151
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Noncoding RNAs in the development, diagnosis, and prognosis of colorectal cancer. Transl Res 2017; 181:108-120. [PMID: 27810413 DOI: 10.1016/j.trsl.2016.10.001] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2016] [Revised: 09/29/2016] [Accepted: 10/06/2016] [Indexed: 12/17/2022]
Abstract
More than 90% of the human genome is actively transcribed, but less than 2% of the total genome encodes protein-coding RNA, and thus, noncoding RNA (ncRNA) is a major component of the human transcriptome. Recently, ncRNA was demonstrated to play important roles in multiple biological processes by directly or indirectly interfering with gene expression, and the dysregulation of ncRNA is associated with a variety of diseases, including cancer. In this review, we summarize the function and mechanism of miRNA, long intergenic ncRNA, and some other types of ncRNAs, such as small nucleolar RNA, circular ncRNA, pseudogene RNA, and even protein-coding mRNA, in the progression of colorectal cancer (CRC). We also presented their clinical application in the diagnosis and prognosis of CRC. The summary of the current state of ncRNA in CRC will contribute to our understanding of the complex processes of CRC initiation and development and will help in the discovery of novel biomarkers and therapeutic targets for CRC diagnosis and treatment.
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152
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Li D, Cheng M, Niu Y, Chi X, Liu X, Fan J, Fan H, Chang Y, Yang W. Identification of a novel human long non-coding RNA that regulates hepatic lipid metabolism by inhibiting SREBP-1c. Int J Biol Sci 2017; 13:349-357. [PMID: 28367099 PMCID: PMC5370442 DOI: 10.7150/ijbs.16635] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 01/14/2017] [Indexed: 12/27/2022] Open
Abstract
Sterol regulatory element binding proteins (SREBPs) are master regulators of hepatic lipid homeostasis. Aberrant expression of SREBPs frequently leads to lipid metabolism dysregulation. Long non-coding RNAs (lncRNAs) have been identified with diverse biological functions, but the effects of lncRNAs on lipid metabolism are rarely reported. Here, we identified a novel human specific lncRNA, lncHR1, as a negative regulator of SREBP-1c expression. Overexpression of lncHR1 inhibited expression of SREBP-1c and fatty acid synthase (FAS) and then repressed oleic acid-induced hepatic cell triglyceride (TG) and lipid droplet (LD) accumulation. In vivo, the data of established transgenic animals showed that mice with lncHR1 expression had less hepatic expression of SREBP-1c, FAS, Acetyl-CoA carboxylase α (ACCα), and less hepatic and plasma TG after being fed a high-fat diet. Therefore, we report a novel lncRNA which can decrease lipid metabolism by repressing SREBP-1c gene expression.
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Affiliation(s)
- Duan Li
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100076, P.R. China;; Department of Microbiology, Xinxiang Medical University, Xinxiang, Henan 453003, P.R. China
| | - Min Cheng
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100076, P.R. China
| | - Yuqiang Niu
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100076, P.R. China
| | - Xiaojing Chi
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100076, P.R. China
| | - Xiuying Liu
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100076, P.R. China
| | - Jingjing Fan
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100076, P.R. China
| | - Heng Fan
- 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
| | - Yongsheng Chang
- 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
| | - Wei Yang
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100076, P.R. China
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153
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Sui W, Shi Z, Xue W, Ou M, Zhu Y, Chen J, Lin H, Liu F, Dai Y. Circular RNA and gene expression profiles in gastric cancer based on microarray chip technology. Oncol Rep 2017; 37:1804-1814. [DOI: 10.3892/or.2017.5415] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 01/09/2017] [Indexed: 12/12/2022] Open
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154
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Lindsay C, Seikaly H, Biron VL. Epigenetics of oropharyngeal squamous cell carcinoma: opportunities for novel chemotherapeutic targets. J Otolaryngol Head Neck Surg 2017; 46:9. [PMID: 28143553 PMCID: PMC5282807 DOI: 10.1186/s40463-017-0185-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 01/20/2017] [Indexed: 12/29/2022] Open
Abstract
Epigenetic modifications are heritable changes in gene expression that do not directly alter DNA sequence. These modifications include DNA methylation, histone post-translational modifications, small and non-coding RNAs. Alterations in epigenetic profiles cause deregulation of fundamental gene expression pathways associated with carcinogenesis. The role of epigenetics in oropharyngeal squamous cell carcinoma (OPSCC) has recently been recognized, with implications for novel biomarkers, molecular diagnostics and chemotherapeutics. In this review, important epigenetic pathways in human papillomavirus (HPV) positive and negative OPSCC are summarized, as well as the potential clinical utility of this knowledge.This material has never been published and is not currently under evaluation in any other peer-reviewed publication.
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Affiliation(s)
- Cameron Lindsay
- Faculty of Medicine and Dentistry, Department of Surgery, Division of Otolaryngology-Head and Neck Surgery, University of Alberta, 1E4.34 WMC, 8440 112 Street, Edmonton, AB, T6G 2B7, Canada
| | - Hadi Seikaly
- Faculty of Medicine and Dentistry, Department of Surgery, Division of Otolaryngology-Head and Neck Surgery, University of Alberta, 1E4.34 WMC, 8440 112 Street, Edmonton, AB, T6G 2B7, Canada
| | - Vincent L Biron
- Faculty of Medicine and Dentistry, Department of Surgery, Division of Otolaryngology-Head and Neck Surgery, University of Alberta, 1E4.34 WMC, 8440 112 Street, Edmonton, AB, T6G 2B7, Canada.
