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Long Non-Coding RNAs in Neuronal Aging. Noncoding RNA 2018; 4:ncrna4020012. [PMID: 29670042 PMCID: PMC6027360 DOI: 10.3390/ncrna4020012] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 04/06/2018] [Accepted: 04/10/2018] [Indexed: 02/07/2023] Open
Abstract
The expansion of long non-coding RNAs (lncRNAs) in organismal genomes has been associated with the emergence of sophisticated regulatory networks that may have contributed to more complex neuronal processes, such as higher-order cognition. In line with the important roles of lncRNAs in the normal functioning of the human brain, dysregulation of lncRNA expression has been implicated in aging and age-related neurodegenerative disorders. In this paper, we discuss the function and expression of known neuronal-associated lncRNAs, their impact on epigenetic changes, the contribution of transposable elements to lncRNA expression, and the implication of lncRNAs in maintaining the 3D nuclear architecture in neurons. Moreover, we discuss how the complex molecular processes that are orchestrated by lncRNAs in the aged brain may contribute to neuronal pathogenesis by promoting protein aggregation and neurodegeneration. Finally, this review explores the possibility that age-related disturbances of lncRNA expression change the genomic and epigenetic regulatory landscape of neurons, which may affect neuronal processes such as neurogenesis and synaptic plasticity.
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Krauskopf J, Caiment F, van Veldhoven K, Chadeau-Hyam M, Sinharay R, Chung KF, Cullinan P, Collins P, Barratt B, Kelly FJ, Vermeulen R, Vineis P, de Kok TM, Kleinjans JC. The human circulating miRNome reflects multiple organ disease risks in association with short-term exposure to traffic-related air pollution. ENVIRONMENT INTERNATIONAL 2018; 113:26-34. [PMID: 29421404 DOI: 10.1016/j.envint.2018.01.014] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 01/17/2018] [Accepted: 01/17/2018] [Indexed: 05/24/2023]
Abstract
Traffic-related air pollution is a complex mixture of particulate matter (PM) and gaseous pollutants, such as nitrogen dioxide (NO2). PM exposure contributes to the pathogenesis of many diseases including several types of cancer, as well as pulmonary, cardiovascular and neurodegenerative diseases. Also exposure to NO2 has been related to increased cardiovascular mortality. In search of an early diagnostic biomarker for improved air pollution-associated health risk assessment, recent human studies have shown that certain circulating miRNAs are altered upon exposure to traffic-related air pollutants. Here, we present for the first time a global analysis of the circulating miRNA genome in an experimental cross-over study of a human population exposed to traffic-related air pollution. By utilizing next-generation sequencing technology and detailed real-time exposure measurements we identified 54 circulating miRNAs to be dose- and pollutant species-dependently associated with PM10, PM2.5, black carbon, ultrafine particles and NO2 already after 2 h of exposure. Bioinformatics analysis suggests that these circulating miRNAs actually reflect the adverse consequences of traffic pollution-induced toxicity in target tissues including the lung, heart, kidney and brain. This study shows the strong potential of circulating miRNAs as novel biomarkers for environmental health risk assessment.
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Affiliation(s)
- Julian Krauskopf
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, The Netherlands.
| | - Florian Caiment
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, The Netherlands
| | - Karin van Veldhoven
- MRC-PHE Centre for Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, Imperial College, London, UK
| | - Marc Chadeau-Hyam
- MRC-PHE Centre for Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, Imperial College, London, UK
| | - Rudy Sinharay
- National Heart and Lung Institute, Imperial College London, UK
| | - Kian Fan Chung
- National Heart and Lung Institute, Imperial College London, UK
| | - Paul Cullinan
- National Heart and Lung Institute, Imperial College London, UK
| | - Peter Collins
- National Heart and Lung Institute, Imperial College London, UK
| | - Benjamin Barratt
- MRC-PHE Centre for Environment and Health, Analytical & Environmental Sciences, King's College London, UK
| | - Frank J Kelly
- MRC-PHE Centre for Environment and Health, Analytical & Environmental Sciences, King's College London, UK
| | - Roel Vermeulen
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht, The Netherlands
| | - Paolo Vineis
- MRC-PHE Centre for Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, Imperial College, London, UK
| | - Theo M de Kok
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, The Netherlands
| | - Jos C Kleinjans
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, The Netherlands
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García-Padilla C, Aránega A, Franco D. The role of long non-coding RNAs in cardiac development and disease. AIMS GENETICS 2018; 5:124-140. [PMID: 31435517 PMCID: PMC6698576 DOI: 10.3934/genet.2018.2.124] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 03/15/2018] [Indexed: 12/12/2022]
Abstract
Cells display a set of RNA molecules at one time point, reflecting thus the cellular transcriptional steady state, configuring therefore its transcriptome. It is basically composed of two different classes of RNA molecules; protein-coding RNAs (cRNAs) and protein non-coding RNAs (ncRNAs). Sequencing of the human genome and subsequently the ENCODE project identified that more than 80% of the genome is transcribed in some type of RNA. Importantly, only 3% of these transcripts correspond to protein-coding RNAs, pointing that ncRNAs are as important or even more as cRNAs. ncRNAs have pivotal roles in development, differentiation and disease. Non-coding RNAs can be classified into two distinct classes according to their length; i.e., small (<200 nt) and long (>200 nt) noncoding RNAs. The structure, biogenesis and functional roles of small non-coding RNA have been widely studied, particularly for microRNAs (miRNAs). In contrast to microRNAs, our current understanding of long non-coding RNAs (lncRNAs) is limited. In this manuscript, we provide state-of-the art review of the functional roles of long non-coding RNAs during cardiac development as well as an overview of the emerging role of these ncRNAs in distinct cardiac diseases.
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Affiliation(s)
| | | | - Diego Franco
- Cardiovascular Development Group, Department of Experimental Biology, University of Jaén, Jaén, Spain
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204
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Osielska MA, Jagodziński PP. Long non-coding RNA as potential biomarkers in non-small-cell lung cancer: What do we know so far? Biomed Pharmacother 2018; 101:322-333. [PMID: 29499406 DOI: 10.1016/j.biopha.2018.02.099] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 02/19/2018] [Accepted: 02/21/2018] [Indexed: 12/29/2022] Open
Abstract
Non-small-cell lung cancer (NSCLC) remains one of the most frequent types of lung cancer characterized by its local advancement at diagnosis. Therefore, identification of new prognostic biomarkers has become one of the most important issue in NSCLC therapy. It is now well understood that genetic and epigenetic alterations are responsible for NSCLC development. Moreover, it has been recently revealed that the non-protein coding regions of the genome may serve as a template for transcription of various type of RNAs, collectively referred to as non-coding RNAs. Non-coding RNAs, including long non-coding RNAs (lncRNAs) are involved in multiple cellular processes and it has been suggested that aberrant expression of lncRNAs may lead to tumour development, including NSCLC. Furthermore, some of the established risk factors for NSCLC may have an impact on expression level of several types of lncRNAs, and thus, affect the lung carcinogenesis through lncRNAs regulation. In this review, we would like to summarise the to-date knowledge about lncRNAs as potential biomarkers in NSCLC and the role of various environmental factors, such as smoking and air pollution, in development and progression of this tumour and their effect on lncRNAs expression.
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Affiliation(s)
- Maria Aleksandra Osielska
- Department of Biochemistry and Molecular Biology, Poznań University of Medical Sciences, Poznań, Poland.
| | - Paweł Piotr Jagodziński
- Department of Biochemistry and Molecular Biology, Poznań University of Medical Sciences, Poznań, Poland
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205
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Noh JH, Kim KM, McClusky WG, Abdelmohsen K, Gorospe M. Cytoplasmic functions of long noncoding RNAs. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018. [PMID: 29516680 DOI: 10.1002/wrna.1471] [Citation(s) in RCA: 270] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Long noncoding RNAs (lncRNAs) are transcripts longer than 200 nucleotides found throughout the cell that lack protein-coding function. Their functions are closely linked to their interaction with RNA-binding proteins (RBPs) and nucleic acids. Nuclear lncRNAs have been studied extensively, revealing complexes with structural and regulatory roles that enable gene organization and control transcription. Cytoplasmic lncRNAs are less well understood, but accumulating evidence indicates that they also form complexes with diverse structural and regulatory functions. Here, we review our current knowledge of cytoplasmic lncRNAs and the different levels of gene regulation controlled by cytoplasmic lncRNA complexes, including mRNA turnover, translation, protein stability, sponging of cytosolic factors, and modulation of signaling pathways. We conclude by discussing areas of future study needed to elucidate comprehensively the biology of lncRNAs, to further understand the impact of lncRNAs on physiology and design lncRNA-centered therapeutic strategies. This article is categorized under: RNA Export and Localization > RNA Localization Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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Affiliation(s)
- Ji Heon Noh
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, Maryland
| | - Kyoung Mi Kim
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, Maryland
| | - Waverly G McClusky
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, Maryland
| | - Kotb Abdelmohsen
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, Maryland
| | - Myriam Gorospe
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, Maryland
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206
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Wanowska E, Kubiak MR, Rosikiewicz W, Makałowska I, Szcześniak MW. Natural antisense transcripts in diseases: From modes of action to targeted therapies. WILEY INTERDISCIPLINARY REVIEWS. RNA 2018; 9:e1461. [PMID: 29341438 PMCID: PMC5838512 DOI: 10.1002/wrna.1461] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 11/28/2017] [Accepted: 11/29/2017] [Indexed: 12/16/2022]
Abstract
Antisense transcription is a widespread phenomenon in mammalian genomes, leading to production of RNAs molecules referred to as natural antisense transcripts (NATs). NATs apply diverse transcriptional and post-transcriptional regulatory mechanisms to carry out a wide variety of biological roles that are important for the normal functioning of living cells, but their dysfunctions can be associated with human diseases. In this review, we attempt to provide a molecular basis for the involvement of NATs in the etiology of human disorders such as cancers and neurodegenerative and cardiovascular diseases. We also discuss the pros and cons of oligonucleotide-based therapies targeted against NATs, and we comment on state-of-the-art progress in this promising area of clinical research. WIREs RNA 2018, 9:e1461. doi: 10.1002/wrna.1461 This article is categorized under: RNA in Disease and Development > RNA in Disease Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA Interactions with Proteins and Other Molecules > Small Molecule-RNA Interactions.
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Affiliation(s)
- Elżbieta Wanowska
- Institute of Antropology, Laboratory of Integrative GenomicsAdam Mickiewicz UniversityPoznanPoland
| | - Magdalena Regina Kubiak
- Institute of Antropology, Laboratory of Integrative GenomicsAdam Mickiewicz UniversityPoznanPoland
| | - Wojciech Rosikiewicz
- Institute of Antropology, Laboratory of Integrative GenomicsAdam Mickiewicz UniversityPoznanPoland
| | - Izabela Makałowska
- Institute of Antropology, Laboratory of Integrative GenomicsAdam Mickiewicz UniversityPoznanPoland
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207
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Idda ML, Munk R, Abdelmohsen K, Gorospe M. Noncoding RNAs in Alzheimer's disease. WILEY INTERDISCIPLINARY REVIEWS. RNA 2018; 9. [PMID: 29327503 PMCID: PMC5847280 DOI: 10.1002/wrna.1463] [Citation(s) in RCA: 124] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 11/24/2017] [Accepted: 11/29/2017] [Indexed: 12/12/2022]
Abstract
Alzheimer's disease (AD) is a progressive neurodegenerative disorder and the main cause of dementia among the elderly worldwide. Despite intense efforts to develop drugs for preventing and treating AD, no effective therapies are available as yet, posing a growing burden at the personal, medical, and socioeconomic levels. AD is characterized by the production and aggregation of amyloid β (Aβ) peptides derived from amyloid precursor protein (APP), the presence of hyperphosphorylated microtubule-associated protein Tau (MAPT), and chronic inflammation leading to neuronal loss. Aβ accumulation and hyperphosphorylated Tau are responsible for the main histopathological features of AD, Aβ plaques, and neurofibrillary tangles (NFTs), respectively. However, the full spectrum of molecular factors that contribute to AD pathogenesis is not known. Noncoding (nc)RNAs, including microRNAs (miRNAs), long noncoding RNAs (lncRNAs), and circular RNAs (circRNAs), regulate gene expression at the transcriptional and posttranscriptional levels in various diseases, serving as biomarkers and potential therapeutic targets. There is rising recognition that ncRNAs have been implicated in both the onset and pathogenesis of AD. Here, we review the ncRNAs implicated posttranscriptionally in the main AD pathways and discuss the growing interest in targeting regulatory ncRNAs therapeutically to combat AD pathology. WIREs RNA 2018, 9:e1463. doi: 10.1002/wrna.1463 This article is categorized under: RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- M Laura Idda
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, Maryland
| | - Rachel Munk
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, Maryland
| | - Kotb Abdelmohsen
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, Maryland
| | - Myriam Gorospe
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, Maryland
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208
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Yuan J, Li J, Yang Y, Tan C, Zhu Y, Hu L, Qi Y, Lu ZJ. Stress-responsive regulation of long non-coding RNA polyadenylation in Oryza sativa. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 93:814-827. [PMID: 29265542 DOI: 10.1111/tpj.13804] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 11/18/2017] [Accepted: 11/28/2017] [Indexed: 05/22/2023]
Abstract
Recently, long non-coding RNAs (lncRNAs) have been demonstrated to be involved in many biological processes of plants; however, a systematic study on transcriptional and, in particular, post-transcriptional regulation of stress-responsive lncRNAs in Oryza sativa (rice) is lacking. We sequenced three types of RNA libraries (poly(A)+, poly(A)- and nuclear RNAs) under four abiotic stresses (cold, heat, drought and salt). Based on an integrative bioinformatics approach and ~200 high-throughput data sets, ~170 of which have been published, we revealed over 7000 lncRNAs, nearly half of which were identified for the first time. Notably, we found that the majority of the ~500 poly(A) lncRNAs that were differentially expressed under stress were significantly downregulated, but approximately 25% were found to have upregulated non-poly(A) forms. Moreover, hundreds of lncRNAs with downregulated polyadenylation (DPA) tend to be highly conserved, show significant nuclear retention and are co-expressed with protein-coding genes that function under stress. Remarkably, these DPA lncRNAs are significantly enriched in quantitative trait loci (QTLs) for stress tolerance or development, suggesting their potential important roles in rice growth under various stresses. In particular, we observed substantially accumulated DPA lncRNAs in plants exposed to drought and salt, which is consistent with the severe reduction of RNA 3'-end processing factors under these conditions. Taken together, the results of this study reveal that polyadenylation and subcellular localization of many rice lncRNAs are likely to be regulated at the post-transcriptional level. Our findings strongly suggest that many upregulated/downregulated lncRNAs previously identified by traditional RNA-seq analyses need to be carefully reviewed to assess the influence of post-transcriptional modification.
