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Zeinelabdeen Y, Abaza T, Yasser MB, Elemam NM, Youness RA. MIAT LncRNA: A multifunctional key player in non-oncological pathological conditions. Noncoding RNA Res 2024; 9:447-462. [PMID: 38511054 PMCID: PMC10950597 DOI: 10.1016/j.ncrna.2024.01.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 12/27/2023] [Accepted: 01/14/2024] [Indexed: 03/22/2024] Open
Abstract
The discovery of non-coding RNAs (ncRNAs) has unveiled a wide range of transcripts that do not encode proteins but play key roles in several cellular and molecular processes. Long noncoding RNAs (lncRNAs) are specific class of ncRNAs that are longer than 200 nucleotides and have gained significant attention due to their diverse mechanisms of action and potential involvement in various pathological conditions. In the current review, the authors focus on the role of lncRNAs, specifically highlighting the Myocardial Infarction Associated Transcript (MIAT), in non-oncological context. MIAT is a nuclear lncRNA that has been directly linked to myocardial infarction and is reported to control post-transcriptional processes as a competitive endogenous RNA (ceRNA) molecule. It interacts with microRNAs (miRNAs), thereby limiting the translation and expression of their respective target messenger RNA (mRNA) and regulating protein expression. Yet, MIAT has been implicated in other numerous pathological conditions such as other cardiovascular diseases, autoimmune disease, neurodegenerative diseases, metabolic diseases, and many others. In this review, the authors emphasize that MIAT exhibits distinct expression patterns and functions across different pathological conditions and is emerging as potential diagnostic, prognostic, and therapeutic agent. Additionally, the authors highlight the regulatory role of MIAT and shed light on the involvement of lncRNAs and specifically MIAT in various non-oncological pathological conditions.
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Affiliation(s)
- Yousra Zeinelabdeen
- Molecular Genetics Research Team, Molecular Biology and Biochemistry Department, Faculty of Biotechnology, German International University (GIU), Cairo, 11835, Egypt
- Faculty of Medical Sciences/UMCG, University of Groningen, Antonius Deusinglaan 1, Groningen, 9713 AV, the Netherlands
| | - Tasneem Abaza
- Molecular Genetics Research Team, Molecular Biology and Biochemistry Department, Faculty of Biotechnology, German International University (GIU), Cairo, 11835, Egypt
- Biotechnology and Biomolecular Biochemistry Program, Faculty of Science, Cairo University, Cairo, Egypt
| | - Montaser Bellah Yasser
- Bioinformatics Group, Center for Informatics Sciences (CIS), School of Information Technology and Computer Science (ITCS), Nile University, Giza, Egypt
| | - Noha M. Elemam
- Clinical Sciences Department, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
| | - Rana A. Youness
- Molecular Genetics Research Team, Molecular Biology and Biochemistry Department, Faculty of Biotechnology, German International University (GIU), Cairo, 11835, Egypt
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2
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Li X, Cao Q, Xu C, Wang J, Pan T, Liu Q, Xie P, Hu Z. Exosomal lncRNA-MIAT promotes neovascularization via the miR-133a-3p/MMP-X1 axis in diabetic retinopathy. Exp Eye Res 2024; 243:109912. [PMID: 38670210 DOI: 10.1016/j.exer.2024.109912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 04/11/2024] [Accepted: 04/23/2024] [Indexed: 04/28/2024]
Abstract
Diabetic retinopathy (DR), a most common microangiopathy of diabetes, causes vision loss and even blindness. The mechanisms of exosomal lncRNA remain unclear in the development of DR. Here, we first identifed the pro-angiogenic effect of exosomes derived from vitreous humor of proliferative diabetic retinopathy patients, where lncRNA-MIAT was enriched inside. Secondly, lncRNA-MIAT was demonstrated significantly increased in exosomes from high glucose induced human retinal vascular endothelial cell, and can regulate tube formation, migration and proliferation ability to promote angiogenesis in vitro and in vivo. Mechanistically, the pro-angiogenic effect of lncRNA-MIAT was via the lncRNA-MIAT/miR-133a-3p/MMP-X1 axis. The reduced level of lncRNA-MIAT in this axis mitigated the generation of retinal neovascular in mouse model of oxygen-induced retinopathy (OIR), providing crucial evidence for lncRNA-MIAT as a potential clinical target. These findings enhance our understanding of the role of exosomal lncRNA-MIAT in retinal angiogenesis, and propose a promising therapeutic strategy against diabetic retinopathy.
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Affiliation(s)
- Xinsheng Li
- Department of Ophthalmology, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou School of Clinical Medicine, Nanjing Medical University, Taizhou, jiangsu, China
| | - Qiuchen Cao
- Department of Ophthalmology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, jiangsu, China
| | - Changlin Xu
- Department of Ophthalmology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, jiangsu, China
| | - Jinfan Wang
- Department of Ophthalmology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, jiangsu, China
| | - Ting Pan
- Department of Ophthalmology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, jiangsu, China
| | - Qinghuai Liu
- Department of Ophthalmology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, jiangsu, China.
| | - Ping Xie
- Department of Ophthalmology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, jiangsu, China.
| | - Zizhong Hu
- Department of Ophthalmology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, jiangsu, China.
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3
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Gasic V, Karan-Djurasevic T, Pavlovic D, Zukic B, Pavlovic S, Tosic N. Diagnostic and Therapeutic Implications of Long Non-Coding RNAs in Leukemia. Life (Basel) 2022; 12:1770. [PMID: 36362925 PMCID: PMC9695865 DOI: 10.3390/life12111770] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 10/27/2022] [Accepted: 10/29/2022] [Indexed: 08/26/2023] Open
Abstract
Leukemia is a heterogenous group of hematological malignancies categorized in four main types (acute myeloid leukemia (AML), acute lymphoblastic leukemia (ALL), chronic myeloid leukemia (CML) and chronic lymphocytic leukemia (CLL). Several cytogenetic and molecular markers have become a part of routine analysis for leukemia patients. These markers have been used in diagnosis, risk-stratification and targeted therapy application. Recent studies have indicated that numerous regulatory RNAs, such as long non-coding RNAs (lncRNAs), have a role in tumor initiation and progression. When it comes to leukemia, data for lncRNA involvement in its etiology, progression, diagnosis, treatment and prognosis is limited. The aim of this review is to summarize research data on lncRNAs in different types of leukemia, on their expression pattern, their role in leukemic transformation and disease progression. The usefulness of this information in the clinical setting, i.e., for diagnostic and prognostic purposes, will be emphasized. Finally, how particular lncRNAs could be used as potential targets for the application of targeted therapy will be considered.
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Affiliation(s)
- Vladimir Gasic
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 11042 Belgrade, Serbia
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4
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Gimbel AT, Koziarek S, Theodorou K, Schulz JF, Stanicek L, Kremer V, Ali T, Günther S, Kumar S, Jo H, Hübner N, Maegdefessel L, Dimmeler S, van Heesch S, Boon RA. Aging-regulated TUG1 is dispensable for endothelial cell function. PLoS One 2022; 17:e0265160. [PMID: 36173935 PMCID: PMC9522302 DOI: 10.1371/journal.pone.0265160] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 07/12/2022] [Indexed: 11/29/2022] Open
Abstract
The evolutionary conserved Taurine Upregulated Gene 1 (TUG1) is a ubiquitously expressed gene that is one of the highest expressed genes in human and rodent endothelial cells (ECs). We here show that TUG1 expression decreases significantly in aging mouse carotid artery ECs and human ECs in vitro, indicating a potential role in the aging endothelial vasculature system. We therefore investigated if, and how, TUG1 might function in aging ECs, but despite extensive phenotyping found no alterations in basal EC proliferation, apoptosis, barrier function, migration, mitochondrial function, or monocyte adhesion upon TUG1 silencing in vitro. TUG1 knockdown did slightly and significantly decrease cumulative sprout length upon vascular endothelial growth factor A stimulation in human umbilical vein endothelial cells (HUVECs), though TUG1-silenced HUVECs displayed no transcriptome-wide mRNA expression changes explaining this effect. Further, ectopic expression of the highly conserved and recently discovered 153 amino acid protein translated from certain TUG1 transcript isoforms did not alter angiogenic sprouting in vitro. Our data show that, despite a high expression and strong evolutionary conservation of both the TUG1 locus and the protein sequence it encodes, TUG1 does not seem to play a major role in basic endothelial cell function.
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Affiliation(s)
- Anna Theresa Gimbel
- Centre of Molecular Medicine, Institute of Cardiovascular Regeneration, Goethe-University, Frankfurt am Main, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Rhine-Main, Frankfurt, Germany
| | - Susanne Koziarek
- Centre of Molecular Medicine, Institute of Cardiovascular Regeneration, Goethe-University, Frankfurt am Main, Germany
| | - Kosta Theodorou
- Centre of Molecular Medicine, Institute of Cardiovascular Regeneration, Goethe-University, Frankfurt am Main, Germany
| | - Jana Felicitas Schulz
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, Berlin, Germany
| | - Laura Stanicek
- Centre of Molecular Medicine, Institute of Cardiovascular Regeneration, Goethe-University, Frankfurt am Main, Germany
- Department of Physiology, Amsterdam Cardiovascular Sciences, VU University Medical Centre, Amsterdam, Netherlands
| | - Veerle Kremer
- Department of Physiology, Amsterdam Cardiovascular Sciences, VU University Medical Centre, Amsterdam, Netherlands
| | - Tamer Ali
- Centre of Molecular Medicine, Institute of Cardiovascular Regeneration, Goethe-University, Frankfurt am Main, Germany
| | - Stefan Günther
- DZHK (German Centre for Cardiovascular Research), Partner Site Rhine-Main, Frankfurt, Germany
- Max Planck Institute for Heart and Lung Research, Bioinformatics and Deep Sequencing Platform, Bad Nauheim, Germany
| | - Sandeep Kumar
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia, United States of America
- Division of Cardiology, Emory University, Atlanta, Georgia, United States of America
| | - Hanjoong Jo
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia, United States of America
- Division of Cardiology, Emory University, Atlanta, Georgia, United States of America
| | - Norbert Hübner
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, Berlin, Germany
- Charité-Universitätsmedizin, Berlin, Germany
| | - Lars Maegdefessel
- Department of Vascular and Endovascular Surgery, Technical University Munich, Munich, Germany
- German Center for Cardiovascular Research DZHK, Partner Site Munich, Munich, Germany
- Department of Medicine, Karolinska Institute, Stockholm, Sweden
| | - Stefanie Dimmeler
- Centre of Molecular Medicine, Institute of Cardiovascular Regeneration, Goethe-University, Frankfurt am Main, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Rhine-Main, Frankfurt, Germany
| | | | - Reinier A. Boon
- Centre of Molecular Medicine, Institute of Cardiovascular Regeneration, Goethe-University, Frankfurt am Main, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Rhine-Main, Frankfurt, Germany
- Department of Physiology, Amsterdam Cardiovascular Sciences, VU University Medical Centre, Amsterdam, Netherlands
- * E-mail:
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5
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Baruah C, Nath P, Barah P. LncRNAs in neuropsychiatric disorders and computational insights for their prediction. Mol Biol Rep 2022; 49:11515-11534. [PMID: 36097122 DOI: 10.1007/s11033-022-07819-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 07/20/2022] [Accepted: 07/24/2022] [Indexed: 12/06/2022]
Abstract
Long non-coding RNAs (lncRNAs) are 200 nucleotide extended transcripts that do not encode proteins or possess limited coding ability. LncRNAs epigenetically control several biological functions such as gene regulation, transcription, mRNA splicing, protein interaction, and genomic imprinting. Over the years, drastic progress in understanding the role of lncRNAs in diverse biological processes has been made. LncRNAs are reported to show tissue-specific expression patterns suggesting their potential as novel candidate biomarkers for diseases. Among all other non-coding RNAs, lncRNAs are highly expressed within the brain-enriched or brain-specific regions of the neural tissues. They are abundantly expressed in the neocortex and pre-mature frontal regions of the brain. LncRNAs are co-expressed with the protein-coding genes and have a significant role in the evolution of functions of the brain. Any deregulation in the lncRNAs contributes to disruptions in normal brain functions resulting in multiple neurological disorders. Neuropsychiatric disorders such as schizophrenia, bipolar disease, autism spectrum disorders, and anxiety are associated with the abnormal expression and regulation of lncRNAs. This review aims to highlight the understanding of lncRNAs concerning normal brain functions and their deregulation associated with neuropsychiatric disorders. We have also provided a survey on the available computational tools for the prediction of lncRNAs, their protein coding potentials, and sub-cellular locations, along with a section on existing online databases with known lncRNAs, and their interactions with other molecules.
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Affiliation(s)
- Cinmoyee Baruah
- Department of Molecular Biology and Biotechnology, Tezpur University, 784028, Napaam, Sonitpur, Assam, India
| | - Prangan Nath
- Department of Molecular Biology and Biotechnology, Tezpur University, 784028, Napaam, Sonitpur, Assam, India
| | - Pankaj Barah
- Department of Molecular Biology and Biotechnology, Tezpur University, 784028, Napaam, Sonitpur, Assam, India.