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155
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Wang W, Zhuang Q, Ji K, Wen B, Lin P, Zhao Y, Li W, Yan C. Identification of miRNA, lncRNA and mRNA-associated ceRNA networks and potential biomarker for MELAS with mitochondrial DNA A3243G mutation. Sci Rep 2017; 7:41639. [PMID: 28139706 PMCID: PMC5282567 DOI: 10.1038/srep41639] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 12/22/2016] [Indexed: 12/25/2022] Open
Abstract
Researchers in the field of mitochondrial biology are increasingly unveiling of the complex mechanisms between mitochondrial dysfunction and noncoding RNAs (ncRNAs). However, roles of ncRNAs underlying mitochondrial myopathy remain unexplored. The aim of this study was to elucidate the regulating networks of dysregulated ncRNAs in Mitochondrial myopathy, Encephalopathy, Lactic Acidosis, and Stroke-like episodes (MELAS) with mitochondrial DNA (mtDNA) A3243G mutation, which might make contributions to the unveiling of the complex mechanisms underlying mitochondrial myopathy and, possibly, new tools applicable to clinical practice. Through high-throughput technology followed by quantitative real-time polymerase chain reaction (qRT-PCR) and bioinformatics analyses, for the first time, we found that the dysregulated muscle miRNAs and lncRNAs between 20 MELAS patients with mtDNA A3243G mutation and 20 controls formed complex regulation networks and participated in immune system, signal transduction, translation, muscle contraction and other pathways in discovery and training phase. Then, selected ncRNAs were validated in muscle and serum in independent validation cohorts by qRT-PCR. Finally, ROC curve analysis indicated reduced serum miR-27b-3p had the better diagnosis value than lactate and might serve as a novel, noninvasive biomarker for MELAS. Follow-up investigation is warranted to better understand roles of ncRNAs in mitochondrial myopathy pathogenesis.
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Affiliation(s)
- Wei Wang
- Laboratory of Neuromuscular Disorders and Department of Neurology, Qilu Hospital, Shandong University, Jinan, China
| | - Qianqian Zhuang
- School of Bioengineering, Qilu University of Technology, Jinan, China
| | - Kunqian Ji
- Laboratory of Neuromuscular Disorders and Department of Neurology, Qilu Hospital, Shandong University, Jinan, China
| | - Bing Wen
- Laboratory of Neuromuscular Disorders and Department of Neurology, Qilu Hospital, Shandong University, Jinan, China
| | - Pengfei Lin
- Laboratory of Neuromuscular Disorders and Department of Neurology, Qilu Hospital, Shandong University, Jinan, China
| | - Yuying Zhao
- Laboratory of Neuromuscular Disorders and Department of Neurology, Qilu Hospital, Shandong University, Jinan, China
| | - Wei Li
- Laboratory of Neuromuscular Disorders and Department of Neurology, Qilu Hospital, Shandong University, Jinan, China
| | - Chuanzhu Yan
- Laboratory of Neuromuscular Disorders and Department of Neurology, Qilu Hospital, Shandong University, Jinan, China.,Key Laboratory for Experimental Teratology of the Ministry of Education, Brain Science Research Institute, Department of Neurology, Qilu Hospital, Shandong University, Jinan, China
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156
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He D, Wang J, Lu Y, Deng Y, Zhao C, Xu L, Chen Y, Hu YC, Zhou W, Lu QR. lncRNA Functional Networks in Oligodendrocytes Reveal Stage-Specific Myelination Control by an lncOL1/Suz12 Complex in the CNS. Neuron 2016; 93:362-378. [PMID: 28041882 DOI: 10.1016/j.neuron.2016.11.044] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 10/09/2016] [Accepted: 11/21/2016] [Indexed: 12/22/2022]
Abstract
Long noncoding RNAs (lncRNAs) are emerging as important regulators of cellular functions, but their roles in oligodendrocyte myelination remain undefined. Through de novo transcriptome reconstruction, we establish dynamic expression profiles of lncRNAs at different stages of oligodendrocyte development and uncover a cohort of stage-specific oligodendrocyte-restricted lncRNAs, including a conserved chromatin-associated lncOL1. Co-expression network analyses further define the association of distinct oligodendrocyte-expressing lncRNA clusters with protein-coding genes and predict lncRNA functions in oligodendrocyte myelination. Overexpression of lncOL1 promotes precocious oligodendrocyte differentiation in the developing brain, whereas genetic inactivation of lncOL1 causes defects in CNS myelination and remyelination following injury. Functional analyses illustrate that lncOL1 interacts with Suz12, a component of polycomb repressive complex 2, to promote oligodendrocyte maturation, in part, through Suz12-mediated repression of a differentiation inhibitory network that maintains the precursor state. Together, our findings reveal a key lncRNA epigenetic circuitry through interaction with chromatin-modifying complexes in control of CNS myelination and myelin repair.
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Affiliation(s)
- Danyang He
- Divisions of Experimental Hematology and Cancer Biology & Developmental Biology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Integrative Biology Graduate Training Program, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jincheng Wang
- Divisions of Experimental Hematology and Cancer Biology & Developmental Biology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Zhejiang Province Key Laboratory of Anti-cancer Drug Research, Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, Zhejiang University, 310058 Hangzhou, China
| | - Yulan Lu
- Key Laboratory of Birth Defects, Children's Hospital of Fudan University, 201102 Shanghai, China
| | - Yaqi Deng
- Divisions of Experimental Hematology and Cancer Biology & Developmental Biology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Chuntao Zhao
- Divisions of Experimental Hematology and Cancer Biology & Developmental Biology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Lingli Xu
- Divisions of Experimental Hematology and Cancer Biology & Developmental Biology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Key Laboratory of Birth Defects, Children's Hospital of Fudan University, 201102 Shanghai, China
| | - Yinhuai Chen
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Yueh-Chiang Hu
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Wenhao Zhou
- Key Laboratory of Birth Defects, Children's Hospital of Fudan University, 201102 Shanghai, China
| | - Q Richard Lu
- Divisions of Experimental Hematology and Cancer Biology & Developmental Biology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Integrative Biology Graduate Training Program, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Key Laboratory of Birth Defects, Children's Hospital of Fudan University, 201102 Shanghai, China.
