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Rajabi D, Khanmohammadi S, Rezaei N. The role of long noncoding RNAs in amyotrophic lateral sclerosis. Rev Neurosci 2024; 0:revneuro-2023-0155. [PMID: 38452377 DOI: 10.1515/revneuro-2023-0155] [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: 12/14/2023] [Accepted: 02/18/2024] [Indexed: 03/09/2024]
Abstract
Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease with a poor prognosis leading to death. The diagnosis and treatment of ALS are inherently challenging due to its complex pathomechanism. Long noncoding RNAs (lncRNAs) are transcripts longer than 200 nucleotides involved in different cellular processes, incisively gene expression. In recent years, more studies have been conducted on lncRNA classes and interference in different disease pathologies, showing their promising contribution to diagnosing and treating neurodegenerative diseases. In this review, we discussed the role of lncRNAs like NEAT1 and C9orf72-as in ALS pathogenesis mechanisms caused by mutations in different genes, including TAR DNA-binding protein-43 (TDP-43), fused in sarcoma (FUS), superoxide dismutase type 1 (SOD1). NEAT1 is a well-established lncRNA in ALS pathogenesis; hence, we elaborate on its involvement in forming paraspeckles, stress response, inflammatory response, and apoptosis. Furthermore, antisense lncRNAs (as-lncRNAs), a key group of transcripts from the opposite strand of genes, including ZEB1-AS1 and ATXN2-AS, are discussed as newly identified components in the pathology of ALS. Ultimately, we review the current standing of using lncRNAs as biomarkers and therapeutic agents and the future vision of further studies on lncRNA applications.
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Affiliation(s)
- Darya Rajabi
- School of Medicine, Tehran University of Medical Sciences, Felestin St., Keshavarz Blvd., Tehran, 1416634793, Iran
| | - Shaghayegh Khanmohammadi
- School of Medicine, Tehran University of Medical Sciences, Felestin St., Keshavarz Blvd., Tehran, 1416634793, Iran
- Research Center for Immunodeficiencies, Children's Medical Center, No 63, Gharib Ave, Keshavarz Blv, Tehran, 1419733151, Iran
- Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Children's Medical Center, No 63, Gharib Ave, Keshavarz Blv, Tehran, 1419733151, Iran
| | - Nima Rezaei
- Research Center for Immunodeficiencies, Children's Medical Center, No 63, Gharib Ave, Keshavarz Blv, Tehran, 1419733151, Iran
- Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Children's Medical Center, No 63, Gharib Ave, Keshavarz Blv, Tehran, 1419733151, Iran
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Felestin St., Keshavarz Blvd., Tehran, 1416634793, Iran
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2
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Han Y, Zhu Y, Dutta S, Almuntashiri S, Wang X, Zhang D. A proinflammatory long noncoding RNA Lncenc1 regulates inflammasome activation in macrophage. Am J Physiol Lung Cell Mol Physiol 2023; 324:L584-L595. [PMID: 36880658 PMCID: PMC10085550 DOI: 10.1152/ajplung.00056.2022] [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: 02/15/2022] [Revised: 02/13/2023] [Accepted: 02/28/2023] [Indexed: 03/08/2023] Open
Abstract
Mammalian genomes encode thousands of long noncoding RNAs (lncRNAs). LncRNAs are extensively expressed in various immune cells. The lncRNAs have been reported to be involved in diverse biological processes, including the regulation of gene expression, dosage compensation, and genomic imprinting. However, very little research has been conducted to explore how they alter innate immune responses during host-pathogen interactions. In this study, we found that a lncRNA, named long noncoding RNA, embryonic stem cells expressed 1 (Lncenc1), was strikingly increased in mouse lungs after gram-negative (G-) bacterial infection or exposure to lipopolysaccharides (LPS). Interestingly, our data indicated that Lncenc1 was upregulated in macrophages but not in primary epithelial cells (PECs) or polymorphonuclear leukocytes (PMN). The upregulation was also observed in human THP-1 and U937 macrophages. Besides, Lncenc1 was highly induced during ATP-induced inflammasome activation. Functionally, Lncenc1 showed proinflammatory effects in macrophages as demonstrated by increased expressions of cytokine and chemokines, as well as enhanced NF-κB promoter activity. Overexpression of Lncenc1 promoted the releases of IL-1β and IL-18, and Caspase-1 activity in macrophages, suggesting a role in inflammasome activation. Consistently, knockdown of Lncenc1 inhibited inflammasome activation in LPS-treated macrophages. Moreover, knockdown of Lncenc1 using antisense oligo (ASO)-loaded exosomes (EXO) attenuated LPS-induced lung inflammation in mice. Similarly, Lncenc1 deficiency protects mice from bacteria-induced lung injury and inflammasome activation. Taken together, our work identified Lncenc1 as a modulator of inflammasome activation in macrophages during bacterial infection. Our study suggested that Lncenc1 could serve as a therapeutic target for lung inflammation and injury.