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6
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Keady J, Fisher M, Anderson E, LeMalenfant R, Turner J. Age-specific impacts of nicotine and withdrawal on hippocampal neuregulin signalling. Eur J Neurosci 2022; 56:4705-4719. [PMID: 35899607 PMCID: PMC9710301 DOI: 10.1111/ejn.15780] [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: 02/09/2022] [Revised: 05/30/2022] [Accepted: 07/20/2022] [Indexed: 11/29/2022]
Abstract
Smoking remains the leading cause of preventable death in the United States, with 87% of smokers starting before the age of 18. Age of initiation is a major predictive factor for smoking frequency and successful smoking cessation. People who initiate smoking during adolescences are 2.33 times more likely to become heavy smokers and half as likely to quit compared with smokers who started during adulthood. Additionally, schizophrenia, a disease state linked to altered neurodevelopment during adolescence, is a major predictive factor for smoking status. Smoking rates among people suffering from schizophrenia are between 60% and 90%. Interestingly, the Neuregulin Signalling Pathway (NSP), which plays an important role in neurodevelopment, is implicated in both schizophrenia and nicotine use disorder. Specifically, SNPS in neuregulin 3 (Nrg3) and Erb-B2 Receptor Tyrosine Kinase 4 (ErbB4) have been associated with smoking cessation outcomes and schizophrenia. Here, we examine the effects of chronic nicotine (18 mg/kg/day) and 24-h withdrawal on NSP gene expression in the hippocampus of adult (20-week-old) and adolescent (4-week-old) mice. We show that withdrawal from chronic nicotine decreased the expression of Erbb4 mRNA in the hippocampus of the adult mice but increased the expression of cytosolic Erbb4 protein in adolescent mice. Nrg3 mRNA and protein expression was not altered by chronic nicotine or withdrawal in the adult or adolescent cohorts, but Nrg3 mRNA and synaptosomal protein expression was lower in the adult withdrawal group when compared with their adolescent counterparts. These results highlight the age-specific effects of nicotine withdrawal on the NSP and may contribute to the lower quit rate and higher cigarette consumption of smokers who initiation during adolescences.
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Affiliation(s)
- Jack Keady
- Department of Pharmaceutical Sciences, University of Kentucky College of Pharmacy, Lexington, Kentucky 40536–0596, USA
| | - Miranda Fisher
- Department of Pharmaceutical Sciences, University of Kentucky College of Pharmacy, Lexington, Kentucky 40536–0596, USA
| | - Erin Anderson
- Department of Drug Discovery and Biomedical Sciences, South Carolina College of Pharmacy, University of South Carolina, Columbia, SC, USA
| | - Rachel LeMalenfant
- Department of Drug Discovery and Biomedical Sciences, South Carolina College of Pharmacy, University of South Carolina, Columbia, SC, USA
| | - Jill Turner
- Department of Pharmaceutical Sciences, University of Kentucky College of Pharmacy, Lexington, Kentucky 40536–0596, USA
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7
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Denham AN, Drake J, Gavrilov M, Taylor ZN, Bacanu SA, Vladimirov VI. Long Non-Coding RNAs: The New Frontier into Understanding the Etiology of Alcohol Use Disorder. Noncoding RNA 2022; 8:ncrna8040059. [PMID: 36005827 PMCID: PMC9415279 DOI: 10.3390/ncrna8040059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 07/29/2022] [Accepted: 08/02/2022] [Indexed: 11/28/2022] Open
Abstract
Alcohol use disorder (AUD) is a complex, chronic, debilitating condition impacting millions worldwide. Genetic, environmental, and epigenetic factors are known to contribute to the development of AUD. Long non-coding RNAs (lncRNAs) are a class of regulatory RNAs, commonly referred to as the “dark matter” of the genome, with little to no protein-coding potential. LncRNAs have been implicated in numerous processes critical for cell survival, suggesting that they play important functional roles in regulating different cell processes. LncRNAs were also shown to display higher tissue specificity than protein-coding genes and have a higher abundance in the brain and central nervous system, demonstrating a possible role in the etiology of psychiatric disorders. Indeed, genetic (e.g., genome-wide association studies (GWAS)), molecular (e.g., expression quantitative trait loci (eQTL)) and epigenetic studies from postmortem brain tissues have identified a growing list of lncRNAs associated with neuropsychiatric and substance use disorders. Given that the expression patterns of lncRNAs have been associated with widespread changes in the transcriptome, including methylation, chromatin architecture, and activation or suppression of translational activity, the regulatory nature of lncRNAs may be ubiquitous and an innate component of gene regulation. In this review, we present a synopsis of the functional impact that lncRNAs may play in the etiology of AUD. We also discuss the classifications of lncRNAs, their known functional roles, and therapeutic advancements in the field of lncRNAs to further clarify the functional relationship between lncRNAs and AUD.
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Affiliation(s)
- Allie N. Denham
- Department of Psychiatry and Behavioral Sciences, Texas A&M University, Bryan, TX 77807, USA
- Department of Psychiatry, College of Medicine, University of Arizona Phoenix, Phoenix, AZ 85004, USA
- Correspondence:
| | - John Drake
- Department of Psychiatry and Behavioral Sciences, Texas A&M University, Bryan, TX 77807, USA
- Department of Psychiatry, College of Medicine, University of Arizona Phoenix, Phoenix, AZ 85004, USA
- MSCI Program, Texas A&M University, Bryan, TX 77807, USA
| | - Matthew Gavrilov
- Department of Psychiatry and Behavioral Sciences, Texas A&M University, Bryan, TX 77807, USA
| | - Zachary N. Taylor
- Department of Psychiatry and Behavioral Sciences, Texas A&M University, Bryan, TX 77807, USA
- Department of Psychiatry, College of Medicine, University of Arizona Phoenix, Phoenix, AZ 85004, USA
| | - Silviu-Alin Bacanu
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA 23219, USA
- Departent of Psychiatry, Virginia Commonwealth University, Richmond, VA 23219, USA
| | - Vladimir I. Vladimirov
- Department of Psychiatry and Behavioral Sciences, Texas A&M University, Bryan, TX 77807, USA
- Department of Psychiatry, College of Medicine, University of Arizona Phoenix, Phoenix, AZ 85004, USA
- Departent of Psychiatry, Virginia Commonwealth University, Richmond, VA 23219, USA
- Texas A&M Institute for Neuroscience, College Station, Texas A&M University, College Station, TX 77843, USA
- Genetics Interdisciplinary Program, College Station, Texas A&M University, College Station, TX 77843, USA
- Lieber Institute for Brain Development, Johns Hopkins University, Baltimore, MD 21205, USA
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8
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Long Intergenic Noncoding RNAs Affect Biological Pathways Underlying Autoimmune and Neurodegenerative Disorders. Mol Neurobiol 2022; 59:5785-5808. [PMID: 35796900 PMCID: PMC9395482 DOI: 10.1007/s12035-022-02941-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 06/23/2022] [Indexed: 11/25/2022]
Abstract
Long intergenic noncoding RNAs (lincRNAs) are a class of independently transcribed molecules longer than 200 nucleotides that do not overlap known protein-coding genes. LincRNAs have diverse roles in gene expression and participate in a spectrum of biological processes. Dysregulation of lincRNA expression can abrogate cellular homeostasis, cell differentiation, and development and can also deregulate the immune and nervous systems. A growing body of literature indicates their important and multifaceted roles in the pathogenesis of several different diseases. Furthermore, certain lincRNAs can be considered potential therapeutic targets and valuable diagnostic or prognostic biomarkers capable of predicting the onset of a disease, its degree of activity, or the progression phase. In this review, we discuss possible mechanisms and molecular functions of lincRNAs in the pathogenesis of selected autoimmune and neurodegenerative disorders: multiple sclerosis, rheumatoid arthritis, systemic lupus erythematosus, Sjögren’s syndrome, Huntington’s disease, Parkinson’s disease, Alzheimer’s disease, and amyotrophic lateral sclerosis. This summary can provide new ideas for future research, diagnosis, and treatment of these highly prevalent and devastating diseases.
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Zakutansky PM, Feng Y. The Long Non-Coding RNA GOMAFU in Schizophrenia: Function, Disease Risk, and Beyond. Cells 2022; 11:1949. [PMID: 35741078 PMCID: PMC9221589 DOI: 10.3390/cells11121949] [Citation(s) in RCA: 10] [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: 05/16/2022] [Revised: 06/10/2022] [Accepted: 06/14/2022] [Indexed: 02/05/2023] Open
Abstract
Neuropsychiatric diseases are among the most common brain developmental disorders, represented by schizophrenia (SZ). The complex multifactorial etiology of SZ remains poorly understood, which reflects genetic vulnerabilities and environmental risks that affect numerous genes and biological pathways. Besides the dysregulation of protein-coding genes, recent discoveries demonstrate that abnormalities associated with non-coding RNAs, including microRNAs and long non-coding RNAs (lncRNAs), also contribute to the pathogenesis of SZ. lncRNAs are an actively evolving family of non-coding RNAs that harbor greater than 200 nucleotides but do not encode for proteins. In general, lncRNA genes are poorly conserved. The large number of lncRNAs specifically expressed in the human brain, together with the genetic alterations and dysregulation of lncRNA genes in the SZ brain, suggests a critical role in normal cognitive function and the pathogenesis of neuropsychiatric diseases. A particular lncRNA of interest is GOMAFU, also known as MIAT and RNCR2. Growing evidence suggests the function of GOMAFU in governing neuronal development and its potential roles as a risk factor and biomarker for SZ, which will be reviewed in this article. Moreover, we discuss the potential mechanisms through which GOMAFU regulates molecular pathways, including its subcellular localization and interaction with RNA-binding proteins, and how interruption to GOMAFU pathways may contribute to the pathogenesis of SZ.
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Affiliation(s)
- Paul M. Zakutansky
- Graduate Program in Biochemistry, Cell and Developmental Biology, Emory University, Atlanta, GA 30322, USA;
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Yue Feng
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
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LncRNA MIAT Promotes Spinal Cord Injury Recovery in Rats by Regulating RBFOX2-Mediated Alternative Splicing of MCL-1. Mol Neurobiol 2022; 59:4854-4868. [PMID: 35641779 DOI: 10.1007/s12035-022-02896-2] [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: 12/29/2021] [Accepted: 05/21/2022] [Indexed: 10/18/2022]
Abstract
LncRNA myocardial infarction-associated transcript (MIAT) alleviates acute spinal cord injury (ASCI)-induced neuronal cell apoptosis, but the specific mechanism of it involved in regulating SCI progression needs further exploration. Here, a SCI rat model was established, followed by administration with adenovirus-mediated MIAT overexpression vector (Ad-MIAT) alone or together with Ad-RBFOX2 (RNA binding fox-1 homolog 2). The data indicated that MIAT overexpression promoted motor function recovery, improved morphology of injured tissues, and restrained neuron loss and cell apoptosis in SCI rats. Then, PC-12 cells were treated with H2O2 to induce cell injury. And highly expressed MIAT suppressed H2O2-caused decrease in cell viability and increase in cell apoptosis. MIAT stabilized RBFOX2 protein expression by binding to RBFOX2, thereby promoting RBFOX2-induced upregulation of anti-apoptotic MCL-1L (myeloid cell leukemia sequence 1) and reduction of pro-apoptotic MCL-1S. And silencing RBFOX2 in vitro blocked the inhibitory effect of MIAT on cell apoptosis. Moreover, MCL-1-specific steric-blocking oligonucleotides (SBOs) were used to transfer the MCL-1 pre-mRNA splicing pattern from MCL-1L to MCL-1S. SBOs reversed the protection effect of RBFOX2 overexpression on H2O2-induced cell injury. Furthermore, overexpression of MCL-1L instead of MCL-1S facilitated autophagy activation in H2O2-stimulated cells. Interestingly, co-overexpression of MIAT and RBFOX2 had a better promoting effect on SCI recovery. In conclusion, MIAT mitigated SCI by promoting RBFOX2-mediated alternative splicing of MCL-1. Our findings might provide a promising therapeutic target for SCI.
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11
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Dey S, Misra A, Selvi Bharathavikru R. Long Non-coding RNAs, Lnc (ing) RNA Metabolism to Cancer Biology. Subcell Biochem 2022; 100:175-199. [PMID: 36301495 DOI: 10.1007/978-3-031-07634-3_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The eukaryotic genome is represented by a vast proportion of non-coding regions, which in recent years have been attributed to have important functional roles in gene regulation through a myriad of processes, ranging from proper localization, correct folding and, most importantly, spatial and temporally regulated expression of genes. One of the major contributing factors in these processes is ribonucleic acid (RNA) metabolism, which comprises the RNA-nucleoprotein (RNP) complexes that interact with and instruct the genome to function. Long non-coding RNAs are an integral component of several RNPs, and herein we provide an overview of the understanding of the long non-coding RNAs, their characteristics, their function and their balancing act as dual modulators in cancer manifestation and progression.
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Affiliation(s)
- Sourav Dey
- RNP Biology Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER)-Berhampur, Transit Campus, Govt ITI Building, Engineering School Junction, Berhampur, Ganjam, Odisha, India
| | - Arushi Misra
- RNP Biology Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER)-Berhampur, Transit Campus, Govt ITI Building, Engineering School Junction, Berhampur, Ganjam, Odisha, India
| | - R Selvi Bharathavikru
- RNP Biology Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER)-Berhampur, Transit Campus, Govt ITI Building, Engineering School Junction, Berhampur, Ganjam, Odisha, India.
