclerosis, prion disease and Huntington's disease. The release of EVs from a cell provides crucial information to what is happening inside the cell and thus could be used in diagnostics and therapy. We will discuss and explore new avenues for the clinical applications of using engineered MSC-EVs and their potential therapeutic benefit in treating neurodegenerative diseases.
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Affiliation(s)
- Ayaz M. Belkozhayev
- Al-Farabi Kazakh National University, Faculty of Biology and Biotechnology, Almaty, Republic of Kazakhstan
- Structural and Functional Genomics Laboratory of M.A. Aitkhozhin Institute of Molecular Biology and Biochemistry, Almaty, Republic of Kazakhstan
| | - Minnatallah Al-Yozbaki
- Canterbury Christ Church University, School of Human and Life Sciences, Life Sciences Industry Liaison Lab, Sandwich, UK
| | - Alex George
- Canterbury Christ Church University, School of Human and Life Sciences, Life Sciences Industry Liaison Lab, Sandwich, UK
- Jubilee Centre for Medical Research, Jubilee Mission Medical College & Research Institute, Thrissur, Kerala, India
| | - Raigul Ye Niyazova
- Al-Farabi Kazakh National University, Faculty of Biology and Biotechnology, Almaty, Republic of Kazakhstan
| | - Kamalidin O. Sharipov
- Structural and Functional Genomics Laboratory of M.A. Aitkhozhin Institute of Molecular Biology and Biochemistry, Almaty, Republic of Kazakhstan
| | - Lee J. Byrne
- Canterbury Christ Church University, School of Human and Life Sciences, Life Sciences Industry Liaison Lab, Sandwich, UK
| | - Cornelia M. Wilson
- Canterbury Christ Church University, School of Human and Life Sciences, Life Sciences Industry Liaison Lab, Sandwich, UK
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Chen QY, Wen T, Wu P, Jia R, Zhang R, Dang J. Exosomal Proteins and miRNAs as Mediators of Amyotrophic Lateral Sclerosis. Front Cell Dev Biol 2021; 9:718803. [PMID: 34568332 PMCID: PMC8461026 DOI: 10.3389/fcell.2021.718803] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 08/13/2021] [Indexed: 12/14/2022] Open
Abstract
Recent advances in the neurobiology and neurogenerative diseases have attracted growing interest in exosomes and their ability to carry and propagate active biomolecules as a means to reprogram recipient cells. Alterations in exosomal protein content and nucleic acid profiles found in human biological fluids have been correlated with various diseases including amyotrophic lateral sclerosis (ALS). In ALS pathogenesis, these lipid-bound nanoscale vesicles have emerged as valuable candidates for diagnostic biomarkers. Moreover, their capacity to spread misfolded proteins and functional non-coding RNAs to interconnected neuronal cells make them putative mediators for the progressive motor degeneration found remarkably apparent in ALS. This review outlines current knowledge concerning the biogenesis, heterogeneity, and function of exosomes in the brain as well as a comprehensive probe of currently available literature on ALS-related exosomal proteins and microRNAs. Lastly, with the rapid development of employing nanoparticles for drug delivery, we explore the therapeutic potentials of exosomes as well as underlying limitations in current isolation and detection methodologies.
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Affiliation(s)
- Qiao Yi Chen
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, China
| | - Ting Wen
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, China
| | - Peng Wu
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, China
| | - Rui Jia
- Department of Neurology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Ronghua Zhang
- Department of Neurology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Jingxia Dang
- Department of Neurology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
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49
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Laneve P, Tollis P, Caffarelli E. RNA Deregulation in Amyotrophic Lateral Sclerosis: The Noncoding Perspective. Int J Mol Sci 2021; 22:10285. [PMID: 34638636 PMCID: PMC8508793 DOI: 10.3390/ijms221910285] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/17/2021] [Accepted: 09/22/2021] [Indexed: 12/18/2022] Open
Abstract
RNA metabolism is central to cellular physiopathology. Almost all the molecular pathways underpinning biological processes are affected by the events governing the RNA life cycle, ranging from transcription to degradation. The deregulation of these processes contributes to the onset and progression of human diseases. In recent decades, considerable efforts have been devoted to the characterization of noncoding RNAs (ncRNAs) and to the study of their role in the homeostasis of the nervous system (NS), where they are highly enriched. Acting as major regulators of gene expression, ncRNAs orchestrate all the steps of the differentiation programs, participate in the mechanisms underlying neural functions, and are crucially implicated in the development of neuronal pathologies, among which are neurodegenerative diseases. This review aims to explore the link between ncRNA dysregulation and amyotrophic lateral sclerosis (ALS), the most frequent motoneuron (MN) disorder in adults. Notably, defective RNA metabolism is known to be largely associated with this pathology, which is often regarded as an RNA disease. We also discuss the potential role that these transcripts may play as diagnostic biomarkers and therapeutic targets.
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Affiliation(s)
- Pietro Laneve
- Institute of Molecular Biology and Pathology, National Research Council, 00185 Rome, Italy
| | - Paolo Tollis
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, 00185 Rome, Italy;
| | - Elisa Caffarelli
- Institute of Molecular Biology and Pathology, National Research Council, 00185 Rome, Italy
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50
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Chen L, Lu Q, Deng F, Peng S, Yuan J, Liu C, Du X. miR-103a-3p Could Attenuate Sepsis-Induced Liver Injury by Targeting HMGB1. Inflammation 2021; 43:2075-2086. [PMID: 32556802 DOI: 10.1007/s10753-020-01275-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The liver is one of the most vulnerable organs during sepsis. Current studies have proven that microRNAs play important roles in injury and inflammation. The current study aimed to investigate the role of miR-103 in septic liver injury. The sepsis model was established by cecal ligation and puncture in mice. Then, the mice were divided into four groups: normal group, sepsis group, sepsis + miR-103a-3p agomir group, and sepsis + negative control group. Liver injury was observed by hematoxylin-eosin staining and electron microscopic studies. The sepsis-induced apoptosis in liver tissues was assessed by TUNEL staining. The levels of inflammatory cytokines in liver tissues were determined by enzyme-linked immunosorbent assay kits. The targeted gene of miR-103a-3p in cells was predicted by bioinformatics algorithm and confirmed by dual-luciferase reporter assay. The expression of miR-103a-3p, HMBG1, and the apoptosis-relative proteins was examined by quantitative real-time polymerase chain reaction and Western blotting. miR-103a-3p was downregulated in liver tissues of sepsis animals. miR-103a-3p agomir could alleviate liver injury including the tissue injury and mitochondrial damage, inhibit the secretion of inflammatory factors, and decrease the apoptosis of liver cells. The high-mobility group B1 (HMGB1) was overregulated in sepsis, and it was a downstream target gene of miR-103a-3p. The results of the rescue assay confirmed that miR-103a-3p had a protection role in septic liver injury by targeting HMGB1. In summary, HMGB1 was one of the genes targeted by miR-103a-3p, which played roles in septic injury. These data may provide novel insight for the identification of new target and treatment strategies for septic liver injury.
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Affiliation(s)
- Leifeng Chen
- Department of General Surgery, Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Qiang Lu
- Department of Anesthesiology, Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Fumou Deng
- Department of Anesthesiology, Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Shengliang Peng
- Department of Anesthesiology, Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Jiajia Yuan
- Department of Anesthesiology, Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Chunfang Liu
- Department of Anesthesiology, Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Xiaohong Du
- Department of Anesthesiology, Second Affiliated Hospital of Nanchang University, Nanchang, China.
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