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Affiliation(s)
- Jiapei Yuan
- MOE Key Laboratory of Bioinformatics, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Jingrui Li
- MOE Key Laboratory of Bioinformatics, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yang Yang
- MOE Key Laboratory of Bioinformatics, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Chang Tan
- MOE Key Laboratory of Bioinformatics, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yumin Zhu
- MOE Key Laboratory of Bioinformatics, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Long Hu
- MOE Key Laboratory of Bioinformatics, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yijun Qi
- MOE Key Laboratory of Bioinformatics, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Zhi John Lu
- MOE Key Laboratory of Bioinformatics, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
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209
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Dan J, Wang J, Wang Y, Zhu M, Yang X, Peng Z, Jiang H, Chen L. LncRNA-MEG3 inhibits proliferation and metastasis by regulating miRNA-21 in gastric cancer. Biomed Pharmacother 2018; 99:931-938. [DOI: 10.1016/j.biopha.2018.01.164] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 01/30/2018] [Accepted: 01/30/2018] [Indexed: 12/14/2022] Open
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Di Mauro V, Barandalla-Sobrados M, Catalucci D. The noncoding-RNA landscape in cardiovascular health and disease. Noncoding RNA Res 2018; 3:12-19. [PMID: 30159435 PMCID: PMC6084835 DOI: 10.1016/j.ncrna.2018.02.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 12/27/2017] [Accepted: 02/08/2018] [Indexed: 12/22/2022] Open
Abstract
The cardiovascular system plays a pivotal role in regulating and maintaining homeostasis in the human body. Therefore any alteration in regulatory networks that orchestrate heart development as well as adaptation to physiological and environmental stress might result in pathological conditions, which represent the leading cause of death worldwide [1]. The latest advances in genome-wide techniques challenged the "protein-central dogma" with the discovery of the so-called non-coding RNAs (ncRNAs). Despite their lack of protein coding potential, ncRNAs have been largely demonstrated to regulate the majority of biological processes and have also been largely implicated in cardiovascular disorders. This review will first discuss the important mechanistic aspects of some of the classes of ncRNAs such as biogenesis, mechanism of action, as well as their involvement in cardiac diseases. The ncRNA potential uses as therapeutic molecules, with a specific focus on the latest technologies for their in vivo delivery as drug targets, will be described.
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Affiliation(s)
- Vittoria Di Mauro
- National Research Council, Institute of Genetics and Biomedical Research, Milan Unit, Milan, Italy
- Humanitas Clinical and Research Center, Rozzano, Milan, Italy
| | - Maria Barandalla-Sobrados
- National Research Council, Institute of Genetics and Biomedical Research, Milan Unit, Milan, Italy
- Humanitas Clinical and Research Center, Rozzano, Milan, Italy
| | - Daniele Catalucci
- National Research Council, Institute of Genetics and Biomedical Research, Milan Unit, Milan, Italy
- Humanitas Clinical and Research Center, Rozzano, Milan, Italy
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211
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O'Brien EM, Selfe JL, Martins AS, Walters ZS, Shipley JM. The long non-coding RNA MYCNOS-01 regulates MYCN protein levels and affects growth of MYCN-amplified rhabdomyosarcoma and neuroblastoma cells. BMC Cancer 2018; 18:217. [PMID: 29466962 PMCID: PMC5822637 DOI: 10.1186/s12885-018-4129-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 02/13/2018] [Indexed: 12/02/2022] Open
Abstract
Background MYCN is amplified in small cell lung cancers and several pediatric tumors, including alveolar rhabdomyosarcomas and neuroblastomas. MYCN protein is known to play a key oncogenic role in both alveolar rhabdomyosarcomas and neuroblastomas. MYCN opposite strand (MYCNOS) is a gene located on the antisense strand to MYCN that encodes alternatively spliced transcripts, two of which (MYCNOS-01 and MYCNOS-02) are known to be expressed in neuroblastoma and small cell lung cancer with reciprocal regulation between MYCNOS-02 and MYCN reported for neuroblastomas. We sought to determine a functional role for MYCNOS-01 in alveolar rhabdomyosarcoma and neuroblastoma cells and identify any associated regulatory effects between MYCN and MYCNOS-01. Methods MYCNOS-01, MYCNOS-02 and MYCN expression levels were assessed in alveolar rhabdomyosarcoma and neuroblastoma cell lines and tumor samples from patients using Affymetrix microarray data and quantitative RT-PCR. Following MYCNOS-01 or MYCN siRNA knockdown and MYCNOS-01 overexpression, transcript levels were assayed by quantitative RT-PCR and MYCN protein expression assessed by Western blot and immunofluorescence. Additionally, effects on cell growth, apoptosis and cell cycle profiles were determined by a metabolic assay, caspase activity and flow cytometry, respectively. Results MYCNOS-01 transcript levels were generally higher in NB and RMS tumor samples and cell lines with MYCN genomic amplification. RNA interference of MYCNOS-01 expression did not alter MYCN transcript levels but decreased MYCN protein levels. Conversely, MYCN reduction increased MYCNOS-01 transcript levels, creating a negative feedback loop on MYCN protein levels. Reduction of MYCNOS-01 or MYCN expression decreased cell growth in MYCN-amplified alveolar rhabdomyosarcoma and neuroblastoma cell lines. This is consistent with MYCNOS-01-mediated regulation of MYCN contributing to the phenotype observed. Conclusions An alternative transcript of MYCNOS, MYCNOS-01, post-transcriptionally regulates MYCN levels and affects growth in MYCN-amplified rhabdomyosarcoma and neuroblastoma cells. Electronic supplementary material The online version of this article (10.1186/s12885-018-4129-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Eleanor M O'Brien
- Sarcoma Molecular Pathology Team, Divisions of Molecular Pathology and Cancer Therapeutics, Institute of Cancer Research, Surrey, Sutton, SM2 5NG, UK
| | - Joanna L Selfe
- Sarcoma Molecular Pathology Team, Divisions of Molecular Pathology and Cancer Therapeutics, Institute of Cancer Research, Surrey, Sutton, SM2 5NG, UK
| | - Ana Sofia Martins
- Sarcoma Molecular Pathology Team, Divisions of Molecular Pathology and Cancer Therapeutics, Institute of Cancer Research, Surrey, Sutton, SM2 5NG, UK
| | - Zoë S Walters
- Sarcoma Molecular Pathology Team, Divisions of Molecular Pathology and Cancer Therapeutics, Institute of Cancer Research, Surrey, Sutton, SM2 5NG, UK
| | - Janet M Shipley
- Sarcoma Molecular Pathology Team, Divisions of Molecular Pathology and Cancer Therapeutics, Institute of Cancer Research, Surrey, Sutton, SM2 5NG, UK.
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212
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Pan Y, Pan Y, Cheng Y, Yang F, Yao Z, Wang O. Knockdown of LncRNA MAPT-AS1 inhibites proliferation and migration and sensitizes cancer cells to paclitaxel by regulating MAPT expression in ER-negative breast cancers. Cell Biosci 2018; 8:7. [PMID: 29441192 PMCID: PMC5799917 DOI: 10.1186/s13578-018-0207-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 01/28/2018] [Indexed: 01/23/2023] Open
Abstract
Background MAPT-AS1, a long non-coding RNA, has not been reported in any previous research about its function in cancers. In this study, we investigated the role of MAPT-AS1 in the progression and paclitaxel resistance in breast cancer, and the regulation between MAPT-AS1 and its natural comparable sense transcripts MAPT. Methods We analysed the breast cancer patients’ clinical information and explored the function of MAPT-AS1 by gain- and loss-of function assays in vitro and in vivo. The regulation between MAPT-AS1 and MAPT was confirmed by gene expression analysis and rescue assays. To verify the hypothesis that MAPT-AS1 and MAPT might form a duplex structure, we performed RT-PCR assays on RNA after α-amanitin treatment. Results By analysing the breast cancer patients’ clinical information from the TCGA database, we found that ER-negative patients with younger age (< 60), larger tumors (≥ 2 cm), metastatic lymph nodes and stages (III–IV) had higher expression of MAPT-AS1. MAPT-AS1 is correlated with the cell growth, invasiveness and paclitaxel resistance by regulating its natural comparable sense transcripts MAPT in ER-negative breast cancer cells. The result revealed that MAPT-AS1 overexpression could partially protect the MAPT mRNA from degradation, while MAPT-AS1 knockdown decreased the stability of MAPT mRNA. Meanwhile, MAPT knockdown decreased the expression of MAPT-AS1 mRNA. MAPT-AS1 expressed coordinately with MAPT in breast tumor tissues. Conclusion Our study is the first to report a novel lncRNA MAPT-AS1 in human cancer. ER-negative patients with younger age (< 60), larger tumors (≥ 2 cm), metastatic lymph nodes and stages (III–IV) had higher expression of MAPT-AS1. MAPT-AS1 is correlated with the cell growth, invasiveness and paclitaxel resistance in ER-negative breast cancer cells through antisense pairing with MAPT. MAPT-AS1 may serve as a potential therapeutic target in ER-negative breast cancers. Electronic supplementary material The online version of this article (10.1186/s13578-018-0207-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yiyuan Pan
- 1Department of Surgical Oncology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000 China
| | - Yiqi Pan
- 2Wenzhou Medical University, Wenzhou, 325000 China
| | - Yue Cheng
- 1Department of Surgical Oncology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000 China
| | - Fan Yang
- 1Department of Surgical Oncology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000 China
| | - Zhihan Yao
- 1Department of Surgical Oncology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000 China
| | - Ouchen Wang
- 1Department of Surgical Oncology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000 China
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213
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Yamamura S, Imai-Sumida M, Tanaka Y, Dahiya R. Interaction and cross-talk between non-coding RNAs. Cell Mol Life Sci 2018; 75:467-484. [PMID: 28840253 PMCID: PMC5765200 DOI: 10.1007/s00018-017-2626-6] [Citation(s) in RCA: 214] [Impact Index Per Article: 35.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 08/07/2017] [Accepted: 08/09/2017] [Indexed: 02/06/2023]
Abstract
Non-coding RNA (ncRNA) has been shown to regulate diverse cellular processes and functions through controlling gene expression. Long non-coding RNAs (lncRNAs) act as a competing endogenous RNAs (ceRNAs) where microRNAs (miRNAs) and lncRNAs regulate each other through their biding sites. Interactions of miRNAs and lncRNAs have been reported to trigger decay of the targeted lncRNAs and have important roles in target gene regulation. These interactions form complicated and intertwined networks. Certain lncRNAs encode miRNAs and small nucleolar RNAs (snoRNAs), and may regulate expression of these small RNAs as precursors. SnoRNAs have also been reported to be precursors for PIWI-interacting RNAs (piRNAs) and thus may regulate the piRNAs as a precursor. These miRNAs and piRNAs target messenger RNAs (mRNAs) and regulate gene expression. In this review, we will present and discuss these interactions, cross-talk, and co-regulation of ncRNAs and gene regulation due to these interactions.
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Affiliation(s)
- Soichiro Yamamura
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA.