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12
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Yang C, Zhang Y, Yang B. MIAT, a potent CVD-promoting lncRNA. Cell Mol Life Sci 2021; 79:43. [PMID: 34921634 PMCID: PMC11072732 DOI: 10.1007/s00018-021-04046-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 10/30/2021] [Accepted: 11/17/2021] [Indexed: 12/13/2022]
Abstract
The initial identification of long non-coding RNA myocardial infarction associated transcript (MIAT) as a genetic risk factor of myocardial infarction has made this lncRNA (designated as lncR-MIAT here) a focus of intensive studies worldwide. Emerging evidence supports that lncR-MIAT is susceptible in its expression to multiple deleterious factors like angiotensin II, isoproterenol, hypoxia, and infection and is anomaly overexpressed in serum, plasma, blood cells and myocardial tissues under a variety of cardiovascular conditions including myocardial infarction, cardiac hypertrophy, diabetic cardiomyopathy, dilated cardiomyopathy, sepsis cardiomyopathy, atrial fibrillation and microvascular dysfunction. Experimental results consistently demonstrated that upregulation of lncR-MIAT plays active roles in the pathological processes of the cardiovascular system and knockdown of this lncRNA effectively ameliorates the adverse conditions. The available data revealed that lncR-MIAT acts through multiple mechanisms such as competitive endogenous RNA, natural antisense RNA and RNA/protein interactions. Moreover, the functional domains of lncR-MIAT accounting for certain specific cellular functions of the full-length transcript have been identified and characterized. These insights will not only tremendously advance our understanding of lncRNA biology and pathophysiology, but also offer good opportunities for more innovative and precise design of agents that have the potential to be developed into new drugs for better therapy of cardiovascular diseases (CVDs) in the future. Herein, we provide an overview of lncR-MIAT, focusing on its roles in cardiovascular diseases, underline the unique cellular/molecular mechanisms for its actions, and speculate the perspectives about the translational studies on the potential diagnostic and therapeutic applications of lncR-MIAT.
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Affiliation(s)
- Chao Yang
- Department of Pharmacology (The State-Province Key Laboratories of Biomedicine Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, 157 Baojian Road, Nangang District, Harbin, Heilongjiang, 150081, People's Republic of China
- Department of Biochemistry, Qiqihar Medical University, Qiqihar, 161000, Heilongjiang, People's Republic of China
| | - Yong Zhang
- Department of Pharmacology (The State-Province Key Laboratories of Biomedicine Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, 157 Baojian Road, Nangang District, Harbin, Heilongjiang, 150081, People's Republic of China
- Institute of Metabolic Disease, Heilongjiang Academy of Medical Science, Harbin, 150086, People's Republic of China
| | - Baofeng Yang
- Department of Pharmacology (The State-Province Key Laboratories of Biomedicine Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, 157 Baojian Road, Nangang District, Harbin, Heilongjiang, 150081, People's Republic of China.
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13
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Irwin AB, Bahabry R, Lubin FD. A putative role for lncRNAs in epigenetic regulation of memory. Neurochem Int 2021; 150:105184. [PMID: 34530054 PMCID: PMC8552959 DOI: 10.1016/j.neuint.2021.105184] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 08/29/2021] [Accepted: 08/31/2021] [Indexed: 12/12/2022]
Abstract
The central dogma of molecular genetics is defined as encoded genetic information within DNA, transcribed into messenger RNA, which contain the instructions for protein synthesis, thus imparting cellular functionality and ultimately life. This molecular genetic theory has given birth to the field of neuroepigenetics, and it is now well established that epigenetic regulation of gene transcription is critical to the learning and memory process. In this review, we address a potential role for a relatively new player in the field of epigenetic crosstalk - long non-coding RNAs (lncRNAs). First, we briefly summarize epigenetic mechanisms in memory formation and examine what little is known about the emerging role of lncRNAs during this process. We then focus discussions on how lncRNAs interact with epigenetic mechanisms to control transcriptional programs under various conditions in the brain, and how this may be applied to regulation of gene expression necessary for memory formation. Next, we explore how epigenetic crosstalk in turn serves to regulate expression of various individual lncRNAs themselves. To highlight the importance of further exploring the role of lncRNA in epigenetic regulation of gene expression, we consider the significant relationship between lncRNA dysregulation and declining memory reserve with aging, Alzheimer's disease, and epilepsy, as well as the promise of novel therapeutic interventions. Finally, we conclude with a discussion of the critical questions that remain to be answered regarding a role for lncRNA in memory.
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Affiliation(s)
- Ashleigh B Irwin
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Rudhab Bahabry
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Farah D Lubin
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, Alabama, USA.
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14
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Zhou J. LncRNA MIAT promotes hypoxia-induced H9C2 cell pyroptosis via binding to SF1 to inhibit CGRP transcription. Exp Physiol 2021; 107:58-67. [PMID: 34713933 DOI: 10.1113/ep089833] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 10/26/2021] [Indexed: 12/26/2022]
Abstract
NEW FINDINGS What is the central question of this study? How does long non-coding RNA myocardial infarction-associated transcript (lncRNA MIAT) function in hypoxia-induced H9C2 cells? What is the main finding and its importance? LncRNA MIAT inhibited transcription of calcitonin gene-related peptide by binding to splicing factor 1, thereby promoting hypoxia-induced H9C2 cell pyroptosis. This study provides a new theoretical basis for the treatment of acute myocardial infarction by using lncRNA MIAT as a molecular target to mediate cardiomyocyte pyrodeath. ABSTRACT Hypoxia induces severe cardiomyocyte pyroptosis, contributing to acute myocardial infarction. The aim of this study was to analyse the molecular mechanism of long non-coding RNA myocardial infarction-associated transcript (lncRNA MIAT) in hypoxia-induced H9C2 cell pyroptosis. A hypoxic H9C2 cell model was established. Cell viability was detected via the Cell Counting Kit-8 method. Levels of lactate dehydrogenase, malondialdehyde and superoxide dismutase and expressions of pyroptotic markers, lncRNA MIAT, splicing factor 1 (SF1) and calcitonin gene-related peptide (CGRP) were detected via qRT-PCR. The subcellular localization of lncRNA MIAT was predicted and confirmed via LncATLAS and nuclear/cytosol fractionation assay. The binding relationships between lncRNA MIAT and SF1 and between SF1 and the CGRP promotor were verified via RNA immunoprecipitation. Rescue experiments were designed to confirm the role of lncRNA MIAT/SF1/CGRP in H9C2 cell pyroptosis. LncRNA MIAT was overexpressed in hypoxia-induced H9C2 cells. Hypoxia induced pyroptosis in H9C2 cells. Silencing of lncRNA MIAT enhanced cell viability and alleviated pyroptosis. LncRNA MIAT inhibited CGRP transcription via binding to SF1. Overexpression of SF1 promoted CGRP transcription and relieved H9C2 cell pyroptosis. Downregulation of CGRP reversed the role of silencing lncRNA MIAT in H9C2 cell pyroptosis. Overall, lncRNA MIAT inhibited CGRP transcription via binding to SF1, thereby promoting hypoxia-induced H9C2 cell pyroptosis.
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Affiliation(s)
- Jingli Zhou
- Department of Cardiology, Shanxi Provincial People's Hospital, Taiyuan City, Shanxi Province, 030000, PR China
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15
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Bhattacharyya N, Pandey V, Bhattacharyya M, Dey A. Regulatory role of long non coding RNAs (lncRNAs) in neurological disorders: From novel biomarkers to promising therapeutic strategies. Asian J Pharm Sci 2021; 16:533-550. [PMID: 34849161 PMCID: PMC8609388 DOI: 10.1016/j.ajps.2021.02.006] [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: 11/18/2020] [Revised: 01/28/2021] [Accepted: 02/18/2021] [Indexed: 01/12/2023] Open
Abstract
Long non coding RNAs (lncRNAs) are non-protein or low-protein coding transcripts that contain more than 200 nucleotides. They representing a large share of the cell's transcriptional output, demonstrate functional attributes viz. tissue-specific expression, determination of cell fate, controlled expression, RNA processing and editing, dosage compensation, genomic imprinting, conserved evolutionary traits etc. These long non coding variants are well associated with pathogenicity of various diseases including the neurological disorders like Alzheimer's disease, schizophrenia, Huntington's disease, Parkinson's disease etc. Neurological disorders are widespread and there knowing the underlying mechanisms become crucial. The lncRNAs take part in the pathogenesis by a plethora of mechanisms like decoy, scaffold, mi-RNA sequestrator, histone modifiers and in transcriptional interference. Detailed knowledge of the role of lncRNAs can help to use them further as novel biomarkers for therapeutic aspects. Here, in this review we discuss regulation and functional roles of lncRNAs in eight neurological diseases and psychiatric disorders, and the mechanisms by which they act. With these, we try to establish their roles as potential markers and viable diagnostic tools in these disorders.
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Affiliation(s)
| | - Vedansh Pandey
- Department of Life Sciences, Presidency University, Kolkata, India
| | | | - Abhijit Dey
- Department of Life Sciences, Presidency University, Kolkata, India
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16
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Pant T, DiStefano JK, Logan S, Bosnjak ZJ. Emerging Role of Long Noncoding RNAs in Perioperative Neurocognitive Disorders and Anesthetic-Induced Developmental Neurotoxicity. Anesth Analg 2021; 132:1614-1625. [PMID: 33332892 DOI: 10.1213/ane.0000000000005317] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Preclinical investigations in animal models have consistently demonstrated neurobiological changes and life-long cognitive deficits following exposure to widely used anesthetics early in life. However, the mechanisms by which these exposures affect brain function remain poorly understood, therefore, limiting the efficacy of current diagnostic and therapeutic options in human studies. The human brain exhibits an abundant expression of long noncoding RNAs (lncRNAs). These biologically active transcripts play critical roles in a diverse array of functions, including epigenetic regulation. Changes in lncRNA expression have been linked with brain development, normal CNS processes, brain injuries, and the development of neurodegenerative diseases, and many lncRNAs are known to have brain-specific expression. Aberrant lncRNA expression has also been implicated in areas of growing importance in anesthesia-related research, including anesthetic-induced developmental neurotoxicity (AIDN), a condition defined by neurological changes occurring in patients repeatedly exposed to anesthesia, and the related condition of perioperative neurocognitive disorder (PND). In this review, we detail recent advances in PND and AIDN research and summarize the evidence supporting roles for lncRNAs in the brain under both normal and pathologic conditions. We also discuss lncRNAs that have been linked with PND and AIDN, and conclude with a discussion of the clinical potential for lncRNAs to serve as diagnostic and therapeutic targets for the prevention of these neurocognitive disorders and the challenges facing the identification and characterization of associated lncRNAs.
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Affiliation(s)
- Tarun Pant
- Department of Diabetes and Fibrotic Disease Unit, Translational Genomic Research Institute, Phoenix, Arizona
| | | | - Sara Logan
- Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Zeljko J Bosnjak
- From the Department of Medicine, Medical College of Wisconsin, Milwaukee, Wisconsin.,Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin
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17
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Singh N. Role of mammalian long non-coding RNAs in normal and neuro oncological disorders. Genomics 2021; 113:3250-3273. [PMID: 34302945 DOI: 10.1016/j.ygeno.2021.07.015] [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: 05/24/2021] [Revised: 07/10/2021] [Accepted: 07/14/2021] [Indexed: 12/09/2022]
Abstract
Long non-coding RNAs (lncRNAs) are expressed at lower levels than protein-coding genes but have a crucial role in gene regulation. LncRNA is distinct, they are being transcribed using RNA polymerase II, and their functionality depends on subcellular localization. Depending on their niche, they specifically interact with DNA, RNA, and proteins and modify chromatin function, regulate transcription at various stages, forms nuclear condensation bodies and nucleolar organization. lncRNAs may also change the stability and translation of cytoplasmic mRNAs and hamper signaling pathways. Thus, lncRNAs affect the physio-pathological states and lead to the development of various disorders, immune responses, and cancer. To date, ~40% of lncRNAs have been reported in the nervous system (NS) and are involved in the early development/differentiation of the NS to synaptogenesis. LncRNA expression patterns in the most common adult and pediatric tumor suggest them as potential biomarkers and provide a rationale for targeting them pharmaceutically. Here, we discuss the mechanisms of lncRNA synthesis, localization, and functions in transcriptional, post-transcriptional, and other forms of gene regulation, methods of lncRNA identification, and their potential therapeutic applications in neuro oncological disorders as explained by molecular mechanisms in other malignant disorders.
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Affiliation(s)
- Neetu Singh
- Molecular Biology Unit, Department of Centre for Advance Research, King George's Medical University, Lucknow, Uttar Pradesh 226 003, India.