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157
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Guo JC, Li CQ, Wang QY, Zhao JM, Ding JY, Li EM, Xu LY. Protein-coding genes combined with long non-coding RNAs predict prognosis in esophageal squamous cell carcinoma patients as a novel clinical multi-dimensional signature. MOLECULAR BIOSYSTEMS 2016; 12:3467-3477. [PMID: 27714034 DOI: 10.1039/c6mb00585c] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Esophageal carcinoma is one of the most malignant gastrointestinal cancers worldwide, and has a high mortality rate. Both protein-coding genes (PCGs) and long non-coding RNAs (lncRNAs) have been shown to play an important role in the development of malignant tumors. However, the clinical significance of PCGs combined lncRNAs is yet to be investigated in esophageal squamous cell carcinoma (ESCC). Using probe re-annotation, univariable Cox regression and the random survival forest algorithm to identify PCG-lncRNA combinations predictive of the overall survival, we found a signature comprised of three PCGs (ANGPTL7, OBP2A, SLC27A5) and two lncRNAs (RP11-702B10.1, RP11-523H24.3) to have the highest accurate prediction, with an area under ROC curve (AUC) of 0.85 in the training group and 0.63 in the test group, and it was significantly associated with the survival of ESCC patients in the training group (median survival: 32.2 months > 60 months, P < 0.001). The application of the signature to the test group showed similar prognostic values (median survival: 39.3 months vs. >60 months, P = 0.03). The chi-square test and multivariable Cox regression analysis showed that the three-PCG, two-lncRNA signature was an independent prognostic factor for patients with ESCC. Stratified analysis suggested that the PCG-lncRNA signature combined with the TNM stage could more accurately categorize ESCC patients. Our study suggests that the three-PCG, two-lncRNA signature has clinical significance for the prognosis of patients with ESCC. This signature can serve as a potential auxiliary biomarker of the TNM stage to subdivide ESCC patients more precisely.
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Affiliation(s)
- Jin-Cheng Guo
- Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou 515041, China and Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou 515041, China.
| | - Chun-Quan Li
- Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou 515041, China and Institute of Oncologic Pathology, Shantou University Medical College, Shantou 515041, China.
| | - Qiu-Yu Wang
- Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou 515041, China and Institute of Oncologic Pathology, Shantou University Medical College, Shantou 515041, China.
| | - Jian-Mei Zhao
- Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou 515041, China and Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou 515041, China.
| | - Ji-Yu Ding
- Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou 515041, China and Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou 515041, China.
| | - En-Min Li
- Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou 515041, China and Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou 515041, China.
| | - Li-Yan Xu
- Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou 515041, China and Institute of Oncologic Pathology, Shantou University Medical College, Shantou 515041, China.
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158
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Predicting the Organelle Location of Noncoding RNAs Using Pseudo Nucleotide Compositions. Interdiscip Sci 2016; 9:540-544. [PMID: 27739055 DOI: 10.1007/s12539-016-0193-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 09/28/2016] [Accepted: 10/06/2016] [Indexed: 11/27/2022]
Abstract
Noncoding RNAs (ncRNAs) are implicated in various biological processes. Recent findings have demonstrated that the function of ncRNAs correlates with their provenance. Therefore, the recognition of ncRNAs from different organelle genomes will be helpful to understand their molecular functions. However, the weakness of experimental techniques limits the progress toward studying organellar ncRNAs and their functional relevance. As a complement of experiments, computational method provides an important choice to identify ncRNA in different organelles. Thus, a computational model was developed to identify ncRNAs from kinetoplast and mitochondrion organelle genomes. In this model, RNA sequences are encoded by "pseudo dinucleotide composition." It was observed by the jackknife test that the overall success rate achieved by the proposed model was 90.08 %. We hope that the proposed method will be helpful in predicting ncRNA organellar locations.
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159
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Long Noncoding RNA lncCAMTA1 Promotes Proliferation and Cancer Stem Cell-Like Properties of Liver Cancer by Inhibiting CAMTA1. Int J Mol Sci 2016; 17:ijms17101617. [PMID: 27669232 PMCID: PMC5085650 DOI: 10.3390/ijms17101617] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 09/03/2016] [Accepted: 09/05/2016] [Indexed: 12/14/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is the most common subtype of liver malignancy, and it is characterized by poor prognosis because of cancer stem cell (CSC)-mediated high postsurgical recurrence rates. Thus, targeting CSCs, or HCC cells with CSC-like properties, is an effective strategy for HCC therapy. Here, using long noncoding RNA (lncRNA) microarray analysis, we identified a novel lncRNA termed lncCAMTA1 that is increased in both liver CSCs and HCC. High lncCAMTA1 expression in HCC indicates poor clinical outcome. In vitro and in vivo functional experiments showed that overexpression of lncCAMTA1 promotes HCC cell proliferation, CSC-like properties, and tumorigenesis. Conversely, depletion of lncCAMTA1 inhibits HCC cell proliferation, CSC-like properties, and tumorigenesis. Mechanistically, we demonstrated that lncCAMTA1 physically associates with the calmodulin binding transcription activator 1 (CAMTA1) promoter, induces a repressive chromatin structure, and inhibits CAMTA1 transcription. Furthermore, CAMTA1 is required for the effects of lncCAMTA1 on HCC cell proliferation and CSC-like properties, and the expression of lncCAMTA1 and CAMTA1 is significantly negatively correlated in HCC tissues. Collectively, our study revealed the important roles and underlying molecular mechanisms of lncCAMTA1 on HCC, and suggested that lncCAMTA1 could be an effective prognostic factor and a potential therapeutic target for HCC.
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160
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Abstract
An individual's risk of developing a common disease typically depends on an interaction of genetic and environmental factors. Epigenetic research is uncovering novel ways through which environmental factors such as diet, air pollution, and chemical exposure can affect our genes. DNA methylation and histone modifications are the most commonly studied epigenetic mechanisms. The role of long non-coding RNAs (lncRNAs) in epigenetic processes has been more recently highlighted. LncRNAs are defined as transcribed RNA molecules greater than 200 nucleotides in length with little or no protein-coding capability. While few functional lncRNAs have been well characterized to date, they have been demonstrated to control gene regulation at every level, including transcriptional gene silencing via regulation of the chromatin structure and DNA methylation. This review aims to provide a general overview of lncRNA function with a focus on their role as key regulators of health and disease and as biomarkers of environmental exposure.
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Affiliation(s)
- Oskar Karlsson
- Center for Molecular Medicine, Department of Clinical Neuroscience, Karolinska Institutet, 171 76, Stockholm, Sweden.