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Affiliation(s)
- Yohan Han
- Clinical and Experimental Therapeutics, College of Pharmacy, University of Georgia, Augusta, Georgia, United States
- Charlie Norwood Department of Veterans Affairs Medical Center, Augusta, Georgia, United States
| | - Yin Zhu
- Clinical and Experimental Therapeutics, College of Pharmacy, University of Georgia, Augusta, Georgia, United States
- Charlie Norwood Department of Veterans Affairs Medical Center, Augusta, Georgia, United States
| | - Saugata Dutta
- Clinical and Experimental Therapeutics, College of Pharmacy, University of Georgia, Augusta, Georgia, United States
- Charlie Norwood Department of Veterans Affairs Medical Center, Augusta, Georgia, United States
| | - Sultan Almuntashiri
- Clinical and Experimental Therapeutics, College of Pharmacy, University of Georgia, Augusta, Georgia, United States
- Charlie Norwood Department of Veterans Affairs Medical Center, Augusta, Georgia, United States
- Department of Clinical Pharmacy, College of Pharmacy, University of Hail, Hail, Saudi Arabia
| | - Xiaoyun Wang
- Clinical and Experimental Therapeutics, College of Pharmacy, University of Georgia, Augusta, Georgia, United States
- Charlie Norwood Department of Veterans Affairs Medical Center, Augusta, Georgia, United States
| | - Duo Zhang
- Clinical and Experimental Therapeutics, College of Pharmacy, University of Georgia, Augusta, Georgia, United States
- Charlie Norwood Department of Veterans Affairs Medical Center, Augusta, Georgia, United States
- Department of Medicine, Medical College of Georgia, Augusta University, Augusta, Georgia, United States
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Rey F, Berardo C, Maghraby E, Mauri A, Messa L, Esposito L, Casili G, Ottolenghi S, Bonaventura E, Cuzzocrea S, Zuccotti G, Tonduti D, Esposito E, Paterniti I, Cereda C, Carelli S. Redox Imbalance in Neurological Disorders in Adults and Children. Antioxidants (Basel) 2023; 12:antiox12040965. [PMID: 37107340 PMCID: PMC10135575 DOI: 10.3390/antiox12040965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 04/03/2023] [Accepted: 04/14/2023] [Indexed: 04/29/2023] Open
Abstract
Oxygen is a central molecule for numerous metabolic and cytophysiological processes, and, indeed, its imbalance can lead to numerous pathological consequences. In the human body, the brain is an aerobic organ and for this reason, it is very sensitive to oxygen equilibrium. The consequences of oxygen imbalance are especially devastating when occurring in this organ. Indeed, oxygen imbalance can lead to hypoxia, hyperoxia, protein misfolding, mitochondria dysfunction, alterations in heme metabolism and neuroinflammation. Consequently, these dysfunctions can cause numerous neurological alterations, both in the pediatric life and in the adult ages. These disorders share numerous common pathways, most of which are consequent to redox imbalance. In this review, we will focus on the dysfunctions present in neurodegenerative disorders (specifically Alzheimer's disease, Parkinson's disease and amyotrophic lateral sclerosis) and pediatric neurological disorders (X-adrenoleukodystrophies, spinal muscular atrophy, mucopolysaccharidoses and Pelizaeus-Merzbacher Disease), highlighting their underlining dysfunction in redox and identifying potential therapeutic strategies.