- San Francisco Veterans Affairs Medical Center, San Francisco, CA, USA.
| | - Mitsuho Imai-Sumida
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- San Francisco Veterans Affairs Medical Center, San Francisco, CA, USA
| | - Yuichiro Tanaka
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- San Francisco Veterans Affairs Medical Center, San Francisco, CA, USA
| | - Rajvir Dahiya
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- San Francisco Veterans Affairs Medical Center, San Francisco, CA, USA
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214
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Shin CH, Ryu S, Kim HH. hnRNPK-regulated PTOV1-AS1 modulates heme oxygenase-1 expression via miR-1207-5p. BMB Rep 2018; 50:220-225. [PMID: 28228215 PMCID: PMC5437967 DOI: 10.5483/bmbrep.2017.50.4.024] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Indexed: 11/20/2022] Open
Abstract
Antisense transcripts were initially identified as transcriptional noise, but have since been reported to play an important role in the quality control of miRNA functions. In this report, we tested the hypothesis that heterogeneous nuclear ribonucleoprotein K (hnRNPK) regulates miRNA function via competitive endogenous RNAs, such as pseudogenes, long non-coding RNAs, and antisense transcripts. Based on analyses of RNA sequencing data, the knockdown of hnRNPK decreased the antisense PTOV1-AS1 transcript which harbors five binding sites for miR-1207-5p. We identified heme oxygenase-1 (HO-1) mRNA as a novel target of miR-1207-5p by western blotting and Ago2 immunoprecipitation. The knockdown of hnRNPK or PTOV1-AS1 suppressed HO-1 expression by increasing the enrichment of HO-1 mRNA in miR-1207-5p-mediated miRISC. Downregulation of HO-1 by a miR-1207-5p mimic or knockdown of hnRNPK and PTOV1-AS1 inhibited the proliferation and clonogenic ability of HeLa cells. Taken together, our results demonstrate that hnRNPKregulated PTOV1-AS1 modulates HO-1 expression via miR- 1207-5p. [BMB Reports 2017; 50(4): 220-225].
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Affiliation(s)
- Chang Hoon Shin
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul 06351, Korea
| | - Seongho Ryu
- Soonchunhyang Institute of Medi-bio Science (SIMS), Soonchunhyang University, Cheonan 31151, Korea
| | - Hyeon Ho Kim
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul 06351, Korea; Institute for Future Medicine, Samsung Medical Center, Seoul 06351, Korea
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215
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Lee KT, Nam JW. Post-transcriptional and translational regulation of mRNA-like long non-coding RNAs by microRNAs in early developmental stages of zebrafish embryos. BMB Rep 2018; 50:226-231. [PMID: 28320503 PMCID: PMC5437968 DOI: 10.5483/bmbrep.2017.50.4.025] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2017] [Indexed: 01/16/2023] Open
Abstract
At the post-transcriptional and translational levels, microRNA (miRNA) represses protein-coding genes via seed pairing to the 3′ untranslated regions (UTRs) of mRNA. Although working models of miRNA-mediated gene silencing are successfully established using miRNA transfections and knockouts, the regulatory interaction between miRNA and long non-coding RNA (lncRNA) remain unknown. In particular, how the mRNA-resembling lncRNAs with 5′ cap, 3′ poly(A)-tail, or coding features, are regulated by miRNA is yet to be examined. We therefore investigated the functional interaction between miRNAs and lncRNAs with/without those features, in miRNA-transfected early zebrafish embryos. We observed that the greatest determinants of the miRNA-mediated silencing of lncRNAs were the 5′ cap and 3′ poly(A)-tails in lncRNAs, at both the post-transcriptional and translational levels. The lncRNAs confirmed to contain 5′ cap, 3′ poly(A)-tail, and the canonical miRNA target sites, were observed to be repressed in the level of both RNA and ribosome-protected fragment, while those with the miRNA target sites and without 5′ cap and 3′ poly(A)-tail, were not robustly repressed by miRNA introduction, thus suggesting a role as a miRNA-decoy.
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Affiliation(s)
- Kyung-Tae Lee
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul 133791, Korea
| | - Jin-Wu Nam
- Department of Life Science, College of Natural Sciences, Hanyang University; Research Institute for Natural Sciences, Hanyang University; Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul 133791, Korea
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216
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Feng L, Liao YT, He JC, Xie CL, Chen SY, Fan HH, Su ZP, Wang Z. Plasma long non-coding RNA BACE1 as a novel biomarker for diagnosis of Alzheimer disease. BMC Neurol 2018; 18:4. [PMID: 29316899 PMCID: PMC5761117 DOI: 10.1186/s12883-017-1008-x] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Accepted: 12/20/2017] [Indexed: 12/28/2022] Open
Abstract
Backgrounds Long non-coding RNA (LncRNA) have been reported to be involved in the pathogenesis of neurodegenerative diseases, but whether it can serve as a biomarker for Alzheimer disease (AD) is not yet known. Methods The present study selected four specific LncRNA (17A, 51A, BACE1 and BC200) as possible AD biomarker. RT-qPCR was performed to validate the LncRNA. Receiver operating characteristic curve (ROC) and area under the ROC curve (AUC) were applied to study the potential of LncRNA as a biomarker in a population of 88 AD patients and 72 control individuals. Results We found that the plasma LncRNA BACE1 level of AD patients was significantly higher than that of healthy controls (p = 0.006). Plasma level of LncRNA 17A, 51A and BC200 did not show a significant difference between two groups (p = 0.098, p = 0.204 and p = 0.232, respectively). ROC curve analysis showed that LncRNA BACE1 was the best candidate of these LncRNA (95% CI: 0.553–0.781, p = 0.003). In addition, no correlation was found for expression of these LncRNA in both control and AD groups with age or MMSE scale (p > 0.05). Conclusions Our present study compared the plasma level of four LncRNA between AD and non-AD patients, and found that the level of the BACE1 is increased in the plasma of AD patients and have a high specificity (88%) for AD, indicating BACE1 may be a potential candidate biomarker to predict AD. Electronic supplementary material The online version of this article (10.1186/s12883-017-1008-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Liang Feng
- Department of Neurology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Yu-Ting Liao
- Institute of public health management of Wenzhou Medical University, Wenzhou, Wenzhou, 325000, China
| | - Jin-Cai He
- Department of Neurology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Cheng-Long Xie
- Department of Neurology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Si-Yan Chen
- Department of Neurology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Hui-Hui Fan
- Institute of public health management of Wenzhou Medical University, Wenzhou, Wenzhou, 325000, China
| | - Zhi-Peng Su
- Department of Neurosurgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China.
| | - Zhen Wang
- Department of Neurology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China.
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217
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Qureshi IA, Mehler MF. Epigenetic mechanisms underlying nervous system diseases. HANDBOOK OF CLINICAL NEUROLOGY 2018; 147:43-58. [PMID: 29325627 DOI: 10.1016/b978-0-444-63233-3.00005-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Epigenetic mechanisms act as control systems for modulating genomic structure and activity in response to evolving profiles of cell-extrinsic, cell-cell, and cell-intrinsic signals. These dynamic processes are responsible for mediating cell- and tissue-specific gene expression and function and gene-gene and gene-environmental interactions. The major epigenetic mechanisms include DNA methylation and hydroxymethylation; histone protein posttranslational modifications, nucleosome remodeling/repositioning, and higher-order chromatin reorganization; noncoding RNA regulation; and RNA editing. These mechanisms are intimately involved in executing fundamental genomic programs, including gene transcription, posttranscriptional RNA processing and transport, translation, X-chromosome inactivation, genomic imprinting, retrotransposon regulation, DNA replication, and DNA repair and the maintenance of genomic stability. For the nervous system, epigenetics offers a novel and robust framework for explaining how brain development and aging occur, neural cellular diversity is generated, synaptic and neural network connectivity and plasticity are mediated, and complex cognitive and behavioral phenotypes are inherited transgenerationally. Epigenetic factors and processes are, not surprisingly, implicated in nervous system disease pathophysiology through several emerging paradigms - mutations and genetic variation in genes encoding epigenetic factors; impairments in epigenetic factor expression, localization, and function; epigenetic mechanisms modulating disease-associated factors and pathways; and the presence of deregulated epigenetic profiles in central and peripheral tissues.
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Affiliation(s)
- Irfan A Qureshi
- Roslyn and Leslie Goldstein Laboratory for Stem Cell Biology and Regenerative Medicine; Institute for Brain Disorders and Neural Regeneration; Departments of Neurology, Neuroscience, Psychiatry and Behavioral Sciences and Rose F. Kennedy Center for Research on Intellectual and Developmental Disabilities, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Mark F Mehler
- Roslyn and Leslie Goldstein Laboratory for Stem Cell Biology and Regenerative Medicine; Institute for Brain Disorders and Neural Regeneration; Departments of Neurology, Neuroscience, Psychiatry and Behavioral Sciences; Rose F. Kennedy Center for Research on Intellectual and Developmental Disabilities; Einstein Cancer Center; Ruth L. and David S. Gottesman Stem Cell Institute; and Center for Epigenomics and Institute for Aging Research, Albert Einstein College of Medicine, Bronx, NY, United States.
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218
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Raut SK, Khullar M. The Big Entity of New RNA World: Long Non-Coding RNAs in Microvascular Complications of Diabetes. Front Endocrinol (Lausanne) 2018; 9:300. [PMID: 29915562 PMCID: PMC5994400 DOI: 10.3389/fendo.2018.00300] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2017] [Accepted: 05/18/2018] [Indexed: 12/14/2022] Open
Abstract
A major part of the genome is known to be transcribed into non-protein coding RNAs (ncRNAs), such as microRNA and long non-coding RNA (lncRNA). The importance of ncRNAs is being increasingly recognized in physiological and pathological processes. lncRNAs are a novel class of ncRNAs that do not code for proteins and are important regulators of gene expression. In the past, these molecules were thought to be transcriptional "noise" with low levels of evolutionary conservation. However, recent studies provide strong evidence indicating that lncRNAs are (i) regulated during various cellular processes, (ii) exhibit cell type-specific expression, (iii) localize to specific organelles, and (iv) associated with human diseases. Emerging evidence indicates an aberrant expression of lncRNAs in diabetes and diabetes-related microvascular complications. In the present review, we discuss the current state of knowledge of lncRNAs, their genesis from genome, and the mechanism of action of individual lncRNAs in the pathogenesis of microvascular complications of diabetes and therapeutic approaches.
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219
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Long Non-coding RNAs, Novel Culprits, or Bodyguards in Neurodegenerative Diseases. MOLECULAR THERAPY. NUCLEIC ACIDS 2017; 10:269-276. [PMID: 29499939 PMCID: PMC5787881 DOI: 10.1016/j.omtn.2017.12.011] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 12/19/2017] [Accepted: 12/19/2017] [Indexed: 12/14/2022]
Abstract
Long non-coding RNA (lncRNA) is a kind of non-coding RNA (ncRNA), with a length of 200 nt to 100 kb, that lacks a significant open reading frame (ORF) encoding a protein. lncRNAs are widely implicated in various physiological and pathological processes, such as epigenetic regulation, cell cycle regulation, cell differentiation regulation, cancer, and neurodegenerative diseases, through their interactions with chromatin, protein, and other RNAs. Numerous studies have suggested that lncRNAs are closely linked with the occurrence and development of a variety of diseases, especially neurodegenerative diseases, of which the etiologies are complicated and the underlying mechanisms remain elusive. Determining the roles of lncRNA in the pathogenesis of neurodegenerative diseases will not only deepen understanding of the physiological and pathological processes that occur in those diseases but also provide new ideas and solutions for their diagnosis and prevention. This review aims to highlight the progress of lncRNA research in the pathological and behavioral changes of neurodegenerative diseases. Specifically, we focus on how lncRNA dysfunctions are involved in the pathogenesis of Alzheimer’s disease, Parkinson’s disease, Huntington’s disease, and amyotrophic lateral sclerosis.
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220
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Antisense transcription regulates the expression of sense gene via alternative polyadenylation. Protein Cell 2017; 9:540-552. [PMID: 29273853 PMCID: PMC5966356 DOI: 10.1007/s13238-017-0497-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 11/27/2017] [Indexed: 01/23/2023] Open
Abstract
Natural antisense transcripts (NAT) and alternative polyadenylation (APA) of messenger RNA (mRNA) are important contributors of transcriptome complexity, each playing a critical role in multiple biological processes. However, whether they have crosstalk and function collaboratively is unclear. We discovered that APA enriched in human sense-antisense (S-AS) gene pairs, and finally focused on RNASEH2C-KAT5 S-AS pair for further study. In cis but not in trans over-expression of the antisense KAT5 gene promoted the usage of distal polyA (pA) site in sense gene RNASEH2C, which generated longer 3' untranslated region (3'UTR) and produced less protein, accompanying with slowed cell growth. Mechanistically, elevated Pol II occupancy coupled with SRSF3 could explain the higher usage of distal pA site. Finally, NAT-mediated downregulation of sense gene's protein level in RNASEH2C-KAT5 pair was specific for human rather than mouse, which lacks the distal pA site of RNASEH2C. We provided the first evidence to support that certain gene affected phenotype may not by the protein of its own, but by affecting the expression of its overlapped gene through APA, implying an unexpected view for understanding the link between genotype and phenotype.
