151
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Li W, Ren Y, Si Y, Wang F, Yu J. Long non-coding RNAs in hematopoietic regulation. CELL REGENERATION 2018; 7:27-32. [PMID: 30671227 PMCID: PMC6326246 DOI: 10.1016/j.cr.2018.08.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Revised: 08/11/2018] [Accepted: 08/21/2018] [Indexed: 02/09/2023]
Abstract
Long non-coding RNAs (lncRNAs) have crucial roles via tethering with DNA, RNA or protein in diverse biological processes. These lncRNA-mediated interactions enhance gene regulatory networks and modulate a wide range of downstream genes. It has been demonstrated that several lncRNAs act as key regulators in hematopoiesis. This review highlights the roles of lncRNAs in normal hematopoietic development and discusses how lncRNA dysregulation correlates with disease prognoses and phenotypes.
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Affiliation(s)
- Weiqian Li
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry & Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS), Peking Union Medical College (PUMC), Beijing, 100005, China.,Key Laboratory of RNA and Hematopoietic Regulation, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Yue Ren
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry & Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS), Peking Union Medical College (PUMC), Beijing, 100005, China.,Key Laboratory of RNA and Hematopoietic Regulation, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Yanmin Si
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry & Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS), Peking Union Medical College (PUMC), Beijing, 100005, China.,Key Laboratory of RNA and Hematopoietic Regulation, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Fang Wang
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry & Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS), Peking Union Medical College (PUMC), Beijing, 100005, China.,Key Laboratory of RNA and Hematopoietic Regulation, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Jia Yu
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry & Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS), Peking Union Medical College (PUMC), Beijing, 100005, China.,Key Laboratory of RNA and Hematopoietic Regulation, Chinese Academy of Medical Sciences, Beijing, 100730, China
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152
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Han BW, Ye H, Wei PP, He B, Han C, Chen ZH, Chen YQ, Wang WT. Global identification and characterization of lncRNAs that control inflammation in malignant cholangiocytes. BMC Genomics 2018; 19:735. [PMID: 30305026 PMCID: PMC6180422 DOI: 10.1186/s12864-018-5133-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 09/28/2018] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Long noncoding RNAs (lncRNAs) are known to play important roles in different cell contexts, including cancers. However, little is known about lncRNAs in cholangiocarcinoma (CCA), a cholangiocyte malignancy with poor prognosis, and associated with chronic inflammation and damage to the biliary epithelium. This study determined whether lncRNAs were dysregulated and participated in disease diagnosis or pivotal inflammation pathways through a genome-wide lncRNA screening and functional analysis. RESULTS We firstly identified a large number of lncRNAs abnormally expressed between 9 pairs of cancerous and adjacent tissues of CCA, and between intra-hepatic CCA and extra-hepatic CCA through a genome-wide profiling. A set of aberrant differentially expressed lncRNAs were further validated in a training set (16 pairs) and a test set (11 pairs) of CCA patient samples. Following assessment of the diagnostic value of the 7 differentially expressed lncRNAs, we confirmed the optimal combination of H19, C3P1, AC005550.3, PVT1, and LPAL2 with area under the curve of 0.8828 [95% CI: 0.7441-1.021, P < 0.001], with 93.75% sensitivity and 81.25% specificity, at the cutoff point of - 0.2884 to distinguish the CCA tissue from the normal ones, suggesting that specific lncRNAs may have potential for detecting CCA. More importantly, the genome-wide locus and lncRNA/mRNA co-expression analyses revealed a set of lncRNAs that participated in inflammation and oxidative stress response pathways by regulating genes in cis or in trans. Finally, APOC1P1, PVT1, and LPAL2 were validated to regulate the migration and some pivotal inflammation genes under the CCA pathogenesis. CONCLUSIONS Our findings are the first to show that lncRNAs may not only be potential biomarkers of CCA progression but also respond to inflammation in CCA.
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Affiliation(s)
- Bo-Wei Han
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou, 510275, People's Republic of China
| | - Hua Ye
- Department of Hepatobiliary, and Department of Anesthesiology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China
| | - Pan-Pan Wei
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou, 510275, People's Republic of China
| | - Bo He
- Department of Hepatobiliary, and Department of Anesthesiology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China
| | - Cai Han
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou, 510275, People's Republic of China
| | - Zhen-Hua Chen
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou, 510275, People's Republic of China
| | - Yue-Qin Chen
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou, 510275, People's Republic of China.
| | - Wen-Tao Wang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou, 510275, People's Republic of China.
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153
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Li X, Li N. LncRNAs on guard. Int Immunopharmacol 2018; 65:60-63. [PMID: 30286432 DOI: 10.1016/j.intimp.2018.09.031] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 09/07/2018] [Accepted: 09/21/2018] [Indexed: 02/07/2023]
Abstract
Long noncoding RNAs (lncRNAs) are emerging as crucial regulators of gene expression in immune system. It has been reported that lncRNAs participate in regulation of immune responses through both transcriptional and post-transcriptional mechanisms. In this review, we summarize the molecular functions of lncRNAs and discuss their binding to DNA, RNA and protein targets. We focus on the regulatory function of lncRNAs in both innate and adaptive immunity, as well as in autoimmunity and cancer immunology. In addition, we point out the limitation in current knowledge and future directions for the study of lncRNAs in the immune system.
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Affiliation(s)
- Xue Li
- Department of Immunology, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, 17 3rd Section Ren min South Road, 509 Yifu Building, Chengdu, Sichuan 610041, China
| | - Nan Li
- Department of Immunology, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, 17 3rd Section Ren min South Road, 509 Yifu Building, Chengdu, Sichuan 610041, China.
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154
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Zhao CN, Mao YM, Liu LN, Li XM, Wang DG, Pan HF. Emerging role of lncRNAs in systemic lupus erythematosus. Biomed Pharmacother 2018; 106:584-592. [DOI: 10.1016/j.biopha.2018.06.175] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 06/26/2018] [Accepted: 06/29/2018] [Indexed: 12/13/2022] Open
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155
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Sun W, Shi Y, Wang Z, Zhang J, Cai H, Zhang J, Huang D. Interaction of long-chain non-coding RNAs and important signaling pathways on human cancers (Review). Int J Oncol 2018; 53:2343-2355. [PMID: 30272345 DOI: 10.3892/ijo.2018.4575] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 08/24/2018] [Indexed: 11/05/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) usually refer to non-coding RNA transcripts >200 nucleotides in length. In terms of the full genomic transcript, the proportion of lncRNAs far exceeds that of coding RNA. Initially, lncRNAs were considered to be the transcriptional noise of genes, but it has since been demonstrated that lncRNAs serve an important role in the regulation of cellular activities through interaction with DNA, RNA and protein. Numerous studies have demonstrated that various intricate signaling pathways are closely related to lncRNAs. Here, we focus on a large number of studies regarding the interaction of lncRNAs with important signaling pathways. It is comprehensively illustrated that lncRNAs regulate key metabolic components and regulatory factors of signaling pathways to affect the biological activities of tumor cells. Evidence suggests that the abnormal expression or mutation of lncRNAs in human tumor cells, and their interaction with signaling pathways, may provide a basis and potential target for the diagnosis and treatment of human cancers.
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Affiliation(s)
- Wei Sun
- Department of Postgraduates, Bengbu Medical College, Bengbu, Anhui 233000, P.R. China
| | - Ying Shi
- Department of Obstetrics, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310014, P.R. China
| | - Zhifei Wang
- Department of Hepatobiliary and Pancreatic Surgery and Minimally Invasive Surgery, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310014, P.R. China
| | - Jiye Zhang
- Department of Hepatobiliary and Pancreatic Surgery and Minimally Invasive Surgery, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310014, P.R. China
| | - Hanhui Cai
- Department of Hepatobiliary and Pancreatic Surgery and Minimally Invasive Surgery, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310014, P.R. China
| | - Jungang Zhang
- Department of Hepatobiliary and Pancreatic Surgery and Minimally Invasive Surgery, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310014, P.R. China
| | - Dongsheng Huang
- Department of Hepatobiliary and Pancreatic Surgery and Minimally Invasive Surgery, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310014, P.R. China
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156
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Brajic A, Franckaert D, Burton O, Bornschein S, Calvanese AL, Demeyer S, Cools J, Dooley J, Schlenner S, Liston A. The Long Non-coding RNA Flatr Anticipates Foxp3 Expression in Regulatory T Cells. Front Immunol 2018; 9:1989. [PMID: 30319599 PMCID: PMC6167443 DOI: 10.3389/fimmu.2018.01989] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 08/13/2018] [Indexed: 12/30/2022] Open
Abstract
Mammalian genomes encode a plethora of long non-coding RNA (lncRNA). These transcripts are thought to regulate gene expression, influencing biological processes from development to pathology. Results from the few lncRNA that have been studied in the context of the immune system have highlighted potentially critical functions as network regulators. Here we explored the nature of the lncRNA transcriptome in regulatory T cells (Tregs), a subset of CD4+ T cells required to establish and maintain immunological self-tolerance. The identified Treg lncRNA transcriptome showed distinct differences from that of non-regulatory CD4+ T cells, with evidence of direct shaping of the lncRNA transcriptome by Foxp3, the master transcription factor driving the distinct mRNA profile of Tregs. Treg lncRNA changes were disproportionally reversed in the absence of Foxp3, with an enrichment for colocalisation with Foxp3 DNA binding sites, indicating a direct coordination of transcription by Foxp3 independent of the mRNA coordination function. We further identified a novel lncRNA Flatr, as a member of the core Treg lncRNA transcriptome. Flatr expression anticipates Foxp3 expression during in vitro Treg conversion, and Flatr-deficient mice show a mild delay in in vitro and peripheral Treg induction. These results implicate Flatr as part of the upstream cascade leading to Treg conversion, and may provide clues as to the nature of this process.