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA.
| | - Andrea A Baccarelli
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
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161
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Motterle A, Sanchez-Parra C, Regazzi R. Role of long non-coding RNAs in the determination of β-cell identity. Diabetes Obes Metab 2016; 18 Suppl 1:41-50. [PMID: 27615130 DOI: 10.1111/dom.12714] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 05/04/2016] [Indexed: 12/22/2022]
Abstract
Pancreatic β-cells are highly specialized cells committed to secrete insulin in response to changes in the level of nutrients, hormones and neurotransmitters. Chronic exposure to elevated concentrations of glucose, fatty acids or inflammatory mediators can result in modifications in β-cell gene expression that alter their functional properties. This can lead to the release of insufficient amount of insulin to cover the organism's needs, and thus to the development of diabetes mellitus. Although most of the studies carried out in the last decades to elucidate the causes of β-cell dysfunction under disease conditions have focused on protein-coding genes, we now know that insulin-secreting cells also contain thousands of molecules of RNA that do not encode polypeptides but play key roles in the acquisition and maintenance of a highly differentiated state. In this review, we will highlight the involvement of long non-coding RNAs (lncRNAs), a particular class of non-coding transcripts, in the differentiation of β-cells and in the regulation of their specialized tasks. We will also discuss the crosstalk between the activities of lncRNAs and microRNAs and present the emerging evidence of a potential contribution of particular lncRNAs to the development of both type 1 and type 2 diabetes.
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Affiliation(s)
- A Motterle
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland.
| | - C Sanchez-Parra
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland
| | - R Regazzi
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland
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162
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Rayner KJ, Liu PP. Long Noncoding RNAs in the Heart: The Regulatory Roadmap of Cardiovascular Development and Disease. ACTA ACUST UNITED AC 2016; 9:101-3. [PMID: 27094196 DOI: 10.1161/circgenetics.116.001413] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Katey J Rayner
- From the University of Ottawa Heart Institute; Departments of Medicine, Cellular & Molecular Medicine, and Biochemistry, Microbiology and Immunology, Ottawa, Ontario, Canada
| | - Peter P Liu
- From the University of Ottawa Heart Institute; Departments of Medicine, Cellular & Molecular Medicine, and Biochemistry, Microbiology and Immunology, Ottawa, Ontario, Canada.
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163
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Xia J, Inagaki Y, Sawakami T, Song P, Cai Y, Hasegawa K, Sakamoto Y, Akimitsu N, Tang W, Kokudo N. Preliminary investigation of five novel long non-coding RNAs in hepatocellular carcinoma cell lines. Biosci Trends 2016; 10:315-9. [PMID: 27499103 DOI: 10.5582/bst.2016.01140] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Hepatocellular carcinoma (HCC) is a highly prevalent cancer with a high mortality rate and HCC is always accompanied with a hepatitis B virus (HBV) infection, unlike many other types of cancers. Over the past few years, cancer-related long non-coding RNAs (lncRNAs) and virus-related lncRNAs have attracted the attention of many researchers, and a number of previous studies have examined the relationship between lncRNAs and various cancers and viruses. The current study used The Cancer Genome Atlas database to screen for lncRNAs up-regulated in HCC in order to identify cancer biomarkers. Results revealed five lncRNAs that were the most up-regulated. This result was then verified in 10 HCC cell lines and two normal liver cell lines. Quantitative real-time PCR revealed that the five lncRNAs were substantially up-regulated in HCC cell lines. Several of the five lncRNAs were expressed at higher levels in a few HCC cell lines that were infected with HBV or that were positive for its protein or DNA than in HCC cell lines that were not infected with HBV or that were negative for its protein or DNA. These findings suggest that the five lncRNAs might play a role in the progression of HCC and/or HBV infection, and these findings need to be studied in further detail.
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Affiliation(s)
- Jufeng Xia
- Hepato-Biliary-Pancreatic Surgery Division, Department of Surgery, Graduate School of Medicine, The University of Tokyo
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164
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Li J, Jin W, Qin Y, Zhao W, Chang C, Xu C. Expression Profile and Function Analysis of LncRNAs during Priming Phase of Rat Liver Regeneration. PLoS One 2016; 11:e0156128. [PMID: 27326854 PMCID: PMC4915705 DOI: 10.1371/journal.pone.0156128] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 06/06/2016] [Indexed: 01/18/2023] Open
Abstract
Emerging evidences have revealed that long non-coding RNAs (lncRNAs) functioned in a wide range of physiological and pathophysiological processes including rat liver regeneration, and could regulate gene expression in the transcriptional and post-transcriptional levels. However, the underlying mechanism for lncRNAs participation in liver regeneration is largely unknown. To define the mechanisms how the lncRNAs regulate LR, we performed bio-chip technology, high-throughput sequencing and RT-PCR to detect the expression of lncRNAs at 0, 2 and 6 h during LR after 2/3 hepatectomy (PH). The results indicated that 28 lncRNAs were involved in LR. Bioinformatics analysis predicated 465 co-expression target genes including 10 regulatory genes were related to these 28 lncRNAs. Ingenuity Pathway Analysis (IPA) was employed to analyze the signaling pathways and physiological activities that regulated by these genes, and the results suggested that these genes were potentially related to ILK, SAPK/JNK and ERK/MAPK signaling pathways, and possibly regulate many important physiological activities in LR in terms of cell proliferation, cell differentiation, cell survival, apoptosis and necrosis.