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221
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Leggio L, Vivarelli S, L'Episcopo F, Tirolo C, Caniglia S, Testa N, Marchetti B, Iraci N. microRNAs in Parkinson's Disease: From Pathogenesis to Novel Diagnostic and Therapeutic Approaches. Int J Mol Sci 2017; 18:ijms18122698. [PMID: 29236052 PMCID: PMC5751299 DOI: 10.3390/ijms18122698] [Citation(s) in RCA: 146] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 12/07/2017] [Accepted: 12/09/2017] [Indexed: 01/09/2023] Open
Abstract
Parkinson’s disease (PD) is the most prevalent central nervous system (CNS) movement disorder and the second most common neurodegenerative disease overall. PD is characterized by the progressive loss of dopaminergic (DAergic) neurons in the substantia nigra pars compacta (SNpc) within the midbrain, accumulation of alpha-synuclein (α-SYN) in Lewy bodies and neurites and excessive neuroinflammation. The neurodegenerative processes typically begin decades before the appearance of clinical symptoms. Therefore, the diagnosis is achievable only when the majority of the relevant DAergic neurons have already died and for that reason available treatments are only palliative at best. The causes and mechanism(s) of this devastating disease are ill-defined but complex interactions between genetic susceptibility and environmental factors are considered major contributors to the etiology of PD. In addition to the role of classical gene mutations in PD, the importance of regulatory elements modulating gene expression has been increasingly recognized. One example is the critical role played by microRNAs (miRNAs) in the development and homeostasis of distinct populations of neurons within the CNS and, in particular, in the context of PD. Recent reports demonstrate how distinct miRNAs are involved in the regulation of PD genes, whereas profiling approaches are unveiling variations in the abundance of certain miRNAs possibly relevant either to the onset or to the progression of the disease. In this review, we provide an overview of the miRNAs recently found to be implicated in PD etiology, with particular focus on their potential relevance as PD biomarkers, as well as their possible use in PD targeted therapy.
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Affiliation(s)
- Loredana Leggio
- Department of Biomedical and Biotechnological Sciences (BIOMETEC), University of Catania, Torre Biologica, Via S. Sofia 97, 95125 Catania, Italy.
| | - Silvia Vivarelli
- Department of Biomedical and Biotechnological Sciences (BIOMETEC), University of Catania, Torre Biologica, Via S. Sofia 97, 95125 Catania, Italy.
| | - Francesca L'Episcopo
- Neuropharmacology Section, OASI Institute for Research and Care on Mental Retardation and Brain Aging (IRCCS), 94018 Troina, Italy.
| | - Cataldo Tirolo
- Neuropharmacology Section, OASI Institute for Research and Care on Mental Retardation and Brain Aging (IRCCS), 94018 Troina, Italy.
| | - Salvo Caniglia
- Neuropharmacology Section, OASI Institute for Research and Care on Mental Retardation and Brain Aging (IRCCS), 94018 Troina, Italy.
| | - Nunzio Testa
- Neuropharmacology Section, OASI Institute for Research and Care on Mental Retardation and Brain Aging (IRCCS), 94018 Troina, Italy.
| | - Bianca Marchetti
- Department of Biomedical and Biotechnological Sciences (BIOMETEC), University of Catania, Torre Biologica, Via S. Sofia 97, 95125 Catania, Italy.
- Neuropharmacology Section, OASI Institute for Research and Care on Mental Retardation and Brain Aging (IRCCS), 94018 Troina, Italy.
| | - Nunzio Iraci
- Department of Biomedical and Biotechnological Sciences (BIOMETEC), University of Catania, Torre Biologica, Via S. Sofia 97, 95125 Catania, Italy.
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Sartor GC, Powell SK, Velmeshev D, Lin DY, Magistri M, Wiedner HJ, Malvezzi AM, Andrade NS, Faghihi MA, Wahlestedt C. Cocaine alters Homer1 natural antisense transcript in the nucleus accumbens. Mol Cell Neurosci 2017; 85:183-189. [PMID: 29055697 PMCID: PMC5698162 DOI: 10.1016/j.mcn.2017.10.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 09/19/2017] [Accepted: 10/09/2017] [Indexed: 12/29/2022] Open
Abstract
Natural antisense transcripts (NATs) are an abundant class of long noncoding RNAs that have recently been shown to be key regulators of chromatin dynamics and gene expression in nervous system development and neurological disorders. However, it is currently unclear if NAT-based mechanisms also play a role in drug-induced neuroadaptations. Aberrant regulation of gene expression is one critical factor underlying the long-lasting behavioral abnormalities that characterize substance use disorder, and it is possible that some drug-induced transcriptional responses are mediated, in part, by perturbations in NAT activity. To test this hypothesis, we used an automated algorithm that mines the NCBI AceView transcriptomics database to identify NAT overlapping genes linked to addiction. We found that 22% of the genes examined contain NATs and that expression of Homer1 natural antisense transcript (Homer1-AS) was altered in the nucleus accumbens (NAc) of mice 2h and 10days following repeated cocaine administration. In in vitro studies, depletion of Homer1-AS lead to an increase in the corresponding sense gene expression, indicating a potential regulatory mechanisms of Homer1 expression by its corresponding antisense transcript. Future in vivo studies are needed to definitely determine a role for Homer1-AS in cocaine-induced behavioral and molecular adaptations.
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Affiliation(s)
- Gregory C Sartor
- Center for Therapeutic Innovation and Department of Psychiatry and Behavioral Sciences, University of Miami Miller School of Medicine, Miami, FL 33136, United States
| | - Samuel K Powell
- Center for Therapeutic Innovation and Department of Psychiatry and Behavioral Sciences, University of Miami Miller School of Medicine, Miami, FL 33136, United States
| | - Dmitry Velmeshev
- Center for Therapeutic Innovation and Department of Psychiatry and Behavioral Sciences, University of Miami Miller School of Medicine, Miami, FL 33136, United States
| | - David Y Lin
- Center for Therapeutic Innovation and Department of Psychiatry and Behavioral Sciences, University of Miami Miller School of Medicine, Miami, FL 33136, United States
| | - Marco Magistri
- Center for Therapeutic Innovation and Department of Psychiatry and Behavioral Sciences, University of Miami Miller School of Medicine, Miami, FL 33136, United States
| | - Hannah J Wiedner
- Center for Therapeutic Innovation and Department of Psychiatry and Behavioral Sciences, University of Miami Miller School of Medicine, Miami, FL 33136, United States
| | - Andrea M Malvezzi
- Center for Therapeutic Innovation and Department of Psychiatry and Behavioral Sciences, University of Miami Miller School of Medicine, Miami, FL 33136, United States
| | - Nadja S Andrade
- Center for Therapeutic Innovation and Department of Psychiatry and Behavioral Sciences, University of Miami Miller School of Medicine, Miami, FL 33136, United States
| | - Mohammad A Faghihi
- Center for Therapeutic Innovation and Department of Psychiatry and Behavioral Sciences, University of Miami Miller School of Medicine, Miami, FL 33136, United States
| | - Claes Wahlestedt
- Center for Therapeutic Innovation and Department of Psychiatry and Behavioral Sciences, University of Miami Miller School of Medicine, Miami, FL 33136, United States.
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223
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Zinad HS, Natasya I, Werner A. Natural Antisense Transcripts at the Interface between Host Genome and Mobile Genetic Elements. Front Microbiol 2017; 8:2292. [PMID: 29209299 PMCID: PMC5701935 DOI: 10.3389/fmicb.2017.02292] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 11/06/2017] [Indexed: 12/26/2022] Open
Abstract
Non-coding RNAs are involved in epigenetic processes, playing a role in the regulation of gene expression at the transcriptional and post-transcriptional levels. A particular group of ncRNA are natural antisense transcripts (NATs); these are transcribed in the opposite direction to protein coding transcripts and are widespread in eukaryotes. Their abundance, evidence of phylogenetic conservation and an increasing number of well-characterized examples of antisense-mediated gene regulation are indicative of essential biological roles of NATs. There is evidence to suggest that they interfere with their corresponding sense transcript to elicit concordant and discordant regulation. The main mechanisms involved include transcriptional interference as well as dsRNA formation. Sense–antisense hybrid formation can trigger RNA interference, RNA editing or protein kinase R. However, the exact molecular mechanisms elicited by NATs in the context of these regulatory roles are currently poorly understood. Several examples confirm that ectopic expression of antisense transcripts trigger epigenetic silencing of the related sense transcript. Genomic approaches suggest that the antisense transcriptome carries a broader biological significance which goes beyond the physiological regulation of the directly related sense transcripts. Because NATs show evidence of conservation we speculate that they played a role in evolution, with early eukaryotes gaining selective advantage through the regulatory effects. With the surge of genome and transcriptome sequencing projects, there is promise of a more comprehensive understanding of the biological role of NATs and the regulatory mechanisms involved.
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Affiliation(s)
- Hany S Zinad
- RNA Interest Group, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Inas Natasya
- RNA Interest Group, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Andreas Werner
- RNA Interest Group, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, United Kingdom
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Knap P, Tebaldi T, Di Leva F, Biagioli M, Dalla Serra M, Viero G. The Unexpected Tuners: Are LncRNAs Regulating Host Translation during Infections? Toxins (Basel) 2017; 9:E357. [PMID: 29469820 PMCID: PMC5705972 DOI: 10.3390/toxins9110357] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 10/30/2017] [Accepted: 10/31/2017] [Indexed: 12/27/2022] Open
Abstract
Pathogenic bacteria produce powerful virulent factors, such as pore-forming toxins, that promote their survival and cause serious damage to the host. Host cells reply to membrane stresses and ionic imbalance by modifying gene expression at the epigenetic, transcriptional and translational level, to recover from the toxin attack. The fact that the majority of the human transcriptome encodes for non-coding RNAs (ncRNAs) raises the question: do host cells deploy non-coding transcripts to rapidly control the most energy-consuming process in cells-i.e., host translation-to counteract the infection? Here, we discuss the intriguing possibility that membrane-damaging toxins induce, in the host, the expression of toxin-specific long non-coding RNAs (lncRNAs), which act as sponges for other molecules, encoding small peptides or binding target mRNAs to depress their translation efficiency. Unravelling the function of host-produced lncRNAs upon bacterial infection or membrane damage requires an improved understanding of host lncRNA expression patterns, their association with polysomes and their function during this stress. This field of investigation holds a unique opportunity to reveal unpredicted scenarios and novel approaches to counteract antibiotic-resistant infections.
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Affiliation(s)
- Primoz Knap
- Institute of Biophysics, CNR Unit at Trento, Via Sommarive 18, Povo Trento 38123, Italy.
| | - Toma Tebaldi
- Yale Cancer Center, Yale University School of Medicine, New Haven, CT 06520, USA.
| | - Francesca Di Leva
- Centre for Integrative Biology, University of Trento, Via Sommarive 9, Povo Trento 38123, Italy.
| | - Marta Biagioli
- Centre for Integrative Biology, University of Trento, Via Sommarive 9, Povo Trento 38123, Italy.
| | - Mauro Dalla Serra
- Institute of Biophysics, CNR Unit at Trento, Via Sommarive 18, Povo Trento 38123, Italy.
| | - Gabriella Viero
- Institute of Biophysics, CNR Unit at Trento, Via Sommarive 18, Povo Trento 38123, Italy.
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225
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Napoli S, Piccinelli V, Mapelli SN, Pisignano G, Catapano CV. Natural antisense transcripts drive a regulatory cascade controlling c-MYC transcription. RNA Biol 2017; 14:1742-1755. [PMID: 28805496 PMCID: PMC5731802 DOI: 10.1080/15476286.2017.1356564] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Cis-natural antisense transcripts (cis-NATs) are long noncoding RNAs transcribed from the opposite strand and overlapping coding and noncoding genes on the sense strand. cis-NATs are widely present in the human genome and can be involved in multiple mechanisms of gene regulation. Here, we describe the presence of cis-NATs in the 3′ distal region of the c-MYC locus and investigate their impact on transcriptional regulation of this key oncogene in human cancers. We found that cis-NATs are produced as consequence of the activation of cryptic transcription initiation sites in the 3′ distal region downstream of the c-MYC 3′UTR. The process is tightly regulated and leads to the formation of two main transcripts, NAT6531 and NAT6558, which differ in their ability to fold into stem-loop secondary structures. NAT6531 acts as a substrate for DICER and as a source of small RNAs capable of modulating c-MYC transcription. This complex system, based on the interplay between cis-NATs and NAT-derived small RNAs, may represent an important layer of epigenetic regulation of the expression of c-MYC and other genes in human cells.