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Affiliation(s)
- Aleksandra Brajic
- Laboratory of Translational Immunology, VIB Center for Brain and Disease Research, VIB, Leuven, Belgium.,Department of Microbiology and Immunology, University of Leuven, Leuven, Belgium
| | - Dean Franckaert
- Laboratory of Translational Immunology, VIB Center for Brain and Disease Research, VIB, Leuven, Belgium.,Department of Microbiology and Immunology, University of Leuven, Leuven, Belgium
| | - Oliver Burton
- Laboratory of Translational Immunology, VIB Center for Brain and Disease Research, VIB, Leuven, Belgium.,Department of Microbiology and Immunology, University of Leuven, Leuven, Belgium
| | - Simon Bornschein
- Laboratory of Translational Immunology, VIB Center for Brain and Disease Research, VIB, Leuven, Belgium.,Department of Microbiology and Immunology, University of Leuven, Leuven, Belgium.,VIB Cancer Research Center, VIB, Leuven, Belgium
| | - Anna L Calvanese
- Laboratory of Translational Immunology, VIB Center for Brain and Disease Research, VIB, Leuven, Belgium.,Department of Microbiology and Immunology, University of Leuven, Leuven, Belgium
| | | | - Jan Cools
- VIB Cancer Research Center, VIB, Leuven, Belgium
| | - James Dooley
- Laboratory of Translational Immunology, VIB Center for Brain and Disease Research, VIB, Leuven, Belgium.,Department of Microbiology and Immunology, University of Leuven, Leuven, Belgium
| | - Susan Schlenner
- Laboratory of Translational Immunology, VIB Center for Brain and Disease Research, VIB, Leuven, Belgium.,Department of Microbiology and Immunology, University of Leuven, Leuven, Belgium
| | - Adrian Liston
- Laboratory of Translational Immunology, VIB Center for Brain and Disease Research, VIB, Leuven, Belgium.,Department of Microbiology and Immunology, University of Leuven, Leuven, Belgium
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157
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Abstract
SIGNIFICANCE RNA is a heterogeneous class of molecules with the minority being protein coding. Noncoding RNAs (ncRNAs) are involved in translation and epigenetic control mechanisms of gene expression. Recent Advances: In recent years, the number of identified ncRNAs has dramatically increased and it is now clear that ncRNAs provide a complex layer of differential gene expression control. CRITICAL ISSUES NcRNAs exhibit interplay with redox regulation. Redox regulation alters the expression of ncRNAs; conversely, ncRNAs alter the expression of generator and effector systems of redox regulation in a complex manner, which will be the focus of this review article. FUTURE DIRECTIONS Understanding the role of ncRNA in redox control will lead to the development of new strategies to alter redox programs. Given that many ncRNAs (particularly microRNAs [miRNAs]) change large gene sets, these molecules are attractive drug candidates; already, now miRNAs can be targeted in patients. Therefore, the development of ncRNA therapies focusing on these molecules is an attractive future strategy. Antioxid. Redox Signal. 29, 793-812.
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Affiliation(s)
- Matthias S Leisegang
- 1 Institute for Cardiovascular Physiology, Goethe-University , Frankfurt, Germany .,2 German Center of Cardiovascular Research (DZHK) , Partner Site RheinMain, Frankfurt, Germany
| | - Katrin Schröder
- 1 Institute for Cardiovascular Physiology, Goethe-University , Frankfurt, Germany .,2 German Center of Cardiovascular Research (DZHK) , Partner Site RheinMain, Frankfurt, Germany
| | - Ralf P Brandes
- 1 Institute for Cardiovascular Physiology, Goethe-University , Frankfurt, Germany .,2 German Center of Cardiovascular Research (DZHK) , Partner Site RheinMain, Frankfurt, Germany
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158
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He J, Tu C, Liu Y. Role of lncRNAs in aging and age-related diseases. Aging Med (Milton) 2018; 1:158-175. [PMID: 31942494 PMCID: PMC6880696 DOI: 10.1002/agm2.12030] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 06/28/2018] [Accepted: 07/03/2018] [Indexed: 01/10/2023] Open
Abstract
Aging is progressive physiological degeneration and consequently declined function, which is linked to senescence on both cellular and organ levels. Accumulating studies indicate that long noncoding RNAs (lncRNAs) play important roles in cellular senescence at all levels-transcriptional, post-transcriptional, translational, and post-translational. Understanding the molecular mechanism of lncRNAs underlying senescence could facilitate interpretation and intervention of aging and age-related diseases. In this review, we describe categories of known and novel lncRNAs that have been involved in the progression of senescence. We also identify the lncRNAs implicated in diseases arising from age-driven degeneration or dysfunction in some representative organs and systems (brains, liver, muscle, cardiovascular system, bone pancreatic islets, and immune system). Improved comprehension of lncRNAs in the aging process on all levels, from cell to organismal, may provide new insights into the amelioration of age-related pathologies and prolonged healthspan.
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Affiliation(s)
- Jieyu He
- Department of GeriatricsThe Second Xiangya HospitalCentral South UniversityChangshaHunanChina
| | - Chao Tu
- Department of OrthopedicsThe Second Xiangya HospitalCentral South UniversityChangshaHunanChina
| | - Youshuo Liu
- Department of GeriatricsThe Second Xiangya HospitalCentral South UniversityChangshaHunanChina
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159
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Juan C, Mao Y, Wang Q, Cao Q, Chen Y, Zhou G. The LncRNA MALAT1 regulates CD80 transcription via the NF-κB signaling pathway in the A549 cell line. Biochem Biophys Res Commun 2018; 503:1674-1681. [DOI: 10.1016/j.bbrc.2018.07.098] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 07/20/2018] [Indexed: 02/02/2023]
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160
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Zheng W, Chen C, Chen S, Fan C, Ruan H. Integrated analysis of long non-coding RNAs and mRNAs associated with peritendinous fibrosis. J Adv Res 2018; 15:49-58. [PMID: 30581612 PMCID: PMC6300459 DOI: 10.1016/j.jare.2018.08.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2018] [Revised: 08/16/2018] [Accepted: 08/29/2018] [Indexed: 02/08/2023] Open
Abstract
The dysregulation of long non-coding RNAs (lncRNAs) is associated with the development of various diseases. However, little is known about the regulatory function of lncRNAs in peritendinous fibrosis. Therefore, the expression profiles of lncRNAs and mRNAs in normal tendon and fibrotic peritendinous tissues were analyzed in this study using RNA sequencing. In total, 219 lncRNAs and 3403 mRNAs were identified that were differentially expressed between the two sets of tissues. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses revealed that the dysregulated mRNAs were mainly associated with immune regulation, inflammation, extracellular matrix (ECM) production and remodeling, and cell cycle regulation. An lncRNA-mRNA co-expression network revealed 181 network pairs comprising eight dysregulated lncRNAs and 146 mRNAs. The results of the bioinformatics analysis indicated that the dysregulated lncRNAs play a role in fibrogenesis through regulation of the cell cycle, inflammation, and ECM production. Furthermore, silencing the lncRNA dnm3os prevented transforming growth factor (TGF)-β1-induced tenocyte proliferation and expression of genes related to fibrogenesis. These findings provide a basis for investigations into the regulatory mechanisms underlying the development and progression of peritendinous fibrosis.
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Affiliation(s)
- Wei Zheng
- Department of Orthopaedics, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, 600 Yishan Road, Shanghai 200233, China
| | - Chen Chen
- Department of Orthopaedics, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, 600 Yishan Road, Shanghai 200233, China.,Department of Arthroscopic Surgery, Shanghai Sixth People's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Shuai Chen
- Department of Orthopaedics, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, 600 Yishan Road, Shanghai 200233, China
| | - Cunyi Fan
- Department of Orthopaedics, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, 600 Yishan Road, Shanghai 200233, China
| | - Hongjiang Ruan
- Department of Orthopaedics, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, 600 Yishan Road, Shanghai 200233, China
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161
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Pearson MJ, Jones SW. Review: Long Noncoding RNAs in the Regulation of Inflammatory Pathways in Rheumatoid Arthritis and Osteoarthritis. Arthritis Rheumatol 2018; 68:2575-2583. [PMID: 27214788 PMCID: PMC5347907 DOI: 10.1002/art.39759] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 05/12/2016] [Indexed: 12/16/2022]
Affiliation(s)
- Mark J Pearson
- Institute of Inflammation and Ageing, MRC-ARK Centre for Musculoskeletal Ageing Research, University of Birmingham, Birmingham, UK
| | - Simon W Jones
- Institute of Inflammation and Ageing, MRC-ARK Centre for Musculoskeletal Ageing Research, University of Birmingham, Birmingham, UK.
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162
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Teng H, Mao F, Liang J, Xue M, Wei W, Li X, Zhang K, Feng D, Liu B, Sun Z. Transcriptomic signature associated with carcinogenesis and aggressiveness of papillary thyroid carcinoma. Theranostics 2018; 8:4345-4358. [PMID: 30214625 PMCID: PMC6134936 DOI: 10.7150/thno.26862] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 07/16/2018] [Indexed: 01/27/2023] Open
Abstract
Papillary thyroid carcinoma (PTC) is the fastest-growing disease caused by numerous molecular alterations in addition to previously reported DNA mutations. There is a compelling need to identify novel transcriptomic alterations that are associated with the pathogenesis of PTC with potential diagnostic and prognostic implications. Methods: We gathered and compared 242 expression profiles between paired PTC and adjacent normal tissues and identified and validated the coding and long non-coding RNAs (lncRNAs) associated with the extrathyroidal extension (ETE) of 655 PTC patients in two independent cohorts, followed by predicting their interactions with drugs. Co-expression, RNA interaction, Kaplan-Meier survival and multivariate Cox proportional regression analyses were performed to identify dysregulated lncRNAs and genes that correlated with clinical outcomes of PTC. Alternative splicing (AS), RNA circularization, and editing were also compared between transcriptomes to expand the repertoire of molecular alterations in PTC. Results: Numerous genes related to cellular microenvironment and steroid hormone response were associated with the ETE of PTC. Drug susceptibility predictions of the expression signature revealed two highly ranked compounds, 6-bromoindirubin-3'-oxime and lovastatin. Co-expression and RNA interaction analysis revealed the essential role of lncRNAs in PTC pathogenesis by modulating extracellular matrix and cell adhesion. Eight genes and two novel lncRNAs were identified that correlated with the aggressive nature and disease-free survival of PTC. Furthermore, this study provided the transcriptome-wide landscape of circRNAs in PTC and uncovered dissimilar expression profiles among circRNAs originating from the same host gene, suggesting the functional complexity of circRNAs in PTC carcinogenesis. The newly identified AS events in the SERPINA1 and FN1 genes may improve the sensitivity and specificity of these diagnostic biomarkers. Conclusions: Our study uncovered a comprehensive transcriptomic signature associated with the carcinogenesis and aggressive behavior of PTC, as well as presents a catalog of 10 potential biomarkers, which would facilitate PTC prognosis and development of new therapeutic strategies for this cancer.
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Affiliation(s)
- Huajing Teng
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Fengbiao Mao
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Jialong Liang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Meiying Xue
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wenqing Wei
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xianfeng Li
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Kun Zhang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Dongdong Feng
- Department of Head and Neck Surgery, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital and Institute, Beijing, China
| | - Baoguo Liu
- Department of Head and Neck Surgery, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital and Institute, Beijing, China
| | - Zhongsheng Sun
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
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163
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Qiu L, Wang T, Tang Q, Li G, Wu P, Chen K. Long Non-coding RNAs: Regulators of Viral Infection and the Interferon Antiviral Response. Front Microbiol 2018; 9:1621. [PMID: 30072977 PMCID: PMC6060254 DOI: 10.3389/fmicb.2018.01621] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 06/28/2018] [Indexed: 11/13/2022] Open
Abstract
Interferons (IFNs) are a family of cytokines providing a robust first line of host innate defense against pathogenic infection, and have now been part of the standard treatment for viral infection. However, IFN based therapy can best be described as modestly effective. Long non-coding RNAs (lncRNAs) are a novel class of non-protein-coding RNAs that are capable of regulating gene expression at different levels, including chromatin, transcription, post-transcription, and translation. Recently, lncRNAs are found to be deregulated upon viral infection or IFN treatment, and some of them can modulate viral infection in an IFN-dependent or -independent manner. Due to the crucial roles of lncRNAs in viral infection and the IFN antiviral response, the modulation of specific lncRNAs may be involved to increase the IFN antiviral response and improve the clinical result of IFN-based therapy. In this review, we summarize lncRNAs that are deregulated by viral infection, with special focus on the functions and underlying mechanisms of some essential lncRNAs, and discuss their roles in viral infection and the antiviral response of IFN.