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Affiliation(s)
- Federica Rey
- Pediatric Clinical Research Center "Romeo ed Enrica Invernizzi", Department of Biomedical and Clinical Sciences, University of Milano, 20157 Milano, Italy
- Center of Functional Genomics and Rare diseases, Department of Pediatrics, Buzzi Children's Hospital, 20154 Milano, Italy
| | - Clarissa Berardo
- Pediatric Clinical Research Center "Romeo ed Enrica Invernizzi", Department of Biomedical and Clinical Sciences, University of Milano, 20157 Milano, Italy
- Center of Functional Genomics and Rare diseases, Department of Pediatrics, Buzzi Children's Hospital, 20154 Milano, Italy
| | - Erika Maghraby
- Pediatric Clinical Research Center "Romeo ed Enrica Invernizzi", Department of Biomedical and Clinical Sciences, University of Milano, 20157 Milano, Italy
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Alessia Mauri
- Pediatric Clinical Research Center "Romeo ed Enrica Invernizzi", Department of Biomedical and Clinical Sciences, University of Milano, 20157 Milano, Italy
- Center of Functional Genomics and Rare diseases, Department of Pediatrics, Buzzi Children's Hospital, 20154 Milano, Italy
| | - Letizia Messa
- Center of Functional Genomics and Rare diseases, Department of Pediatrics, Buzzi Children's Hospital, 20154 Milano, Italy
- Department of Electronics, Information and Bioengineering (DEIB), Politecnico di Milano, 20133 Milano, Italy
| | - Letizia Esposito
- Pediatric Clinical Research Center "Romeo ed Enrica Invernizzi", Department of Biomedical and Clinical Sciences, University of Milano, 20157 Milano, Italy
- Center of Functional Genomics and Rare diseases, Department of Pediatrics, Buzzi Children's Hospital, 20154 Milano, Italy
| | - Giovanna Casili
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, 98166 Messina, Italy
| | - Sara Ottolenghi
- Department of Medicine and Surgery, University of Milano Bicocca, 20126 Milano, Italy
| | - Eleonora Bonaventura
- Child Neurology Unit, Buzzi Children's Hospital, 20154 Milano, Italy
- Center for Diagnosis and Treatment of Leukodystrophies and Genetic Leukoencephalopathies (COALA), Buzzi Children's Hospital, 20154 Milano, Italy
| | - Salvatore Cuzzocrea
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, 98166 Messina, Italy
| | - Gianvincenzo Zuccotti
- Pediatric Clinical Research Center "Romeo ed Enrica Invernizzi", Department of Biomedical and Clinical Sciences, University of Milano, 20157 Milano, Italy
- Department of Pediatrics, Buzzi Children's Hospital, 20154 Milano, Italy
| | - Davide Tonduti
- Pediatric Clinical Research Center "Romeo ed Enrica Invernizzi", Department of Biomedical and Clinical Sciences, University of Milano, 20157 Milano, Italy
- Child Neurology Unit, Buzzi Children's Hospital, 20154 Milano, Italy
- Center for Diagnosis and Treatment of Leukodystrophies and Genetic Leukoencephalopathies (COALA), Buzzi Children's Hospital, 20154 Milano, Italy
| | - Emanuela Esposito
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, 98166 Messina, Italy
| | - Irene Paterniti
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, 98166 Messina, Italy
| | - Cristina Cereda
- Center of Functional Genomics and Rare diseases, Department of Pediatrics, Buzzi Children's Hospital, 20154 Milano, Italy
| | - Stephana Carelli
- Pediatric Clinical Research Center "Romeo ed Enrica Invernizzi", Department of Biomedical and Clinical Sciences, University of Milano, 20157 Milano, Italy
- Center of Functional Genomics and Rare diseases, Department of Pediatrics, Buzzi Children's Hospital, 20154 Milano, Italy
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Rey F, Maghraby E, Messa L, Esposito L, Barzaghini B, Pandini C, Bordoni M, Gagliardi S, Diamanti L, Raimondi MT, Mazza M, Zuccotti G, Carelli S, Cereda C. Identification of a novel pathway in sporadic Amyotrophic Lateral Sclerosis mediated by the long non-coding RNA ZEB1-AS1. Neurobiol Dis 2023; 178:106030. [PMID: 36736597 DOI: 10.1016/j.nbd.2023.106030] [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: 10/11/2022] [Revised: 01/17/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Deregulation of transcription in the pathogenesis of sporadic Amyotrophic Lateral Sclerosis (sALS) is taking central stage with RNA-sequencing analyses from sALS patients tissues highlighting numerous deregulated long non-coding RNAs (lncRNAs). The oncogenic lncRNA ZEB1-AS1 is strongly downregulated in peripheral blood mononuclear cells of sALS patients. In addition, in cancer-derived cell lines, ZEB1-AS1 belongs to a negative feedback loop regulation with hsa-miR-200c, acting as a molecular sponge for this miRNA. The role of the lncRNA ZEB1-AS1 in sALS pathogenesis has not been characterized yet, and its study could help identifying a possible disease-modifying target. METHODS the implication of the ZEB1-AS1/ZEB1/hsa-miR-200c/BMI1 pathway was investigated in multiple patients-derived cellular models (patients-derived peripheral blood mononuclear cells and induced pluripotent stem cells-derived neural stem cells) and in the neuroblastoma cell line SH-SY5Y, where its function was inhibited via RNA interference. Molecular techniques such as Real Time PCR, Western Blot and Immunofluorescence were used to assess the pathway dysregulation. RESULTS Our results show a dysregulation of a signaling pathway involving ZEB1-AS1/hsa-miR-200c/β-Catenin in peripheral blood mononuclear cells and in induced pluripotent stem cells-derived neural stem cells from sALS patients. These results were validated in vitro on the cell line SH-SY5Y with silenced expression of ZEB1-AS1. Moreover, we found an increase for ZEB1-AS1 during neural differentiation with an aberrant expression of β-Catenin, highlighting also its aggregation and possible impact on neurite length. CONCLUSIONS Our results support and describe the role of ZEB1-AS1 pathway in sALS and specifically in neuronal differentiation, suggesting that an impairment of β-Catenin signaling and an alteration of the neuronal phenotype are taking place.
