1
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Khosroshahi PA, Ghanbari M. MicroRNA dysregulation in glutamate and dopamine pathways of schizophrenia: From molecular pathways to diagnostic and therapeutic approaches. Prog Neuropsychopharmacol Biol Psychiatry 2024; 135:111081. [PMID: 39002925 DOI: 10.1016/j.pnpbp.2024.111081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 06/28/2024] [Accepted: 07/07/2024] [Indexed: 07/15/2024]
Abstract
Schizophrenia is a complex psychiatric disorder, and genetic and environmental factors have been implicated in its development. Dysregulated glutamatergic and dopaminergic transmission pathways are involved in schizophrenia development. Besides genetic mutations, epigenetic dysregulation has a considerable role in dysregulating molecular pathways involved in schizophrenia. MicroRNAs (miRNAs) are small, non-coding RNAs that target specific mRNAs and inhibit their translation into proteins. As epigenetic factors, miRNAs regulate many genes involved in glutamate and dopamine signaling pathways; thereby, their dysregulation can contribute to the development of schizophrenia. Secretion of specific miRNAs from damaged cells into body fluids can make them one of the ideal non-invasive biomarkers in the early diagnosis of schizophrenia. Also, understanding the molecular mechanisms of miRNAs in schizophrenia pathogenesis can pave the way for developing novel treatments for patients with schizophrenia. In this study, we reviewed the glutamatergic and dopaminergic pathophysiology and highlighted the role of miRNA dysregulation in schizophrenia development. Besides, we shed light on the significance of circulating miRNAs for schizophrenia diagnosis and the recent findings on the miRNA-based treatment for schizophrenia.
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Affiliation(s)
| | - Mohammad Ghanbari
- Department of Animal Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran.
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2
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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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3
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Poller W, Sahoo S, Hajjar R, Landmesser U, Krichevsky AM. Exploration of the Noncoding Genome for Human-Specific Therapeutic Targets-Recent Insights at Molecular and Cellular Level. Cells 2023; 12:2660. [PMID: 37998395 PMCID: PMC10670380 DOI: 10.3390/cells12222660] [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: 10/06/2023] [Revised: 11/13/2023] [Accepted: 11/14/2023] [Indexed: 11/25/2023] Open
Abstract
While it is well known that 98-99% of the human genome does not encode proteins, but are nevertheless transcriptionally active and give rise to a broad spectrum of noncoding RNAs [ncRNAs] with complex regulatory and structural functions, specific functions have so far been assigned to only a tiny fraction of all known transcripts. On the other hand, the striking observation of an overwhelmingly growing fraction of ncRNAs, in contrast to an only modest increase in the number of protein-coding genes, during evolution from simple organisms to humans, strongly suggests critical but so far essentially unexplored roles of the noncoding genome for human health and disease pathogenesis. Research into the vast realm of the noncoding genome during the past decades thus lead to a profoundly enhanced appreciation of the multi-level complexity of the human genome. Here, we address a few of the many huge remaining knowledge gaps and consider some newly emerging questions and concepts of research. We attempt to provide an up-to-date assessment of recent insights obtained by molecular and cell biological methods, and by the application of systems biology approaches. Specifically, we discuss current data regarding two topics of high current interest: (1) By which mechanisms could evolutionary recent ncRNAs with critical regulatory functions in a broad spectrum of cell types (neural, immune, cardiovascular) constitute novel therapeutic targets in human diseases? (2) Since noncoding genome evolution is causally linked to brain evolution, and given the profound interactions between brain and immune system, could human-specific brain-expressed ncRNAs play a direct or indirect (immune-mediated) role in human diseases? Synergistic with remarkable recent progress regarding delivery, efficacy, and safety of nucleic acid-based therapies, the ongoing large-scale exploration of the noncoding genome for human-specific therapeutic targets is encouraging to proceed with the development and clinical evaluation of novel therapeutic pathways suggested by these research fields.
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Affiliation(s)
- Wolfgang Poller
- Department for Cardiology, Angiology and Intensive Care Medicine, Deutsches Herzzentrum Charité (DHZC), Charité-Universitätsmedizin Berlin, 12200 Berlin, Germany;
- Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 13353 Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Site Berlin, 10785 Berlin, Germany
| | - Susmita Sahoo
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1030, New York, NY 10029, USA;
| | - Roger Hajjar
- Gene & Cell Therapy Institute, Mass General Brigham, 65 Landsdowne St, Suite 143, Cambridge, MA 02139, USA;
| | - Ulf Landmesser
- Department for Cardiology, Angiology and Intensive Care Medicine, Deutsches Herzzentrum Charité (DHZC), Charité-Universitätsmedizin Berlin, 12200 Berlin, Germany;
- German Center for Cardiovascular Research (DZHK), Site Berlin, 10785 Berlin, Germany
- Berlin Institute of Health, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Anna M. Krichevsky
- Department of Neurology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA;
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Shabani K, Pigeon J, Benaissa Touil Zariouh M, Liu T, Saffarian A, Komatsu J, Liu E, Danda N, Becmeur-Lefebvre M, Limame R, Bohl D, Parras C, Hassan BA. The temporal balance between self-renewal and differentiation of human neural stem cells requires the amyloid precursor protein. SCIENCE ADVANCES 2023; 9:eadd5002. [PMID: 37327344 PMCID: PMC10275593 DOI: 10.1126/sciadv.add5002] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 05/11/2023] [Indexed: 06/18/2023]
Abstract
Neurogenesis in the developing human cerebral cortex occurs at a particularly slow rate owing in part to cortical neural progenitors preserving their progenitor state for a relatively long time, while generating neurons. How this balance between the progenitor and neurogenic state is regulated, and whether it contributes to species-specific brain temporal patterning, is poorly understood. Here, we show that the characteristic potential of human neural progenitor cells (NPCs) to remain in a progenitor state as they generate neurons for a prolonged amount of time requires the amyloid precursor protein (APP). In contrast, APP is dispensable in mouse NPCs, which undergo neurogenesis at a much faster rate. Mechanistically, APP cell-autonomously contributes to protracted neurogenesis through suppression of the proneurogenic activator protein-1 transcription factor and facilitation of canonical WNT signaling. We propose that the fine balance between self-renewal and differentiation is homeostatically regulated by APP, which may contribute to human-specific temporal patterns of neurogenesis.