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Affiliation(s)
- Sara Napoli
- a Tumor Biology and Experimental Therapeutics Program , Institute of Oncology Research (IOR), Università della Svizzera italiana (USI) , Bellinzona , Switzerland
| | - Valentina Piccinelli
- a Tumor Biology and Experimental Therapeutics Program , Institute of Oncology Research (IOR), Università della Svizzera italiana (USI) , Bellinzona , Switzerland
| | - Sarah N Mapelli
- a Tumor Biology and Experimental Therapeutics Program , Institute of Oncology Research (IOR), Università della Svizzera italiana (USI) , Bellinzona , Switzerland
| | - Giuseppina Pisignano
- a Tumor Biology and Experimental Therapeutics Program , Institute of Oncology Research (IOR), Università della Svizzera italiana (USI) , Bellinzona , Switzerland
| | - Carlo V Catapano
- a Tumor Biology and Experimental Therapeutics Program , Institute of Oncology Research (IOR), Università della Svizzera italiana (USI) , Bellinzona , Switzerland.,b Department of Oncology , Faculty of Biology and Medicine, University of Lausanne , Lausanne , Switzerland
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Li Y, Zhang H, Zhu B, Ashraf U, Chen Z, Xu Q, Zhou D, Zheng B, Song Y, Chen H, Ye J, Cao S. Microarray Analysis Identifies the Potential Role of Long Non-Coding RNA in Regulating Neuroinflammation during Japanese Encephalitis Virus Infection. Front Immunol 2017; 8:1237. [PMID: 29033949 PMCID: PMC5626832 DOI: 10.3389/fimmu.2017.01237] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 09/19/2017] [Indexed: 01/31/2023] Open
Abstract
Japanese encephalitis virus (JEV) is the leading cause of epidemic encephalitis worldwide. JEV-induced neuroinflammation is characterized by profound neuronal cells damage accompanied by activation of glial cells. Albeit long non-coding RNAs (lncRNAs) have been emerged as important regulatory RNAs with profound effects on various biological processes, it is unknown how lncRNAs regulate JEV-induced inflammation. Here, using microarray approach, we identified 618 lncRNAs and 1,007 mRNAs differentially expressed in JEV-infected mice brain. The functional annotation analysis revealed that differentially regulated transcripts were predominantly involved in various signaling pathways related to host immune and inflammatory responses. The lncRNAs with their potential to regulate JEV-induced inflammatory response were identified by constructing the lncRNA-mRNA coexpression network. Furthermore, silencing of the two selected lncRNAs (E52329 and N54010) resulted in reducing the phosphorylation of JNK and MKK4, which are known to be involved during inflammatory response. Collectively, we first demonstrated the transcriptomic landscape of lncRNAs in mice brain infected with JEV and analyzed the coexpression network of differentially regulated lncRNAs and mRNAs during JEV infection. Our results provide a better understanding of the host response to JEV infection and suggest that the identified lncRNAs may be used as potential therapeutic targets for the management of Japanese encephalitis.
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Affiliation(s)
- Yunchuan Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,Laboratory of Animal Virology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Hao Zhang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,Laboratory of Animal Virology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Bibo Zhu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,Laboratory of Animal Virology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Usama Ashraf
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,Laboratory of Animal Virology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Zheng Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,Laboratory of Animal Virology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Qiuping Xu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,Laboratory of Animal Virology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Dengyuan Zhou
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,Laboratory of Animal Virology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Bohan Zheng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,Laboratory of Animal Virology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Yunfeng Song
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,Laboratory of Animal Virology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Huanchun Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,Laboratory of Animal Virology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Jing Ye
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,Laboratory of Animal Virology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Shengbo Cao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,Laboratory of Animal Virology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
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227
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Hao X, Du Y, Qian L, Li D, Liu X. Upregulation of long noncoding RNA AP003419.16 predicts high risk of aging‑associated idiopathic pulmonary fibrosis. Mol Med Rep 2017; 16:8085-8091. [PMID: 28944926 PMCID: PMC5779893 DOI: 10.3892/mmr.2017.7607] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 07/03/2017] [Indexed: 01/03/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) are able to regulate adjacent genes and thus participate in the incidence in the present study has identified lncRNA AP003419.16, adjacent to the protein-coding gene ribosomal protein S6 kinase B-2 (RPS6KB2). RPS6KB2 is believed to be involved in the process of aging and idiopathic pulmonary fibrosis (IPF), due to its activation by growth factors and regulation by the protein kinase mTOR signaling pathway. The results of the present study indicated that the expression of AP003419.16 increased significantly in patients with IPF, whereas its adjacent gene ribosomal protein S6 kinase B-2 increased simultaneously. AP003419.16 expression may be used to predict an increased risk of aging-associated IPF. The present study provided a molecular hypothesis of IPF occurrence in the aging process, in addition to novel molecular targets for the clinical treatment of IPF.
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Affiliation(s)
- Xiaoyan Hao
- Department of Geriatrics, The First Affiliated Hospital of Shanxi Medical University, Taiyuan, Shanxi 030001, P.R. China
| | - Yufeng Du
- Department of Geriatrics, The First Affiliated Hospital of Shanxi Medical University, Taiyuan, Shanxi 030001, P.R. China
| | - Li Qian
- Department of Geriatrics, The First Affiliated Hospital of Shanxi Medical University, Taiyuan, Shanxi 030001, P.R. China
| | - Dan Li
- Department of Geriatrics, The First Affiliated Hospital of Shanxi Medical University, Taiyuan, Shanxi 030001, P.R. China
| | - Xuejun Liu
- Department of Geriatrics, The First Affiliated Hospital of Shanxi Medical University, Taiyuan, Shanxi 030001, P.R. China
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228
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Kurokawa T, Kohno K, Nagai K, Chiba M, Pak S, Murata S, Fukunaga K, Yasue H, Ohkohchi N. Antisense RNA transcripts in the blood may be novel diagnostic markers for colorectal cancer. Oncol Lett 2017; 14:3487-3493. [PMID: 28927104 PMCID: PMC5587960 DOI: 10.3892/ol.2017.6572] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 01/06/2017] [Indexed: 01/21/2023] Open
Abstract
Numerous genetic studies have been conducted regarding the occurrence of colorectal cancer (CRC) and the prognosis using microarrays. However, adequate investigations into the diagnostic application of microarrays have yet to be performed. The simplicity and accuracy of diagnosis and prognosis tracking are important requirements for its processes, and the use of blood cells for diagnosis is considered to be suitable to meet these requirements. The patients involved in the study were 28 preoperative patients with CRC and 6 healthy individuals who served as controls. RNA was extracted from the blood cells of the patients and analyzed using a sense/antisense RNA custom microarray. In the patients with CRC, the expression levels of 20 sense RNA and 20 antisense RNA species were identified as being significantly altered compared with that of the healthy volunteers (P<0.05; fold-change, >2.0). Cluster analysis of these RNA species revealed that the top 10 antisense RNAs significantly clustered patients with cancer and healthy individuals separately. Patients with stage I or II CRC exhibited significant changes in the expression levels of 33 sense and 39 antisense RNA species, as compared with healthy volunteers (P<0.01; fold-change >2.0). Cluster analysis demonstrated that patients with stage I or II CRC and healthy volunteers formed separate clusters only among the top 20 antisense RNA species. A tracking study of expression levels of haloacid dehalogenase-like hydrolase domain-containing 1 (HDHD1) antisense RNA was performed and a significant difference was identified between the CRC and healthy groups revealing that the levels at one week and three months following surgical removal of the cancerous tissue, decreased to almost same levels of the healthy individuals. The results of the current study indicate that HDHD1 antisense RNA may serve as a potential biomarker for the prognosis of CRC.
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Affiliation(s)
- Tomohiro Kurokawa
- Department of Gastrointestinal and Hepato-Biliary-Pancreatic Surgery, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
| | - Keisuke Kohno
- Department of Gastrointestinal and Hepato-Biliary-Pancreatic Surgery, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
| | - Kentaro Nagai
- Department of Gastrointestinal and Hepato-Biliary-Pancreatic Surgery, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
| | - Mitsuru Chiba
- Department of Biomedical Sciences, Division of Medical Life Sciences, Hirosaki University Graduate School of Health Sciences, Hirosaki, Aomori 036-8564, Japan
| | - Sugiru Pak
- Department of Gastrointestinal and Hepato-Biliary-Pancreatic Surgery, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
| | - Soichiro Murata
- Department of Gastrointestinal and Hepato-Biliary-Pancreatic Surgery, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
| | - Kiyoshi Fukunaga
- Department of Gastrointestinal and Hepato-Biliary-Pancreatic Surgery, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
| | - Hiroshi Yasue
- Genome Resource Unit, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-0901, Japan
| | - Nobuhiro Ohkohchi
- Department of Gastrointestinal and Hepato-Biliary-Pancreatic Surgery, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
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229
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Bunch H. Gene regulation of mammalian long non-coding RNA. Mol Genet Genomics 2017; 293:1-15. [PMID: 28894972 DOI: 10.1007/s00438-017-1370-9] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Accepted: 09/07/2017] [Indexed: 12/14/2022]
Abstract
RNA polymerase II (Pol II) transcribes two classes of RNAs, protein-coding and non-protein-coding (ncRNA) genes. ncRNAs are also synthesized by RNA polymerases I and III (Pol I and III). In humans, the number of ncRNA genes exceeds more than twice that of protein-coding genes. However, the history of studying Pol II-synthesized ncRNA is relatively short. Since early 2000s, important biological and pathological functions of these ncRNA genes have begun to be discovered and intensively studied. And transcription mechanisms of long non-coding RNA (lncRNA) have been recently reported. Transcription of lncRNAs utilizes some transcription factors and mechanisms shared in that of protein-coding genes. In addition, tissue specificity in lncRNA gene expression has been shown. LncRNAs play essential roles in regulating the expression of neighboring or distal genes through different mechanisms. This leads to the implication of lncRNAs in a wide variety of biological pathways and pathological development. In this review, the newly discovered transcription mechanisms, characteristics, and functions of lncRNA are discussed.
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Affiliation(s)
- Heeyoun Bunch
- School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Agriculture & Life Sciences Building 1, Room 207, 80 Dae-Hak Ro, Daegu, Republic of Korea.
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230
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Chakravarthy M, Chen S, Dodd PR, Veedu RN. Nucleic Acid-Based Theranostics for Tackling Alzheimer's Disease. Theranostics 2017; 7:3933-3947. [PMID: 29109789 PMCID: PMC5667416 DOI: 10.7150/thno.21529] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 07/28/2017] [Indexed: 02/07/2023] Open
Abstract
Nucleic acid-based technologies have received significant interest in recent years as novel theranostic strategies for various diseases. The approval by the United States Food and Drug Administration (FDA) of Nusinersen, an antisense oligonucleotide drug, for the treatment of spinal muscular dystrophy highlights the potential of nucleic acids to treat neurological diseases, including Alzheimer's disease (AD). AD is a devastating neurodegenerative disease characterized by progressive impairment of cognitive function and behavior. It is the most common form of dementia; it affects more than 20% of people over 65 years of age and leads to death 7-15 years after diagnosis. Intervention with novel agents addressing the underlying molecular causes is critical. Here we provide a comprehensive review on recent developments in nucleic acid-based theranostic strategies to diagnose and treat AD.
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Affiliation(s)
- Madhuri Chakravarthy
- Centre for Comparative Genomics, Murdoch University, Murdoch, Perth, Australia 6150
- Perron Institute for Neurological and Translational Science, QEII Medical Centre, Nedlands, Perth, Australia 6005
| | - Suxiang Chen
- Centre for Comparative Genomics, Murdoch University, Murdoch, Perth, Australia 6150
- Perron Institute for Neurological and Translational Science, QEII Medical Centre, Nedlands, Perth, Australia 6005
| | - Peter R. Dodd
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Brisbane, Australia 4072
| | - Rakesh N. Veedu
- Centre for Comparative Genomics, Murdoch University, Murdoch, Perth, Australia 6150
- Perron Institute for Neurological and Translational Science, QEII Medical Centre, Nedlands, Perth, Australia 6005
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Brisbane, Australia 4072
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231
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Wei CW, Luo T, Zou SS, Wu AS. Research progress on the roles of microRNAs in governing synaptic plasticity, learning and memory. Life Sci 2017; 188:118-122. [PMID: 28866103 DOI: 10.1016/j.lfs.2017.08.033] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 08/24/2017] [Accepted: 08/25/2017] [Indexed: 12/16/2022]
Abstract
The importance of non-coding RNA involved in biological processes has become apparent in recent years and the mechanism of transcriptional regulation has also been identified. MicroRNAs (miRNAs) represent a class of small regulatory non-coding RNAs of 22bp in length that mediate gene silencing by identifying specific sequences in the target messenger RNAs (mRNAs). Many miRNAs are highly expressed in the central nervous system in a spatially and temporally controlled manner in normal physiology, as well as in certain pathological conditions. There is growing evidence that a considerable number of specific miRNAs play important roles in synaptic plasticity, learning and memory function. In addition, the dysfunction of these molecules may also contribute to the etiology of several neurodegenerative diseases. Here we provide an overview of the current literatures, which support non-coding RNA-mediated gene function regulation represents an important but underappreciated, layer of epigenetic control that facilitates learning and memory functions.