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18
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Yang L, Deng J, Ma W, Qiao A, Xu S, Yu Y, Boriboun C, Kang X, Han D, Ernst P, Zhou L, Shi J, Zhang E, Li TS, Qiu H, Nakagawa S, Blackshaw S, Zhang J, Qin G. Ablation of lncRNA Miat attenuates pathological hypertrophy and heart failure. Am J Cancer Res 2021; 11:7995-8007. [PMID: 34335976 PMCID: PMC8315059 DOI: 10.7150/thno.50990] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 04/29/2021] [Indexed: 12/11/2022] Open
Abstract
Rationale: The conserved long non-coding RNA (lncRNA) myocardial infarction associate transcript (Miat) was identified for its multiple single-nucleotide polymorphisms that are strongly associated with susceptibility to MI, but its role in cardiovascular biology remains elusive. Here we investigated whether Miat regulates cardiac response to pathological hypertrophic stimuli. Methods: Both an angiotensin II (Ang II) infusion model and a transverse aortic constriction (TAC) model were used in adult WT and Miat-null knockout (Miat-KO) mice to induce pathological cardiac hypertrophy. Heart structure and function were evaluated by echocardiography and histological assessments. Gene expression in the heart was evaluated by RNA sequencing (RNA-seq), quantitative real-time RT-PCR (qRT-PCR), and Western blotting. Primary WT and Miat-KO mouse cardiomyocytes were isolated and used in Ca2+ transient and contractility measurements. Results: Continuous Ang II infusion for 4 weeks induced concentric hypertrophy in WT mice, but to a lesser extent in Miat-KO mice. Surgical TAC for 6 weeks resulted in decreased systolic function and heart failure in WT mice but not in Miat-KO mice. In both models, Miat-KO mice displayed reduced heart-weight to tibia-length ratio, cardiomyocyte cross-sectional area, cardiomyocyte apoptosis, and cardiac interstitial fibrosis and a better-preserved capillary density, as compared to WT mice. In addition, Ang II treatment led to significantly reduced mRNA and protein expression of the Ca2+ cycling genes Sarcoplasmic/endoplasmic reticulum Ca2+ ATPase 2a (SERCA2a) and ryanodine receptor 2 (RyR2) and a dramatic increase in global RNA splicing events in the left ventricle (LV) of WT mice, and these changes were largely blunted in Miat-KO mice. Consistently, cardiomyocytes isolated from Miat-KO mice demonstrated more efficient Ca2+ cycling and greater contractility. Conclusions: Ablation of Miat attenuates pathological hypertrophy and heart failure, in part, by enhancing cardiomyocyte contractility.
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19
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Keihani S, Kluever V, Fornasiero EF. Brain Long Noncoding RNAs: Multitask Regulators of Neuronal Differentiation and Function. Molecules 2021; 26:molecules26133951. [PMID: 34203457 PMCID: PMC8272081 DOI: 10.3390/molecules26133951] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 06/21/2021] [Accepted: 06/24/2021] [Indexed: 02/07/2023] Open
Abstract
The extraordinary cellular diversity and the complex connections established within different cells types render the nervous system of vertebrates one of the most sophisticated tissues found in living organisms. Such complexity is ensured by numerous regulatory mechanisms that provide tight spatiotemporal control, robustness and reliability. While the unusual abundance of long noncoding RNAs (lncRNAs) in nervous tissues was traditionally puzzling, it is becoming clear that these molecules have genuine regulatory functions in the brain and they are essential for neuronal physiology. The canonical view of RNA as predominantly a 'coding molecule' has been largely surpassed, together with the conception that lncRNAs only represent 'waste material' produced by cells as a side effect of pervasive transcription. Here we review a growing body of evidence showing that lncRNAs play key roles in several regulatory mechanisms of neurons and other brain cells. In particular, neuronal lncRNAs are crucial for orchestrating neurogenesis, for tuning neuronal differentiation and for the exact calibration of neuronal excitability. Moreover, their diversity and the association to neurodegenerative diseases render them particularly interesting as putative biomarkers for brain disease. Overall, we foresee that in the future a more systematic scrutiny of lncRNA functions will be instrumental for an exhaustive understanding of neuronal pathophysiology.
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20
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Aliperti V, Skonieczna J, Cerase A. Long Non-Coding RNA (lncRNA) Roles in Cell Biology, Neurodevelopment and Neurological Disorders. Noncoding RNA 2021; 7:36. [PMID: 34204536 PMCID: PMC8293397 DOI: 10.3390/ncrna7020036] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 06/14/2021] [Accepted: 06/15/2021] [Indexed: 02/08/2023] Open
Abstract
Development is a complex process regulated both by genetic and epigenetic and environmental clues. Recently, long non-coding RNAs (lncRNAs) have emerged as key regulators of gene expression in several tissues including the brain. Altered expression of lncRNAs has been linked to several neurodegenerative, neurodevelopmental and mental disorders. The identification and characterization of lncRNAs that are deregulated or mutated in neurodevelopmental and mental health diseases are fundamental to understanding the complex transcriptional processes in brain function. Crucially, lncRNAs can be exploited as a novel target for treating neurological disorders. In our review, we first summarize the recent advances in our understanding of lncRNA functions in the context of cell biology and then discussing their association with selected neuronal development and neurological disorders.
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Affiliation(s)
- Vincenza Aliperti
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy
| | - Justyna Skonieczna
- Centre for Genomics and Child Health, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK;
| | - Andrea Cerase
- Centre for Genomics and Child Health, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK;
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21
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Yang S, Lim KH, Kim SH, Joo JY. Molecular landscape of long noncoding RNAs in brain disorders. Mol Psychiatry 2021; 26:1060-1074. [PMID: 33173194 DOI: 10.1038/s41380-020-00947-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 09/28/2020] [Accepted: 10/27/2020] [Indexed: 02/08/2023]
Abstract
According to current paradigms, various risk factors, such as genetic mutations, oxidative stress, neural network dysfunction, and abnormal protein degradation, contribute to the progression of brain disorders. Through the cooperation of gene transcripts in biological processes, the study of noncoding RNAs can lead to insights into the cause and treatment of brain disorders. Recently, long noncoding RNAs (lncRNAs) which are longer than 200 nucleotides in length have been suggested as key factors in various brain disorders. Accumulating evidence suggests the potential of lncRNAs as diagnostic or prognostic biomarkers and therapeutic targets. High-throughput screening-based sequencing has been instrumental in identification of lncRNAs that demand new approaches to understanding the progression of brain disorders. In this review, we discuss the recent progress in the study of lncRNAs, and addresses the pathogenesis of brain disorders that involve lncRNAs and describes the associations of lncRNAs with neurodegenerative disorders such as Alzheimer disease (AD), Parkinson disease (PD), and neurodevelopmental disorders. We also discuss potential targets of lncRNAs and their promise as novel therapeutics and biomarkers in brain disorders.
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Affiliation(s)
- Sumin Yang
- Neurodegenerative Disease Research Group, Korea Brain Research Institute, Daegu, 41062, Republic of Korea
| | - Key-Hwan Lim
- Neurodegenerative Disease Research Group, Korea Brain Research Institute, Daegu, 41062, Republic of Korea
| | - Sung-Hyun Kim
- Neurodegenerative Disease Research Group, Korea Brain Research Institute, Daegu, 41062, Republic of Korea
| | - Jae-Yeol Joo
- Neurodegenerative Disease Research Group, Korea Brain Research Institute, Daegu, 41062, Republic of Korea.
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22
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Yoshimoto R, Chhipi-Shrestha JK, Schneider-Poetsch T, Furuno M, Burroughs AM, Noma S, Suzuki H, Hayashizaki Y, Mayeda A, Nakagawa S, Kaida D, Iwasaki S, Yoshida M. Spliceostatin A interaction with SF3B limits U1 snRNP availability and causes premature cleavage and polyadenylation. Cell Chem Biol 2021; 28:1356-1365.e4. [PMID: 33784500 DOI: 10.1016/j.chembiol.2021.03.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 01/07/2021] [Accepted: 03/09/2021] [Indexed: 12/01/2022]
Abstract
RNA splicing, a highly conserved process in eukaryotic gene expression, is seen as a promising target for anticancer agents. Splicing is associated with other RNA processing steps, such as transcription and nuclear export; however, our understanding of the interaction between splicing and other RNA regulatory mechanisms remains incomplete. Moreover, the impact of chemical splicing inhibition on long non-coding RNAs (lncRNAs) has been poorly understood. Here, we demonstrate that spliceostatin A (SSA), a chemical splicing modulator that binds to the SF3B subcomplex of the U2 small nuclear ribonucleoprotein particle (snRNP), limits U1 snRNP availability in splicing, resulting in premature cleavage and polyadenylation of MALAT1, a nuclear lncRNA, as well as protein-coding mRNAs. Therefore, truncated transcripts are exported into the cytoplasm and translated, resulting in aberrant protein products. Our work demonstrates that active recycling of the splicing machinery maintains homeostasis of RNA processing beyond intron excision.
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Affiliation(s)
- Rei Yoshimoto
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan; Division of Gene Expression Mechanism, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Aichi 470-1192, Japan
| | - Jagat K Chhipi-Shrestha
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan; Department of Biotechnology, Graduate School of Agricultural Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Tilman Schneider-Poetsch
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Masaaki Furuno
- RIKEN Center for Integrative Medical Sciences, Tsurumi-ku, Yokohama 230-0045, Japan
| | - A Maxwell Burroughs
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Shohei Noma
- RIKEN Center for Integrative Medical Sciences, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Harukazu Suzuki
- RIKEN Center for Integrative Medical Sciences, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Yoshihide Hayashizaki
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Saitama 351-0198, Japan
| | - Akila Mayeda
- Division of Gene Expression Mechanism, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Aichi 470-1192, Japan
| | - Shinichi Nakagawa
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Hokkaido 060-0812, Japan
| | - Daisuke Kaida
- Department of Gene Expression and Regulation, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Sugitani, Toyama 930-0194, Japan
| | - Shintaro Iwasaki
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan; Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8561, Japan; AMED-CREST, Japan Agency for Medical Research and Development, Chiyoda-ku, Tokyo 100-0004 Japan.
| | - Minoru Yoshida
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan; Department of Biotechnology, Graduate School of Agricultural Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan; Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan.
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23
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Pisignano G, Ladomery M. Epigenetic Regulation of Alternative Splicing: How LncRNAs Tailor the Message. Noncoding RNA 2021; 7:ncrna7010021. [PMID: 33799493 PMCID: PMC8005942 DOI: 10.3390/ncrna7010021] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 02/05/2021] [Accepted: 02/22/2021] [Indexed: 12/23/2022] Open
Abstract
Alternative splicing is a highly fine-tuned regulated process and one of the main drivers of proteomic diversity across eukaryotes. The vast majority of human multi-exon genes is alternatively spliced in a cell type- and tissue-specific manner, and defects in alternative splicing can dramatically alter RNA and protein functions and lead to disease. The eukaryotic genome is also intensively transcribed into long and short non-coding RNAs which account for up to 90% of the entire transcriptome. Over the years, lncRNAs have received considerable attention as important players in the regulation of cellular processes including alternative splicing. In this review, we focus on recent discoveries that show how lncRNAs contribute significantly to the regulation of alternative splicing and explore how they are able to shape the expression of a diverse set of splice isoforms through several mechanisms. With the increasing number of lncRNAs being discovered and characterized, the contribution of lncRNAs to the regulation of alternative splicing is likely to grow significantly.
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Affiliation(s)
- Giuseppina Pisignano
- Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK
- Correspondence: (G.P.); (M.L.)
| | - Michael Ladomery
- Faculty of Health and Applied Sciences, University of the West of England, Coldharbour Lane, Frenchay, Bristol BS16 1QY, UK
- Correspondence: (G.P.); (M.L.)
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24
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Alcohol use disorder causes global changes in splicing in the human brain. Transl Psychiatry 2021; 11:2. [PMID: 33414398 PMCID: PMC7790816 DOI: 10.1038/s41398-020-01163-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 12/09/2020] [Accepted: 12/10/2020] [Indexed: 01/11/2023] Open
Abstract
Alcohol use disorder (AUD) is a widespread disease leading to the deterioration of cognitive and other functions. Mechanisms by which alcohol affects the brain are not fully elucidated. Splicing constitutes a nuclear process of RNA maturation, which results in the formation of the transcriptome. We tested the hypothesis as to whether AUD impairs splicing in the superior frontal cortex (SFC), nucleus accumbens (NA), basolateral amygdala (BLA), and central nucleus of the amygdala (CNA). To evaluate splicing, bam files from STAR alignments were indexed with samtools for use by rMATS software. Computational analysis of affected pathways was performed using Gene Ontology Consortium, Gene Set Enrichment Analysis, and LncRNA Ontology databases. Surprisingly, AUD was associated with limited changes in the transcriptome: expression of 23 genes was altered in SFC, 14 in NA, 102 in BLA, and 57 in CNA. However, strikingly, mis-splicing in AUD was profound: 1421 mis-splicing events were detected in SFC, 394 in NA, 1317 in BLA, and 469 in CNA. To determine the mechanism of mis-splicing, we analyzed the elements of the spliceosome: small nuclear RNAs (snRNAs) and splicing factors. While snRNAs were not affected by alcohol, expression of splicing factor heat shock protein family A (Hsp70) member 6 (HSPA6) was drastically increased in SFC, BLA, and CNA. Also, AUD was accompanied by aberrant expression of long noncoding RNAs (lncRNAs) related to splicing. In summary, alcohol is associated with genome-wide changes in splicing in multiple human brain regions, likely due to dysregulation of splicing factor(s) and/or altered expression of splicing-related lncRNAs.