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Affiliation(s)
- Khadijeh Shabani
- Institut du Cerveau–Paris Brain Institute–ICM, Sorbonne Université, INSERM, CNRS, Hôpital Pitié-Salpêtrière, Paris, France
| | - Julien Pigeon
- Institut du Cerveau–Paris Brain Institute–ICM, Sorbonne Université, INSERM, CNRS, Hôpital Pitié-Salpêtrière, Paris, France
| | - Marwan Benaissa Touil Zariouh
- Institut du Cerveau–Paris Brain Institute–ICM, Sorbonne Université, INSERM, CNRS, Hôpital Pitié-Salpêtrière, Paris, France
| | - Tengyuan Liu
- Institut du Cerveau–Paris Brain Institute–ICM, Sorbonne Université, INSERM, CNRS, Hôpital Pitié-Salpêtrière, Paris, France
| | - Azadeh Saffarian
- Scipio bioscience, iPEPS-ICM, Hôpital Pitié-Salpêtrière, Paris, France
| | - Jun Komatsu
- Scipio bioscience, iPEPS-ICM, Hôpital Pitié-Salpêtrière, Paris, France
| | - Elise Liu
- Institut du Cerveau–Paris Brain Institute–ICM, Sorbonne Université, INSERM, CNRS, Hôpital Pitié-Salpêtrière, Paris, France
| | - Natasha Danda
- Institut du Cerveau–Paris Brain Institute–ICM, Sorbonne Université, INSERM, CNRS, Hôpital Pitié-Salpêtrière, Paris, France
| | - Mathilde Becmeur-Lefebvre
- Genetics and Foetopathology, Centre Hospitalier Regional d’Orleans–Hôpital de la Source, Orleans, France
| | - Ridha Limame
- Institut du Cerveau–Paris Brain Institute–ICM, Sorbonne Université, INSERM, CNRS, Hôpital Pitié-Salpêtrière, Paris, France
| | - Delphine Bohl
- Institut du Cerveau–Paris Brain Institute–ICM, Sorbonne Université, INSERM, CNRS, Hôpital Pitié-Salpêtrière, Paris, France
| | - Carlos Parras
- Institut du Cerveau–Paris Brain Institute–ICM, Sorbonne Université, INSERM, CNRS, Hôpital Pitié-Salpêtrière, Paris, France
| | - Bassem A. Hassan
- Institut du Cerveau–Paris Brain Institute–ICM, Sorbonne Université, INSERM, CNRS, Hôpital Pitié-Salpêtrière, Paris, France
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5
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Lukiw WJ. MicroRNA (miRNA) Complexity in Alzheimer's Disease (AD). BIOLOGY 2023; 12:788. [PMID: 37372073 DOI: 10.3390/biology12060788] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 05/11/2023] [Accepted: 05/18/2023] [Indexed: 06/29/2023]
Abstract
AD is a complex, progressive, age-related neurodegenerative disorder representing the most common cause of senile dementia and neurological dysfunction in our elderly domestic population. The widely observed heterogeneity of AD is a reflection of the complexity of the AD process itself and the altered molecular-genetic mechanisms operating in the diseased human brain and CNS. One of the key players in this complex regulation of gene expression in human pathological neurobiology are microRNAs (miRNAs) that, through their actions, shape the transcriptome of brain cells that normally associate with very high rates of genetic activity, gene transcription and messenger RNA (mRNA) generation. The analysis of miRNA populations and the characterization of their abundance, speciation and complexity can further provide valuable clues to our molecular-genetic understanding of the AD process, especially in the sporadic forms of this common brain disorder. Current in-depth analyses of high-quality AD and age- and gender-matched control brain tissues are providing pathophysiological miRNA-based signatures of AD that can serve as a basis for expanding our mechanistic understanding of this disorder and the future design of miRNA- and related RNA-based therapeutics. This focused review will consolidate the findings from multiple laboratories as to which are the most abundant miRNA species, both free and exosome-bound in the human brain and CNS, which miRNA species appear to be the most prominently affected by the AD process and review recent developments and advancements in our understanding of the complexity of miRNA signaling in the hippocampal CA1 region of AD-affected brains.
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Affiliation(s)
- Walter J Lukiw
- LSU Neuroscience Center, Louisiana State University Health Science Center, New Orleans, LA 70112, USA
- Alchem Biotech Research, Toronto, ON M5S 1A8, Canada
- Department of Ophthalmology, LSU Health Science Center, New Orleans, LA 70112, USA
- Department Neurology, Louisiana State University Health Science Center, New Orleans, LA 70112, USA
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6
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Guo Z, Kuang Z, Deng Y, Li L, Yang X. Identification of Species-Specific MicroRNAs Provides Insights into Dynamic Evolution of MicroRNAs in Plants. Int J Mol Sci 2022; 23:ijms232214273. [PMID: 36430750 PMCID: PMC9698635 DOI: 10.3390/ijms232214273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/08/2022] [Accepted: 11/15/2022] [Indexed: 11/19/2022] Open
Abstract
MicroRNAs (miRNAs) are an important class of regulatory small RNAs that program gene expression, mainly at the post-transcriptional level. Although sporadic examples of species-specific miRNAs (termed SS-miRNAs) have been reported, a genome-scale study across a variety of distant species has not been assessed. Here, by comprehensively analyzing miRNAs in 81 plant species phylogenetically ranging from chlorophytes to angiosperms, we identified 8048 species-specific miRNAs from 5499 families, representing over 61.2% of the miRNA families in the examined species. An analysis of the conservation from different taxonomic levels supported the high turnover rate of SS-miRNAs, even over short evolutionary distances. A comparison of the intrinsic features between SS-miRNAs and NSS-miRNAs (non-species-specific miRNAs) indicated that the AU content of mature miRNAs was the most striking difference. Our data further illustrated a significant bias of the genomic coordinates towards SS-miRNAs lying close to or within genes. By analyzing the 125,267 putative target genes for the 7966 miRNAs, we found the preferentially regulated functions of SS-miRNAs related to diverse metabolic processes. Collectively, these findings underscore the dynamic evolution of miRNAs in the species-specific lineages.
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Affiliation(s)
- Zhonglong Guo
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Zheng Kuang
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Yang Deng
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Lei Li
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
- Correspondence: (L.L.); (X.Y.)
| | - Xiaozeng Yang
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
- Correspondence: (L.L.); (X.Y.)