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Affiliation(s)
- Lipeng Qiu
- Institute of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Tao Wang
- Institute of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Qi Tang
- Institute of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Guohui Li
- Institute of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Peng Wu
- Institute of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Keping Chen
- Institute of Life Sciences, Jiangsu University, Zhenjiang, China
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164
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Meydan C, Bekenstein U, Soreq H. Molecular Regulatory Pathways Link Sepsis With Metabolic Syndrome: Non-coding RNA Elements Underlying the Sepsis/Metabolic Cross-Talk. Front Mol Neurosci 2018; 11:189. [PMID: 29922126 PMCID: PMC5996041 DOI: 10.3389/fnmol.2018.00189] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 05/15/2018] [Indexed: 01/04/2023] Open
Abstract
Sepsis and metabolic syndrome (MetS) are both inflammation-related entities with high impact for human health and the consequences of concussions. Both represent imbalanced parasympathetic/cholinergic response to insulting triggers and variably uncontrolled inflammation that indicates shared upstream regulators, including short microRNAs (miRs) and long non-coding RNAs (lncRNAs). These may cross talk across multiple systems, leading to complex molecular and clinical outcomes. Notably, biomedical and RNA-sequencing based analyses both highlight new links between the acquired and inherited pathogenic, cardiac and inflammatory traits of sepsis/MetS. Those include the HOTAIR and MIAT lncRNAs and their targets, such as miR-122, −150, −155, −182, −197, −375, −608 and HLA-DRA. Implicating non-coding RNA regulators in sepsis and MetS may delineate novel high-value biomarkers and targets for intervention.
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Affiliation(s)
- Chanan Meydan
- Department of Internal Medicine, Mayanei Hayeshua Medical Center, Bnei Brak, Israel
| | - Uriya Bekenstein
- The Department of Biological Chemistry, The Edmond and Lilly Safra Center for Brain Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Hermona Soreq
- The Department of Biological Chemistry, The Edmond and Lilly Safra Center for Brain Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
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165
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Abstract
Cytokines and long noncoding RNAs (lncRNAs) are intertwined in the regulatory circuit controlling immunity. lncRNA expression levels are altered following cytokine stimulation in a cell-type-specific fashion. lncRNAs, in turn, regulate the inducible expression of cytokines following immune activation. These studies position lncRNAs as important regulators of gene expression within the complex pathways of the immune system. Our understanding of the functions of lncRNAs is just beginning. Current methodologies for functionally understanding how these transcripts mediate their effects are unable to keep up with the speed of genomic outputs cataloging thousands of these novel genes. In this review, we highlight the interplay between cytokines and lncRNAs and speculate on the future utility of these genes as potential biomarkers and therapeutic targets for the treatment of inflammatory disorders.
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Affiliation(s)
- Susan Carpenter
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, California 95064
| | - Katherine A Fitzgerald
- Program in Innate Immunity, Division of Infectious Diseases, University of Massachusetts Medical School, Worcester, Massachusetts 01655
- Centre for Molecular Inflammation Research, Department of Cancer Research and Molecular Medicine, NTNU, 7491 Trondheim, Norway
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166
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Seo W, Taniuchi I. Regulation of hematopoiesis and immune responses by long non-coding RNAs. Int Immunol 2018; 29:165-172. [PMID: 28444293 DOI: 10.1093/intimm/dxx021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 04/12/2017] [Indexed: 12/19/2022] Open
Abstract
Since the first draft of the human genome sequence was released in 2001, unprecedentedly rapid progress has been made in whole genome-wide approaches by utilizing next-generation-sequencing technologies. The last decade alone has generated enormous data in the forms of exome sequencing, transcriptomes, transcription factor occupancy, genomic variation profiling and epigenetic modifications. One of the most striking realizations from sequencing studies has been the discovery and characterization of non-coding RNAs (ncRNAs). Although the extent to which ncRNAs are functional in vivo is still a controversial topic, there is at least a consensus that some ncRNAs are functional and that they play various roles in biology. Among the several kinds of ncRNAs, long ncRNAs (lncRNAs) in particular have received more attention because they have a larger potential to act as multifunctional regulators. Not surprisingly, researchers in the field of immunology have started to examine ncRNAs as new regulatory mechanisms. In this review, we will summarize some lncRNAs that have been reported to function in the immune system and then argue that there is still a long way to go before we can achieve a complete understanding of lncRNAs.
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Affiliation(s)
- Wooseok Seo
- Laboratory for Transcriptional Regulation, RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Ichiro Taniuchi
- Laboratory for Transcriptional Regulation, RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
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167
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Ahmed W, Liu ZF. Long Non-Coding RNAs: Novel Players in Regulation of Immune Response Upon Herpesvirus Infection. Front Immunol 2018; 9:761. [PMID: 29706968 PMCID: PMC5906719 DOI: 10.3389/fimmu.2018.00761] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 03/27/2018] [Indexed: 12/13/2022] Open
Abstract
Herpesviruses have developed a variety of sophisticated immune evasion strategies to establish lifelong latent infection, including the use of long non-coding RNAs (lncRNAs). In this review, we summarize the lncRNA action modes, i.e., RNA-protein, RNA-RNA, and RNA-DNA interactions, involved in regulating important aspects of immunity by controlling gene expression at various stages. Upon herpesvirus infection, host lncRNAs, such as nuclear paraspeckle assembly transcript 1, negative regulator of antiviral, and B-cell integration cluster have been functionally characterized as negative or positive antiviral regulators in the immune response. Herpesviruses have also evolved multiple strategies to modulate the host immune response using lncRNAs, such as latency-associated transcript, β 2.7 RNA, 5 kb and 7.2 kb lncRNAs, Epstein-Barr virus-encoded non-coding RNA, BamH I-A rightward transcripts, polyadenylated nuclear, and herpesvirus saimiri U-rich RNAs. We discuss the various mechanisms of immune-related lncRNAs, and their diversified and important functions in the modulation of innate and adaptive immunity upon herpesvirus infection as well as in host-pathogen interactions, which will facilitate our understanding of rational design of novel strategies to combat herpesvirus infection.
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Affiliation(s)
- Waqas Ahmed
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- College of Life Sciences, Guangzhou University, Guangzhou, China
| | - Zheng-Fei Liu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
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168
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Long non-coding RNAs regulating macrophage functions in homeostasis and disease. Vascul Pharmacol 2018; 114:122-130. [PMID: 29548902 DOI: 10.1016/j.vph.2018.02.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 02/09/2018] [Accepted: 02/26/2018] [Indexed: 12/29/2022]
Abstract
Non-coding RNAs, once considered "genomic junk", are now known to play central roles in the dynamic control of transcriptional and post-transcriptional gene expression. Long non-coding RNAs (lncRNAs) are an expansive class of transcripts broadly described as greater than 200 nucleotides in length. While most lncRNAs are species-specific, their lack of conservation does not imbue a lack of function. LncRNAs have been found to regulate numerous diverse biological functions, including those central to macrophage differentiation and activation. Through their ability to form RNA-DNA, RNA-protein and RNA-RNA interactions, lncRNAs have been implicated in the regulation of myeloid lineage determination, and innate and adaptive immune functions, among others. In this review, we discuss recent advances, current challenges and future opportunities in understanding the roles of lncRNAs in macrophage functions in homeostasis and disease.
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169
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Ye Y, Xu Y, Lai Y, He W, Li Y, Wang R, Luo X, Chen R, Chen T. Long non-coding RNA cox-2 prevents immune evasion and metastasis of hepatocellular carcinoma by altering M1/M2 macrophage polarization. J Cell Biochem 2018; 119:2951-2963. [PMID: 29131381 DOI: 10.1002/jcb.26509] [Citation(s) in RCA: 159] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 11/09/2017] [Indexed: 12/14/2022]
Abstract
Macrophages have been shown to demonstrate a high level of plasticity, with the ability to undergo dynamic transition between M1 and M2 polarized phenotypes. We investigate long non-coding RNA (lncRNA) cox-2 in macrophage polarization and the regulatory mechanism functions in hepatocellular carcinoma (HCC). Lipopolysaccharide (LPS) was used to induce RAW264.7 macrophages into M1 type, and IL-4 was to induce RAW264.7 macrophages into M2 type. We selected mouse hepatic cell line Hepal-6 and hepatoma cell line HepG2 for co-incubation with M1 or M2 macrophages. Quantitative real-time PCR was used to detect the expressions of lncRNA cox-2 and mRNAs. ELISA was conducted for testing IL-12 and IL-10 expressions; Western blotting for epithelial mesenchymal transition related factors (E-cadherin and Vimentin). An MTT, colony formation assay, flow cytometry, transwell assay, and stretch test were conducted to test cell abilities. The M1 macrophages had higher lncRNA cox-2 expression than that in the non-polarized macrophages and M2 macrophages. The lncRNA cox-2 siRNA decreased the expression levels of IL-12, iNOS, and TNF-α in M1 macrophages, increased the expression levels of IL-10, Arg-1, and Fizz-1 in M2 macrophages (all P < 0.05). The lncRNA cox-2 siRNA reduces the ability of M1 macrophages to inhibit HCC cell proliferation, invasion, migration, EMT, angiogenesis and facilitate apoptosis while strengthening the ability of M2 macrophages to promote proliferation HCC cell growth and inhibit apoptosis. These findings indicate that lncRNA cox-2 inhibits HCC immune evasion and tumor growth by inhibiting the polarization of M2 macrophages.