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25
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Du JX, Zhu GQ, Cai JL, Wang B, Luo YH, Chen C, Cai CZ, Zhang SJ, Zhou J, Fan J, Zhu W, Dai Z. Splicing factors: Insights into their regulatory network in alternative splicing in cancer. Cancer Lett 2020; 501:83-104. [PMID: 33309781 DOI: 10.1016/j.canlet.2020.11.043] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 11/24/2020] [Accepted: 11/26/2020] [Indexed: 12/18/2022]
Abstract
More than 95% of all human genes are alternatively spliced after transcription, which enriches the diversity of proteins and regulates transcript and/or protein levels. The splicing isoforms produced from the same gene can manifest distinctly, even exerting opposite effects. Mounting evidence indicates that the alternative splicing (AS) mechanism is ubiquitous in various cancers and drives the generation and maintenance of various hallmarks of cancer, such as enhanced proliferation, inhibited apoptosis, invasion and metastasis, and angiogenesis. Splicing factors (SFs) play pivotal roles in the recognition of splice sites and the assembly of spliceosomes during AS. In this review, we mainly discuss the similarities and differences of SF domains, the details of SF function in AS, the effect of SF-driven pathological AS on different hallmarks of cancer, and the main drivers of SF expression level and subcellular localization. In addition, we briefly introduce the application prospects of targeted therapeutic strategies, including small-molecule inhibitors, siRNAs and splice-switching oligonucleotides (SSOs), from three perspectives (drivers, SFs and pathological AS). Finally, we share our insights into the potential direction of research on SF-centric AS-related regulatory networks.
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Affiliation(s)
- Jun-Xian Du
- Department of General Surgery, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China
| | - Gui-Qi Zhu
- Liver Cancer Institute, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China; Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai, 200032, China
| | - Jia-Liang Cai
- Liver Cancer Institute, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China; Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai, 200032, China
| | - Biao Wang
- Liver Cancer Institute, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China; Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai, 200032, China
| | - Yi-Hong Luo
- Department of General Surgery, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China
| | - Cong Chen
- Department of General Surgery, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China
| | - Cheng-Zhe Cai
- Department of General Surgery, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China
| | - Si-Jia Zhang
- Department of General Surgery, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China
| | - Jian Zhou
- Liver Cancer Institute, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China; Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai, 200032, China
| | - Jia Fan
- Liver Cancer Institute, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China; Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai, 200032, China
| | - Wei Zhu
- Department of General Surgery, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China.
| | - Zhi Dai
- Liver Cancer Institute, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China; Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai, 200032, China.
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26
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Aznaourova M, Schmerer N, Schmeck B, Schulte LN. Disease-Causing Mutations and Rearrangements in Long Non-coding RNA Gene Loci. Front Genet 2020; 11:527484. [PMID: 33329688 PMCID: PMC7735109 DOI: 10.3389/fgene.2020.527484] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 11/02/2020] [Indexed: 12/12/2022] Open
Abstract
The classic understanding of molecular disease-mechanisms is largely based on protein-centric models. During the past decade however, genetic studies have identified numerous disease-loci in the human genome that do not encode proteins. Such non-coding DNA variants increasingly gain attention in diagnostics and personalized medicine. Of particular interest are long non-coding RNA (lncRNA) genes, which generate transcripts longer than 200 nucleotides that are not translated into proteins. While most of the estimated ~20,000 lncRNAs currently remain of unknown function, a growing number of genetic studies link lncRNA gene aberrations with the development of human diseases, including diabetes, AIDS, inflammatory bowel disease, or cancer. This suggests that the protein-centric view of human diseases does not capture the full complexity of molecular patho-mechanisms, with important consequences for molecular diagnostics and therapy. This review illustrates well-documented lncRNA gene aberrations causatively linked to human diseases and discusses potential lessons for molecular disease models, diagnostics, and therapy.
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Affiliation(s)
- Marina Aznaourova
- Institute for Lung Research, Philipps University Marburg, Marburg, Germany
| | - Nils Schmerer
- Institute for Lung Research, Philipps University Marburg, Marburg, Germany
| | - Bernd Schmeck
- Institute for Lung Research, Philipps University Marburg, Marburg, Germany.,Systems Biology Platform, German Center for Lung Research (DZL), Philipps University Marburg, Marburg, Germany.,Center for Synthetic Microbiology (SYNMIKRO), Philipps University Marburg, Marburg, Germany
| | - Leon N Schulte
- Institute for Lung Research, Philipps University Marburg, Marburg, Germany.,Systems Biology Platform, German Center for Lung Research (DZL), Philipps University Marburg, Marburg, Germany
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27
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Wu M, Fu P, Qu L, Liu J, Lin A. Long Noncoding RNAs, New Critical Regulators in Cancer Immunity. Front Oncol 2020; 10:550987. [PMID: 33194608 PMCID: PMC7662117 DOI: 10.3389/fonc.2020.550987] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 09/09/2020] [Indexed: 12/11/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) play crucial roles in various aspects of cellular functions. Recent studies have revealed that lncRNAs are critical players in the immune system by modulating immune cell differentiation and functions, particularly in cancer immunity. Here we systematically summarize how lncRNAs are involved in different processes of the cancer immunity cycle, including immune cell differentiation, proliferation, trafficking, and infiltration. Moreover, the limitations of the current understanding of lncRNA’s functions in cancer immunity are described, such as the complexity of the cancer immunity system, the inclusive functions of lncRNAs in this system, and the associated immune response. In sum, the comprehensive investigation of the roles of lncRNAs in cancer immunity aids in cancer diagnosis and therapies.
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Affiliation(s)
- Minjie Wu
- Breast Center of the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Peifen Fu
- Breast Center of the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Lei Qu
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Jian Liu
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, Durham, NC, United States
| | - Aifu Lin
- Breast Center of the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
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28
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Blokhin IO, Khorkova O, Saveanu RV, Wahlestedt C. Molecular mechanisms of psychiatric diseases. Neurobiol Dis 2020; 146:105136. [PMID: 33080337 DOI: 10.1016/j.nbd.2020.105136] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 09/24/2020] [Accepted: 10/09/2020] [Indexed: 12/16/2022] Open
Abstract
For most psychiatric diseases, pathogenetic concepts as well as paradigms underlying neuropsychopharmacologic approaches currently revolve around neurotransmitters such as dopamine, serotonin, and norepinephrine. However, despite the fact that several generations of neurotransmitter-based psychotropics including atypical antipsychotics, selective serotonin reuptake inhibitors, and serotonin-norepinephrine reuptake inhibitors are available, the effectiveness of these medications is limited, and relapse rates in psychiatric diseases are relatively high, indicating potential involvement of other pathogenetic pathways. Indeed, recent high-throughput studies in genetics and molecular biology have shown that pathogenesis of major psychiatric illnesses involves hundreds of genes and numerous pathways via such fundamental processes as DNA methylation, transcription, and splicing. Current review summarizes these and other molecular mechanisms of such psychiatric illnesses as schizophrenia, major depressive disorder, and alcohol use disorder and suggests a conceptual framework for future studies.
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Affiliation(s)
- Ilya O Blokhin
- Center for Therapeutic Innovation, University of Miami, Miami, FL, United States of America; Department of Psychiatry and Behavioral Sciences, University of Miami, Miami, FL, United States of America; Jackson Memorial Hospital, Miami, FL, United States of America
| | - Olga Khorkova
- OPKO Health Inc., Miami, FL, United States of America
| | - Radu V Saveanu
- Department of Psychiatry and Behavioral Sciences, University of Miami, Miami, FL, United States of America
| | - Claes Wahlestedt
- Center for Therapeutic Innovation, University of Miami, Miami, FL, United States of America; Department of Psychiatry and Behavioral Sciences, University of Miami, Miami, FL, United States of America.
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29
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Angeles AK, Heckmann D, Flosdorf N, Duensing S, Sültmann H. The ERG-Regulated LINC00920 Promotes Prostate Cancer Cell Survival via the 14-3-3ε-FOXO Pathway. Mol Cancer Res 2020; 18:1545-1559. [PMID: 32646965 DOI: 10.1158/1541-7786.mcr-20-0021] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 06/04/2020] [Accepted: 06/29/2020] [Indexed: 11/16/2022]
Abstract
Numerous noncoding transcripts have been reported to correlate with cancer development and progression. Nevertheless, there remains a paucity of long noncoding RNAs (lncRNA) with well-elucidated functional roles. Here, we leverage the International Cancer Genome Consortium-Early Onset Prostate Cancer transcriptome and identify the previously uncharacterized lncRNA LINC00920 to be upregulated in prostate tumors. Phenotypic characterization of LINC00920 revealed its positive impact on cellular proliferation, colony formation, and migration. We demonstrate that LINC00920 transcription is directly activated by ERG, an oncogenic transcription factor overexpressed in 50% of prostate cancers. Chromatin isolation by RNA purification-mass spectrometry revealed the interaction of LINC00920 with the 14-3-3ε protein, leading to enhanced sequestration of tumor suppressive FOXO1. Altogether, our results provide a rationale on how ERG overexpression, partly by driving LINC00920 transcription, could confer survival advantage to prostate cancer cells and potentially prime PTEN-intact prostate cells for cellular transformation through FOXO inactivation. IMPLICATIONS: The study describes a novel lncRNA-mediated mechanism of regulating the FOXO signaling pathway and provides additional insight into the role of ERG in prostate cancer cells.
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Affiliation(s)
- Arlou Kristina Angeles
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), and National Center for Tumor Diseases (NCT), Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Doreen Heckmann
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), and National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Niclas Flosdorf
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), and National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Stefan Duensing
- Department of Urology, Section of Molecular Urooncology, University Hospital Heidelberg, Heidelberg, Germany
| | - Holger Sültmann
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), and National Center for Tumor Diseases (NCT), Heidelberg, Germany.
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30
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Da CM, Gong CY, Nan W, Zhou KS, Wu ZL, Zhang HH. The role of long non-coding RNA MIAT in cancers. Biomed Pharmacother 2020; 129:110359. [PMID: 32535389 DOI: 10.1016/j.biopha.2020.110359] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 05/25/2020] [Accepted: 06/02/2020] [Indexed: 02/07/2023] Open
Abstract
Long non-coding RNAs (lncRNAs), a kind of non-coding single-strand RNAs, play an important role as carcinogenic genes or tumor suppressors in the development of human cancer. Myocardial infarction-associated transcript (MIAT) was first identified as a lncRNA in 2006 and originally isolated as a candidate gene for myocardial infarction. Later, it was reported that MIAT exhibits regulatory effects on the human cell cycle. Since its discovery, MIAT has also been identified as a carcinogenic regulator in many malignant tumors. High expression of MIAT is related to the clinicopathological characteristics of cancer patients. It can also regulate cell proliferation, invasion, metastasis, and anti-apoptosis through a variety of mechanisms. Therefore, MIAT is considered a potential biomarker and therapeutic target in cancer. In this review, we summarize the biological function, mechanism, and potential clinical significance of MIAT during tumorigenesis.
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Affiliation(s)
- Chao-Ming Da
- The Second Clinical Medical College of Lanzhou University, 82 Cuiying Men, Lanzhou 730030, PR China; Orthopaedics Key Laboratory of Gansu Province, Lanzhou 730000, PR China
| | - Chao-Yang Gong
- The Second Clinical Medical College of Lanzhou University, 82 Cuiying Men, Lanzhou 730030, PR China; Orthopaedics Key Laboratory of Gansu Province, Lanzhou 730000, PR China
| | - Wei Nan
- The Second Clinical Medical College of Lanzhou University, 82 Cuiying Men, Lanzhou 730030, PR China
| | - Kai-Sheng Zhou
- The Second Clinical Medical College of Lanzhou University, 82 Cuiying Men, Lanzhou 730030, PR China
| | - Zuo-Long Wu
- The Second Clinical Medical College of Lanzhou University, 82 Cuiying Men, Lanzhou 730030, PR China; Orthopaedics Key Laboratory of Gansu Province, Lanzhou 730000, PR China
| | - Hai-Hong Zhang
- The Second Clinical Medical College of Lanzhou University, 82 Cuiying Men, Lanzhou 730030, PR China; Orthopaedics Key Laboratory of Gansu Province, Lanzhou 730000, PR China.
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31
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Paterson C, Cumming B, Law AJ. Temporal Dynamics of the Neuregulin-ErbB Network in the Murine Prefrontal Cortex across the Lifespan. Cereb Cortex 2020; 30:3325-3339. [PMID: 31897479 DOI: 10.1093/cercor/bhz312] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Neuregulin-ErbB signaling is essential for numerous functions in the developing, adult, and aging brain, particularly in the prefrontal cortex (PFC). Mouse models with disrupted Nrg and/or ErbB genes are relevant to psychiatric, developmental, and age-related disorders, displaying a range of abnormalities stemming from cortical circuitry impairment. Many of these models display nonoverlapping phenotypes dependent upon the gene target and timing of perturbation, suggesting that cortical expression of the Nrg-ErbB network undergoes temporal regulation across the lifespan. Here, we report a comprehensive temporal expression mapping study of the Nrg-ErbB signaling network in the mouse PFC across postnatal development through aging. We find that Nrg and ErbB genes display distinct expression profiles; moreover, splice isoforms of these genes are differentially expressed across the murine lifespan. We additionally find a developmental switch in ErbB4 splice isoform expression potentially mediated through coregulation of the lncRNA Miat expression. Our results are the first to comprehensively and quantitatively map the expression patterns of the Nrg-ErbB network in the mouse PFC across the postnatal lifespan and may help disentangle the pathway's involvement in normal cortical sequences of events across the lifespan, as well as shedding light on the pathophysiological mechanisms of abnormal Nrg-ErbB signaling in neurological disease.