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Affiliation(s)
- Jun Li
- College of Life Science, Henan Normal University, Xinxiang 453007, Henan Province, China
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation and Henan Bioengineering Key Laboratory, Henan. Normal University, Xinxiang 453007, Henan Province, China
- Henan engineering laboratory for bioengineering and drug development, Henan Normal University, Xinxiang 453007, Henan Province, China
| | - Wei Jin
- College of Life Science, Henan Normal University, Xinxiang 453007, Henan Province, China
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation and Henan Bioengineering Key Laboratory, Henan. Normal University, Xinxiang 453007, Henan Province, China
- Henan engineering laboratory for bioengineering and drug development, Henan Normal University, Xinxiang 453007, Henan Province, China
| | - Yanli Qin
- College of Life Science, Henan Normal University, Xinxiang 453007, Henan Province, China
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation and Henan Bioengineering Key Laboratory, Henan. Normal University, Xinxiang 453007, Henan Province, China
- Henan engineering laboratory for bioengineering and drug development, Henan Normal University, Xinxiang 453007, Henan Province, China
| | - Weiming Zhao
- College of Life Science, Henan Normal University, Xinxiang 453007, Henan Province, China
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation and Henan Bioengineering Key Laboratory, Henan. Normal University, Xinxiang 453007, Henan Province, China
- Henan engineering laboratory for bioengineering and drug development, Henan Normal University, Xinxiang 453007, Henan Province, China
| | - Cuifang Chang
- College of Life Science, Henan Normal University, Xinxiang 453007, Henan Province, China
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation and Henan Bioengineering Key Laboratory, Henan. Normal University, Xinxiang 453007, Henan Province, China
- Henan engineering laboratory for bioengineering and drug development, Henan Normal University, Xinxiang 453007, Henan Province, China
- * E-mail: (CFC); (CSX)
| | - Cunshuan Xu
- College of Life Science, Henan Normal University, Xinxiang 453007, Henan Province, China
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation and Henan Bioengineering Key Laboratory, Henan. Normal University, Xinxiang 453007, Henan Province, China
- Henan engineering laboratory for bioengineering and drug development, Henan Normal University, Xinxiang 453007, Henan Province, China
- * E-mail: (CFC); (CSX)
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165
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Li W, Xie P, Ruan WH. Overexpression of lncRNA UCA1 promotes osteosarcoma progression and correlates with poor prognosis. J Bone Oncol 2016; 5:80-5. [PMID: 27335776 PMCID: PMC4908186 DOI: 10.1016/j.jbo.2016.05.003] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2016] [Accepted: 05/06/2016] [Indexed: 10/28/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) have been proved to play important roles in the tumorigenesis and development of several human malignancies. Our study aims to investigate the expression and function of lncRNA-UCA1 in osteosarcoma. lncRNA-UCA1 expression was detected in osteosarcoma tissues and cell lines by using qRT-PCR. Association between lncRNA-UCA1 levels and clinicopathological factors and patient's prognosis was analyzed. The roles of lncRNA-UCA1 in regulating osteosarcoma cell proliferation, apoptosis, migration, and invasion were evaluated in vitro. We found that lncRNA-UCA1 expression was upregulated in osteosarcoma tissues and cell lines. High lncRNA-UCA1 expression was significantly correlated with large tumor size, high tumor grade, positive distant metastasis, and advanced clinical stage. Multivariate regression analysis identified lncRNA-UCA1 overexpression as an independent unfavorable prognostic factor. lncRNA-UCA1 knockdown inhibited osteosarcoma cell proliferation, promoted cell apoptosis, and suppressed cell invasion and migration, whereas lncRNA-UCA1 overexpression showed opposite effects. These findings suggested that lncRNA-UCA1 may contribute to osteosarcoma initiation and progression, and would be not only a novel prognostic marker but also a potential therapeutic target for this disease.
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Affiliation(s)
- Wei Li
- Department of spine surgery, Hanzhong Municipal Central Hospital, Hanzhong 723000, Shaanxi Province, China
| | - Peng Xie
- Department of bone and joint trauma, Hanzhong Municipal Central Hospital, Hanzhong 723000, Shaanxi Province, China
| | - Wen-hui Ruan
- Department of bone and joint trauma, Hanzhong Municipal Central Hospital, Hanzhong 723000, Shaanxi Province, China
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166
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Long noncoding RNA signatures define oncogenic subtypes in T-cell acute lymphoblastic leukemia. Leukemia 2016; 30:1927-30. [PMID: 27168467 DOI: 10.1038/leu.2016.82] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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167
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Peng H, Ishida M, Li L, Saito A, Kamiya A, Hamilton JP, Fu R, Olaru AV, An F, Popescu I, Iacob R, Dima S, Alexandrescu ST, Grigorie R, Nastase A, Berindan-Neagoe I, Tomuleasa C, Graur F, Zaharia F, Torbenson MS, Mezey E, Lu M, Selaru FM. Pseudogene INTS6P1 regulates its cognate gene INTS6 through competitive binding of miR-17-5p in hepatocellular carcinoma. Oncotarget 2016; 6:5666-77. [PMID: 25686840 PMCID: PMC4467393 DOI: 10.18632/oncotarget.3290] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Accepted: 01/02/2015] [Indexed: 12/13/2022] Open
Abstract
The complex regulation of tumor suppressive gene and its pseudogenes play key roles in the pathogenesis of hepatocellular cancer (HCC). However, the roles played by pseudogenes in the pathogenesis of HCC are still incompletely elucidated. This study identifies the putative tumor suppressor INTS6 and its pseudogene INTS6P1 in HCC through the whole genome microarray expression. Furthermore, the functional studies – include growth curves, cell death, migration assays and in vivo studies – verify the tumor suppressive roles of INTS6 and INTS6P1 in HCC. Finally, the mechanistic experiments indicate that INTS6 and INTS6P1 are reciprocally regulated through competition for oncomiR-17-5p. Taken together, these findings demonstrate INTS6P1 and INTS6 exert the tumor suppressive roles through competing for oncomiR-17-5p. Our investigation of this regulatory circuit reveals novel insights into the underlying mechanisms of hepatocarcinogenesis.