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Affiliation(s)
- Yibiao Ye
- Department of Hepatobilliary Surgery, Sun Yat-sen Memorial Hospitall, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Malignant Tumor Gene Regulation and Target Therapy of Guangdong Higher Education Institutes, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yunxiuxiu Xu
- Department of Hepatobilliary Surgery, Sun Yat-sen Memorial Hospitall, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Malignant Tumor Gene Regulation and Target Therapy of Guangdong Higher Education Institutes, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yu Lai
- Key Laboratory of Malignant Tumor Gene Regulation and Target Therapy of Guangdong Higher Education Institutes, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
- Department of Gastroenterology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Wenguang He
- Department of General Surgery, Zengcheng District People's Hospital of Guangzhou, Guangzhou, China
| | - Yanshan Li
- Key Laboratory of Malignant Tumor Gene Regulation and Target Therapy of Guangdong Higher Education Institutes, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
- Department of Blood Transfusion, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Ruomei Wang
- Department of Hepatobilliary Surgery, Sun Yat-sen Memorial Hospitall, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Malignant Tumor Gene Regulation and Target Therapy of Guangdong Higher Education Institutes, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xinxi Luo
- Key Laboratory of Malignant Tumor Gene Regulation and Target Therapy of Guangdong Higher Education Institutes, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
- Department of Gastrointestinal Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Rufu Chen
- Department of Hepatobilliary Surgery, Sun Yat-sen Memorial Hospitall, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Malignant Tumor Gene Regulation and Target Therapy of Guangdong Higher Education Institutes, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Tao Chen
- Key Laboratory of Malignant Tumor Gene Regulation and Target Therapy of Guangdong Higher Education Institutes, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
- Department of Biliary Pancreatic Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
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170
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lncRNAs Regulate Innate Immune Responses and Their Roles in Macrophage Polarization. Mediators Inflamm 2018; 2018:8050956. [PMID: 29599646 PMCID: PMC5828099 DOI: 10.1155/2018/8050956] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 12/04/2017] [Indexed: 02/07/2023] Open
Abstract
The innate immune system is the first line of defense against microbial pathogens. The activated innate immune system plays important roles in eliciting antimicrobial defenses. Despite the benefits of innate immune responses, excessive inflammation will cause host damage. Thus, tight regulation of these processes is required for the maintenance of immune homeostasis. Recently, a new class of long noncoding RNAs (lncRNAs) has emerged as important regulators in many physiological and pathological processes. Dysregulated lncRNAs have been found to be associated with excessive or uncontrolled inflammation. In this brief review, we summarize the roles of functional lncRNAs in regulating innate immune responses. We also discuss the roles of lncRNAs in macrophage polarization, an important molecular event in the innate immune responses.
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171
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Simion V, Haemmig S, Feinberg MW. LncRNAs in vascular biology and disease. Vascul Pharmacol 2018; 114:145-156. [PMID: 29425892 DOI: 10.1016/j.vph.2018.01.003] [Citation(s) in RCA: 122] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 01/09/2018] [Accepted: 01/16/2018] [Indexed: 12/14/2022]
Abstract
Accumulating studies indicate that long non-coding RNAs (lncRNAs) play important roles in the regulation of diverse biological processes involved in homeostatic control of the vessel wall in health and disease. However, our knowledge of the mechanisms by which lncRNAs control gene expression and cell signaling pathways is still nascent. Furthermore, only a handful of lncRNAs has been functionally evaluated in response to pathophysiological stimuli or in vascular disease states. For example, lncRNAs may regulate endothelial dysfunction by modulating endothelial cell proliferation (e.g. MALAT1, H19) or angiogenesis (e.g. MEG3, MANTIS). LncRNAs have also been implicated in modulating vascular smooth muscle cell (VSMC) phenotypes or vascular remodeling (e.g. ANRIL, SMILR, SENCR, MYOSLID). Finally, emerging studies have implicated lncRNAs in leukocytes activation (e.g. lincRNA-Cox2, linc00305, THRIL), macrophage polarization (e.g. GAS5), and cholesterol metabolism (e.g. LeXis). This review summarizes recent findings on the expression, mechanism, and function of lncRNAs implicated in a range of vascular disease states from mice to human subjects. An improved understanding of lncRNAs in vascular disease may provide new pathophysiological insights and opportunities for the generation of a new class of RNA-based biomarkers and therapeutic targets.
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Affiliation(s)
- Viorel Simion
- Department of Medicine, Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Stefan Haemmig
- Department of Medicine, Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Mark W Feinberg
- Department of Medicine, Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
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172
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Sun Q, Hao Q, Prasanth KV. Nuclear Long Noncoding RNAs: Key Regulators of Gene Expression. Trends Genet 2018; 34:142-157. [PMID: 29249332 PMCID: PMC6002860 DOI: 10.1016/j.tig.2017.11.005] [Citation(s) in RCA: 388] [Impact Index Per Article: 64.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 11/16/2017] [Accepted: 11/21/2017] [Indexed: 02/06/2023]
Abstract
A significant portion of the human genome encodes genes that transcribe long nonprotein-coding RNAs (lncRNAs). A large number of lncRNAs localize in the nucleus, either enriched on the chromatin or localized to specific subnuclear compartments. Nuclear lncRNAs participate in several biological processes, including chromatin organization, and transcriptional and post-transcriptional gene expression, and also act as structural scaffolds of nuclear domains. Here, we highlight recent studies demonstrating the role of lncRNAs in regulating gene expression and nuclear organization in mammalian cells. In addition, we update current knowledge about the involvement of the most-abundant and conserved lncRNA, metastasis-associated lung adenocarcinoma transcript 1 (MALAT1), in gene expression control.
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Affiliation(s)
- Qinyu Sun
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601 S Goodwin Avenue, Urbana, IL 61801, USA; These authors contributing equally
| | - Qinyu Hao
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601 S Goodwin Avenue, Urbana, IL 61801, USA; These authors contributing equally
| | - Kannanganattu V Prasanth
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601 S Goodwin Avenue, Urbana, IL 61801, USA.
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173
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Saha P, Verma S, Pathak RU, Mishra RK. Long Noncoding RNAs in Mammalian Development and Diseases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1008:155-198. [PMID: 28815540 DOI: 10.1007/978-981-10-5203-3_6] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Following analysis of sequenced genomes and transcriptome of many eukaryotes, it is evident that virtually all protein-coding genes have already been discovered. These advances have highlighted an intriguing paradox whereby the relative amount of protein-coding sequences remain constant but nonprotein-coding sequences increase consistently in parallel to increasing evolutionary complexity. It is established that differences between species map to nonprotein-coding regions of the genome that surprisingly is transcribed extensively. These transcripts regulate epigenetic processes and constitute an important layer of regulatory information essential for organismal development and play a causative role in diseases. The noncoding RNA-directed regulatory circuit controls complex characteristics. Sequence variations in noncoding RNAs influence evolution, quantitative traits, and disease susceptibility. This chapter presents an account on a class of such noncoding transcripts that are longer than 200 nucleotides (long noncoding RNA-lncRNA) in mammalian development and diseases.
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Affiliation(s)
- Parna Saha
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500007, India
| | - Shreekant Verma
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500007, India
| | - Rashmi U Pathak
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500007, India.
| | - Rakesh K Mishra
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500007, India.
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174
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Cen X, Huang XQ, Sun WT, Liu Q, Liu J. Long noncoding RNAs: a new regulatory code in osteoarthritis. Am J Transl Res 2017; 9:4747-4755. [PMID: 29218077 PMCID: PMC5714763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2017] [Accepted: 10/30/2017] [Indexed: 06/07/2023]
Abstract
It is reported that long noncoding RNAs (lncRNAs) were expressed aberrantly in cartilage of osteoarthritis (OA). Current evidence indicates that lncRNAs not only serve as positive or negative regulators of OA, but also crosstalk with multiple potential targets to impact on the critical events in OA process. This review summarized the lncRNAs identified in OA to date, discussed their influence on the survival of chondrocytes and synoviocytes, arthritis-associated factors, and angiogenesis, and indicated the potential in diagnosis, therapy, and prognosis.
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Affiliation(s)
- Xiao Cen
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Oral and Maxillofacial Surgery, West China Hospital of Stomatology, Sichuan UniversityChengdu, China
| | - Xin-Qi Huang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Orthodontics, West China Hospital of Stomatology, Sichuan UniversityChengdu, China
| | - Wen-Tian Sun
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Orthodontics, West China Hospital of Stomatology, Sichuan UniversityChengdu, China
| | - Qing Liu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Orthodontics, West China Hospital of Stomatology, Sichuan UniversityChengdu, China
| | - Jun Liu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Orthodontics, West China Hospital of Stomatology, Sichuan UniversityChengdu, China
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175
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Yu CK, Xu T, Assoian RK, Rader DJ. Mining the Stiffness-Sensitive Transcriptome in Human Vascular Smooth Muscle Cells Identifies Long Noncoding RNA Stiffness Regulators. Arterioscler Thromb Vasc Biol 2017; 38:164-173. [PMID: 29051139 DOI: 10.1161/atvbaha.117.310237] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 09/26/2017] [Indexed: 02/06/2023]
Abstract
OBJECTIVE Vascular extracellular matrix stiffening is a risk factor for aortic and coronary artery disease. How matrix stiffening regulates the transcriptome profile of human aortic and coronary vascular smooth muscle cells (VSMCs) is not well understood. Furthermore, the role of long noncoding RNAs (lncRNAs) in the cellular response to stiffening has never been explored. This study characterizes the stiffness-sensitive (SS) transcriptome of human aortic and coronary VSMCs and identifies potential key lncRNA regulators of stiffness-dependent VSMC functions. APPROACH AND RESULTS Aortic and coronary VSMCs were cultured on hydrogel substrates mimicking physiological and pathological extracellular matrix stiffness. Total RNAseq was performed to compare the SS transcriptome profiles of aortic and coronary VSMCs. We identified 3098 genes (2842 protein coding and 157 lncRNA) that were stiffness sensitive in both aortic and coronary VSMCs (false discovery rate <1%). Hierarchical clustering revealed that aortic and coronary VSMCs grouped by stiffness rather than cell origin. Conservation analyses also revealed that SS genes were more conserved than stiffness-insensitive genes. These VSMC SS genes were less tissue-type specific and expressed in more tissues than stiffness-insensitive genes. Using unbiased systems analyses, we identified MALAT1 as an SS lncRNA that regulates stiffness-dependent VSMC proliferation and migration in vitro and in vivo. CONCLUSIONS This study provides the transcriptomic landscape of human aortic and coronary VSMCs in response to extracellular matrix stiffness and identifies novel SS human lncRNAs. Our data suggest that the SS transcriptome is evolutionarily important to VSMCs function and that SS lncRNAs can act as regulators of stiffness-dependent phenotypes.