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Affiliation(s)
- Clare Paterson
- Department of Psychiatry, University of Colorado, School of Medicine Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Brooke Cumming
- Department of Psychiatry, University of Colorado, School of Medicine Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Amanda J Law
- Department of Psychiatry, University of Colorado, School of Medicine Anschutz Medical Campus, Aurora, CO 80045, USA.,Department of Cell and Developmental Biology, University of Colorado, School of Medicine Anschutz Medical Campus, Aurora, CO 80045, USA.,Department of Medicine, University of Colorado, School of Medicine Anschutz Medical Campus, Aurora, CO 80045, USA
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32
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Rigo R, Bazin J, Romero‐Barrios N, Moison M, Lucero L, Christ A, Benhamed M, Blein T, Huguet S, Charon C, Crespi M, Ariel F. The Arabidopsis lncRNA ASCO modulates the transcriptome through interaction with splicing factors. EMBO Rep 2020; 21:e48977. [PMID: 32285620 PMCID: PMC7202219 DOI: 10.15252/embr.201948977] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 03/09/2020] [Accepted: 03/10/2020] [Indexed: 12/31/2022] Open
Abstract
Alternative splicing (AS) is a major source of transcriptome diversity. Long noncoding RNAs (lncRNAs) have emerged as regulators of AS through different molecular mechanisms. In Arabidopsis thaliana, the AS regulators NSRs interact with the ALTERNATIVE SPLICING COMPETITOR (ASCO) lncRNA. Here, we analyze the effect of the knock-down and overexpression of ASCO at the genome-wide level and find a large number of deregulated and differentially spliced genes related to flagellin responses and biotic stress. In agreement, ASCO-silenced plants are more sensitive to flagellin. However, only a minor subset of deregulated genes overlaps with the AS defects of the nsra/b double mutant, suggesting an alternative way of action for ASCO. Using biotin-labeled oligonucleotides for RNA-mediated ribonucleoprotein purification, we show that ASCO binds to the highly conserved spliceosome component PRP8a. ASCO overaccumulation impairs the recognition of specific flagellin-related transcripts by PRP8a. We further show that ASCO also binds to another spliceosome component, SmD1b, indicating that it interacts with multiple splicing factors. Hence, lncRNAs may integrate a dynamic network including spliceosome core proteins, to modulate transcriptome reprogramming in eukaryotes.
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Affiliation(s)
- Richard Rigo
- Institute of Plant Sciences Paris‐Saclay (IPS2)CNRSINRAUniversities Paris‐Sud, Evry and Paris‐DiderotSorbonne Paris‐CiteUniversity of Paris‐SaclayOrsayFrance
| | - Jérémie Bazin
- Institute of Plant Sciences Paris‐Saclay (IPS2)CNRSINRAUniversities Paris‐Sud, Evry and Paris‐DiderotSorbonne Paris‐CiteUniversity of Paris‐SaclayOrsayFrance
| | - Natali Romero‐Barrios
- Institute of Plant Sciences Paris‐Saclay (IPS2)CNRSINRAUniversities Paris‐Sud, Evry and Paris‐DiderotSorbonne Paris‐CiteUniversity of Paris‐SaclayOrsayFrance
| | - Michaël Moison
- Institute of Plant Sciences Paris‐Saclay (IPS2)CNRSINRAUniversities Paris‐Sud, Evry and Paris‐DiderotSorbonne Paris‐CiteUniversity of Paris‐SaclayOrsayFrance
- Instituto de Agrobiotecnología del Litoral, CONICET, FBCBUniversidad Nacional del LitoralSanta FeArgentina
| | - Leandro Lucero
- Instituto de Agrobiotecnología del Litoral, CONICET, FBCBUniversidad Nacional del LitoralSanta FeArgentina
| | - Aurélie Christ
- Institute of Plant Sciences Paris‐Saclay (IPS2)CNRSINRAUniversities Paris‐Sud, Evry and Paris‐DiderotSorbonne Paris‐CiteUniversity of Paris‐SaclayOrsayFrance
| | - Moussa Benhamed
- Institute of Plant Sciences Paris‐Saclay (IPS2)CNRSINRAUniversities Paris‐Sud, Evry and Paris‐DiderotSorbonne Paris‐CiteUniversity of Paris‐SaclayOrsayFrance
| | - Thomas Blein
- Institute of Plant Sciences Paris‐Saclay (IPS2)CNRSINRAUniversities Paris‐Sud, Evry and Paris‐DiderotSorbonne Paris‐CiteUniversity of Paris‐SaclayOrsayFrance
| | - Stéphanie Huguet
- Institute of Plant Sciences Paris‐Saclay (IPS2)CNRSINRAUniversities Paris‐Sud, Evry and Paris‐DiderotSorbonne Paris‐CiteUniversity of Paris‐SaclayOrsayFrance
| | - Céline Charon
- Institute of Plant Sciences Paris‐Saclay (IPS2)CNRSINRAUniversities Paris‐Sud, Evry and Paris‐DiderotSorbonne Paris‐CiteUniversity of Paris‐SaclayOrsayFrance
| | - Martin Crespi
- Institute of Plant Sciences Paris‐Saclay (IPS2)CNRSINRAUniversities Paris‐Sud, Evry and Paris‐DiderotSorbonne Paris‐CiteUniversity of Paris‐SaclayOrsayFrance
| | - Federico Ariel
- Instituto de Agrobiotecnología del Litoral, CONICET, FBCBUniversidad Nacional del LitoralSanta FeArgentina
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Rusconi F, Battaglioli E, Venturin M. Psychiatric Disorders and lncRNAs: A Synaptic Match. Int J Mol Sci 2020; 21:ijms21093030. [PMID: 32344798 PMCID: PMC7246907 DOI: 10.3390/ijms21093030] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 04/15/2020] [Accepted: 04/21/2020] [Indexed: 12/15/2022] Open
Abstract
Psychiatric disorders represent a heterogeneous class of multifactorial mental diseases whose origin entails a pathogenic integration of genetic and environmental influences. Incidence of these pathologies is dangerously high, as more than 20% of the Western population is affected. Despite the diverse origins of specific molecular dysfunctions, these pathologies entail disruption of fine synaptic regulation, which is fundamental to behavioral adaptation to the environment. The synapses, as functional units of cognition, represent major evolutionary targets. Consistently, fine synaptic tuning occurs at several levels, involving a novel class of molecular regulators known as long non-coding RNAs (lncRNAs). Non-coding RNAs operate mainly in mammals as epigenetic modifiers and enhancers of proteome diversity. The prominent evolutionary expansion of the gene number of lncRNAs in mammals, particularly in primates and humans, and their preferential neuronal expression does represent a driving force that enhanced the layering of synaptic control mechanisms. In the last few years, remarkable alterations of the expression of lncRNAs have been reported in psychiatric conditions such as schizophrenia, autism, and depression, suggesting unprecedented mechanistic insights into disruption of fine synaptic tuning underlying severe behavioral manifestations of psychosis. In this review, we integrate literature data from rodent pathological models and human evidence that proposes the biology of lncRNAs as a promising field of neuropsychiatric investigation.
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Affiliation(s)
- Francesco Rusconi
- Correspondence: (F.R.); (M.V.); Tel.: +39-02-503-30445 (F.R.); +39-02-503-30443 (M.V.)
| | | | - Marco Venturin
- Correspondence: (F.R.); (M.V.); Tel.: +39-02-503-30445 (F.R.); +39-02-503-30443 (M.V.)
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34
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RNA-Binding Proteins as Important Regulators of Long Non-Coding RNAs in Cancer. Int J Mol Sci 2020; 21:ijms21082969. [PMID: 32340118 PMCID: PMC7215867 DOI: 10.3390/ijms21082969] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 04/20/2020] [Accepted: 04/21/2020] [Indexed: 12/20/2022] Open
Abstract
The majority of the genome is transcribed into pieces of non-(protein) coding RNA, among which long non-coding RNAs (lncRNAs) constitute a large group of particularly versatile molecules that govern basic cellular processes including transcription, splicing, RNA stability, and translation. The frequent deregulation of numerous lncRNAs in cancer is known to contribute to virtually all hallmarks of cancer. An important regulatory mechanism of lncRNAs is the post-transcriptional regulation mediated by RNA-binding proteins (RBPs). So far, however, only a small number of known cancer-associated lncRNAs have been found to be regulated by the interaction with RBPs like human antigen R (HuR), ARE/poly(U)-binding/degradation factor 1 (AUF1), insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1), and tristetraprolin (TTP). These RBPs regulate, by various means, two aspects in particular, namely the stability and the localization of lncRNAs. Importantly, these RBPs themselves are commonly deregulated in cancer and might thus play a major role in the deregulation of cancer-related lncRNAs. There are, however, still many open questions, for example regarding the context specificity of these regulatory mechanisms that, in part, is based on the synergistic or competitive interaction between different RBPs. There is also a lack of knowledge on how RBPs facilitate the transport of lncRNAs between different cellular compartments.
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35
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Kazimierczyk M, Kasprowicz MK, Kasprzyk ME, Wrzesinski J. Human Long Noncoding RNA Interactome: Detection, Characterization and Function. Int J Mol Sci 2020; 21:E1027. [PMID: 32033158 PMCID: PMC7037361 DOI: 10.3390/ijms21031027] [Citation(s) in RCA: 113] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 01/31/2020] [Accepted: 02/02/2020] [Indexed: 01/17/2023] Open
Abstract
The application of a new generation of sequencing techniques has revealed that most of the genome has already been transcribed. However, only a small part of the genome codes proteins. The rest of the genome "dark matter" belongs to divergent groups of non-coding RNA (ncRNA), that is not translated into proteins. There are two groups of ncRNAs, which include small and long non-coding RNAs (sncRNA and lncRNA respectively). Over the last decade, there has been an increased interest in lncRNAs and their interaction with cellular components. In this review, we presented the newest information about the human lncRNA interactome. The term lncRNA interactome refers to cellular biomolecules, such as nucleic acids, proteins, and peptides that interact with lncRNA. The lncRNA interactome was characterized in the last decade, however, understanding what role the biomolecules associated with lncRNA play and the nature of these interactions will allow us to better understand lncRNA's biological functions in the cell. We also describe a set of methods currently used for the detection of lncRNA interactome components and the analysis of their interactions. We think that such a holistic and integrated analysis of the lncRNA interactome will help to better understand its potential role in the development of organisms and cancers.
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Affiliation(s)
| | | | | | - Jan Wrzesinski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland (M.K.K.); (M.E.K.)
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36
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Krasikova A, Kulikova T. Identification of Genomic Loci Responsible for the Formation of Nuclear Domains Using Lampbrush Chromosomes. Noncoding RNA 2019; 6:ncrna6010001. [PMID: 31881720 PMCID: PMC7151628 DOI: 10.3390/ncrna6010001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 12/19/2019] [Accepted: 12/22/2019] [Indexed: 12/12/2022] Open
Abstract
In the cell nuclei, various types of nuclear domains assemble as a result of transcriptional activity at specific chromosomal loci. Giant transcriptionally active lampbrush chromosomes, which form in oocyte nuclei of amphibians and birds enable the mapping of genomic sequences with high resolution and the visualization of individual transcription units. This makes avian and amphibian oocyte nuclei an advantageous model for studying locus-specific nuclear domains. We developed two strategies for identification and comprehensive analysis of the genomic loci involved in nuclear domain formation on lampbrush chromosomes. The first approach was based on the sequential FISH-mapping of BAC clones containing genomic DNA fragments with a known chromosomal position close to the locus of a nuclear domain. The second approach involved mechanical microdissection of the chromosomal region adjacent to the nuclear domain followed by the generation of FISH-probes and DNA sequencing. Furthermore, deciphering the DNA sequences from the dissected material by high throughput sequencing technologies and their mapping to the reference genome helps to identify the genomic region responsible for the formation of the nuclear domain. For those nuclear domains structured by nascent transcripts, identification of genomic loci of their formation is a crucial step in the identification of scaffold RNAs.