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Affiliation(s)
- Haoran Peng
- Division of Gastroenterology and Hepatology, Department of Medicine, The Johns Hopkins Hospital, Baltimore, Maryland, USA.,Liver Transplantation Center, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, P.R. China
| | - Masaharu Ishida
- Division of Gastroenterology and Hepatology, Department of Medicine, The Johns Hopkins Hospital, Baltimore, Maryland, USA
| | - Ling Li
- Division of Gastroenterology and Hepatology, Department of Medicine, The Johns Hopkins Hospital, Baltimore, Maryland, USA
| | - Atsushi Saito
- Department of Psychiatry and Behavioral Sciences, The Johns Hopkins Hospital, Baltimore, Maryland, USA
| | - Atsushi Kamiya
- Department of Psychiatry and Behavioral Sciences, The Johns Hopkins Hospital, Baltimore, Maryland, USA
| | - James P Hamilton
- Division of Gastroenterology and Hepatology, Department of Medicine, The Johns Hopkins Hospital, Baltimore, Maryland, USA
| | - Rongdang Fu
- Liver Transplantation Center, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, P.R. China
| | - Alexandru V Olaru
- Division of Gastroenterology and Hepatology, Department of Medicine, The Johns Hopkins Hospital, Baltimore, Maryland, USA
| | - Fangmei An
- Department of Gastroenterology, Wuxi People's Hospital Affiliated to Nanjing Medical University, Wuxi, Jiangsu, P.R. China
| | - Irinel Popescu
- Dan Setlacec Center of General Surgery and Liver Transplantation, Fundeni Clinical Institute, Bucharest, Romania
| | - Razvan Iacob
- Dan Setlacec Center of General Surgery and Liver Transplantation, Fundeni Clinical Institute, Bucharest, Romania
| | - Simona Dima
- Dan Setlacec Center of General Surgery and Liver Transplantation, Fundeni Clinical Institute, Bucharest, Romania
| | - Sorin T Alexandrescu
- Dan Setlacec Center of General Surgery and Liver Transplantation, Fundeni Clinical Institute, Bucharest, Romania
| | - Razvan Grigorie
- Dan Setlacec Center of General Surgery and Liver Transplantation, Fundeni Clinical Institute, Bucharest, Romania
| | - Anca Nastase
- Dan Setlacec Center of General Surgery and Liver Transplantation, Fundeni Clinical Institute, Bucharest, Romania
| | - Ioana Berindan-Neagoe
- Department of Immunology, The Iuliu Hatieganu University of Medicine and Pharmacy, Cluj Napoca, Romania.,Department of Functional Genomics, The Oncology Institute Ion Chiricuta, Cluj Napoca, Romania.,The Research Center for Functional Genomics, Biomedicine and Translational Medicine, The Iuliu Hatieganu University of Medicine and Pharmacy, Cluj Napoca, Romania
| | - Ciprian Tomuleasa
- The Research Center for Functional Genomics, Biomedicine and Translational Medicine, The Iuliu Hatieganu University of Medicine and Pharmacy, Cluj Napoca, Romania.,Department of Hematology, The Oncology Institute Ion Chiricuta, Cluj Napoca, Romania
| | - Florin Graur
- Department of Surgery, The Iuliu Hatieganu University of Medicine and Pharmacy, Cluj Napoca, Romania.,Department of Surgery, Regional Institute of Gastroenterology and Hepatology "Octavian Fodor", Cluj Napoca, Romania
| | - Florin Zaharia
- Department of Surgery, The Iuliu Hatieganu University of Medicine and Pharmacy, Cluj Napoca, Romania.,Department of Surgery, Regional Institute of Gastroenterology and Hepatology "Octavian Fodor", Cluj Napoca, Romania
| | - Michael S Torbenson
- Department of Pathology, The Johns Hopkins Hospital, Baltimore, Maryland, USA
| | - Esteban Mezey
- Division of Gastroenterology and Hepatology, Department of Medicine, The Johns Hopkins Hospital, Baltimore, Maryland, USA
| | - Minqiang Lu
- Liver Transplantation Center, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, P.R. China
| | - Florin M Selaru
- Division of Gastroenterology and Hepatology, Department of Medicine, The Johns Hopkins Hospital, Baltimore, Maryland, USA.,The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins Hospital, Baltimore, Maryland, USA
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168
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Reciprocal Changes of Circulating Long Non-Coding RNAs ZFAS1 and CDR1AS Predict Acute Myocardial Infarction. Sci Rep 2016; 6:22384. [PMID: 26928231 PMCID: PMC4772828 DOI: 10.1038/srep22384] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 02/10/2016] [Indexed: 01/07/2023] Open
Abstract
This study sought to evaluate the potential of circulating long non-coding RNAs (lncRNAs) as biomarkers for acute myocardial infarction (AMI). We measured the circulating levels of 15 individual lncRNAs, known to be relevant to cardiovascular disease, using the whole blood samples collected from 103 AMI patients, 149 non-AMI subjects, and 95 healthy volunteers. We found that only two of them, Zinc finger antisense 1 (ZFAS1) and Cdr1 antisense (CDR1AS), showed significant differential expression between AMI patients and control subjects. Circulating level of ZFAS1 was significantly lower in AMI (0.74 ± 0.07) than in non-AMI subjects (1.0 ± 0.05, P < 0.0001), whereas CDR1AS showed the opposite changes with its blood level markedly higher in AMI (2.18 ± 0.24) than in non-AMI subjects (1.0 ± 0.05, P < 0.0001). When comparison was made between AMI and non-AMI, the area under ROC curve was 0.664 for ZFAS1 alone or 0.671 for CDR1AS alone, and 0.691 for ZFAS1 and CDR1AS combination. Univariate and multivariate analyses identified these two lncRNAs as independent predictors for AMI. Similar changes of circulating ZFAS1 and CDR1AS were consistently observed in an AMI mouse model. Reciprocal changes of circulating ZFAS1 and CDR1AS independently predict AMI and may be considered novel biomarkers of AMI.
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169
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Piccoli MT, Bär C, Thum T. Non-coding RNAs as modulators of the cardiac fibroblast phenotype. J Mol Cell Cardiol 2016; 92:75-81. [PMID: 26764220 DOI: 10.1016/j.yjmcc.2015.12.023] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 12/22/2015] [Accepted: 12/24/2015] [Indexed: 01/21/2023]
Abstract
Cardiac fibroblasts represent one of the most frequent cell type in the heart of rodents and humans and alterations of their phenotype have a great impact on cardiac function. Due to aging, ischemic injuries, valvular dysfunctions, hypertension and aortic stenosis, multiple signals trigger the accumulation of extracellular matrix in the cardiac interstitium and perivascular space, leading to structural and functional detrimental changes in the heart. Cardiac fibroblasts are the principal orchestrators of matrix formation and degradation and indirectly regulate cardiac hypertrophy and inflammation. Understanding the molecular bases of their action could provide tools for the treatment of cardiac remodeling. This review summarizes recent evidences on non-coding RNAs, including microRNAs and long non-coding RNAs that modulate the phenotype of cardiac fibroblasts and may serve in the future as targets for novel therapeutic strategies against cardiac fibrosis.