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Affiliation(s)
- Chang-Wei Wei
- Department of Anesthesiology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing 100020, China
| | - Ting Luo
- Department of Anesthesiology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing 100020, China
| | - Shan-Shan Zou
- Department of Anesthesiology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing 100020, China
| | - An-Shi Wu
- Department of Anesthesiology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing 100020, China.
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232
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Matsui A, Iida K, Tanaka M, Yamaguchi K, Mizuhashi K, Kim JM, Takahashi S, Kobayashi N, Shigenobu S, Shinozaki K, Seki M. Novel Stress-Inducible Antisense RNAs of Protein-Coding Loci Are Synthesized by RNA-Dependent RNA Polymerase. PLANT PHYSIOLOGY 2017; 175:457-472. [PMID: 28710133 PMCID: PMC5580770 DOI: 10.1104/pp.17.00787] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 07/12/2017] [Indexed: 05/03/2023]
Abstract
Our previous study identified approximately 6,000 abiotic stress-responsive noncoding transcripts existing on the antisense strand of protein-coding genes and implied that a type of antisense RNA was synthesized from a sense RNA template by RNA-dependent RNA polymerase (RDR). Expression analyses revealed that the expression of novel abiotic stress-induced antisense RNA on 1,136 gene loci was reduced in the rdr1/2/6 mutants. RNase protection indicated that the RD29A antisense RNA and other RDR1/2/6-dependent antisense RNAs are involved in the formation of dsRNA. The accumulation of stress-inducible antisense RNA was decreased and increased in dcp5 and xrn4, respectively, but not changed in dcl2/3/4, nrpd1a and nrpd1b RNA-seq analyses revealed that the majority of the RDR1/2/6-dependent antisense RNA loci did not overlap with RDR1/2/6-dependent 20-30 nt RNA loci. Additionally, rdr1/2/6 mutants decreased the degradation rate of the sense RNA and exhibited arrested root growth during the recovery stage following a drought stress, whereas dcl2/3/4 mutants did not. Collectively, these results indicate that RDRs have stress-inducible antisense RNA synthesis activity and a novel biological function that is different from the known endogenous small RNA pathways from protein-coding genes. These data reveal a novel mechanism of RNA regulation during abiotic stress response that involves complex RNA degradation pathways.
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Affiliation(s)
- Akihiro Matsui
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Kei Iida
- Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Maho Tanaka
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Katsushi Yamaguchi
- NIBB Core Research Facilities, National Institute for Basic Biology, Myodaiji, Okazaki, Aichi 444-8585, Japan
| | - Kayoko Mizuhashi
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Jong-Myong Kim
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Satoshi Takahashi
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Norio Kobayashi
- Computational Engineering Applications Unit, Advanced Center for Computing and Communication, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Shuji Shigenobu
- NIBB Core Research Facilities, National Institute for Basic Biology, Myodaiji, Okazaki, Aichi 444-8585, Japan
| | - Kazuo Shinozaki
- Gene Discovery Research Group, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Motoaki Seki
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa 244-0813, Japan
- Core Research for Evolutional Science and Technology, Japan Science and Technology, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
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233
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Human Long Noncoding RNA Regulation of Stem Cell Potency and Differentiation. Stem Cells Int 2017; 2017:6374504. [PMID: 28951743 PMCID: PMC5603141 DOI: 10.1155/2017/6374504] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 07/12/2017] [Accepted: 08/02/2017] [Indexed: 12/15/2022] Open
Abstract
Because of their capability of differentiation into lineage-specific cells, stem cells are an attractive therapeutic modality in regenerative medicine. To develop an effective stem cell-based therapeutic strategy with predictable results, deeper understanding of the underlying molecular mechanisms of stem cell differentiation and/or pluripotency maintenance is required. Thus, reviewing the key factors involved in the transcriptional and epigenetic regulation of stem cell differentiation and maintenance is important. Accumulating data indicate that long noncoding RNAs (lncRNAs) mediate numerous biological processes, including stem cell differentiation and maintenance. Here, we review recent findings on the human lncRNA regulation of stem cell potency and differentiation. Although the clinical implication of these lncRNAs is only beginning to be elucidated, it is anticipated that lncRNAs will become important therapeutic targets in the near future.
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234
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Lucafò M, Di Silvestre A, Romano M, Avian A, Antonelli R, Martelossi S, Naviglio S, Tommasini A, Stocco G, Ventura A, Decorti G, De Iudicibus S. Role of the Long Non-Coding RNA Growth Arrest-Specific 5 in Glucocorticoid Response in Children with Inflammatory Bowel Disease. Basic Clin Pharmacol Toxicol 2017; 122:87-93. [PMID: 28722800 DOI: 10.1111/bcpt.12851] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 07/06/2017] [Indexed: 12/27/2022]
Abstract
Glucocorticoids (GCs) are widely employed in inflammatory, autoimmune and neoplastic diseases, and, despite the introduction of novel therapies, remain the first-line treatment for inducing remission in inflammatory bowel disease (IBD). Given the high incidence of suboptimal response, associated with a significant number of side-effects, that are particularly severe in paediatric patients, the identification of subjects that are most likely to respond poorly to GCs is extremely important. Recent evidence suggests that the long non-coding RNA (lncRNA) GAS5 could be a potential marker of GC resistance. To address this issue, we evaluated the association between the lncRNA GAS5 and the efficacy of steroids, in terms of inhibition of proliferation, in two cell lines derived from colon and ovarian cancers, to confirm the sensitivity and specificity of these lncRNAs. These cells showed a different sensitivity to GCs and revealed differential expression of GAS5 after treatment. GAS5 was up-regulated in GC-resistant cells and accumulated more in the cytoplasm compared to the nucleus in response to the drug. The functions of GAS5 were assessed by silencing, and we found that GAS5 knock-down reduced the proliferation during GC treatment. Furthermore, for the first time, we measured GAS5 levels in 19 paediatric IBD patients at diagnosis and after the first cycle of GCs, and we demonstrated an up-regulation of the lncRNA in patients with unfavourable steroid response. Our preliminary results indicate that GAS5 could be considered a novel pharmacogenomic marker useful for the personalization of GC therapy.
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Affiliation(s)
- Marianna Lucafò
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy
| | - Alessia Di Silvestre
- PhD School in Science of Reproduction and Development, University of Trieste, Trieste, Italy
| | - Maurizio Romano
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Alice Avian
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Roberta Antonelli
- Department of Neurosciences, Scuola Internazionale Superiore di Studi Avanzati, Trieste, Italy
| | - Stefano Martelossi
- Institute for Maternal and Child Health - IRCCS 'Burlo Garofolo', Trieste, Italy
| | - Samuele Naviglio
- PhD School in Science of Reproduction and Development, University of Trieste, Trieste, Italy
| | - Alberto Tommasini
- Institute for Maternal and Child Health - IRCCS 'Burlo Garofolo', Trieste, Italy
| | - Gabriele Stocco
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Alessandro Ventura
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy.,Institute for Maternal and Child Health - IRCCS 'Burlo Garofolo', Trieste, Italy
| | - Giuliana Decorti
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy.,Institute for Maternal and Child Health - IRCCS 'Burlo Garofolo', Trieste, Italy
| | - Sara De Iudicibus
- Institute for Maternal and Child Health - IRCCS 'Burlo Garofolo', Trieste, Italy
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235
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Sun W, Pei L, Liang Z. mRNA and Long Non-coding RNA Expression Profiles in Rats Reveal Inflammatory Features in Sepsis-Associated Encephalopathy. Neurochem Res 2017; 42:3199-3219. [DOI: 10.1007/s11064-017-2357-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 07/07/2017] [Accepted: 07/12/2017] [Indexed: 01/31/2023]
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236
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Schoch KM, Miller TM. Antisense Oligonucleotides: Translation from Mouse Models to Human Neurodegenerative Diseases. Neuron 2017. [PMID: 28641106 DOI: 10.1016/j.neuron.2017.04.010] [Citation(s) in RCA: 196] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Multiple neurodegenerative diseases are characterized by single-protein dysfunction and aggregation. Treatment strategies for these diseases have often targeted downstream pathways to ameliorate consequences of protein dysfunction; however, targeting the source of that dysfunction, the affected protein itself, seems most judicious to achieve a highly effective therapeutic outcome. Antisense oligonucleotides (ASOs) are small sequences of DNA able to target RNA transcripts, resulting in reduced or modified protein expression. ASOs are ideal candidates for the treatment of neurodegenerative diseases, given numerous advancements made to their chemical modifications and delivery methods. Successes achieved in both animal models and human clinical trials have proven ASOs both safe and effective. With proper considerations in mind regarding the human applicability of ASOs, we anticipate ongoing in vivo research and clinical trial development of ASOs for the treatment of neurodegenerative diseases.
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Affiliation(s)
- Kathleen M Schoch
- Department of Neurology, Hope Center for Neurological Disorders, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Timothy M Miller
- Department of Neurology, Hope Center for Neurological Disorders, Washington University in St. Louis, St. Louis, MO 63110, USA.
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237
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Simvastatin ameliorate memory deficits and inflammation in clinical and mouse model of Alzheimer’s disease via modulating the expression of miR-106b. Biomed Pharmacother 2017; 92:46-57. [DOI: 10.1016/j.biopha.2017.05.060] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 05/10/2017] [Accepted: 05/10/2017] [Indexed: 12/16/2022] Open
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238
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Zhao J, Yue D, Zhou Y, Jia L, Wang H, Guo M, Xu H, Chen C, Zhang J, Xu L. The Role of MicroRNAs in Aβ Deposition and Tau Phosphorylation in Alzheimer's Disease. Front Neurol 2017; 8:342. [PMID: 28769871 PMCID: PMC5513952 DOI: 10.3389/fneur.2017.00342] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 06/30/2017] [Indexed: 12/22/2022] Open
Abstract
Alzheimer’s disease (AD), with main clinical features of progressive impairment in cognitive and behavioral functions, is the most common degenerative disease of the central nervous system. Recent evidence showed that microRNAs (miRNAs) played important roles in the pathological progression of AD. In this article, we reviewed the promising role of miRNAs in both Aβ deposition and Tau phosphorylation, two key pathological characters in the pathological progression of AD, which might be helpful for the understanding of pathogenesis and the development of new strategies of clinical diagnosis and treatment of AD.
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Affiliation(s)
- Juanjuan Zhao
- Department of Immunology, Zunyi Medical College, Guizhou, China
| | - Dongxu Yue
- Department of Immunology, Zunyi Medical College, Guizhou, China
| | - Ya Zhou
- Department of Medical Physics, Zunyi Medical College, Guizhou, China
| | - Li Jia
- Department of Immunology, Zunyi Medical College, Guizhou, China
| | - Hairong Wang
- Department of Immunology, Zunyi Medical College, Guizhou, China
| | - Mengmeng Guo
- Department of Immunology, Zunyi Medical College, Guizhou, China
| | - Hualin Xu
- Department of Immunology, Zunyi Medical College, Guizhou, China
| | - Chao Chen
- Department of Immunology, Zunyi Medical College, Guizhou, China
| | - Jidong Zhang
- Department of Immunology, Zunyi Medical College, Guizhou, China
| | - Lin Xu
- Department of Immunology, Zunyi Medical College, Guizhou, China
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239
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Salhi A, Essack M, Alam T, Bajic VP, Ma L, Radovanovic A, Marchand B, Schmeier S, Zhang Z, Bajic VB. DES-ncRNA: A knowledgebase for exploring information about human micro and long noncoding RNAs based on literature-mining. RNA Biol 2017; 14:963-971. [PMID: 28387604 PMCID: PMC5546543 DOI: 10.1080/15476286.2017.1312243] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Revised: 02/23/2017] [Accepted: 03/24/2017] [Indexed: 01/08/2023] Open
Abstract
Noncoding RNAs (ncRNAs), particularly microRNAs (miRNAs) and long ncRNAs (lncRNAs), are important players in diseases and emerge as novel drug targets. Thus, unraveling the relationships between ncRNAs and other biomedical entities in cells are critical for better understanding ncRNA roles that may eventually help develop their use in medicine. To support ncRNA research and facilitate retrieval of relevant information regarding miRNAs and lncRNAs from the plethora of published ncRNA-related research, we developed DES-ncRNA ( www.cbrc.kaust.edu.sa/des_ncrna ). DES-ncRNA is a knowledgebase containing text- and data-mined information from public scientific literature and other public resources. Exploration of mined information is enabled through terms and pairs of terms from 19 topic-specific dictionaries including, for example, antibiotics, toxins, drugs, enzymes, mutations, pathways, human genes and proteins, drug indications and side effects, mutations, diseases, etc. DES-ncRNA contains approximately 878,000 associations of terms from these dictionaries of which 36,222 (5,373) are with regards to miRNAs (lncRNAs). We provide several ways to explore information regarding ncRNAs to users including controlled generation of association networks as well as hypotheses generation. We show an example how DES-ncRNA can aid research on Alzheimer disease and suggest potential therapeutic role for Fasudil. DES-ncRNA is a powerful tool that can be used on its own or as a complement to the existing resources, to support research in human ncRNA. To our knowledge, this is the only knowledgebase dedicated to human miRNAs and lncRNAs derived primarily through literature-mining enabling exploration of a broad spectrum of associated biomedical entities, not paralleled by any other resource.