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7
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Domingo‐Rodriguez L, Cabana‐Domínguez J, Fernàndez‐Castillo N, Cormand B, Martín‐García E, Maldonado R. Differential expression of miR‐1249‐3p and miR‐34b‐5p between vulnerable and resilient phenotypes of cocaine addiction. Addict Biol 2022; 27:e13201. [PMID: 36001423 PMCID: PMC9286869 DOI: 10.1111/adb.13201] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 05/13/2022] [Accepted: 06/03/2022] [Indexed: 11/28/2022]
Affiliation(s)
- Laura Domingo‐Rodriguez
- Laboratory of Neuropharmacology‐Neurophar, Department of Medicine and Life Sciences Universitat Pompeu Fabra (UPF) Barcelona Spain
| | - Judit Cabana‐Domínguez
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia Universitat de Barcelona Barcelona Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) Barcelona Spain
- Institut de Biomedicina de la Universitat de Barcelona (IBUB), Universitat de Barcelona Barcelona Spain
- Institut de Recerca Sant Joan de Déu (IR‐SJD) Barcelona Spain
| | - Noèlia Fernàndez‐Castillo
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia Universitat de Barcelona Barcelona Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) Barcelona Spain
- Institut de Biomedicina de la Universitat de Barcelona (IBUB), Universitat de Barcelona Barcelona Spain
- Institut de Recerca Sant Joan de Déu (IR‐SJD) Barcelona Spain
| | - Bru Cormand
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia Universitat de Barcelona Barcelona Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) Barcelona Spain
- Institut de Biomedicina de la Universitat de Barcelona (IBUB), Universitat de Barcelona Barcelona Spain
- Institut de Recerca Sant Joan de Déu (IR‐SJD) Barcelona Spain
| | - Elena Martín‐García
- Laboratory of Neuropharmacology‐Neurophar, Department of Medicine and Life Sciences Universitat Pompeu Fabra (UPF) Barcelona Spain
- Hospital del Mar Medical Research Institute (IMIM) Barcelona Spain
| | - Rafael Maldonado
- Laboratory of Neuropharmacology‐Neurophar, Department of Medicine and Life Sciences Universitat Pompeu Fabra (UPF) Barcelona Spain
- Hospital del Mar Medical Research Institute (IMIM) Barcelona Spain
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8
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Yang JH, Chang MW, Tsitsipatis D, Yang X, Martindale J, Munk R, Cheng A, Izydore E, Pandey PR, Piao Y, Mazan-Mamczarz K, De S, Abdelmohsen K, Gorospe M. LncRNA OIP5-AS1-directed miR-7 degradation promotes MYMX production during human myogenesis. Nucleic Acids Res 2022; 50:7115-7133. [PMID: 35736212 PMCID: PMC9262585 DOI: 10.1093/nar/gkac524] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 05/22/2022] [Accepted: 06/01/2022] [Indexed: 12/24/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) and microRNAs (miRNAs) modulate gene expression programs in physiology and disease. Here, we report a noncoding RNA regulatory network that modulates myoblast fusion into multinucleated myotubes, a process that occurs during muscle development and muscle regeneration after injury. In early stages of human myogenesis, the levels of lncRNA OIP5-AS1 increased, while the levels of miR-7 decreased. Moreover, OIP5-AS1 bound and induced miR-7 decay via target RNA-directed miRNA decay; accordingly, loss of OIP5-AS1 attenuated, while antagonizing miR-7 accelerated, myotube formation. We found that the OIP5-AS1-mediated miR-7 degradation promoted myoblast fusion, as it derepressed the miR-7 target MYMX mRNA, which encodes the fusogenic protein myomixer (MYMX). Remarkably, an oligonucleotide site blocker interfered with the OIP5-AS1-directed miR-7 degradation, allowing miR-7 to accumulate, lowering MYMX production and suppressing myotube formation. These results highlight a mechanism whereby lncRNA OIP5-AS1-mediated miR-7 decay promotes myotube formation by stimulating a myogenic fusion program.
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Affiliation(s)
- Jen-Hao Yang
- Correspondence may also be addressed to Jen-Hao Yang. Tel: +1 410 454 8392;
| | - Ming-Wen Chang
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, 251 Bayview Blvd, Baltimore, MD 21224, USA
| | - Dimitrios Tsitsipatis
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, 251 Bayview Blvd, Baltimore, MD 21224, USA
| | - Xiaoling Yang
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, 251 Bayview Blvd, Baltimore, MD 21224, USA
| | - Jennifer L Martindale
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, 251 Bayview Blvd, Baltimore, MD 21224, USA
| | - Rachel Munk
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, 251 Bayview Blvd, Baltimore, MD 21224, USA
| | - Aiwu Cheng
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, 251 Bayview Blvd, Baltimore, MD 21224, USA
| | - Elizabeth Izydore
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, 251 Bayview Blvd, Baltimore, MD 21224, USA
| | - Poonam R Pandey
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, 251 Bayview Blvd, Baltimore, MD 21224, USA
| | - Yulan Piao
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, 251 Bayview Blvd, Baltimore, MD 21224, USA
| | - Krystyna Mazan-Mamczarz
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, 251 Bayview Blvd, Baltimore, MD 21224, USA
| | - Supriyo De
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, 251 Bayview Blvd, Baltimore, MD 21224, USA
| | - Kotb Abdelmohsen
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, 251 Bayview Blvd, Baltimore, MD 21224, USA
| | - Myriam Gorospe
- To whom correspondence should be addressed. Tel: +1 410 454 8412;
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9
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Yang Q, Hong Y, Zhao T, Song H, Ming GL. What Makes Organoids Good Models of Human Neurogenesis? Front Neurosci 2022; 16:872794. [PMID: 35495031 PMCID: PMC9048596 DOI: 10.3389/fnins.2022.872794] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 03/02/2022] [Indexed: 01/03/2023] Open
Abstract
Human neurogenesis occurs mainly in embryonic, fetal, and neonatal stages and generates tremendously diverse neural cell types that constitute the human nervous system. Studies on human neurogenesis have been limited due to a lack of access to human embryonic and fetal tissues. Brain organoids derived from human pluripotent stem cells not only recapitulate major developmental processes during neurogenesis, but also exhibit human-specific features, thus providing an unprecedented opportunity to study human neurodevelopment. First, three-dimensional brain organoids resemble early human neurogenesis with diverse stem cell pools, including the presence of primate-enriched outer radial glia cells. Second, brain organoids recapitulate human neurogenesis at the cellular level, generating diverse neuronal cell types and forming stratified cortical layers. Third, brain organoids also capture gliogenesis with the presence of human-specific astrocytes. Fourth, combined with genome-editing technologies, brain organoids are promising models for investigating functions of human-specific genes at different stages of human neurogenesis. Finally, human organoids derived from patient iPSCs can recapitulate specific disease phenotypes, providing unique models for studying developmental brain disorders of genetic and environmental causes, and for mechanistic studies and drug screening. The aim of this review is to illustrate why brain organoids are good models to study various steps of human neurogenesis, with a focus on corticogenesis. We also discuss limitations of current brain organoid models and future improvements.