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Affiliation(s)
- Maria-Teresa Piccoli
- Institute of Molecular and Translational Therapeutic Strategies, Hannover Medical School, Hannover, Germany
| | - Christian Bär
- Institute of Molecular and Translational Therapeutic Strategies, Hannover Medical School, Hannover, Germany
| | - Thomas Thum
- Institute of Molecular and Translational Therapeutic Strategies, Hannover Medical School, Hannover, Germany.
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170
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Moyo B, Nicholson SA, Arbuthnot PB. The role of long non-coding RNAs in hepatitis B virus-related hepatocellular carcinoma. Virus Res 2016; 212:103-13. [DOI: 10.1016/j.virusres.2015.07.025] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 07/26/2015] [Accepted: 07/28/2015] [Indexed: 02/06/2023]
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171
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LncRNAs: key players and novel insights into cervical cancer. Tumour Biol 2015; 37:2779-88. [PMID: 26715267 DOI: 10.1007/s13277-015-4663-9] [Citation(s) in RCA: 157] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 12/16/2015] [Indexed: 01/17/2023] Open
Abstract
Cervical cancer contributed the second highest number of deaths in female cancers, exceeded only by breast cancer, carrying high risks of morbidity and mortality. There was a great need and urgency in searching novel treatment targets and prognosis biomarkers to improve the survival rate of cervical cancer patients. Many long non-coding RNAs (lncRNAs) were emerging as pivotal regulators in various biological processes and took vitally an effect on the oncogenesis and progression of cervical cancer. In this review, we summarized the origin and overview function of lncRNAs; highlighted the roles of lncRNAs in cervical cancer in terms of prognosis and tumor progression, invasion and metastasis, apoptosis, and radio-resistance; and outlined the molecular mechanisms of lncRNAs in cervical cancer from the aspects of the interaction of lncRNAs with proteins/mRNAs (especially in HPV protein) and miRNAs, as well as RNA N-methyladenosine (m6A) methylation of lncRNAs. Meanwhile, the application of lncRNAs as biomarkers in cervical cancer prognosis and predictors for metastasis was also discussed. An overview of these researches will be valuable for broadening horizons into mechanisms, selection of meritorious biomarkers for diagnosis as well as prognosis, and future targeted therapy of cervical cancer.
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172
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Zhu H, Wang Q, Yao Y, Fang J, Sun F, Ni Y, Shen Y, Wang H, Shao S. Microarray analysis of Long non-coding RNA expression profiles in human gastric cells and tissues with Helicobacter pylori Infection. BMC Med Genomics 2015; 8:84. [PMID: 26690385 PMCID: PMC4687289 DOI: 10.1186/s12920-015-0159-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 12/11/2015] [Indexed: 01/14/2023] Open
Abstract
Background Although Helicobacter pylori (H.pylori) is the dominant gastrointestinal pathogen, the genetic and molecular mechanisms underlying H.pylori-related diseases have not been fully elucidated. Long non-coding RNAs (lncRNAs) have been identified in eukaryotic cells, many of which play important roles in regulating biological processes and pathogenesis. However, the expression changes of lncRNAs in human infected by H.pylori have been rarely reported. This study aimed to identify the dysregulated lncRNAs in human gastric epithelial cells and tissues infected with H.pylori. Methods The aberrant expression profiles of lncRNAs and mRNAs in GES-1 cells with or without H.pylori infection were explored by microarray analysis. LncRNA-mRNA co-expression network was constructed based on Pearson correlation analysis. Gene Ontology (GO) and KEGG Pathway analyses of aberrantly expressed mRNAs were performed to identify the related biological functions and pathologic pathways. The expression changes of target lncRNAs were validated by qRT-PCR to confirm the microarray data in both cells and clinical specimens. Results Three hundred three lncRNAs and 565 mRNAs were identified as aberrantly expressed transcripts (≥2 or ≤0.5-fold change, P < 0.05) in cells with H.pylori infection compared to controls. LncRNA-mRNA co-expression network showed the core lncRNAs/mRNAs which might play important roles in H.pylori-related pathogenesis. GO and KEGG analyses have indicated that the functions of aberrantly expressed mRNAs in H.pylori infection were related closely with inflammation and carcinogenesis. QRT-PCR data confirmed the expression pattern of 8 (n345630, XLOC_004787, n378726, LINC00473, XLOC_005517, LINC00152, XLOC_13370, and n408024) lncRNAs in infected cells. Additionally, four down-regulated (n345630, XLOC_004787, n378726, and LINC00473) lncRNAs were verified in H.pylori-positive gastric samples. Conclusion Our study provided a preliminary exploration of lncRNAs expression profiles in H.pylori-infected cells by microarray. These dysregulated lncRNAs might contribute to the pathological processes during H.pylori infection. Electronic supplementary material The online version of this article (doi:10.1186/s12920-015-0159-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hong Zhu
- School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu, 212013, China.
| | - Qiang Wang
- Department of Gastroenterology, The Second People's Hospital of Changzhou, Changzhou, Jiangsu, 213003, China.
| | - Yizheng Yao
- School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu, 212013, China.
| | - Jian Fang
- School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu, 212013, China.
| | - Fengying Sun
- School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu, 212013, China.
| | - Ying Ni
- School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu, 212013, China.
| | - Yixin Shen
- School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu, 212013, China.
| | - Hua Wang
- School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu, 212013, China.
| | - Shihe Shao
- School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu, 212013, China.