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Emerging Roles of Long Non-Coding RNAs as Drivers of Brain Evolution. Cells 2019; 8:cells8111399. [PMID: 31698782 PMCID: PMC6912723 DOI: 10.3390/cells8111399] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 11/01/2019] [Accepted: 11/03/2019] [Indexed: 01/09/2023] Open
Abstract
Mammalian genomes encode tens of thousands of long-noncoding RNAs (lncRNAs), which are capable of interactions with DNA, RNA and protein molecules, thereby enabling a variety of transcriptional and post-transcriptional regulatory activities. Strikingly, about 40% of lncRNAs are expressed specifically in the brain with precisely regulated temporal and spatial expression patterns. In stark contrast to the highly conserved repertoire of protein-coding genes, thousands of lncRNAs have newly appeared during primate nervous system evolution with hundreds of human-specific lncRNAs. Their evolvable nature and the myriad of potential functions make lncRNAs ideal candidates for drivers of human brain evolution. The human brain displays the largest relative volume of any animal species and the most remarkable cognitive abilities. In addition to brain size, structural reorganization and adaptive changes represent crucial hallmarks of human brain evolution. lncRNAs are increasingly reported to be involved in neurodevelopmental processes suggested to underlie human brain evolution, including proliferation, neurite outgrowth and synaptogenesis, as well as in neuroplasticity. Hence, evolutionary human brain adaptations are proposed to be essentially driven by lncRNAs, which will be discussed in this review.
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Hanly D, Esteller M, Berdasco M. Altered Long Non-coding RNA Expression in Cancer: Potential Biomarkers and Therapeutic Targets? ACTA ACUST UNITED AC 2019. [DOI: 10.1007/7355_2019_83] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Non-coding RNAs: Regulators of glioma cell epithelial-mesenchymal transformation. Pathol Res Pract 2019; 215:152539. [DOI: 10.1016/j.prp.2019.152539] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Revised: 06/29/2019] [Accepted: 07/12/2019] [Indexed: 12/14/2022]
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Hanly DJ, Esteller M, Berdasco M. Interplay between long non-coding RNAs and epigenetic machinery: emerging targets in cancer? Philos Trans R Soc Lond B Biol Sci 2019; 373:rstb.2017.0074. [PMID: 29685978 PMCID: PMC5915718 DOI: 10.1098/rstb.2017.0074] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/03/2017] [Indexed: 12/21/2022] Open
Abstract
Of the diverse array of putative molecular and biological functions assigned to long non-coding RNAs (lncRNAs), one attractive perspective in epigenetic research has been the hypothesis that lncRNAs directly interact with the proteins involved in the modulation of chromatin conformation. Indeed, epigenetic modifiers are among the most frequent protein partners of lncRNAs that have been identified to date, of which histone methyltransferases and protein members of the Polycomb Repressive Complex PRC2 have received considerable attention. This review is focused on how lncRNAs interface with epigenetic factors to shape the outcomes of crucial biological processes such as regulation of gene transcription, modulation of nuclear architecture, X inactivation in females and pre-mRNA splicing. Because of our increasing knowledge of their role in development and cellular differentiation, more research is beginning to be done into the deregulation of lncRNAs in human disorders. Focusing on cancer, we describe some key examples of disease-focused lncRNA studies. This knowledge has significantly contributed to our ever-improving understanding of how lncRNAs interact with epigenetic factors of human disease, and has also provided a plethora of much-needed novel prognostic biomarker candidates or potential therapeutic targets. Finally, current limitations and perspectives on lncRNA research are discussed here.This article is part of a discussion meeting issue 'Frontiers in epigenetic chemical biology'.
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Affiliation(s)
- David J Hanly
- Cancer Epigenetics Group, Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 Barcelona, Spain
| | - Manel Esteller
- Cancer Epigenetics Group, Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 Barcelona, Spain.,Department of Physiological Sciences II, School of Medicine, University of Barcelona, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), 08908 Barcelona, Spain
| | - María Berdasco
- Cancer Epigenetics Group, Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 Barcelona, Spain
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Walter Costa MB, Höner zu Siederdissen C, Dunjić M, Stadler PF, Nowick K. SSS-test: a novel test for detecting positive selection on RNA secondary structure. BMC Bioinformatics 2019; 20:151. [PMID: 30898084 PMCID: PMC6429701 DOI: 10.1186/s12859-019-2711-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 03/03/2019] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) play an important role in regulating gene expression and are thus important for determining phenotypes. Most attempts to measure selection in lncRNAs have focused on the primary sequence. The majority of small RNAs and at least some parts of lncRNAs must fold into specific structures to perform their biological function. Comprehensive assessments of selection acting on RNAs therefore must also encompass structure. Selection pressures acting on the structure of non-coding genes can be detected within multiple sequence alignments. Approaches of this type, however, have so far focused on negative selection. Thus, a computational method for identifying ncRNAs under positive selection is needed. RESULTS We introduce the SSS-test (test for Selection on Secondary Structure) to identify positive selection and thus adaptive evolution. Benchmarks with biological as well as synthetic controls yield coherent signals for both negative and positive selection, demonstrating the functionality of the test. A survey of a lncRNA collection comprising 15,443 families resulted in 110 candidates that appear to be under positive selection in human. In 26 lncRNAs that have been associated with psychiatric disorders we identified local structures that have signs of positive selection in the human lineage. CONCLUSIONS It is feasible to assay positive selection acting on RNA secondary structures on a genome-wide scale. The detection of human-specific positive selection in lncRNAs associated with cognitive disorder provides a set of candidate genes for further experimental testing and may provide insights into the evolution of cognitive abilities in humans. AVAILABILITY The SSS-test and related software is available at: https://github.com/waltercostamb/SSS-test . The databases used in this work are available at: http://www.bioinf.uni-leipzig.de/Software/SSS-test/ .
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Affiliation(s)
- Maria Beatriz Walter Costa
- Embrapa Agroenergia, Parque Estação Biológica (PqEB), Asa Norte, Brasília, DF, 70770-901 Brazil
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universität Leipzig, Härtelstraße 16–18, Leipzig, 04107 Germany
| | - Christian Höner zu Siederdissen
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universität Leipzig, Härtelstraße 16–18, Leipzig, 04107 Germany
| | - Marko Dunjić
- Human Biology Group, Institute for Biology, Department of Biology, Chemistry, Pharmacy, Freie Universitaet Berlin, Königin-Luise-Straße 1-3, Berlin, 14195 Germany
- Center for Human Molecular Genetics, Faculty of Biology, University of Belgrade, Studentski trg 16, PO box 43, Belgrade, 11000 Serbia
| | - Peter F. Stadler
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universität Leipzig, Härtelstraße 16–18, Leipzig, 04107 Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig & Competence Center for Scalable Data Services and Solutions Dresden-Leipzig & Leipzig Research Center for Civilization Diseases, University Leipzig, Leipzig, 04107 Germany
- Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, Leipzig, 04103 Germany
- Department of Theoretical Chemistry, University of Vienna, Währinger Straße 17, Vienna, A-1090 Austria
- Center for non-coding RNA in Technology and Health, University of Copenhagen, Grønnegårdsvej 3, Frederiksberg C, DK-1870 Denmark
- Faculdad de Ciencias, Universidad Nacional de Colombia, Sede Bogotá, Ciudad Universitaria, Bogotá, D.C., COL-111321 Colombia
- Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM87501 USA
| | - Katja Nowick
- Human Biology Group, Institute for Biology, Department of Biology, Chemistry, Pharmacy, Freie Universitaet Berlin, Königin-Luise-Straße 1-3, Berlin, 14195 Germany
- TFome Research Group, Bioinformatics Group, Interdisciplinary Center of Bioinformatics, Department of Computer Science, University of Leipzig, Härtelstraße 16-18, Leipzig, 04107 Germany
- Paul-Flechsig-Institute for Brain Research, University of Leipzig, Liebigstraße 19. Haus C, Leipzig, 04103 Germany
- Bioinformatics, Faculty of Agricultural Sciences, Institute of Animal Science, University of Hohenheim, Garbenstraße 13, Stuttgart, 70593 Germany
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Bountali A, Tonge DP, Mourtada-Maarabouni M. RNA sequencing reveals a key role for the long non-coding RNA MIAT in regulating neuroblastoma and glioblastoma cell fate. Int J Biol Macromol 2019; 130:878-891. [PMID: 30836187 DOI: 10.1016/j.ijbiomac.2019.03.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 02/28/2019] [Accepted: 03/01/2019] [Indexed: 12/29/2022]
Abstract
Myocardial Infarction Associated Transcript (MIAT) is a subnuclear lncRNA that interferes with alternative splicing and is associated with increased risk of various heart conditions and nervous system tumours. The current study aims to elucidate the role of MIAT in cell survival, apoptosis and migration in neuroblastoma and glioblastoma multiforme. To this end, MIAT was silenced by MIAT-specific siRNAs in neuroblastoma and glioblastoma cell lines, and RNA sequencing together with a series of functional assays were performed. The RNA sequencing has revealed that the expression of an outstanding number of genes is altered, including genes involved in cancer-related processes, such as cell growth and survival, apoptosis, reactive oxygen species (ROS) production and migration. Furthermore, the functional studies have confirmed the RNA sequencing leads, with our key findings suggesting that MIAT knockdown eliminates long-term survival and migration and increases basal apoptosis in neuroblastoma and glioblastoma cell lines. Taken together with the recent demonstration of the involvement of MIAT in glioblastoma, our observations suggest that MIAT could possess tumour-promoting properties, thereby acting as an oncogene, and has the potential to be used as a reliable biomarker for neuroblastoma and glioblastoma and be employed for prognostic, predictive and, potentially, therapeutic purposes for these cancers.
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Affiliation(s)
- Aikaterini Bountali
- School of Life Sciences, Faculty of Natural Sciences, Keele University, Newcastle-under-Lyme ST5 5BG, UK
| | - Daniel P Tonge
- School of Life Sciences, Faculty of Natural Sciences, Keele University, Newcastle-under-Lyme ST5 5BG, UK
| | - Mirna Mourtada-Maarabouni
- School of Life Sciences, Faculty of Natural Sciences, Keele University, Newcastle-under-Lyme ST5 5BG, UK.
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Fakhr-Eldeen A, Toraih EA, Fawzy MS. Long non-coding RNAs MALAT1, MIAT and ANRIL gene expression profiles in beta-thalassemia patients: a cross-sectional analysis. ACTA ACUST UNITED AC 2019; 24:308-317. [PMID: 30665334 DOI: 10.1080/16078454.2019.1570616] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
OBJECTIVES Beta-thalassemia (β-thal) is one of the most common genetic disorders worldwide. Multiple genetic and epigenetic mechanisms could be implicated in the pathogenesis and/or phenotype variations. We sought to explore the serum expression profile of three disease-related long non-coding RNAs (lncRNAs) in a sample of Egyptian β-thal patients with correlation to the patients' clinicolaboratory data. METHODS Fifty consecutive β-thal patients and 50 unrelated controls were enrolled in the study. Quantification of circulating lncRNAs; MALAT1 (metastasis-associated lung adenocarcinoma transcript 1), MIAT (myocardial infarction associated transcript), and ANRIL (antisense non-coding RNA in the INK4 locus) was done by Real-time qRT-PCR. RESULTS Significant higher expression levels of the studied lncRNAs in β-thal patients compared to the controls (all P values < 0.001) were identified. There was no significant difference between β-thal-major and intermedia patients at the level of any of the studied lncRNAs. Higher MALAT1 expression profile was associated with early age at onset, early age at first blood transfusion, and a higher frequency of splenomegaly. Whereas, up-regulated MIAT levels were associated with early age at first blood transfusion. CONCLUSIONS Taken together, the studied lncRNAs MALAT1, MIAT, and ANRIL might be implicated in β-thal pathogenesis and could provide new molecular biomarkers for β-thalassemia after validation in large-scale future studies.
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Affiliation(s)
- Abeer Fakhr-Eldeen
- a Department of Clinical Pathology, Faculty of Medicine , Sohag University , Sohag , Egypt.,b Department of Pathology, Faculty of Medicine , Northern Border University , Arar , Saudi Arabia
| | - Eman A Toraih
- c Genetics Unit, Department of Histology and Cell Biology, Faculty of Medicine , Suez Canal University , Ismailia , Egypt.,d Center of Excellence of Molecular and Cellular Medicine , Suez Canal University , Ismailia , Egypt
| | - Manal S Fawzy
- e Department of Biochemistry, Faculty of Medicine , Northern Border University , Arar , Saudi Arabia.,f Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine , Suez Canal University , Ismailia , Egypt
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Laneve P, Rea J, Caffarelli E. Long Noncoding RNAs: Emerging Players in Medulloblastoma. Front Pediatr 2019; 7:67. [PMID: 30923703 PMCID: PMC6426782 DOI: 10.3389/fped.2019.00067] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 02/18/2019] [Indexed: 01/02/2023] Open
Abstract
Central Nervous System tumors are the leading cause of cancer-related death in children, and medulloblastoma has the highest incidence rate. The current therapies achieve a 5-year survival rate of 50-80%, but often inflict severe secondary effects demanding the urgent development of novel, effective, and less toxic therapeutic strategies. Historically identified on a histopathological basis, medulloblastoma was later classified into four major subgroups-namely WNT, SHH, Group 3, and Group 4-each characterized by distinct transcriptional profiles, copy-number aberrations, somatic mutations, and clinical outcomes. Additional complexity was recently provided by integrating gene- and non-gene-based data, which indicates that each subclass can be further subdivided into specific subtypes. These deeper classifications, while getting over the typical tumor heterogeneity, indicate that different forms of medulloblastoma hold different molecular drivers that can be successfully exploited for a greater diagnostic accuracy and for the development of novel, targeted treatments. Long noncoding RNAs are transcripts that lack coding potential and play relevant roles as regulators of gene expression in mammalian differentiation and developmental processes. Their cell type- and tissue-specificity, higher than mRNAs, make them more informative about cell- type identity than protein-coding genes. Remarkably, about 40% of long noncoding RNAs are expressed in the brain and their aberrant expression has been linked to neuro-oncological disorders. However, while their involvement in gliomas and neuroblastomas has been extensively studied, their role in medulloblastoma is still poorly explored. Here, we present an overview of current knowledge regarding the function played by long noncoding RNAs in medulloblastoma biology.