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Affiliation(s)
- Qian Yang
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Yan Hong
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Ting Zhao
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Hongjun Song
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States,Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States,Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA, United States,The Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Guo-li Ming
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States,Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States,Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA, United States,Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States,*Correspondence: Guo-li Ming,
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10
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Rajagopal R, Baltazar MT, Carmichael PL, Dent MP, Head J, Li H, Muller I, Reynolds J, Sadh K, Simpson W, Spriggs S, White A, Kukic P. Beyond AOPs: A Mechanistic Evaluation of NAMs in DART Testing. FRONTIERS IN TOXICOLOGY 2022; 4:838466. [PMID: 35295212 PMCID: PMC8915803 DOI: 10.3389/ftox.2022.838466] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 01/31/2022] [Indexed: 12/22/2022] Open
Abstract
New Approach Methodologies (NAMs) promise to offer a unique opportunity to enable human-relevant safety decisions to be made without the need for animal testing in the context of exposure-driven Next Generation Risk Assessment (NGRA). Protecting human health against the potential effects a chemical may have on embryo-foetal development and/or aspects of reproductive biology using NGRA is particularly challenging. These are not single endpoint or health effects and risk assessments have traditionally relied on data from Developmental and Reproductive Toxicity (DART) tests in animals. There are numerous Adverse Outcome Pathways (AOPs) that can lead to DART, which means defining and developing strict testing strategies for every AOP, to predict apical outcomes, is neither a tenable goal nor a necessity to ensure NAM-based safety assessments are fit-for-purpose. Instead, a pragmatic approach is needed that uses the available knowledge and data to ensure NAM-based exposure-led safety assessments are sufficiently protective. To this end, the mechanistic and biological coverage of existing NAMs for DART were assessed and gaps to be addressed were identified, allowing the development of an approach that relies on generating data relevant to the overall mechanisms involved in human reproduction and embryo-foetal development. Using the knowledge of cellular processes and signalling pathways underlying the key stages in reproduction and development, we have developed a broad outline of endpoints informative of DART. When the existing NAMs were compared against this outline to determine whether they provide comprehensive coverage when integrated in a framework, we found them to generally cover the reproductive and developmental processes underlying the traditionally evaluated apical endpoint studies. The application of this safety assessment framework is illustrated using an exposure-led case study.
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11
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Mead B, Tomarev S. The role of miRNA in retinal ganglion cell health and disease. Neural Regen Res 2022; 17:516-522. [PMID: 34380881 PMCID: PMC8504366 DOI: 10.4103/1673-5374.320974] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 01/19/2021] [Accepted: 04/15/2021] [Indexed: 12/03/2022] Open
Abstract
miRNA are short non-coding RNA responsible for the knockdown of proteins through their targeting and silencing of complimentary mRNA sequences. The miRNA landscape of a cell thus affects the levels of its proteins and has significant consequences to its health. Deviations in this miRNA landscape have been implicated in a variety of neurodegenerative diseases and have also garnered interest as targets for treatment. Retinal ganglion cells are the sole projection neuron of the retina with their axons making up the optic nerve. They are a focus of study not only for their importance in vision and the myriad of blinding diseases characterized by their dysfunction and loss, but also as a model of other central nervous system diseases such as spinal cord injury and traumatic brain injury. This review summarizes current knowledge on the role of miRNA in retinal ganglion cell function, highlighting how perturbations can result in disease, and how modulating their abundance may provide a novel avenue of therapeutic research.
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Affiliation(s)
- Ben Mead
- School of Optometry and Vision Sciences, Cardiff University, Cardiff, UK
| | - Stanislav Tomarev
- Section of Retinal Ganglion Cell Biology, Laboratory of Retinal Cell and Molecular Biology, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
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12
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Tsamou M, Carpi D, Pistollato F, Roggen EL. Sporadic Alzheimer's Disease- and Neurotoxicity-Related microRNAs Affecting Key Events of Tau-Driven Adverse Outcome Pathway Toward Memory Loss. J Alzheimers Dis 2022; 86:1427-1457. [PMID: 35213375 DOI: 10.3233/jad-215434] [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] [Indexed: 12/13/2022]
Abstract
BACKGROUND A complex network of aging-related homeostatic pathways that are sensitive to further deterioration in the presence of genetic, systemic, and environmental risk factors, and lifestyle, is implicated in the pathogenesis of progressive neurodegenerative diseases, such as sporadic (late-onset) Alzheimer's disease (sAD). OBJECTIVE Since sAD pathology and neurotoxicity share microRNAs (miRs) regulating common as well as overlapping pathological processes, environmental neurotoxic compounds are hypothesized to exert a risk for sAD initiation and progression. METHODS Literature search for miRs associated with human sAD and environmental neurotoxic compounds was conducted. Functional miR analysis using PathDip was performed to create miR-target interaction networks. RESULTS The identified miRs were successfully linked to the hypothetical starting point and key events of the earlier proposed tau-driven adverse outcome pathway toward memory loss. Functional miR analysis confirmed most of the findings retrieved from literature and revealed some interesting findings. The analysis identified 40 miRs involved in both sAD and neurotoxicity that dysregulated processes governing the plausible adverse outcome pathway for memory loss. CONCLUSION Creating miR-target interaction networks related to pathological processes involved in sAD initiation and progression, and environmental chemical-induced neurotoxicity, respectively, provided overlapping miR-target interaction networks. This overlap offered an opportunity to create an alternative picture of the mechanisms underlying sAD initiation and early progression. Looking at initiation and progression of sAD from this new angle may open for new biomarkers and novel drug targets for sAD before the appearance of the first clinical symptoms.