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Affiliation(s)
- Federica Rey
- Pediatric Research Center "Romeo ed Enrica Invernizzi", Department of Biomedical and Clinical Sciences, University of Milan, Milan, Italy
| | - Erika Maghraby
- Pediatric Research Center "Romeo ed Enrica Invernizzi", Department of Biomedical and Clinical Sciences, University of Milan, Milan, Italy; Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy
| | - Letizia Messa
- Center of Functional Genomics and Rare Diseases, Department of Pediatrics, Buzzi Children's Hospital, Milan, Italy; Department of Electronics, Information and Bioengineering (DEIB), Politecnico di Milano, Milan, Italy
| | - Letizia Esposito
- Pediatric Research Center "Romeo ed Enrica Invernizzi", Department of Biomedical and Clinical Sciences, University of Milan, Milan, Italy
| | - Bianca Barzaghini
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Milan, Italy
| | - Cecilia Pandini
- Department of Biosciences, University of Milan, Milan, Italy
| | - Matteo Bordoni
- Cellular Models and Neuroepigenetics Unit, IRCCS Mondino Foundation, Pavia, Italy
| | - Stella Gagliardi
- Molecular Biology and Transcriptomics Unit, IRCCS Mondino Foundation, Pavia, Italy
| | - Luca Diamanti
- Neuroncology Unit, IRCCS Mondino Foundation, Pavia, Italy
| | - Manuela Teresa Raimondi
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Milan, Italy
| | - Massimiliano Mazza
- Immunotherapy, Cell Therapy and Biobank (ITCB), IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Gianvincenzo Zuccotti
- Pediatric Research Center "Romeo ed Enrica Invernizzi", Department of Biomedical and Clinical Sciences, University of Milan, Milan, Italy; Department of Pediatrics, Buzzi Children's Hospital, Milan, Italy
| | - Stephana Carelli
- Pediatric Research Center "Romeo ed Enrica Invernizzi", Department of Biomedical and Clinical Sciences, University of Milan, Milan, Italy.
| | - Cristina Cereda
- Center of Functional Genomics and Rare Diseases, Department of Pediatrics, Buzzi Children's Hospital, Milan, Italy
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Rey F, Messa L, Maghraby E, Casili G, Ottolenghi S, Barzaghini B, Raimondi MT, Cereda C, Cuzzocrea S, Zuccotti G, Esposito E, Paterniti I, Carelli S. Oxygen Sensing in Neurodegenerative Diseases: Current Mechanisms, Implication of Transcriptional Response, and Pharmacological Modulation. Antioxid Redox Signal 2023; 38:160-182. [PMID: 35793106 DOI: 10.1089/ars.2022.0046] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Significance: Oxygen (O2) sensing is the fundamental process through which organisms respond to changes in O2 levels. Complex networks exist allowing the maintenance of O2 levels through the perception, capture, binding, transport, and delivery of molecular O2. The brain extreme sensitivity to O2 balance makes the dysregulation of related processes crucial players in the pathogenesis of neurodegenerative diseases (NDs). In this study, we wish to review the most relevant advances in O2 sensing in relation to Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis. Recent Advances: Over the years, it has been clarified that most NDs share common pathways, a great number of which are in relation to O2 imbalance. These include hypoxia, hyperoxia, reactive oxygen species production, metabolism of metals, protein misfolding, and neuroinflammation. Critical Issues: There is still a gap in knowledge concerning how O2 sensing plays a role in the above indicated neurodegenerations. Specifically, O2 concentrations are perceived in body sites that are not limited to the brain, but primarily reside in other organs. Moreover, the mechanisms of O2 sensing, gene expression, and signal transduction seem to correlate with neurodegeneration, but many aspects are mechanistically still unexplained. Future Directions: Future studies should focus on the precise characterization of O2 level disruption and O2 sensing mechanisms in NDs. Moreover, advances need to be made also concerning the techniques used to assess O2 sensing dysfunctions in these diseases. There is also the need to develop innovative therapies targeting this precise mechanism rather than its secondary effects, as early intervention is necessary. Antioxid. Redox Signal. 38, 160-182.