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Affiliation(s)
- Pietro Laneve
- Institute of Molecular Biology and Pathology, National Research Council, Rome, Italy
| | - Jessica Rea
- Department of Biology and Biotechnology, Sapienza University of Rome, Rome, Italy
| | - Elisa Caffarelli
- Institute of Molecular Biology and Pathology, National Research Council, Rome, Italy
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Komatsu T, Yokoi S, Fujii K, Mito M, Kimura Y, Iwasaki S, Nakagawa S. UPA-seq: prediction of functional lncRNAs using differential sensitivity to UV crosslinking. RNA (NEW YORK, N.Y.) 2018; 24:1785-1802. [PMID: 30232101 PMCID: PMC6239193 DOI: 10.1261/rna.067611.118] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 09/12/2018] [Indexed: 05/16/2023]
Abstract
While a large number of long noncoding RNAs (lncRNAs) are transcribed from the genome of higher eukaryotes, systematic prediction of their functionality has been challenging due to the lack of conserved sequence motifs or structures. Assuming that some lncRNAs function as large ribonucleoprotein complexes and thus are easily crosslinked to proteins upon UV irradiation, we performed RNA-seq analyses of RNAs recovered from the aqueous phase after UV irradiation and phenol-chloroform extraction (UPA-seq). As expected, the numbers of UPA-seq reads mapped to known functional lncRNAs were remarkably reduced upon UV irradiation. Comparison with ENCODE eCLIP data revealed that lncRNAs that exhibited greater decreases upon UV irradiation preferentially associated with proteins containing prion-like domains (PrLDs). Fluorescent in situ hybridization (FISH) analyses revealed the nuclear localization of novel functional lncRNA candidates, including one that accumulated at the site of transcription. We propose that UPA-seq provides a useful tool for the selection of lncRNA candidates to be analyzed in depth in subsequent functional studies.
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Affiliation(s)
- Taiwa Komatsu
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
- Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan
| | - Saori Yokoi
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Koichi Fujii
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Mari Mito
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Saitama 351-0198, Japan
| | - Yusuke Kimura
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Saitama 351-0198, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8561, Japan
| | - Shintaro Iwasaki
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Saitama 351-0198, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8561, Japan
| | - Shinichi Nakagawa
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
- Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan
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Pan B, Zhao M, Xu L. Long noncoding RNA gastric cancer-associated transcript 3 plays oncogenic roles in glioma through sponging miR-3127-5p. J Cell Physiol 2018; 234:8825-8833. [PMID: 30317610 DOI: 10.1002/jcp.27542] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 09/13/2018] [Indexed: 02/02/2023]
Abstract
Evidence is emerging that long noncoding RNAs (lncRNAs) play vital roles in tumorigenesis. LncRNA gastric cancer-associated transcript 3 (GACAT3) is reported to participate in the development of breast cancer, colorectal cancer, nonsmall cell lung cancer, and gastric cancer. However, whether it is implicated in glioma has not been elucidated. Here, we found that GACAT3 level was aberrantly elevated in glioma tissues and cell lines. Higher GACAT3 expression predicted lower survival rate. Knockdown of GACAT3 suppressed the proliferation, colony formation, migration, and invasion but promoting apoptosis in glioma cells. Next, we determined that GACAT3 contributes to glioma progression through inhibiting microRNA (miR)-3127-5p. Subsequently, ELAVL1 was identified as a direct target of miR-3127-5p by bioinformatics analysis and luciferase reporter assay. Moreover, we confirmed that GACAT3 promoted ELAVL1 expression through sponging miR-3127-5p, leading to glioma progression. Taken together, our study elucidated that GACAT3/miR-3127-5p/ELAVL1 signaling regulates glioma development and might be a promising therapeutic target.
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Affiliation(s)
- Bailin Pan
- Department of Neurosurgery, Zhuji People's Hospital of Zhejiang Province, Zhuji Affiliated Hospital of Wenzhou Medical University, Zhuji, China
| | - Ming Zhao
- Department of Neurosurgery, Zhuji People's Hospital of Zhejiang Province, Zhuji Affiliated Hospital of Wenzhou Medical University, Zhuji, China
| | - Longbiao Xu
- Department of Neurosurgery, Zhuji People's Hospital of Zhejiang Province, Zhuji Affiliated Hospital of Wenzhou Medical University, Zhuji, China
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Yang C, Kelaini S, Caines R, Margariti A. RBPs Play Important Roles in Vascular Endothelial Dysfunction Under Diabetic Conditions. Front Physiol 2018; 9:1310. [PMID: 30294283 PMCID: PMC6158626 DOI: 10.3389/fphys.2018.01310] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Accepted: 08/30/2018] [Indexed: 12/17/2022] Open
Abstract
Diabetes is one of the major health care problems worldwide leading to huge suffering and burden to patients and society. Diabetes is also considered as a cardiovascular disorder because of the correlation between diabetes and an increased incidence of cardiovascular disease. Vascular endothelial cell dysfunction is a major mediator of diabetic vascular complications. It has been established that diabetes contributes to significant alteration of the gene expression profile of vascular endothelial cells. Post-transcriptional regulation by RNA binding proteins (RBPs) plays an important role in the alteration of gene expression profile under diabetic conditions. The review focuses on the roles and mechanisms of critical RBPs toward diabetic vascular endothelial dysfunction. Deeper understanding of the post- transcriptional regulation by RBPs could lead to new therapeutic strategies against diabetic manifestation in the future.
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Affiliation(s)
- Chunbo Yang
- Centre for Experimental Medicine, Queens University Belfast, Belfast, United Kingdom
| | - Sophia Kelaini
- Centre for Experimental Medicine, Queens University Belfast, Belfast, United Kingdom
| | - Rachel Caines
- Centre for Experimental Medicine, Queens University Belfast, Belfast, United Kingdom
| | - Andriana Margariti
- Centre for Experimental Medicine, Queens University Belfast, Belfast, United Kingdom
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He J, Tu C, Liu Y. Role of lncRNAs in aging and age-related diseases. Aging Med (Milton) 2018; 1:158-175. [PMID: 31942494 PMCID: PMC6880696 DOI: 10.1002/agm2.12030] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 06/28/2018] [Accepted: 07/03/2018] [Indexed: 01/10/2023] Open
Abstract
Aging is progressive physiological degeneration and consequently declined function, which is linked to senescence on both cellular and organ levels. Accumulating studies indicate that long noncoding RNAs (lncRNAs) play important roles in cellular senescence at all levels-transcriptional, post-transcriptional, translational, and post-translational. Understanding the molecular mechanism of lncRNAs underlying senescence could facilitate interpretation and intervention of aging and age-related diseases. In this review, we describe categories of known and novel lncRNAs that have been involved in the progression of senescence. We also identify the lncRNAs implicated in diseases arising from age-driven degeneration or dysfunction in some representative organs and systems (brains, liver, muscle, cardiovascular system, bone pancreatic islets, and immune system). Improved comprehension of lncRNAs in the aging process on all levels, from cell to organismal, may provide new insights into the amelioration of age-related pathologies and prolonged healthspan.
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Affiliation(s)
- Jieyu He
- Department of GeriatricsThe Second Xiangya HospitalCentral South UniversityChangshaHunanChina
| | - Chao Tu
- Department of OrthopedicsThe Second Xiangya HospitalCentral South UniversityChangshaHunanChina
| | - Youshuo Liu
- Department of GeriatricsThe Second Xiangya HospitalCentral South UniversityChangshaHunanChina
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Fenoglio C, Oldoni E, Serpente M, De Riz MA, Arcaro M, D'Anca M, Pietroboni AM, Calvi A, Lecchi E, Goris A, Mallants K, Dubois B, Comi C, Cantello R, Scarpini E, Galimberti D. LncRNAs expression profile in peripheral blood mononuclear cells from multiple sclerosis patients. J Neuroimmunol 2018; 324:129-135. [PMID: 30170791 DOI: 10.1016/j.jneuroim.2018.08.008] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 07/20/2018] [Accepted: 08/14/2018] [Indexed: 01/10/2023]
Abstract
LncRNA PCR arrays containing 90 common LncRNAs were used to screen lncRNA expression levels in PBMC from a discovery population of patients with MS. Data from discovery and replications cohorts showed a generalized dysregulation of lncRNA levels in MS patients compared with controls. MALAT1, MEG9, NRON, ANRIL, TUG1, XIST, SOX2OT, GOMAFU, HULC, BACE-1AS were significantly downregulated in MS patients in comparison with controls. Therefore, we performed a validation analysis in an independent cohort of Belgian origin. In this study, NRON and TUG1 downregulations in MS patients compared with controls were confirmed (p ≤ .05 and p ≤ .0001 respectively), whereas considering the other lncRNAs, the statistical threshold was not reached. LncRNAs profiling could thus represent a new challenge in the research of easy detectable biomarkers of disease susceptibility and progression.
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Affiliation(s)
| | - Emanuela Oldoni
- University of Milan, Dino Ferrari Center, Milan, Italy; Laboratory for Neuroimmunology, Department of Neurosciences, KU Leuven, Herestraat 49 bus 1022, 3000 Leuven, Belgium.
| | | | - Milena A De Riz
- Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Neurodegenerative Diseases Unit, Milan, Italy.
| | - Marina Arcaro
- Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Neurodegenerative Diseases Unit, Milan, Italy.
| | | | - Anna M Pietroboni
- Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Neurodegenerative Diseases Unit, Milan, Italy.
| | - Alberto Calvi
- University of Milan, Dino Ferrari Center, Milan, Italy.
| | - Elisabetta Lecchi
- Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Neurodegenerative Diseases Unit, Milan, Italy
| | - An Goris
- Laboratory for Neuroimmunology, Department of Neurosciences, KU Leuven, Herestraat 49 bus 1022, 3000 Leuven, Belgium.
| | - Klara Mallants
- Laboratory for Neuroimmunology, Department of Neurosciences, KU Leuven, Herestraat 49 bus 1022, 3000 Leuven, Belgium.
| | - Bénédicte Dubois
- Laboratory for Neuroimmunology, Department of Neurosciences, KU Leuven, Herestraat 49 bus 1022, 3000 Leuven, Belgium; Department of Neurology, University Hospitals Leuven, Herestraat 49, 3000 Leuven, Belgium.
| | - Cristoforo Comi
- Department of Translational Medicine, Section of Neurology, University of Eastern Piedmont Amedeo Avogadro, Novara, Italy.
| | - Roberto Cantello
- Department of Translational Medicine, Section of Neurology, University of Eastern Piedmont Amedeo Avogadro, Novara, Italy.
| | - Elio Scarpini
- University of Milan, Dino Ferrari Center, Milan, Italy; Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Neurodegenerative Diseases Unit, Milan, Italy.
| | - Daniela Galimberti
- University of Milan, Dino Ferrari Center, Milan, Italy; Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Neurodegenerative Diseases Unit, Milan, Italy.
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Blokhin I, Khorkova O, Hsiao J, Wahlestedt C. Developments in lncRNA drug discovery: where are we heading? Expert Opin Drug Discov 2018; 13:837-849. [PMID: 30078338 DOI: 10.1080/17460441.2018.1501024] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
INTRODUCTION The central dogma of molecular biology, which states that the only role of long RNA transcripts is to convey information from gene to protein, was brought into question in recent years due to discovery of the extensive presence and complex roles of long noncoding RNAs (lncRNAs). Furthermore, lncRNAs were found to be involved in pathogenesis of multiple diseases and thus represent a new class of therapeutic targets. Translational efforts in the lncRNA field have been augmented by progress in optimizing the chemistry and delivery platforms of lncRNA-targeting modalities, including oligonucleotide-based drugs and CRISPR-Cas9. Areas covered: This review covers the current advances in characterizing diversity and biological functions of lncRNA focusing on their therapeutic potential in selected therapeutic areas. Expert opinion: Due to accelerating parallel progress in lncRNA biology and lncRNA-compatible therapeutic modalities, it is likely that lncRNA-dependent mechanisms of pathogenesis will soon be targeted in various disorders, including neurological, psychiatric, cardiovascular, infectious diseases, and cancer. Significant efforts, however, are still required to better understand the biology of both lncRNAs and lncRNA-targeting drugs. Further work is needed in the areas of lncRNA nomenclature, database representation, intra/interfield communication, and education of the community at large.
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Affiliation(s)
- Ilya Blokhin
- a Center for Therapeutic Innovation and Department of Psychiatry and Behavioral Sciences , University of Miami Miller School of Medicine , Miami , FL , USA
| | | | | | - Claes Wahlestedt
- a Center for Therapeutic Innovation and Department of Psychiatry and Behavioral Sciences , University of Miami Miller School of Medicine , Miami , FL , USA
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