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Affiliation(s)
- Maria Tsamou
- ToxGenSolutions (TGS), Maastricht, The Netherlands
| | - Donatella Carpi
- European Commission, Joint Research Centre (JRC), Ispra VA, Italy
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13
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PM10 Alters Trophoblast Cell Function and Modulates miR-125b-5p Expression. BIOMED RESEARCH INTERNATIONAL 2022; 2022:3697944. [PMID: 35036432 PMCID: PMC8759905 DOI: 10.1155/2022/3697944] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 11/05/2021] [Accepted: 11/10/2021] [Indexed: 12/16/2022]
Abstract
Air pollution is one of the largest global environmental health hazards that threaten premature mortality or morbidity. Particulate matter 10 (PM10) has been demonstrated to contribute to several human diseases via dysregulated miRNA expression. Trophoblast cells play a key role in implantation and placentation for a successful pregnancy. Nonetheless, the PM10 associated trophoblast cell functions during pregnancy and miRNA expression are still unknown. Our study showed that PM10 affected HTR-8/SVneo cell viability and also decreased cell proliferation, migration, and invasion. A high concentration of PM10 caused an increase in HTR-8/SVneo cell apoptosis. Treatment with PM10 induced inflammation through the upregulated IL-1β, IL-6, and TNF-α expression in trophoblast cells. In PM10-treated HTR-8/SVneo cells, miR-125b-5p expression was considerably increased and TXNRD1 was found to be negatively related to miR-125b-5p. Collectively, our findings revealed that PM10 could alter miR-125b-5p expression by targeting TXNRD1 and suppressing trophoblast cell functions. Additional investigations relating to the function of miR-125b-5p and its target on particulate pollution exposure in trophoblast are warranted for future biomarker or effective therapeutic approaches.
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14
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Marino M, Mele E, Pastorino GMG, Meccariello R, Operto FF, Santoro A, Viggiano A. Neuroinflammation: Molecular Mechanisms And Therapeutic Perspectives. Cent Nerv Syst Agents Med Chem 2022; 22:160-174. [PMID: 36177627 DOI: 10.2174/1871524922666220929153215] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 08/01/2022] [Accepted: 08/22/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Neuroinflammation is a key component in the etiopathogenesis of neurological diseases and brain aging. This process involves the brain immune system that modulates synaptic functions and protects neurons from infection or damage. Hence, the knowledge of neuroinflammation related pathways and modulation by drugs or natural compounds is functional to developing therapeutic strategies aimed at preserving, maintaining and restoring brain health. OBJECTIVE This review article summarizes the basics of neuroinflammation and related signaling pathways, the success of the dietary intervention in clinical practice and the possible development of RNA-based strategies for treating neurological diseases. METHODS Pubmed search from 2012 to 2022 with the keywords neuroinflammation and molecular mechanisms in combination with diet, miRNA and non-coding RNA. RESULTS Glial cells-play a crucial role in neuroinflammation, but several pathways can be activated in response to different inflammatory stimuli, inducing cell death by apoptosis, pyroptosis or necroptosis. The dietary intervention has immunomodulatory effects and could limit the inflammatory process induced by microglia and astrocytes. Thus by inhibiting neuroinflammation and improving the symptoms of a variety of neurological diseases, diet exerts pleiotropic neuroprotective effects independently from the spectrum of pathophysiological mechanisms underlying the specific disorder. Furthermore, data from animal models revealed that altered expression of specific noncoding RNAs, in particular microRNAs, contributes to neuroinflammatory diseases; consequently, RNA-based strategies may be promising to alleviate the consequences of neuroinflammation. CONCLUSION Further studies are needed to identify the molecular pathways and the new pharmacological targets in neuroinflammation to lay the basis for more effective and selective therapies to be applied, in parallel to dietary intervention, in the treatment of neuroinflammation-based diseases.
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Affiliation(s)
- Marianna Marino
- Dipartimento di Medicina, Chirurgia e Odontoiatria "Scuola Medica Salernitana", Università di Salerno, 84081 Baronissi, Italy
| | - Elena Mele
- Dipartimento di Scienze Motorie e del Benessere, Università di Napoli Parthenope, 80133 Napoli, Italy
| | | | - Rosaria Meccariello
- Dipartimento di Scienze Motorie e del Benessere, Università di Napoli Parthenope, 80133 Napoli, Italy
| | - Francesca Felicia Operto
- Child and Adolescent Neuropsychiatry Unit, Medical School, University of Salerno, Salerno, Italy
| | - Antonietta Santoro
- Dipartimento di Medicina, Chirurgia e Odontoiatria "Scuola Medica Salernitana", Università di Salerno, 84081 Baronissi, Italy
| | - Andrea Viggiano
- Dipartimento di Medicina, Chirurgia e Odontoiatria "Scuola Medica Salernitana", Università di Salerno, 84081 Baronissi, Italy
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15
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Prodromidou K, Matsas R. Evolving features of human cortical development and the emerging roles of non-coding RNAs in neural progenitor cell diversity and function. Cell Mol Life Sci 2021; 79:56. [PMID: 34921638 PMCID: PMC11071749 DOI: 10.1007/s00018-021-04063-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 11/25/2021] [Accepted: 11/26/2021] [Indexed: 10/19/2022]
Abstract
The human cerebral cortex is a uniquely complex structure encompassing an unparalleled diversity of neuronal types and subtypes. These arise during development through a series of evolutionary conserved processes, such as progenitor cell proliferation, migration and differentiation, incorporating human-associated adaptations including a protracted neurogenesis and the emergence of novel highly heterogeneous progenitor populations. Disentangling the unique features of human cortical development involves elucidation of the intricate developmental cell transitions orchestrated by progressive molecular events. Crucially, developmental timing controls the fine balance between cell cycle progression/exit and the neurogenic competence of precursor cells, which undergo morphological transitions coupled to transcriptome-defined temporal states. Recent advances in bulk and single-cell transcriptomic technologies suggest that alongside protein-coding genes, non-coding RNAs exert important regulatory roles in these processes. Interestingly, a considerable number of novel long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) have appeared in human and non-human primates suggesting an evolutionary role in shaping cortical development. Here, we present an overview of human cortical development and highlight the marked diversification and complexity of human neuronal progenitors. We further discuss how lncRNAs and miRNAs constitute critical components of the extended epigenetic regulatory network defining intermediate states of progenitors and controlling cell cycle dynamics and fate choices with spatiotemporal precision, during human neurodevelopment.