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Affiliation(s)
- Adil Salhi
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, Kingdom of Saudi Arabia
| | - Magbubah Essack
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, Kingdom of Saudi Arabia
| | - Tanvir Alam
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, Kingdom of Saudi Arabia
| | - Vladan P. Bajic
- VINCA Institute of Nuclear Sciences, Belgrade, Republic of Serbia
| | - Lina Ma
- BIG Data Center, Beijing Institute of Genomics (BIG), Chinese Academy of Sciences, Beijing, China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences (CAS), Beijing, China
| | - Aleksandar Radovanovic
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, Kingdom of Saudi Arabia
| | | | - Sebastian Schmeier
- Massey University Auckland, Institute of Natural and Mathematical Sciences, Albany, Auckland, New Zealand
| | - Zhang Zhang
- BIG Data Center, Beijing Institute of Genomics (BIG), Chinese Academy of Sciences, Beijing, China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences (CAS), Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai, China
| | - Vladimir B. Bajic
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, Kingdom of Saudi Arabia
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240
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Delgado-Morales R, Agís-Balboa RC, Esteller M, Berdasco M. Epigenetic mechanisms during ageing and neurogenesis as novel therapeutic avenues in human brain disorders. Clin Epigenetics 2017; 9:67. [PMID: 28670349 PMCID: PMC5493012 DOI: 10.1186/s13148-017-0365-z] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 06/11/2017] [Indexed: 12/26/2022] Open
Abstract
Ageing is the main risk factor for human neurological disorders. Among the diverse molecular pathways that govern ageing, epigenetics can guide age-associated decline in part by regulating gene expression and also through the modulation of genomic instability and high-order chromatin architecture. Epigenetic mechanisms are involved in the regulation of neural differentiation as well as in functional processes related to memory consolidation, learning or cognition during healthy lifespan. On the other side of the coin, many neurodegenerative diseases are associated with epigenetic dysregulation. The reversible nature of epigenetic factors and, especially, their role as mediators between the genome and the environment make them exciting candidates as therapeutic targets. Rather than providing a broad description of the pathways epigenetically deregulated in human neurological disorders, in this review, we have focused on the potential use of epigenetic enzymes as druggable targets to ameliorate neural decline during normal ageing and especially in neurological disorders. We will firstly discuss recent progress that supports a key role of epigenetic regulation during healthy ageing with an emphasis on the role of epigenetic regulation in adult neurogenesis. Then, we will focus on epigenetic alterations associated with ageing-related human disorders of the central nervous system. We will discuss examples in the context of psychiatric disorders, including schizophrenia and posttraumatic stress disorders, and also dementia or Alzheimer's disease as the most frequent neurodegenerative disease. Finally, methodological limitations and future perspectives are discussed.
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Affiliation(s)
- Raúl Delgado-Morales
- Cancer Epigenetics Group, Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Biomedical Research Institute (IDIBELL), 3rd Floor, Hospital Duran i Reynals, Av. Gran Via 199-203, 08908L'Hospitalet, Barcelona, Catalonia Spain.,Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience (MHeNs), Maastricht University, Maastricht, The Netherlands
| | - Roberto Carlos Agís-Balboa
- Psychiatric Diseases Research Group, Galicia Sur Health Research Institute, Complexo Hospitalario Universitario de Vigo (CHUVI), SERGAS, CIBERSAM, Vigo, Spain
| | - Manel Esteller
- Cancer Epigenetics Group, Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Biomedical Research Institute (IDIBELL), 3rd Floor, Hospital Duran i Reynals, Av. Gran Via 199-203, 08908L'Hospitalet, Barcelona, Catalonia Spain.,Department of Physiological Sciences II, School of Medicine, University of Barcelona, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - María Berdasco
- Cancer Epigenetics Group, Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Biomedical Research Institute (IDIBELL), 3rd Floor, Hospital Duran i Reynals, Av. Gran Via 199-203, 08908L'Hospitalet, Barcelona, Catalonia Spain
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241
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Tracy KM, Tye CE, Page NA, Fritz AJ, Stein JL, Lian JB, Stein GS. Selective expression of long non-coding RNAs in a breast cancer cell progression model. J Cell Physiol 2017; 233:1291-1299. [PMID: 28488769 DOI: 10.1002/jcp.25997] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 05/09/2017] [Indexed: 01/01/2023]
Abstract
Long non-coding RNAs (lncRNAs) are acknowledged as regulators of cancer biology and pathology. Our goal was to perform a stringent profiling of breast cancer cell lines that represent disease progression. We used the MCF-10 series, which includes the normal-like MCF-10A, HRAS-transformed MCF-10AT1 (pre-malignant), and MCF-10CA1a (malignant) cells, to perform transcriptome wide sequencing. From these data, we have identified 346 lncRNAs with dysregulated expression across the progression series. By comparing lncRNAs from these datasets to those from an additional set of cell lines that represent different disease stages and subtypes, MCF-7 (early stage, luminal), and MDA-MB-231 (late stage, basal), 61 lncRNAs that are associated with breast cancer progression were identified. Querying breast cancer patient data from The Cancer Genome Atlas, we selected a lncRNA, IGF-like family member 2 antisense RNA 1 (IGFL2-AS1), of potential clinical relevance for functional characterization. Among the 61 lncRNAs, IGFL2-AS1 was the most significantly decreased. Our results indicate that this lncRNA plays a role in downregulating its nearest neighbor, IGFL1, and affects migration of breast cancer cells. Furthermore, the lncRNAs we identified provide a valuable resource to mechanistically and clinically understand the contribution of lncRNAs in breast cancer progression.
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Affiliation(s)
- Kirsten M Tracy
- Department of Biochemistry and University of Vermont Cancer Center, The University of Vermont Larner College of Medicine, Burlington, Vermont
| | - Coralee E Tye
- Department of Biochemistry and University of Vermont Cancer Center, The University of Vermont Larner College of Medicine, Burlington, Vermont
| | - Natalie A Page
- Department of Biochemistry and University of Vermont Cancer Center, The University of Vermont Larner College of Medicine, Burlington, Vermont
| | - Andrew J Fritz
- Department of Biochemistry and University of Vermont Cancer Center, The University of Vermont Larner College of Medicine, Burlington, Vermont
| | - Janet L Stein
- Department of Biochemistry and University of Vermont Cancer Center, The University of Vermont Larner College of Medicine, Burlington, Vermont
| | - Jane B Lian
- Department of Biochemistry and University of Vermont Cancer Center, The University of Vermont Larner College of Medicine, Burlington, Vermont
| | - Gary S Stein
- Department of Biochemistry and University of Vermont Cancer Center, The University of Vermont Larner College of Medicine, Burlington, Vermont
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242
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Li Y, Ye Y, Feng B, Qi Y. Long Noncoding RNA lncARSR Promotes Doxorubicin Resistance in Hepatocellular Carcinoma via Modulating PTEN-PI3K/Akt Pathway. J Cell Biochem 2017; 118:4498-4507. [PMID: 28464252 DOI: 10.1002/jcb.26107] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 05/01/2017] [Indexed: 12/20/2022]
Abstract
Hepatocellular carcinoma (HCC) is generally resistant to chemotherapy due to intrinsic or acquired drug resistances. Many molecules and signaling pathways are involved in chemo-resistance of HCC cells. However, the contribution of long noncoding RNA (lncRNA) to chemo-resistance of HCC cells is still largely unknown. In this study, we revealed the critical roles of long noncoding RNA lncARSR in chemo-resistance of HCC cells. lncARSR is upregulated in HCC, associated with large tumor size and advanced BCLC stage, and indicts poor prognosis. Functional assays showed that overexpression of lncARSR enhances doxorubicin resistance of HCC cells in vitro and in vivo. And while knockdown of lncARSR increases sensitivity of HCC cells to doxorubicin in vitro and in vivo. Mechanistically, we found that lncARSR physically associates with PTEN mRNA, promotes PTEN mRNA degradation, decreases PTEN expression, and activates PI3K/Akt pathway. PTEN is downregulated in HCC, and the expression of PTEN is negatively correlated with lncARSR in HCC tissues. Furthermore, the effects of lncARSR overexpression on doxorubicin resistance could be reversed by PI3K/Akt pathway inhibitor, and lncARSR knockdown-induced doxorubicin sensitivity could be reversed by PTEN depletion. Taken together, our results showed that upregulated lncARSR promotes doxorubicin resistance in HCC via modulating PTEN-PI3K/Akt pathway, and implied that lncARSR may serve as a promising prognostic biomarker and therapeutic target for HCC chemo-resistance. J. Cell. Biochem. 118: 4498-4507, 2017. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Yaling Li
- Department of Pharmacy, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Yun Ye
- Department of Pharmacy, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Bimin Feng
- Department of Pharmacy, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Yan Qi
- Central Laboratory, Yunnan Provincial Hospital of Traditional Chinese Medicine, Kunming, Yunnan, China
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243
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Singh A, Sen D. MicroRNAs in Parkinson's disease. Exp Brain Res 2017; 235:2359-2374. [PMID: 28526930 DOI: 10.1007/s00221-017-4989-1] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2016] [Accepted: 05/16/2017] [Indexed: 01/11/2023]
Abstract
Parkinson's disease is the second most common neurodegenerative disease commonly affecting the older population. Loss of dopaminergic neurons in the substantia nigra of brain leads to impairment of motor activities as well as cognitive defects. There are many underlying causes to this disease, both genetic and epigenetic, which are yet to be fully explored. Non-coding RNAs are significant part of our genome and are involved in various cellular processes. MicroRNAs, which are small non-coding RNAs having 20-22 nucleotides, are involved in many underlying mechanisms of pathogenesis of several neurodegenerative diseases including Parkinson's. This review focuses on the role played by microRNAs in regulating various genes responsible for the onset and pathogenesis of Parkinson's disease and various literature evidences pointing at the usefulness of targeting specific microRNAs as a potential alternate therapeutic strategy for successful impairment of the disease progression. This review also discusses about various biofluid-based microRNA markers which may be potentially utilized for diagnostic purposes.
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Affiliation(s)
- Abhishek Singh
- School of Bio Sciences and Technology, VIT University, Vellore, India
- Cellular and Molecular Therapeutics Laboratory, Centre for Biomaterials, Cellular and Molecular Theranostics (CBCMT), VIT University, Vellore, Tamil Nadu, 632014, India
| | - Dwaipayan Sen
- Cellular and Molecular Therapeutics Laboratory, Centre for Biomaterials, Cellular and Molecular Theranostics (CBCMT), VIT University, Vellore, Tamil Nadu, 632014, India.
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244
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Millan MJ. Linking deregulation of non-coding RNA to the core pathophysiology of Alzheimer's disease: An integrative review. Prog Neurobiol 2017; 156:1-68. [PMID: 28322921 DOI: 10.1016/j.pneurobio.2017.03.004] [Citation(s) in RCA: 96] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 03/09/2017] [Accepted: 03/09/2017] [Indexed: 02/06/2023]
Abstract
The human genome encodes a vast repertoire of protein non-coding RNAs (ncRNA), some specific to the brain. MicroRNAs, which interfere with the translation of target mRNAs, are of particular interest since their deregulation has been implicated in neurodegenerative disorders like Alzheimer's disease (AD). However, it remains challenging to link the complex body of observations on miRNAs and AD into a coherent framework. Using extensive graphical support, this article discusses how a diverse panoply of miRNAs convergently and divergently impact (and are impacted by) core pathophysiological processes underlying AD: neuroinflammation and oxidative stress; aberrant generation of β-amyloid-42 (Aβ42); anomalies in the production, cleavage and post-translational marking of Tau; impaired clearance of Aβ42 and Tau; perturbation of axonal organisation; disruption of synaptic plasticity; endoplasmic reticulum stress and the unfolded protein response; mitochondrial dysfunction; aberrant induction of cell cycle re-entry; and apoptotic loss of neurons. Intriguingly, some classes of miRNA provoke these cellular anomalies, whereas others act in a counter-regulatory, protective mode. Moreover, changes in levels of certain species of miRNA are a consequence of the above-mentioned anomalies. In addition to miRNAs, circular RNAs, piRNAs, long non-coding RNAs and other types of ncRNA are being increasingly implicated in AD. Overall, a complex mesh of deregulated and multi-tasking ncRNAs reciprocally interacts with core pathophysiological mechanisms underlying AD. Alterations in ncRNAs can be detected in CSF and the circulation as well as the brain and are showing promise as biomarkers, with the ultimate goal clinical exploitation as targets for novel modes of symptomatic and course-altering therapy.
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Affiliation(s)
- Mark J Millan
- Centre for Therapeutic Innovation in Neuropsychiatry, institut de recherche Servier, 125 chemin de ronde, 78290 Croissy sur Seine, France.