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MESH Headings
- Aorta/metabolism
- Aorta/pathology
- Cell Movement
- Cell Proliferation
- Cells, Cultured
- Cluster Analysis
- Computational Biology/methods
- Coronary Vessels/metabolism
- Coronary Vessels/pathology
- Data Mining/methods
- Extracellular Matrix/genetics
- Extracellular Matrix/metabolism
- Extracellular Matrix/pathology
- Gene Expression Profiling/methods
- Gene Expression Regulation
- Humans
- Hydrogels
- Mechanotransduction, Cellular
- Muscle, Smooth, Vascular/metabolism
- Muscle, Smooth, Vascular/pathology
- Myocytes, Smooth Muscle/metabolism
- Myocytes, Smooth Muscle/pathology
- RNA, Long Noncoding/genetics
- RNA, Long Noncoding/metabolism
- Transcriptome
- Vascular Stiffness
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Affiliation(s)
- Christopher K Yu
- From the Perelman School of Medicine (C.K.Y.), Department of Systems Pharmacology and Translational Therapeutics (T.X., R.K.A.), Program in Translational Biomechanics, Institute of Translational Medicine and Therapeutics (T.X., R.K.A.), and Departments of Genetics, Medicine, and Pediatrics, Perelman School of Medicine (D.J.R.), University of Pennsylvania, Philadelphia
- This manuscript was sent to Zahi Fayad, Consulting Editor, for review by expert referees, editorial decision, and final disposition
| | - Tina Xu
- From the Perelman School of Medicine (C.K.Y.), Department of Systems Pharmacology and Translational Therapeutics (T.X., R.K.A.), Program in Translational Biomechanics, Institute of Translational Medicine and Therapeutics (T.X., R.K.A.), and Departments of Genetics, Medicine, and Pediatrics, Perelman School of Medicine (D.J.R.), University of Pennsylvania, Philadelphia
- This manuscript was sent to Zahi Fayad, Consulting Editor, for review by expert referees, editorial decision, and final disposition
| | - Richard K Assoian
- From the Perelman School of Medicine (C.K.Y.), Department of Systems Pharmacology and Translational Therapeutics (T.X., R.K.A.), Program in Translational Biomechanics, Institute of Translational Medicine and Therapeutics (T.X., R.K.A.), and Departments of Genetics, Medicine, and Pediatrics, Perelman School of Medicine (D.J.R.), University of Pennsylvania, Philadelphia
- This manuscript was sent to Zahi Fayad, Consulting Editor, for review by expert referees, editorial decision, and final disposition
| | - Daniel J Rader
- From the Perelman School of Medicine (C.K.Y.), Department of Systems Pharmacology and Translational Therapeutics (T.X., R.K.A.), Program in Translational Biomechanics, Institute of Translational Medicine and Therapeutics (T.X., R.K.A.), and Departments of Genetics, Medicine, and Pediatrics, Perelman School of Medicine (D.J.R.), University of Pennsylvania, Philadelphia.
- This manuscript was sent to Zahi Fayad, Consulting Editor, for review by expert referees, editorial decision, and final disposition.
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176
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Meng J, Yao Z, He Y, Zhang R, Yang H, Yao X, Chen L, Zhang H, Cheng J. Long non-coding RNA expression profiles in different severity EV71-infected hand foot and mouth disease patients. Biochem Biophys Res Commun 2017; 493:1594-1600. [PMID: 28993196 PMCID: PMC7092854 DOI: 10.1016/j.bbrc.2017.09.141] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 09/25/2017] [Indexed: 12/11/2022]
Abstract
Enterovirus 71 (EV71) is associated with the severe hand foot and mouth disease (HFMD) outcomes, however the host-virus interaction mechanism and the pathogenesis remain poorly understood. Long non-coding RNAs (lncRNAs) are involved in variety physiological and pathological processes, but the functions of lncRNAs in EV71 infection remain elusive. Here we profiled the expression of lncRNAs in peripheral blood mononuclear cells (PBMCs) from EV71-infected mild patients, severe patients as well as the healthy controls, and identified 8541 lncRNAs were differentially expressed. Focused on the dynamic changed lncRNAs, we performed systematic bioinformatics analysis with Series Test of Cluster (STC) algorithm, Gene Ontology (GO) analysis, pathway analysis and lncRNA-mRNA co-expression network analysis, and revealed the potential functions and related pathways of these lncRNAs were associated with immunity and inflammation during the clinical process of EV71-infected HFMD. Among the significant dynamic changed lncRNAs, ten lncRNAs were screened whose expression were further validated in EV71-infected mild patients, severe patients and healthy control. These results shed light on the potential roles of lncRNAs in EV71-infected HFMD, especially in distinguishing the mild and severe cases for early diagnose and treatment, moreover, provide deeper insight into the mechanism of EV71-induced immune and inflammatory responses, as well as the pathogenesis of the imbalanced inflammation in severe EV71 infection. LncRNAs expression profile were analyzed with EV71-infected HFMD patients' PBMCs. Dynamic changed lncRNAs were analyzed in different severity EV71-infected patients. Most of the lncRNAs were related to innate immune and inflammatory responses. The candidate lncRNAs may serve as potential markers for EV71-induced severe HFMD.
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Affiliation(s)
- Jun Meng
- Shenzhen Center for Disease Control and Prevention, Shenzhen, Guangdong, China
| | - Zhenyu Yao
- Department of Translational Medicine R&D Center, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong, China
| | - Yaqing He
- Shenzhen Center for Disease Control and Prevention, Shenzhen, Guangdong, China
| | - Renli Zhang
- Shenzhen Center for Disease Control and Prevention, Shenzhen, Guangdong, China
| | - Hong Yang
- Shenzhen Center for Disease Control and Prevention, Shenzhen, Guangdong, China
| | - Xiangjie Yao
- Shenzhen Center for Disease Control and Prevention, Shenzhen, Guangdong, China
| | - Long Chen
- Shenzhen Center for Disease Control and Prevention, Shenzhen, Guangdong, China
| | - Hailong Zhang
- Shenzhen Center for Disease Control and Prevention, Shenzhen, Guangdong, China
| | - Jinquan Cheng
- Shenzhen Center for Disease Control and Prevention, Shenzhen, Guangdong, China.
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177
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Emerging mechanisms of long noncoding RNA function during normal and malignant hematopoiesis. Blood 2017; 130:1965-1975. [PMID: 28928124 DOI: 10.1182/blood-2017-06-788695] [Citation(s) in RCA: 121] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 09/15/2017] [Indexed: 12/22/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are increasingly recognized as vital components of gene programs controlling cell differentiation and function. Central to their functions is an ability to act as scaffolds or as decoys that recruit or sequester effector proteins from their DNA, RNA, or protein targets. lncRNA-modulated effectors include regulators of transcription, chromatin organization, RNA processing, and translation, such that lncRNAs can influence gene expression at multiple levels. Here we review the current understanding of how lncRNAs help coordinate gene expression to modulate cell fate in the hematopoietic system. We focus on a growing number of mechanistic studies to synthesize emerging principles of lncRNA function, emphasizing how they facilitate diversification of gene programming during development. We also survey how disrupted lncRNA function can contribute to malignant transformation, highlighting opportunities for therapeutic intervention in specific myeloid and lymphoid cancers. Finally, we discuss challenges and prospects for further elucidation of lncRNA mechanisms.
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178
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He X, Ou C, Xiao Y, Han Q, Li H, Zhou S. LncRNAs: key players and novel insights into diabetes mellitus. Oncotarget 2017; 8:71325-71341. [PMID: 29050364 PMCID: PMC5642639 DOI: 10.18632/oncotarget.19921] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 07/19/2017] [Indexed: 12/14/2022] Open
Abstract
Long non-coding RNAs (LncRNAs) are a class of endogenous RNA molecules, which have a transcribing length of over 200 nt, lack a complete functional open reading frame (ORF), and rarely encode a functional short peptide. Recent studies have revealed that disruption of LncRNAs levels correlates with several human diseases, including diabetes mellitus (DM), a complex multifactorial metabolic disorder affecting more than 400 million people worldwide. LncRNAs are emerging as pivotal regulators in various biological processes, in the progression of DM and its associated complications, involving pancreatic β-cell disorder, insulin resistance, and epigenetic regulation, etc. Further investigation into the mechanisms of action of LncRNAs in DM will be of great value in the thorough understanding of pathogenesis. However, prior to successful application of LncRNAs, further search for molecular biomarkers and drug targets to provide a new strategy for DM prevention, early diagnosis, and therapy is warranted.
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Affiliation(s)
- Xiaoyun He
- Department of Endocrinology, Affiliated Hospital of Guilin Medical University, Guilin 541001, China
- Department of Endocrinology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Chunlin Ou
- Cancer Research Institute, Central South University, Changsha 410078, China
| | - Yanhua Xiao
- Department of Endocrinology, Affiliated Hospital of Guilin Medical University, Guilin 541001, China
| | - Qing Han
- Department of Endocrinology, Affiliated Hospital of Guilin Medical University, Guilin 541001, China
| | - Hao Li
- Department of Neurology, Affiliated Hospital of Guilin Medical University, Guilin 541001, China
| | - Suxian Zhou
- Department of Endocrinology, Affiliated Hospital of Guilin Medical University, Guilin 541001, China
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179
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Mowel WK, Kotzin JJ, McCright SJ, Neal VD, Henao-Mejia J. Control of Immune Cell Homeostasis and Function by lncRNAs. Trends Immunol 2017; 39:55-69. [PMID: 28919048 DOI: 10.1016/j.it.2017.08.009] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 07/03/2017] [Accepted: 08/24/2017] [Indexed: 12/15/2022]
Abstract
The immune system is composed of diverse cell types that coordinate responses to infection and maintain tissue homeostasis. In each of these cells, extracellular cues determine highly specific epigenetic landscapes and transcriptional profiles to promote immunity while maintaining homeostasis. New evidence indicates that long non-coding RNAs (lncRNAs) play crucial roles in epigenetic and transcriptional regulation in mammals. Thus, lncRNAs have emerged as key regulatory molecules of immune cell gene expression programs in response to microbial and tissue-derived cues. We review here how lncRNAs control the function and homeostasis of cell populations during immune responses, emphasizing the diverse molecular mechanisms by which lncRNAs tune highly contextualized transcriptional programs. In addition, we discuss the new challenges faced in interrogating lncRNA mechanisms and function in the immune system.
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Affiliation(s)
- Walter K Mowel
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; These authors contributed equally to this work
| | - Jonathan J Kotzin
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; These authors contributed equally to this work
| | - Sam J McCright
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Vanessa D Neal
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jorge Henao-Mejia
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Transplant Immunology, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA 19104, USA.
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180
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Perry RBT, Ulitsky I. The functions of long noncoding RNAs in development and stem cells. Development 2017; 143:3882-3894. [PMID: 27803057 DOI: 10.1242/dev.140962] [Citation(s) in RCA: 150] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Eukaryotic genomes are pervasively transcribed, with tens of thousands of RNAs emanating from uni- and bi-directional promoters and from active enhancers. In vertebrates, thousands of loci in each species produce a class of transcripts called long noncoding RNAs (lncRNAs) that are typically expressed at low levels and do not appear to give rise to functional proteins. Substantial numbers of lncRNAs are expressed at specific stages of embryonic development, in many cases from regions flanking key developmental regulators. Here, we review the known biological functions of such lncRNAs and the emerging paradigms of their modes of action. We also provide an overview of the growing arsenal of methods for lncRNA identification, perturbation and functional characterization.