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Affiliation(s)
- Kanella Prodromidou
- Laboratory of Cellular and Molecular Neurobiology-Stem Cells, Department of Neurobiology, Hellenic Pasteur Institute, 127 Vasilissis Sofias Avenue, 11521, Athens, Greece.
| | - Rebecca Matsas
- Laboratory of Cellular and Molecular Neurobiology-Stem Cells, Department of Neurobiology, Hellenic Pasteur Institute, 127 Vasilissis Sofias Avenue, 11521, Athens, Greece
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16
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Liu J, Mosti F, Silver DL. Human brain evolution: Emerging roles for regulatory DNA and RNA. Curr Opin Neurobiol 2021; 71:170-177. [PMID: 34861533 PMCID: PMC8756680 DOI: 10.1016/j.conb.2021.11.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 09/03/2021] [Accepted: 11/02/2021] [Indexed: 12/18/2022]
Abstract
Humans diverge from other primates in numerous ways, including their neuroanatomy and cognitive capacities. Human-specific features are particularly prominent in the cerebral cortex, which has undergone an expansion in size and acquired unique cellular composition and circuitry. Human-specific gene expression is postulated to explain neocortical anatomical differences across evolution. In particular, noncoding regulatory loci are strongly linked to human traits, including progenitor proliferation and cortical size. In this review, we highlight emerging noncoding elements implicated in human cortical evolution, including roles for regulatory DNA and RNA. Further, we discuss the association of human-specific genetic changes with neurodevelopmental diseases.
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Affiliation(s)
- Jing Liu
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Federica Mosti
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA; Department of Neurobiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Debra L Silver
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA; Department of Neurobiology, Duke University Medical Center, Durham, NC 27710, USA; Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA; Duke Regeneration Center and Duke Institute for Brain Sciences, Duke University Medical Center, Durham, NC 277710, USA.
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17
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Guy B, Zhang JS, Duncan LH, Johnston RJ. Human neural organoids: Models for developmental neurobiology and disease. Dev Biol 2021; 478:102-121. [PMID: 34181916 PMCID: PMC8364509 DOI: 10.1016/j.ydbio.2021.06.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 06/08/2021] [Accepted: 06/24/2021] [Indexed: 12/25/2022]
Abstract
Human organoids stand at the forefront of basic and translational research, providing experimentally tractable systems to study human development and disease. These stem cell-derived, in vitro cultures can generate a multitude of tissue and organ types, including distinct brain regions and sensory systems. Neural organoid systems have provided fundamental insights into molecular mechanisms governing cell fate specification and neural circuit assembly and serve as promising tools for drug discovery and understanding disease pathogenesis. In this review, we discuss several human neural organoid systems, how they are generated, advances in 3D imaging and bioengineering, and the impact of organoid studies on our understanding of the human nervous system.
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Affiliation(s)
- Brian Guy
- Department of Biology, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD, 21218, USA
| | - Jingliang Simon Zhang
- Department of Biology, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD, 21218, USA
| | - Leighton H Duncan
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Robert J Johnston
- Department of Biology, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD, 21218, USA.
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18
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Yoshida T, Asano Y, Ui-Tei K. Modulation of MicroRNA Processing by Dicer via Its Associated dsRNA Binding Proteins. Noncoding RNA 2021; 7:ncrna7030057. [PMID: 34564319 PMCID: PMC8482068 DOI: 10.3390/ncrna7030057] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/13/2021] [Accepted: 09/13/2021] [Indexed: 12/12/2022] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that are about 22 nucleotides in length. They regulate gene expression post-transcriptionally by guiding the effector protein Argonaute to its target mRNA in a sequence-dependent manner, causing the translational repression and destabilization of the target mRNAs. Both Drosha and Dicer, members of the RNase III family proteins, are essential components in the canonical miRNA biogenesis pathway. miRNA is transcribed into primary-miRNA (pri-miRNA) from genomic DNA. Drosha then cleaves the flanking regions of pri-miRNA into precursor-miRNA (pre-miRNA), while Dicer cleaves the loop region of the pre-miRNA to form a miRNA duplex. Although the role of Drosha and Dicer in miRNA maturation is well known, the modulation processes that are important for regulating the downstream gene network are not fully understood. In this review, we summarized and discussed current reports on miRNA biogenesis caused by Drosha and Dicer. We also discussed the modulation mechanisms regulated by double-stranded RNA binding proteins (dsRBPs) and the function and substrate specificity of dsRBPs, including the TAR RNA binding protein (TRBP) and the adenosine deaminase acting on RNA (ADAR).
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19
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Fonseca Cabral G, Schaan AP, Cavalcante GC, Sena-dos-Santos C, de Souza TP, Souza Port’s NM, dos Santos Pinheiro JA, Ribeiro-dos-Santos Â, Vidal AF. Nuclear and Mitochondrial Genome, Epigenome and Gut Microbiome: Emerging Molecular Biomarkers for Parkinson's Disease. Int J Mol Sci 2021; 22:9839. [PMID: 34576000 PMCID: PMC8471599 DOI: 10.3390/ijms22189839] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 06/23/2021] [Accepted: 06/28/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Parkinson's disease (PD) is currently the second most common neurodegenerative disorder, burdening about 10 million elderly individuals worldwide. The multifactorial nature of PD poses a difficult obstacle for understanding the mechanisms involved in its onset and progression. Currently, diagnosis depends on the appearance of clinical signs, some of which are shared among various neurologic disorders, hindering early diagnosis. There are no effective tools to prevent PD onset, detect the disease in early stages or accurately report the risk of disease progression. Hence, there is an increasing demand for biomarkers that may identify disease onset and progression, as treatment-based medicine may not be the best approach for PD. Over the last few decades, the search for molecular markers to predict susceptibility, aid in accurate diagnosis and evaluate the progress of PD have intensified, but strategies aimed to improve individualized patient care have not yet been established. CONCLUSIONS Genomic variation, regulation by epigenomic mechanisms, as well as the influence of the host gut microbiome seem to have a crucial role in the onset and progress of PD, thus are considered potential biomarkers. As such, the human nuclear and mitochondrial genome, epigenome, and the host gut microbiome might be the key elements to the rise of personalized medicine for PD patients.