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Affiliation(s)
- Federica Rey
- Department of Biomedical and Clinical Sciences, University of Milano, Milano, Italy.,Department of Biomedical and Clinical Sciences, Pediatric Research Center "Romeo ed Enrica Invernizzi," University of Milano, Milano, Italy
| | - Letizia Messa
- Department of Biomedical and Clinical Sciences, University of Milano, Milano, Italy.,Department of Biomedical and Clinical Sciences, Pediatric Research Center "Romeo ed Enrica Invernizzi," University of Milano, Milano, Italy
| | - Erika Maghraby
- Department of Biomedical and Clinical Sciences, University of Milano, Milano, Italy.,Department of Biomedical and Clinical Sciences, Pediatric Research Center "Romeo ed Enrica Invernizzi," University of Milano, Milano, Italy
| | - Giovanna Casili
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
| | - Sara Ottolenghi
- Department of Medicine and Surgery, University of Milano Bicocca, Milano, Italy
| | - Bianca Barzaghini
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta," Politecnico di Milano, Milano, Italy
| | - Manuela Teresa Raimondi
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta," Politecnico di Milano, Milano, Italy
| | - Cristina Cereda
- Department of Women, Mothers and Neonatal Care, Children's Hospital "V. Buzzi," Milano, Italy
| | - Salvatore Cuzzocrea
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
| | - Gianvincenzo Zuccotti
- Department of Biomedical and Clinical Sciences, University of Milano, Milano, Italy.,Department of Biomedical and Clinical Sciences, Pediatric Research Center "Romeo ed Enrica Invernizzi," University of Milano, Milano, Italy.,Department of Pediatrics, Children's Hospital "V. Buzzi," Milano, Italy
| | - Emanuela Esposito
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
| | - Irene Paterniti
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
| | - Stephana Carelli
- Department of Biomedical and Clinical Sciences, University of Milano, Milano, Italy.,Department of Biomedical and Clinical Sciences, Pediatric Research Center "Romeo ed Enrica Invernizzi," University of Milano, Milano, Italy
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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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Neural Precursor Cells Expanded Inside the 3D Micro-Scaffold Nichoid Present Different Non-Coding RNAs Profiles and Transcript Isoforms Expression: Possible Epigenetic Modulation by 3D Growth. Biomedicines 2021; 9:biomedicines9091120. [PMID: 34572306 PMCID: PMC8472193 DOI: 10.3390/biomedicines9091120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/25/2021] [Accepted: 08/27/2021] [Indexed: 12/24/2022] Open
Abstract
Non-coding RNAs show relevant implications in various biological and pathological processes. Thus, understanding the biological implications of these molecules in stem cell biology still represents a major challenge. The aim of this work is to study the transcriptional dysregulation of 357 non-coding genes, found through RNA-Seq approach, in murine neural precursor cells expanded inside the 3D micro-scaffold Nichoid versus standard culture conditions. Through weighted co-expression network analysis and functional enrichment, we highlight the role of non-coding RNAs in altering the expression of coding genes involved in mechanotransduction, stemness, and neural differentiation. Moreover, as non-coding RNAs are poorly conserved between species, we focus on those with human homologue sequences, performing further computational characterization. Lastly, we looked for isoform switching as possible mechanism in altering coding and non-coding gene expression. Our results provide a comprehensive dissection of the 3D scaffold Nichoid's influence on the biological and genetic response of neural precursor cells. These findings shed light on the possible role of non-coding RNAs in 3D cell growth, indicating that also non-coding RNAs are implicated in cellular response to mechanical stimuli.
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