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Affiliation(s)
- Rotem Ben-Tov Perry
- Department of Biological Regulation, Weizmann Institute of Science, 234 Herzl St, Rehovot 76100, Israel
| | - Igor Ulitsky
- Department of Biological Regulation, Weizmann Institute of Science, 234 Herzl St, Rehovot 76100, Israel
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181
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Roux BT, Heward JA, Donnelly LE, Jones SW, Lindsay MA. Catalog of Differentially Expressed Long Non-Coding RNA following Activation of Human and Mouse Innate Immune Response. Front Immunol 2017; 8:1038. [PMID: 28900427 PMCID: PMC5581803 DOI: 10.3389/fimmu.2017.01038] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 08/11/2017] [Indexed: 12/12/2022] Open
Abstract
Despite increasing evidence to indicate that long non-coding RNAs (lncRNAs) are novel regulators of immunity, there has been no systematic attempt to identify and characterize the lncRNAs whose expression is changed following the induction of the innate immune response. To address this issue, we have employed next-generation sequencing data to determine the changes in the lncRNA profile in four human (monocytes, macrophages, epithelium, and chondrocytes) and four mouse cell types (RAW 264.7 macrophages, bone marrow-derived macrophages, peritoneal macrophages, and splenic dendritic cells) following exposure to the pro-inflammatory mediators, lipopolysaccharides (LPS), or interleukin-1β. We show differential expression of 204 human and 210 mouse lncRNAs, with positional analysis demonstrating correlation with immune-related genes. These lncRNAs are predominantly cell-type specific, composed of large regions of repeat sequences, and show poor evolutionary conservation. Comparison within the human and mouse sequences showed less than 1% sequence conservation, although we identified multiple conserved motifs. Of the 204 human lncRNAs, 21 overlapped with syntenic mouse lncRNAs, of which five were differentially expressed in both species. Among these syntenic lncRNA was IL7-AS (antisense), which was induced in multiple cell types and shown to regulate the production of the pro-inflammatory mediator interleukin-6 in both human and mouse cells. In summary, we have identified and characterized those lncRNAs that are differentially expressed following activation of the human and mouse innate immune responses and believe that these catalogs will provide the foundation for the future analysis of the role of lncRNAs in immune and inflammatory responses.
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Affiliation(s)
- Benoit T Roux
- Department of Pharmacy and Pharmacology, University of Bath, Bath, United Kingdom
| | - James A Heward
- Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Louise E Donnelly
- Airway Disease, National Heart and Lung Institute, Imperial College, London, United Kingdom
| | - Simon W Jones
- Institute of Inflammation and Ageing, MRC-ARUK Centre for Musculoskeletal Ageing Research, University of Birmingham, Birmingham, United Kingdom
| | - Mark A Lindsay
- Department of Pharmacy and Pharmacology, University of Bath, Bath, United Kingdom.,Airway Disease, National Heart and Lung Institute, Imperial College, London, United Kingdom
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182
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Chen YG, Satpathy AT, Chang HY. Gene regulation in the immune system by long noncoding RNAs. Nat Immunol 2017; 18:962-972. [PMID: 28829444 PMCID: PMC9830650 DOI: 10.1038/ni.3771] [Citation(s) in RCA: 502] [Impact Index Per Article: 71.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 03/16/2017] [Indexed: 02/07/2023]
Abstract
Long noncoding RNAs (lncRNAs) are emerging as critical regulators of gene expression in the immune system. Studies have shown that lncRNAs are expressed in a highly lineage-specific manner and control the differentiation and function of innate and adaptive cell types. In this Review, we focus on mechanisms used by lncRNAs to regulate genes encoding products involved in the immune response, including direct interactions with chromatin, RNA and proteins. In addition, we address new areas of lncRNA biology, such as the functions of enhancer RNAs, circular RNAs and chemical modifications to RNA in cellular processes. We emphasize critical gaps in knowledge and future prospects for the roles of lncRNAs in the immune system and autoimmune disease.
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Affiliation(s)
- Y Grace Chen
- Center for Personal Dynamic Regulomes and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, USA.,These authors contributed equally to this work
| | - Ansuman T Satpathy
- Center for Personal Dynamic Regulomes and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, USA.,Department of Pathology, Stanford University School of Medicine, Stanford, California, USA.,These authors contributed equally to this work
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, USA
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183
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Gomes CPC, Spencer H, Ford KL, Michel LYM, Baker AH, Emanueli C, Balligand JL, Devaux Y. The Function and Therapeutic Potential of Long Non-coding RNAs in Cardiovascular Development and Disease. MOLECULAR THERAPY-NUCLEIC ACIDS 2017; 8:494-507. [PMID: 28918050 PMCID: PMC5565632 DOI: 10.1016/j.omtn.2017.07.014] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 07/25/2017] [Indexed: 02/09/2023]
Abstract
The popularization of genome-wide analyses and RNA sequencing led to the discovery that a large part of the human genome, while effectively transcribed, does not encode proteins. Long non-coding RNAs have emerged as critical regulators of gene expression in both normal and disease states. Studies of long non-coding RNAs expressed in the heart, in combination with gene association studies, revealed that these molecules are regulated during cardiovascular development and disease. Some long non-coding RNAs have been functionally implicated in cardiac pathophysiology and constitute potential therapeutic targets. Here, we review the current knowledge of the function of long non-coding RNAs in the cardiovascular system, with an emphasis on cardiovascular development and biology, focusing on hypertension, coronary artery disease, myocardial infarction, ischemia, and heart failure. We discuss potential therapeutic implications and the challenges of long non-coding RNA research, with directions for future research and translational focus.
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Affiliation(s)
- Clarissa P C Gomes
- Cardiovascular Research Unit, Luxembourg Institute of Health, 1526 Luxembourg, Luxembourg
| | - Helen Spencer
- Centre for Cardiovascular Science, University of Edinburgh, Edinburgh EH8 9YL, UK
| | - Kerrie L Ford
- Bristol Heart Institute, University of Bristol, Bristol BS8 1TH, UK
| | - Lauriane Y M Michel
- Unité de Pharmacologie et de Thérapeutique, Institut de Recherche Experimentale et Clinique, Université Catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
| | - Andrew H Baker
- Centre for Cardiovascular Science, University of Edinburgh, Edinburgh EH8 9YL, UK
| | - Costanza Emanueli
- Bristol Heart Institute, University of Bristol, Bristol BS8 1TH, UK; National Heart and Lung Institute, Imperial College London, London SW7 2AZ, UK
| | - Jean-Luc Balligand
- Unité de Pharmacologie et de Thérapeutique, Institut de Recherche Experimentale et Clinique, Université Catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
| | - Yvan Devaux
- Cardiovascular Research Unit, Luxembourg Institute of Health, 1526 Luxembourg, Luxembourg.
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184
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Mirza AH, Kaur S, Pociot F. Long non-coding RNAs as novel players in β cell function and type 1 diabetes. Hum Genomics 2017; 11:17. [PMID: 28738846 PMCID: PMC5525349 DOI: 10.1186/s40246-017-0113-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 07/18/2017] [Indexed: 12/15/2022] Open
Abstract
Background Long non-coding RNAs (lncRNAs) are a sub-class within non-coding RNA repertoire that have emerged as crucial regulators of the gene expression in various pathophysiological conditions. lncRNAs display remarkable versatility and wield their functions through interactions with RNA, DNA, or proteins. Accumulating body of evidence based on multitude studies has highlighted the role of lncRNAs in many autoimmune and inflammatory diseases, including type 1 diabetes (T1D). Main body of abstract This review highlights emerging roles of lncRNAs in immune and islet β cell function as well as some of the challenges and opportunities in understanding the pathogenesis of T1D and its complications. Conclusion We accentuate that the lncRNAs within T1D-loci regions in consort with regulatory variants and enhancer clusters orchestrate the chromatin remodeling in β cells and thereby act as cis/trans-regulatory determinants of islet cell transcriptional programs.
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Affiliation(s)
- Aashiq H Mirza
- CPH-DIRECT, Department of Pediatrics, Herlev University Hospital, Herlev Ringvej 75, DK-2730, Herlev, Denmark.,Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Center for non-coding RNA in Technology and Health, University of Copenhagen, Copenhagen, Denmark
| | - Simranjeet Kaur
- CPH-DIRECT, Department of Pediatrics, Herlev University Hospital, Herlev Ringvej 75, DK-2730, Herlev, Denmark
| | - Flemming Pociot
- CPH-DIRECT, Department of Pediatrics, Herlev University Hospital, Herlev Ringvej 75, DK-2730, Herlev, Denmark. .,Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark. .,Center for non-coding RNA in Technology and Health, University of Copenhagen, Copenhagen, Denmark.
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185
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Lnc-ing inflammation to disease. Biochem Soc Trans 2017; 45:953-62. [PMID: 28687714 DOI: 10.1042/bst20160377] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 05/26/2017] [Accepted: 06/12/2017] [Indexed: 02/06/2023]
Abstract
Termed 'master gene regulators' long ncRNAs (lncRNAs) have emerged as the true vanguard of the 'noncoding revolution'. Functioning at a molecular level, in most if not all cellular processes, lncRNAs exert their effects systemically. Thus, it is not surprising that lncRNAs have emerged as important players in human pathophysiology. As our body's first line of defense upon infection or injury, inflammation has been implicated in the etiology of several human diseases. At the center of the acute inflammatory response, as well as several pathologies, is the pleiotropic transcription factor NF-κβ. In this review, we attempt to capture a summary of lncRNAs directly involved in regulating innate immunity at various arms of the NF-κβ pathway that have also been validated in human disease. We also highlight the fundamental concepts required as lncRNAs enter a new era of diagnostic and therapeutic significance.
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186
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lncRNA HULC promotes the growth of hepatocellular carcinoma cells via stabilizing COX-2 protein. Biochem Biophys Res Commun 2017. [PMID: 28634076 DOI: 10.1016/j.bbrc.2017.06.103] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Highly upregulated in liver cancer (HULC), a lncRNA overexpressed in hepatocellular carcinoma (HCC), has been demonstrated to be involved in the carcinogenesis and progression of HCC. However, the mechanisms of HULC promoting the abnormal growth of HCC cells are still not well elucidated. In the present study, we for the first time demonstrated that HULC promoted the growth of HCC cells through elevating COX-2 protein. Moreover, the study of the corresponding mechanism by which HULC upregulated COX-2 showed that HULC enhanced the level of ubiquitin-specific peptidase 22 (USP22), which decreased ubiquitin-mediated degradation of COX-2 protein by removing the conjugated polyubiquitin chains from COX-2 and finally stabilized COX2 protein. In addition, knockdown of USP22 or COX-2 attenuated HULC-mediated abnormal growth of HCC cells. In conclusion, our results demonstrated that "USP22/COX-2" axis played an important role in HULC promoting growth of HCC cells. The identification of this novel pathway may pave a road for developing new potential anti-HCC strategies.
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187
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Mathy NW, Chen XM. Long non-coding RNAs (lncRNAs) and their transcriptional control of inflammatory responses. J Biol Chem 2017; 292:12375-12382. [PMID: 28615453 DOI: 10.1074/jbc.r116.760884] [Citation(s) in RCA: 185] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) have emerged as potential key regulators of the inflammatory response, particularly by modulating the transcriptional control of inflammatory genes. lncRNAs may act as an enhancer or suppressor to inflammatory transcription, function as scaffold molecules through interactions with RNA-binding proteins in chromatin remodeling complexes, and modulate dynamic and epigenetic control of inflammatory transcription in a gene-specific and time-dependent fashion. Here, we will review recent literature regarding the role of lncRNAs in transcriptional control of inflammatory responses. Better understanding of lncRNA regulation of inflammation will provide novel targets for the development of new therapeutic strategies.