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Affiliation(s)
- Gleyce Fonseca Cabral
- Laboratório de Genética Humana e Médica, Universidade Federal do Pará, R. Augusto Correa, Belém 66075-110, Brazil; (G.F.C.); (A.P.S.); (G.C.C.); (C.S.-d.-S.); (T.P.d.S.); (J.A.d.S.P.)
| | - Ana Paula Schaan
- Laboratório de Genética Humana e Médica, Universidade Federal do Pará, R. Augusto Correa, Belém 66075-110, Brazil; (G.F.C.); (A.P.S.); (G.C.C.); (C.S.-d.-S.); (T.P.d.S.); (J.A.d.S.P.)
| | - Giovanna C. Cavalcante
- Laboratório de Genética Humana e Médica, Universidade Federal do Pará, R. Augusto Correa, Belém 66075-110, Brazil; (G.F.C.); (A.P.S.); (G.C.C.); (C.S.-d.-S.); (T.P.d.S.); (J.A.d.S.P.)
| | - Camille Sena-dos-Santos
- Laboratório de Genética Humana e Médica, Universidade Federal do Pará, R. Augusto Correa, Belém 66075-110, Brazil; (G.F.C.); (A.P.S.); (G.C.C.); (C.S.-d.-S.); (T.P.d.S.); (J.A.d.S.P.)
| | - Tatiane Piedade de Souza
- Laboratório de Genética Humana e Médica, Universidade Federal do Pará, R. Augusto Correa, Belém 66075-110, Brazil; (G.F.C.); (A.P.S.); (G.C.C.); (C.S.-d.-S.); (T.P.d.S.); (J.A.d.S.P.)
| | - Natacha M. Souza Port’s
- Laboratório de Neurofarmacologia Molecular, Universidade de São Paulo, São Paulo 05508-000, Brazil;
| | - Jhully Azevedo dos Santos Pinheiro
- Laboratório de Genética Humana e Médica, Universidade Federal do Pará, R. Augusto Correa, Belém 66075-110, Brazil; (G.F.C.); (A.P.S.); (G.C.C.); (C.S.-d.-S.); (T.P.d.S.); (J.A.d.S.P.)
| | - Ândrea Ribeiro-dos-Santos
- Laboratório de Genética Humana e Médica, Universidade Federal do Pará, R. Augusto Correa, Belém 66075-110, Brazil; (G.F.C.); (A.P.S.); (G.C.C.); (C.S.-d.-S.); (T.P.d.S.); (J.A.d.S.P.)
- Núcleo de Pesquisas em Oncologia, Universidade Federal do Pará–R. dos Mundurucus, Belém 66073-000, Brazil
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Pará, R. Augusto Correa, Belém 66075-110, Brazil
| | - Amanda F. Vidal
- Laboratório de Genética Humana e Médica, Universidade Federal do Pará, R. Augusto Correa, Belém 66075-110, Brazil; (G.F.C.); (A.P.S.); (G.C.C.); (C.S.-d.-S.); (T.P.d.S.); (J.A.d.S.P.)
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Pará, R. Augusto Correa, Belém 66075-110, Brazil
- ITVDS—Instituto Tecnológico Vale Desenvolvimento Sustentável–R. Boaventura da Silva, Belém 66055-090, Brazil
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Ferrari R, Grandi N, Tramontano E, Dieci G. Retrotransposons as Drivers of Mammalian Brain Evolution. Life (Basel) 2021; 11:life11050376. [PMID: 33922141 PMCID: PMC8143547 DOI: 10.3390/life11050376] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 04/20/2021] [Accepted: 04/21/2021] [Indexed: 12/11/2022] Open
Abstract
Retrotransposons, a large and diverse class of transposable elements that are still active in humans, represent a remarkable force of genomic innovation underlying mammalian evolution. Among the features distinguishing mammals from all other vertebrates, the presence of a neocortex with a peculiar neuronal organization, composition and connectivity is perhaps the one that, by affecting the cognitive abilities of mammals, contributed mostly to their evolutionary success. Among mammals, hominids and especially humans display an extraordinarily expanded cortical volume, an enrichment of the repertoire of neural cell types and more elaborate patterns of neuronal connectivity. Retrotransposon-derived sequences have recently been implicated in multiple layers of gene regulation in the brain, from transcriptional and post-transcriptional control to both local and large-scale three-dimensional chromatin organization. Accordingly, an increasing variety of neurodevelopmental and neurodegenerative conditions are being recognized to be associated with retrotransposon dysregulation. We review here a large body of recent studies lending support to the idea that retrotransposon-dependent evolutionary novelties were crucial for the emergence of mammalian, primate and human peculiarities of brain morphology and function.
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Affiliation(s)
- Roberto Ferrari
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy;
| | - Nicole Grandi
- Laboratory of Molecular Virology, Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, 09042 Monserrato, Italy; (N.G.); (E.T.)
| | - Enzo Tramontano
- Laboratory of Molecular Virology, Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, 09042 Monserrato, Italy; (N.G.); (E.T.)