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245
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Greco S, Zaccagnini G, Fuschi P, Voellenkle C, Carrara M, Sadeghi I, Bearzi C, Maimone B, Castelvecchio S, Stellos K, Gaetano C, Menicanti L, Martelli F. Increased BACE1-AS long noncoding RNA and β-amyloid levels in heart failure. Cardiovasc Res 2017; 113:453-463. [DOI: 10.1093/cvr/cvx013] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 01/25/2017] [Indexed: 01/18/2023] Open
Affiliation(s)
- Simona Greco
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, Via Morandi, 30 20097 San Donato, Milanese, Milan, Italy
| | - Germana Zaccagnini
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, Via Morandi, 30 20097 San Donato, Milanese, Milan, Italy
| | - Paola Fuschi
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, Via Morandi, 30 20097 San Donato, Milanese, Milan, Italy
| | - Christine Voellenkle
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, Via Morandi, 30 20097 San Donato, Milanese, Milan, Italy
| | - Matteo Carrara
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, Via Morandi, 30 20097 San Donato, Milanese, Milan, Italy
| | - Iman Sadeghi
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, Via Morandi, 30 20097 San Donato, Milanese, Milan, Italy
| | - Claudia Bearzi
- Institute of Cell Biology and Neurobiology (IBCN), National Research Council of Italy (CNR), Monterotondo Scalo, Rome, Italy
| | - Biagina Maimone
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, Via Morandi, 30 20097 San Donato, Milanese, Milan, Italy
| | | | - Konstantinos Stellos
- Laboratory of RNA Metabolism and Vascular Inflammation, Institute of Cardiovascular Regeneration, Centre of Molecular Medicine, Goethe University Frankfurt, Frankfurt/Main, Germany
| | - Carlo Gaetano
- Division of Cardiovascular Epigenetics, Department of Cardiology and Internal Medicine Clinic III, Department of Cardiology, Goethe University, Frankfurt/Main, Germany
| | - Lorenzo Menicanti
- Department of Cardiac Surgery, IRCCS Policlinico San Donato, Milan, Italy
| | - Fabio Martelli
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, Via Morandi, 30 20097 San Donato, Milanese, Milan, Italy
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246
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Cai Y, Sun Z, Jia H, Luo H, Ye X, Wu Q, Xiong Y, Zhang W, Wan J. Rpph1 Upregulates CDC42 Expression and Promotes Hippocampal Neuron Dendritic Spine Formation by Competing with miR-330-5p. Front Mol Neurosci 2017; 10:27. [PMID: 28223918 PMCID: PMC5293807 DOI: 10.3389/fnmol.2017.00027] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2016] [Accepted: 01/23/2017] [Indexed: 12/12/2022] Open
Abstract
Alzheimer's disease (AD) is a heterogeneous neurodegenerative disease. Recent studies employing microRNA-seq and genome-wide sequencing have identified some non-coding RNAs that are influentially involved in AD pathogenesis. Non-coding RNAs can compete with other endogenous RNAs by microRNA response elements (MREs) and manipulate biological processes, such as tumorigenesis. However, only a few non-coding RNAs have been reported in the pathogenesis of AD. In this study, we constructed the first competing endogenous RNA (ceRNA) network leveraging whole transcriptome sequencing and a previously studied microRNA-seq of APPswe/PS1ΔE9 transgenic mice. The underlying mechanisms for the involvement of ceRNA in AD were validated using the Dual Luciferase Reporter Assay, detection of transcription levels by quantitative RT-PCR and translation levels by Western blotting, and morphological examination in primary cultured neurons. In the ceRNA network, four lncRNAs (C030034L19Rik, Rpph1, A830012C17Rik, and Gm15477) and five miRNAs (miR-182-5p, miR-330-5p, miR-326-3p, miR-132-3p, and miR-484) are enriched in nine pathways and an AD-related gene pool. Among them, Ribonuclease P RNA component H1 (Rpph1) is upregulated in the cortex of APPswe/PS1ΔE9 mice compared to wild type controls. Rpph1 binds to miR326-3p/miR-330-5p and causes the release of their downstream target Cdc42, which leads to CDC42 upregulation. This effect was disrupted upon mutation of the MRE on Rpph1. Moreover, overexpression of Rpph1 increased dendritic spine density in primary cultured hippocampal pyramidal neurons, whereas knocking down of Rpph1 had the reverse effect. In conclusion, Rpph1 modulates CDC42 expression level in a ceRNA-dependent manner, which may represent a compensatory mechanism in the early stage of the AD pathogenesis.
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Affiliation(s)
- Yifei Cai
- Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University - The Hong Kong University of Science and Technology Medical Center Shenzhen, China
| | - Ziling Sun
- Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University - The Hong Kong University of Science and Technology Medical Center Shenzhen, China
| | - Huizhen Jia
- Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University - The Hong Kong University of Science and Technology Medical Center Shenzhen, China
| | - Hongxue Luo
- Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University - The Hong Kong University of Science and Technology Medical Center Shenzhen, China
| | - Xiaoyang Ye
- Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University - The Hong Kong University of Science and Technology Medical Center Shenzhen, China
| | - Qi Wu
- Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University - The Hong Kong University of Science and Technology Medical Center Shenzhen, China
| | - Yi Xiong
- Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University - The Hong Kong University of Science and Technology Medical Center Shenzhen, China
| | - Wei Zhang
- Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University - The Hong Kong University of Science and Technology Medical Center Shenzhen, China
| | - Jun Wan
- Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University - The Hong Kong University of Science and Technology Medical CenterShenzhen, China; Division of Life Science, The Hong Kong University of Science and TechnologyHong Kong, China
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247
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Huang X, Luo YL, Mao YS, Ji JL. The link between long noncoding RNAs and depression. Prog Neuropsychopharmacol Biol Psychiatry 2017; 73:73-78. [PMID: 27318257 DOI: 10.1016/j.pnpbp.2016.06.004] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Revised: 06/07/2016] [Accepted: 06/13/2016] [Indexed: 12/28/2022]
Abstract
The major depressive disorder (MDD) is a relatively common mental disorder from which that hundreds of million people have suffered, leading to displeasing life quality, which is characterized by health damage and even suicidal thoughts. The complicated development and functioning of MDD is still under exploration. Long noncoding RNA (lncRNAs) are highly expressed in the brain, could affect neural stem cell maintenance, neurogenesis and gliogenesis, brain patterning, synaptic and stress responses, and neural plasticity. The dysregulation of certain lncRNAs induces in neurodevelopmental, neurodegenerative and neuroimmunological disorders, primary brain tumors, and psychiatric diseases. Although advances have been made, no fully satisfactory treatments for major depression are available, further investigation is requested. And recently data showed that the expression level of the majority of lncRNAs demonstrated a clear tendency of upregulation, and the certain dysregulated miRNAs and lncRNAs in the MDD have been proved to have a co-synergism mechanism, that is why we speculate lncRNA might get the capability to regulate MDD. Few identified lncRNAs have been deeply studied in detailed experiments up until now, little predictions of their function have been raised, and further researches is calling for discover their signal pathway and related regulatory networks.
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Affiliation(s)
- Xiao Huang
- Department of Psychological Medicine, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Yan-Li Luo
- Department of Psychiatry, Tongji Hospital of Tongji University, Shanghai 200065, China
| | - Yue-Shi Mao
- Department of Neurology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Jian-Lin Ji
- Department of Psychological Medicine, Zhongshan Hospital, Fudan University, Shanghai 200032, China.
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248
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Xu Z, Yan Y, Qian L, Gong Z. Long non-coding RNAs act as regulators of cell autophagy in diseases (Review). Oncol Rep 2017; 37:1359-1366. [PMID: 28184916 PMCID: PMC5364869 DOI: 10.3892/or.2017.5416] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 01/27/2017] [Indexed: 02/07/2023] Open
Abstract
Identification of long non-coding RNAs (lncRNAs) has provided a substantial increase in our understanding of the non-coding transcriptome. Studies have revealed a crucial function of lncRNAs in the modulation of cell autophagy in vitro and in vivo, further contributing to the hallmarks of disease phenotypes. These findings have profoundly altered our understanding of disease pathobiology, and may lead to the emergence of new biological concepts underlying autophagy-associated diseases, such as the carcinomas. Studies on the molecular mechanism of the lncRNA-autophagy axis may offer additional avenues for therapeutic intervention and biomarker assessment. In this review, we discuss recent findings on the multiple molecular roles of regulatory lncRNAs in the signaling pathways of cell autophagy. The emerging knowledge in this rapidly advancing field will offer novel insights into human diseases, especially cancers.
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Affiliation(s)
- Zhijie Xu
- Department of Pathology, Xiangya Hospital, Changsha, Hunan 410008, P.R. China
| | - Yuanliang Yan
- Department of Pharmacy, Xiangya Hospital, Changsha, Hunan 410008, P.R. China
| | - Long Qian
- Department of Pharmacy, Xiangya Hospital, Changsha, Hunan 410008, P.R. China
| | - Zhicheng Gong
- Department of Pharmacy, Xiangya Hospital, Changsha, Hunan 410008, P.R. China
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249
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Zhao HY, Wu HJ, He JL, Zhuang JH, Liu ZY, Huang LQ, Zhao ZX. Chronic Sleep Restriction Induces Cognitive Deficits and Cortical Beta-Amyloid Deposition in Mice via BACE1-Antisense Activation. CNS Neurosci Ther 2017; 23:233-240. [PMID: 28145081 DOI: 10.1111/cns.12667] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 11/27/2016] [Accepted: 11/29/2016] [Indexed: 12/11/2022] Open
Abstract
AIMS To clarify the correlation between chronic sleep restriction (CSR) and sporadic Alzheimer disease (AD), we determined in wild-type mice the impact of CSR, on cognitive performance, beta-amyloid (Aβ) peptides, and its feed-forward regulators regarding AD pathogenesis. METHODS Sixteen nine-month-old C57BL/6 male mice were equally divided into the CSR and control groups. CSR was achieved by application of a slowly rotating drum for 2 months. The Morris water maze test was used to assess cognitive impairment. The concentrations of Aβ peptides, amyloid precursor protein (APP) and β-secretase 1 (BACE1), and the mRNA levels of BACE1 and BACE1-antisense (BACE1-AS) were measured. RESULTS Following CSR, impairments of spatial learning and memory consolidation were observed in the mice, accompanied by Aβ plaque deposition and an increased Aβ concentration in the prefrontal and temporal lobe cortex. CSR also upregulated the β-secretase-induced cleavage of APP by increasing the protein and mRNA levels of BACE1, particularly the BACE1-AS. CONCLUSIONS This study shows that a CSR accelerates AD pathogenesis in wild-type mice. An upregulation of the BACE1 pathway appears to participate in both cortical Aβ plaque deposition and memory impairment caused by CSR. BACE1-AS is likely activated to initiate a cascade of events that lead to AD pathogenesis. Our study provides, therefore, a molecular mechanism that links CSR to sporadic AD.
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Affiliation(s)
- Hong-Yi Zhao
- Department of Neurology, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Hui-Juan Wu
- Department of Neurology, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Jia-Lin He
- Academy of Clinical Medicine, Second Military Medical University, Shanghai, China
| | - Jian-Hua Zhuang
- Department of Neurology, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Zhen-Yu Liu
- Department of Neurology, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Liu-Qing Huang
- Department of Neurology, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Zhong-Xin Zhao
- Department of Neurology, Changzheng Hospital, Second Military Medical University, Shanghai, China
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Inhaled Pollutants: The Molecular Scene behind Respiratory and Systemic Diseases Associated with Ultrafine Particulate Matter. Int J Mol Sci 2017; 18:ijms18020243. [PMID: 28125025 PMCID: PMC5343780 DOI: 10.3390/ijms18020243] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 01/09/2017] [Accepted: 01/13/2017] [Indexed: 01/10/2023] Open
Abstract
Air pollution of anthropogenic origin is largely from the combustion of biomass (e.g., wood), fossil fuels (e.g., cars and trucks), incinerators, landfills, agricultural activities and tobacco smoke. Air pollution is a complex mixture that varies in space and time, and contains hundreds of compounds including volatile organic compounds (e.g., benzene), metals, sulphur and nitrogen oxides, ozone and particulate matter (PM). PM0.1 (ultrafine particles (UFP)), those particles with a diameter less than 100 nm (includes nanoparticles (NP)) are considered especially dangerous to human health and may contribute significantly to the development of numerous respiratory and cardiovascular diseases such as chronic obstructive pulmonary disease (COPD) and atherosclerosis. Some of the pathogenic mechanisms through which PM0.1 may contribute to chronic disease is their ability to induce inflammation, oxidative stress and cell death by molecular mechanisms that include transcription factors such as nuclear factor κB (NF-κB) and nuclear factor (erythroid-derived 2)-like 2 (Nrf2). Epigenetic mechanisms including non-coding RNA (ncRNA) may also contribute towards the development of chronic disease associated with exposure to PM0.1. This paper highlights emerging molecular concepts associated with inhalational exposure to PM0.1 and their ability to contribute to chronic respiratory and systemic disease.
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