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Affiliation(s)
- Nicholas W Mathy
- Department of Medical Microbiology and Immunology, Creighton University School of Medicine, Omaha, Nebraska 68178
| | - Xian-Ming Chen
- Department of Medical Microbiology and Immunology, Creighton University School of Medicine, Omaha, Nebraska 68178.
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188
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LncRNA-mediated regulation of cell signaling in cancer. Oncogene 2017; 36:5661-5667. [PMID: 28604750 PMCID: PMC6450570 DOI: 10.1038/onc.2017.184] [Citation(s) in RCA: 1179] [Impact Index Per Article: 168.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 05/06/2017] [Accepted: 05/08/2017] [Indexed: 12/13/2022]
Abstract
To date, a large number of long non-coding RNAs (lncRNAs) have been recently discovered through functional genomics studies. Importantly, lncRNAs have been shown, in many cases, to function as master regulators for gene expression and thus, they can play a critical role in various biological functions and disease processes including cancer. Although the lncRNA-mediated gene expression involves various mechanisms, such as regulation of transcription, translation, protein modification, and the formation of RNA-protein or protein-protein complexes, in this review we discuss the latest developments primarily in important cell signaling pathways regulated by lncRNAs in cancer.
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189
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Li M, Guan H. Noncoding RNAs Regulating NF-κB Signaling. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 927:317-36. [PMID: 27376741 DOI: 10.1007/978-981-10-1498-7_12] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
As transcription factors that regulate expression of a variety of genes essential for diverse physiological and pathological processes, nuclear factor kappa B (NF-κB) family molecules play important roles in the development and progression of malignant tumor, and constitutive activation of NF-κB has been evidenced in various types of tumor tissues. Underlying its pathologic role, deregulated expression and/or transactivating activity of NF-κB usually involves multiple layers of molecular mechanisms. Noncoding RNAs, including microRNAs (miRNAs) and long noncoding RNAs (lncRNAs), are known to modulate expression and biological functions of regulatory proteins in a variety of cancer contexts. In this chapter, the regulatory role of miRNAs and lncRNAs in NF-κB signaling in malignant diseases will be discussed.
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Affiliation(s)
- Mengfeng Li
- Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan Road II, Guangzhou, China.
| | - Hongyu Guan
- Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan Road II, Guangzhou, China
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190
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Li Q, Liu Q. Noncoding RNAs in Cancer Immunology. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 927:243-64. [PMID: 27376738 DOI: 10.1007/978-981-10-1498-7_9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Cancer immunology is the study of interaction between cancer cells and immune system by the application of immunology principle and theory. With the recent approval of several new drugs targeting immune checkpoints in cancer, cancer immunology has become a very attractive field of research and is thought to be the new hope to conquer cancer. This chapter introduces the aberrant expression and function of noncoding RNAs, mainly microRNAs and long noncoding RNAs, in tumor-infiltrating immune cells, and their significance in tumor immunity. It also illustrates how noncoding RNAs are shuttled between tumor cells and immune cells in tumor microenvironments via exosomes or other microvesicles to modulate tumor immunity.
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Affiliation(s)
- Qian Li
- Sun Yat-sen Memorial Hospital, Sun Yat-sen University, 107, Yanjiang West Road, Guangzhou, 510120, China
| | - Qiang Liu
- Sun Yat-sen Memorial Hospital, Sun Yat-sen University, 107, Yanjiang West Road, Guangzhou, 510120, China.
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191
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Morriss GR, Cooper TA. Protein sequestration as a normal function of long noncoding RNAs and a pathogenic mechanism of RNAs containing nucleotide repeat expansions. Hum Genet 2017; 136:1247-1263. [PMID: 28484853 DOI: 10.1007/s00439-017-1807-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 04/28/2017] [Indexed: 12/12/2022]
Abstract
An emerging class of long noncoding RNAs (lncRNAs) function as decoy molecules that bind and sequester proteins thereby inhibiting their normal functions. Titration of proteins by lncRNAs has wide-ranging effects affecting nearly all steps in gene expression. While decoy lncRNAs play a role in normal physiology, RNAs expressed from alleles containing nucleotide repeat expansions can be pathogenic due to protein sequestration resulting in disruption of normal functions. This review focuses on commonalities between decoy lncRNAs that regulate gene expression by competitive inhibition of protein function through sequestration and specific examples of nucleotide repeat expansion disorders mediated by toxic RNA that sequesters RNA-binding proteins and impedes their normal functions. Understanding how noncoding RNAs compete with various RNA and DNA molecules for binding of regulatory proteins will provide insight into how similar mechanisms contribute to disease pathogenesis.
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Affiliation(s)
- Ginny R Morriss
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Thomas A Cooper
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, 77030, USA. .,Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA. .,Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA.
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192
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Mumtaz PT, Bhat SA, Ahmad SM, Dar MA, Ahmed R, Urwat U, Ayaz A, Shrivastava D, Shah RA, Ganai NA. LncRNAs and immunity: watchdogs for host pathogen interactions. Biol Proced Online 2017; 19:3. [PMID: 28465674 PMCID: PMC5406993 DOI: 10.1186/s12575-017-0052-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 04/06/2017] [Indexed: 01/23/2023] Open
Abstract
Immune responses combat various infectious agents by inducing inflammatory responses, antimicrobial pathways and adaptive immunity. The polygenic responses to these external stimuli are temporally and coordinately regulated. Specific lncRNAs are induced to modulate innate and adaptive immune responses which can function through various target interactions like RNA-DNA, RNA-RNA, and RNA-protein interaction and hence affect the immunogenic regulation at various stages of gene expression. LncRNA are found to be present in various immune cells like monocytes, macrophages, dendritic cells, neutrophils, T cells and B cells. They have been shown to be involved in many biological processes, including the regulation of the expression of genes, the dosage compensation and genomics imprinting, but the knowledge how lncRNAs are regulated and how they alter cell differentiation/function is still obscure. Further dysregulation of lncRNA has been seen in many diseases, but as yet very less research has been carried out to understand the role of lncRNAs in regulation during host-pathogens interactions. In this review, we summarize the functional developments and mechanism of action of lncRNAs, in immunity and defense of host against pathogens.
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Affiliation(s)
- Peerzada Tajamul Mumtaz
- Division of Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, SKUAST-K, Shuhama, Srinagar, Jammu and Kashmir India
- School of Life Sciences Jaipur National University, Jaipur, Rajasthan India
| | - Shakil Ahmad Bhat
- Division of Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, SKUAST-K, Shuhama, Srinagar, Jammu and Kashmir India
| | - Syed Mudasir Ahmad
- Division of Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, SKUAST-K, Shuhama, Srinagar, Jammu and Kashmir India
| | - Mashooq Ahmad Dar
- Division of Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, SKUAST-K, Shuhama, Srinagar, Jammu and Kashmir India
| | - Raashid Ahmed
- Division of Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, SKUAST-K, Shuhama, Srinagar, Jammu and Kashmir India
| | - Uneeb Urwat
- Division of Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, SKUAST-K, Shuhama, Srinagar, Jammu and Kashmir India
| | - Aadil Ayaz
- Division of Animal Breeding and Genetics, Faculty of Veterinary Sciences and Animal Husbandry, SKUAST-K, Shuhama, Srinagar, Jammu and Kashmir India
| | - Divya Shrivastava
- School of Life Sciences Jaipur National University, Jaipur, Rajasthan India
| | - Riaz Ahmad Shah
- Division of Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, SKUAST-K, Shuhama, Srinagar, Jammu and Kashmir India
| | - Nazir Ahmad Ganai
- Division of Animal Breeding and Genetics, Faculty of Veterinary Sciences and Animal Husbandry, SKUAST-K, Shuhama, Srinagar, Jammu and Kashmir India
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193
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Zhang DD, Wang WT, Xiong J, Xie XM, Cui SS, Zhao ZG, Li MJ, Zhang ZQ, Hao DL, Zhao X, Li YJ, Wang J, Chen HZ, Lv X, Liu DP. Long noncoding RNA LINC00305 promotes inflammation by activating the AHRR-NF-κB pathway in human monocytes. Sci Rep 2017; 7:46204. [PMID: 28393844 PMCID: PMC5385552 DOI: 10.1038/srep46204] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 03/13/2017] [Indexed: 02/08/2023] Open
Abstract
Accumulating data from genome-wide association studies (GWAS) have provided a collection of novel candidate genes associated with complex diseases, such as atherosclerosis. We identified an atherosclerosis-associated single-nucleotide polymorphism (SNP) located in the intron of the long noncoding RNA (lncRNA) LINC00305 by searching the GWAS database. Although the function of LINC00305 is unknown, we found that LINC00305 expression is enriched in atherosclerotic plaques and monocytes. Overexpression of LINC00305 promoted the expression of inflammation-associated genes in THP-1 cells and reduced the expression of contractile markers in co-cultured human aortic smooth muscle cells (HASMCs). We showed that overexpression of LINC00305 activated nuclear factor-kappa beta (NF-κB) and that inhibition of NF-κB abolished LINC00305-mediated activation of cytokine expression. Mechanistically, LINC00305 interacted with lipocalin-1 interacting membrane receptor (LIMR), enhanced the interaction of LIMR and aryl-hydrocarbon receptor repressor (AHRR), and promoted protein expression as well as nuclear localization of AHRR. Moreover, LINC00305 activated NF-κB exclusively in the presence of LIMR and AHRR. In light of these findings, we propose that LINC00305 promotes monocyte inflammation by facilitating LIMR and AHRR cooperation and the AHRR activation, which eventually activates NF-κB, thereby inducing HASMC phenotype switching.