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, 09042 Monserrato, Italy
| | - Giorgio Dieci
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy;
- Correspondence:
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Synergism of Proneurogenic miRNAs Provides a More Effective Strategy to Target Glioma Stem Cells. Cancers (Basel) 2021; 13:cancers13020289. [PMID: 33466745 PMCID: PMC7831004 DOI: 10.3390/cancers13020289] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/08/2021] [Accepted: 01/11/2021] [Indexed: 12/16/2022] Open
Abstract
Simple Summary miRNAs function as critical regulators of gene expression and have been defined as contributors of cancer phenotypes by acting as oncogenes or tumor suppressors. Based on these findings, miRNA-based therapies have been explored in the treatment of many different malignancies. The use of single miRNAs has faced some challenges and showed limited success. miRNAs cooperate to regulate distinct biological processes and pathways and, therefore, combination of related miRNAs could amplify the repression of oncogenic factors and the effect on cancer relevant pathways. We established that the combination of tumor suppressor miRNAs miR-124, miR-128, and miR-137 is much more effective than single miRNAs in disrupting proliferation and survival of glioma stem cells and neuroblastoma lines and promoting differentiation and response to radiation. Subsequent genomic analyses showed that other combinations of tumor suppressor miRNAs could be equally effective, and its use could provide new routes to target in special cancer-initiating cell populations. Abstract Tumor suppressor microRNAs (miRNAs) have been explored as agents to target cancer stem cells. Most strategies use a single miRNA mimic and present many disadvantages, such as the amount of reagent required and the diluted effect on target genes. miRNAs work in a cooperative fashion to regulate distinct biological processes and pathways. Therefore, we propose that miRNA combinations could provide more efficient ways to target cancer stem cells. We have previously shown that miR-124, miR-128, and miR-137 function synergistically to regulate neurogenesis. We used a combination of these three miRNAs to treat glioma stem cells and showed that this treatment was much more effective than single miRNAs in disrupting cell proliferation and survival and promoting differentiation and response to radiation. Transcriptomic analyses indicated that transcription regulation, angiogenesis, metabolism, and neuronal differentiation are among the main biological processes affected by transfection of this miRNA combination. In conclusion, we demonstrated the value of using combinations of neurogenic miRNAs to disrupt cancer phenotypes and glioma stem cell growth. The synergistic effect of these three miRNA amplified the repression of oncogenic factors and the effect on cancer relevant pathways. Future therapeutic approaches would benefit from utilizing miRNA combinations, especially when targeting cancer-initiating cell populations.
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Yang MS, Xu XJ, Zhang B, Niu F, Liu BY. Comparative transcriptomic analysis of rat versus mouse cerebral cortex after traumatic brain injury. Neural Regen Res 2021; 16:1235-1243. [PMID: 33318400 PMCID: PMC8284282 DOI: 10.4103/1673-5374.301028] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The heterogeneity of traumatic brain injury (TBI)-induced secondary injury has greatly hampered the development of effective treatments for TBI patients. Targeting common processes across species may be an innovative strategy to combat debilitating TBI. In the present study, a cross-species transcriptome comparison was performed for the first time to determine the fundamental processes of secondary brain injury in Sprague-Dawley rat and C57/BL6 mouse models of TBI, caused by acute controlled cortical impact. The RNA sequencing data from the mouse model of TBI were downloaded from the Gene Expression Omnibus (ID: GSE79441) at the National Center for Biotechnology Information. For the rat data, peri-injury cerebral cortex samples were collected for transcriptomic analysis 24 hours after TBI. Differentially expressed gene-based functional analysis revealed that common features between the two species were mainly involved in the regulation and activation of the innate immune response, including complement cascades as well as Toll-like and nucleotide oligomerization domain-like receptor pathways. These findings were further corroborated by gene set enrichment analysis. Moreover, transcription factor analysis revealed that the families of signal transducers and activators of transcription (STAT), basic leucine zipper (BZIP), Rel homology domain (RHD), and interferon regulatory factor (IRF) transcription factors play vital regulatory roles in the pathophysiological processes of TBI, and are also largely associated with inflammation. These findings suggest that targeting the common innate immune response might be a promising therapeutic approach for TBI. The animal experimental procedures were approved by the Beijing Neurosurgical Institute Animal Care and Use Committee (approval No. 201802001) on June 6, 2018.
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Affiliation(s)
- Meng-Shi Yang
- Beijing Key Laboratory of Central Nervous System Injury, Beijing Neurosurgical Institute; Beijing Key Laboratory of Central Nervous System Injury and Department of Neurosurgery, Beijing Neurosurgical Institute and Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Xiao-Jian Xu
- Beijing Key Laboratory of Central Nervous System Injury, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Bin Zhang
- Beijing Key Laboratory of Central Nervous System Injury, Beijing Neurosurgical Institute; Beijing Key Laboratory of Central Nervous System Injury and Department of Neurosurgery, Beijing Neurosurgical Institute and Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Fei Niu
- Beijing Key Laboratory of Central Nervous System Injury, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Bai-Yun Liu
- Beijing Key Laboratory of Central Nervous System Injury, Beijing Neurosurgical Institute; Beijing Key Laboratory of Central Nervous System Injury and Department of Neurosurgery, Beijing Neurosurgical Institute and Beijing Tiantan Hospital, Capital Medical University; Nerve Injury and Repair Center of Beijing Institute for Brain Disorders; China National Clinical Research Center for Neurological Diseases, Beijing, China
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Lukiw WJ. microRNA-146a Signaling in Alzheimer's Disease (AD) and Prion Disease (PrD). Front Neurol 2020; 11:462. [PMID: 32670176 PMCID: PMC7331828 DOI: 10.3389/fneur.2020.00462] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 04/29/2020] [Indexed: 12/12/2022] Open
Abstract
The mouse- and human-brain-resident, nuclear factor kappa B (NF-κB)-regulated, micro RNA-146a-5p (miRNA-146a-5p) is an inducible, 22-nucleotide, single-stranded non-coding RNA (sncRNA) easily detected in several brain and immunological cell types, and an important epigenetic modulator of inflammatory signaling and the innate-immune response in several neurological disorders. Among all studied microRNAs, miRNA-146a-5p (typically referred to as just miRNA-146a) has been well characterized and its pathological function in progressive, age-related, and lethal human inflammatory neurodegenerative disease states is well documented. This communication will review our current understanding of miRNA-146a, its induction by the NF-kB-stimulating actions of inflammatory mediators, including the secretory products of certain microbial species such as viral vectors, and Gram-negative bacteria (such as Bacteroides fragilis) that are normal residents of the human gastrointestinal (GI) tract microbiome, and how miRNA-146a appears to contribute to neuro-pathological, neuro-inflammatory, and altered neuro-immunological aspects of both Alzheimer's disease (AD) and prion disease (PrD).
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Affiliation(s)
- Walter J Lukiw
- Bollinger Professor of Alzheimer's Disease, Louisiana State University School of Medicine, New Orleans, LA, United States.,LSU Neuroscience Center, Louisiana State University Health Sciences Center, New Orleans, LA, United States.,Department of Ophthalmology, LSUHSC, New Orleans, LA, United States.,Department of Neurology, Louisiana State University Health Sciences Center, New Orleans, LA, United States
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