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Affiliation(s)
- Dan-Dan Zhang
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, P. R. China
| | - Wen-Tian Wang
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, P. R. China
| | - Jian Xiong
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, P. R. China
| | - Xue-Min Xie
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, P. R. China
| | - Shen-Shen Cui
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, P. R. China
| | - Zhi-Guo Zhao
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, P. R. China
| | - Mulin Jun Li
- Department of Biochemistry, The University of Hong Kong, Hong Kong SAR, P. R. China
- Centre for Genomic Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, P. R. China
| | - Zhu-Qin Zhang
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, P. R. China
| | - De-Long Hao
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, P. R. China
| | - Xiang Zhao
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, P. R. China
| | - Yong-Jun Li
- Department of Vascular Surgery, Beijing Hospital, Beijing 100005, P. R. China
| | - Junwen Wang
- Department of Biochemistry, The University of Hong Kong, Hong Kong SAR, P. R. China
- Centre for Genomic Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, P. R. China
- Center for Individualized Medicine, Mayo Clinic Arizona & Department of Biomedical Informatics, Arizona State University, Scottsdale, AZ, 85259, USA
| | - Hou-Zao Chen
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, P. R. China
| | - Xiang Lv
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, P. R. China
- Department of Pathophysiology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, P. R. China
| | - De-Pei Liu
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, P. R. China
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194
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Long Non-Coding RNAs Regulating Immunity in Insects. Noncoding RNA 2017; 3:ncrna3010014. [PMID: 29657286 PMCID: PMC5832008 DOI: 10.3390/ncrna3010014] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2016] [Revised: 03/04/2017] [Accepted: 03/07/2017] [Indexed: 02/06/2023] Open
Abstract
Recent advances in modern technology have led to the understanding that not all genetic information is coded into protein and that the genomes of each and every organism including insects produce non-coding RNAs that can control different biological processes. Among RNAs identified in the last decade, long non-coding RNAs (lncRNAs) represent a repertoire of a hidden layer of internal signals that can regulate gene expression in physiological, pathological, and immunological processes. Evidence shows the importance of lncRNAs in the regulation of host–pathogen interactions. In this review, an attempt has been made to view the role of lncRNAs regulating immune responses in insects.
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195
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Khyzha N, Alizada A, Wilson MD, Fish JE. Epigenetics of Atherosclerosis: Emerging Mechanisms and Methods. Trends Mol Med 2017; 23:332-347. [PMID: 28291707 DOI: 10.1016/j.molmed.2017.02.004] [Citation(s) in RCA: 134] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 02/13/2017] [Accepted: 02/16/2017] [Indexed: 12/26/2022]
Abstract
Atherosclerosis is a vascular pathology characterized by inflammation and plaque build-up within arterial vessel walls. Vessel occlusion, often occurring after plaque rupture, can result in myocardial and cerebral infarction. Epigenetic changes are increasingly being associated with atherosclerosis and are of interest from both therapeutic and biomarker perspectives. Emerging genomic approaches that profile DNA methylation, chromatin accessibility, post-translational histone modifications, transcription factor binding, and RNA expression in low or single cell populations are poised to enhance our spatiotemporal understanding of atherogenesis. Here, we review recent therapeutically relevant epigenetic discoveries and emerging technologies that may generate new opportunities for atherosclerosis research.
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Affiliation(s)
- Nadiya Khyzha
- Toronto General Hospital Research Institute, University Health Network, Toronto, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada; Heart & Stroke Richard Lewar Centre of Excellence in Cardiovascular Research, Toronto, Canada
| | - Azad Alizada
- Heart & Stroke Richard Lewar Centre of Excellence in Cardiovascular Research, Toronto, Canada; Genetics and Genome Biology, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Michael D Wilson
- Heart & Stroke Richard Lewar Centre of Excellence in Cardiovascular Research, Toronto, Canada; Genetics and Genome Biology, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Canada.
| | - Jason E Fish
- Toronto General Hospital Research Institute, University Health Network, Toronto, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada; Heart & Stroke Richard Lewar Centre of Excellence in Cardiovascular Research, Toronto, Canada.
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196
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Let-7e modulates the inflammatory response in vascular endothelial cells through ceRNA crosstalk. Sci Rep 2017; 7:42498. [PMID: 28195197 PMCID: PMC5307339 DOI: 10.1038/srep42498] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 01/11/2017] [Indexed: 02/06/2023] Open
Abstract
The inflammatory responses of vascular endothelial cells (VECs) are critical in the development of many cardio-cerebrovascular diseases. Let-7e is an important regulator of endothelial function and inflammation. However, the effects and mechanisms of let-7e on VECs inflammation have not been studied until recently. Thus, we investigated these issues and found that in addition to proliferation, apoptosis and cell adhesion, let-7e was also implicated in the regulation of inflammatory responses through a complex network, including IκBβ and lncRNA lnc-MKI67IP-3. Let-7e promoted NF-κB activation and translocation to the nucleus by inhibiting its target gene (IκBβ) expression and subsequently increased the expression of inflammatory and adhesion molecules. Meanwhile, lnc-MKI67IP-3 acted as a sponge or competing endogenous RNA (ceRNA) for let-7e, suppressing its pro-inflammatory effects, and let-7e decreased lnc-MKI67IP-3 expression, thereby forming a positive feedback loop to aggravate inflammation. Moreover, let-7e, lnc-MKI67IP-3 and IκBβ were also abnormal in oxLDL-treated VECs and atherosclerotic plaques. The present study revealed let-7e as a pro-inflammatory mediator and a novel regulatory mechanism for the NF-κB pathway through ceRNA crosstalk, comprising let-7e and its target IκBβ and the ceRNA lnc-MKI67IP-3. Thus, this molecule might play important roles in the inflammatory responses of VECs and development of atherosclerosis.
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197
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Tang SH, Gao JH, Wen SL, Tong H, Yan ZP, Liu R, Tang CW. Expression of cyclooxygenase-2 is correlated with lncRNA-COX-2 in cirrhotic mice induced by carbon tetrachloride. Mol Med Rep 2017; 15:1507-1512. [PMID: 28259935 PMCID: PMC5364955 DOI: 10.3892/mmr.2017.6161] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2015] [Accepted: 12/01/2016] [Indexed: 02/05/2023] Open
Abstract
Multiple long non-coding RNAs (lncRNAs) have been demonstrated to be involved in liver disease. Increased cyclooxygenase-2 (COX‑2) levels have also been reported to be involved in the progression of liver cirrhosis. In the present study, the correlations between lncRNA‑COX‑2 RNA expression levels, COX‑2 mRNA expression levels and liver fibrosis were examined. Liver fibrosis was induced by intraperitoneal injection of carbon tetrachloride (CCl4) in mice for 2 months (CCl4‑2M) or 3 months (CCl4‑3M). Liver histopathological evaluation was conducted using hematoxylin and eosin and Masson trichrome staining. Hepatic expression of COX‑2 and lncRNA‑COX‑2 was evaluated by reverse transcription‑quantitative polymerase chain reaction and immunohistochemical staining. Compared with the control group, fibrotic areas were increased four and nine times in the CCl4‑2M group and the CCl4‑3M group, respectively. LncRNA-COX-2 and COX‑2 upregulation were observed in the cirrhotic liver. COX‑2 mRNA expression levels and lncRNA-COX-2 RNA expression levels were significantly positively correlated with the fibrotic area. In addition, COX‑2 mRNA expression was significantly positively correlated with lncRNA‑COX‑2 expression. These results suggest that expression of COX‑2 and lncRNA‑COX‑2 increased with the progression of liver fibrosis. LncRNA-COX-2 may potentially be considered as a novel therapeutic target for liver fibrosis.
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Affiliation(s)
- Shi-Hang Tang
- Department of Gastroenterology, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Jin-Hang Gao
- Department of Gastroenterology, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Shi-Lei Wen
- Department of Human Anatomy, Academy of Preclinical and Forensic Medicine, West China Medicine College, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Huan Tong
- Department of Gastroenterology, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Zhao-Ping Yan
- Department of Gastroenterology, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Rui Liu
- Division of Peptides Related with Human Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Cheng-Wei Tang
- Department of Gastroenterology, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
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198
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Mao X, Su Z, Mookhtiar AK. Long non-coding RNA: a versatile regulator of the nuclear factor-κB signalling circuit. Immunology 2017; 150:379-388. [PMID: 27936492 DOI: 10.1111/imm.12698] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 11/27/2016] [Accepted: 12/01/2016] [Indexed: 12/16/2022] Open
Abstract
The nuclear factor-κB (NF-κB) family of transcription factors play an essential role for the regulation of inflammatory responses, immune function and malignant transformation. Aberrant activity of this signalling pathway may lead to inflammation, autoimmune diseases and oncogenesis. Over the last two decades great progress has been made in the understanding of NF-κB activation and how the response is counteracted for maintaining tissue homeostasis. Therapeutic targeting of this pathway has largely remained ineffective due to the widespread role of this vital pathway and the lack of specificity of the therapies currently available. Besides regulatory proteins and microRNAs, long non-coding RNA (lncRNA) is emerging as another critical layer of the intricate modulatory architecture for the control of the NF-κB signalling circuit. In this paper we focus on recent progress concerning lncRNA-mediated modulation of the NF-κB pathway, and evaluate the potential therapeutic uses and challenges of using lncRNAs that regulate NF-κB activity.
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Affiliation(s)
- Xiaohua Mao
- Department of Biochemistry, Key Laboratory of Ministry of Education for Developmental Genes and Human Diseases, School of Medicine, Southeast University, Nanjing, Jiangsu, China
| | - Zhenyi Su
- Department of Biochemistry, Key Laboratory of Ministry of Education for Developmental Genes and Human Diseases, School of Medicine, Southeast University, Nanjing, Jiangsu, China
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199
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Abstract
The discovery of long noncoding RNAs (lncRNA) has provided a new perspective on gene regulation in diverse biological contexts. lncRNAs are remarkably versatile molecules that interact with RNA, DNA, or proteins to promote or restrain the expression of protein-coding genes. Activation of immune cells is associated with dynamic changes in expression of genes, the products of which combat infectious microorganisms, initiate repair, and resolve inflammatory responses in cells and tissues. Recent evidence indicates that lncRNAs play important roles in directing the development of diverse immune cells and controlling the dynamic transcriptional programs that are a hallmark of immune cell activation. The importance of these molecules is underscored by their newly recognized roles in inflammatory diseases. In this review, we discuss the contribution of lncRNAs in the development and activation of immune cells and their roles in immune-related diseases. We also discuss challenges faced in identifying biological functions for this large and complex class of genes.
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Affiliation(s)
- Maninjay K Atianand
- Program in Innate Immunity, Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605;
| | - Daniel R Caffrey
- Program in Innate Immunity, Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605;
| | - Katherine A Fitzgerald
- Program in Innate Immunity, Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605;
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200
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Long non-coding RNAs: Mechanism of action and functional utility. Noncoding RNA Res 2016; 1:43-50. [PMID: 30159410 PMCID: PMC6096411 DOI: 10.1016/j.ncrna.2016.11.002] [Citation(s) in RCA: 188] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 11/09/2016] [Accepted: 11/10/2016] [Indexed: 12/22/2022] Open
Abstract
Recent RNA sequencing studies have revealed that most of the human genome is transcribed, but very little of the total transcriptomes has the ability to encode proteins. Long non-coding RNAs (lncRNAs) are non-coding transcripts longer than 200 nucleotides. Members of the non-coding genome include microRNA (miRNA), small regulatory RNAs and other short RNAs. Most of long non-coding RNA (lncRNAs) are poorly annotated. Recent recognition about lncRNAs highlights their effects in many biological and pathological processes. LncRNAs are dysfunctional in a variety of human diseases varying from cancerous to non-cancerous diseases. Characterization of these lncRNA genes and their modes of action may allow their use for diagnosis, monitoring of progression and targeted therapies in various diseases. In this review, we summarize the functional perspectives as well as the mechanism of action of lncRNAs.
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