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173
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Mehta SL, Kim T, Vemuganti R. Long Noncoding RNA FosDT Promotes Ischemic Brain Injury by Interacting with REST-Associated Chromatin-Modifying Proteins. J Neurosci 2015; 35:16443-9. [PMID: 26674869 PMCID: PMC4679824 DOI: 10.1523/jneurosci.2943-15.2015] [Citation(s) in RCA: 108] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 10/15/2015] [Accepted: 11/14/2015] [Indexed: 12/17/2022] Open
Abstract
Ischemia induces extensive temporal changes in cerebral transcriptome that influences the neurologic outcome after stroke. In addition to protein-coding RNAs, many classes of noncoding RNAs, including long noncoding RNAs (LncRNAs), also undergo changes in the poststroke brain. We currently evaluated the functional significance of an LncRNA called Fos downstream transcript (FosDT) that is cogenic with Fos gene. Following transient middle cerebral artery occlusion (MCAO) in adult rats, expression of FosDT and Fos was induced. FosDT knockdown significantly ameliorated the postischemic motor deficits and reduced the infarct volume. Focal ischemia also increased FosDT binding to chromatin-modifying proteins (CMPs) Sin3a and coREST (corepressors of the transcription factor REST). Furthermore, FosDT knockdown derepressed REST-downstream genes GRIA2, NFκB2, and GRIN1 in the postischemic brain. Thus, FosDT induction and its interactions with REST-associated CMPs, and the resulting regulation of REST-downstream genes might modulate ischemic brain damage. LncRNAs, such as FosDT, can be therapeutically targeted to minimize poststroke brain damage. SIGNIFICANCE STATEMENT Mammalian brain is abundantly enriched with long noncoding RNAs (LncRNAs). Functional roles of LncRNAs in normal and pathological states are not yet understood. This study identified that LncRNA FosDT induced after transient focal ischemia modulates poststroke behavioral deficits and brain damage. These effects of FosDT in part are due to its interactions with chromatin-modifying proteins Sin3a and coREST (corepressors of the transcription factor REST) and subsequent derepression of REST-downstream genes GRIA2, NFκB2, and GRIN1. Therefore, LncRNA-mediated epigenetic remodeling could determine stroke outcome.
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Affiliation(s)
| | - TaeHee Kim
- Department of Neurological Surgery, Neuroscience Training Program, and
| | - Raghu Vemuganti
- Department of Neurological Surgery, Neuroscience Training Program, and Cellular and Molecular Pathology Training Program, University of Wisconsin, Madison, Wisconsin 53792
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174
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Zhang F, Zhang L, Zhang C. Long noncoding RNAs and tumorigenesis: genetic associations, molecular mechanisms, and therapeutic strategies. Tumour Biol 2015; 37:163-75. [PMID: 26586396 DOI: 10.1007/s13277-015-4445-4] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 11/13/2015] [Indexed: 01/17/2023] Open
Abstract
The human genome contains a large number of nonprotein-coding sequences. Recently, new discoveries in the functions of nonprotein-coding sequences have demonstrated that the "Dark Genome" significantly contributes to human diseases, especially with regard to cancer. Of particular interest in this review are long noncoding RNAs (lncRNAs), which comprise a class of nonprotein-coding transcripts that are longer than 200 nucleotides. Accumulating evidence indicates that a large number of lncRNAs exhibit genetic associations with tumorigenesis, tumor progression, and metastasis. Our current understanding of the molecular bases of these lncRNAs that are associated with cancer indicate that they play critical roles in gene transcription, translation, and chromatin modification. Therapeutic strategies based on the targeting of lncRNAs to disrupt their expression or their functions are being developed. In this review, we briefly summarize and discuss the genetic associations and the aberrant expression of lncRNAs in cancer, with a particular focus on studies that have revealed the molecular mechanisms of lncRNAs in tumorigenesis. In addition, we also discuss different therapeutic strategies that involve the targeting of lncRNAs.
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Affiliation(s)
- Fan Zhang
- Department of Orthopedics, The first Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, 650032, China
| | - Liang Zhang
- Hong-Hui Hospital, Xi'an Jiaotong University, College of Medicine, Xi'an, Shaanxi, 710004, People's Republic of China
| | - Caiguo Zhang
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, 80045, USA.
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175
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Yang Z, Guo X, Li G, Shi Y, Li L. Long noncoding RNAs as potential biomarkers in gastric cancer: Opportunities and challenges. Cancer Lett 2015; 371:62-70. [PMID: 26577810 DOI: 10.1016/j.canlet.2015.11.011] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2015] [Revised: 11/05/2015] [Accepted: 11/05/2015] [Indexed: 02/06/2023]
Abstract
Gastric cancer (GC) is a major threat to human health, and its prognosis is poor due to the lack of appropriate biomarkers. LncRNAs are a group of non-protein-coding RNAs that regulate gene expression at the transcriptional or posttranscriptional level. LncRNAs play essential roles in GC initiation and development in the same way as oncogenes or tumour suppressor genes. Recent investigations have revealed that lncRNAs are often aberrantly expressed in GC; are involved in cell proliferation, apoptosis, migration and invasion; and correlate with the malignant phenotype of GC. LncRNAs, especially the lncRNAs present in the blood and gastric juice, show potential value as biomarkers for the diagnosis of GC or for determining disease prognosis. However, there are still many challenges to be faced before lncRNAs can be used in clinical applications. In this review, we summarise lncRNAs as the potential biomarkers for GC and the current challenges associated with the clinical application.
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Affiliation(s)
- Ziguo Yang
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong University, Jinan 250021, China
| | - Xiaobo Guo
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong University, Jinan 250021, China.
| | - Guimei Li
- Department of Pediatrics, Shandong Provincial Hospital Affiliated to Shandong University, Jinan 250021, China
| | - Yulong Shi
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong University, Jinan 250021, China
| | - Leping Li
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong University, Jinan 250021, China
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176
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Long non-coding RNA CARLo-5 expression is associated with disease progression and predicts outcome in hepatocellular carcinoma patients. Clin Exp Med 2015; 17:33-43. [PMID: 26433964 DOI: 10.1007/s10238-015-0395-9] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 09/14/2015] [Indexed: 12/30/2022]
Abstract
Recently, many studies show that long non-coding RNAs (lncRNAs) play important roles in cancer biology. Although its expression was reported dysregulated during tumorigenesis, the contributions of lncRNAs to hepatocellular carcinoma (HCC) are still largely unknown. In particular, the lncRNA CARLo-5 has a functional role in cell-cycle regulation in colon cancer, while the clinical significance and biological function of CARLo-5 in HCC remain unelucidated. In order to fill those study blanks, the expression level of CARLo-5 in human HCC specimens was tested, and its correlation with clinicopathologic features as well as the prognosis for patients with HCC was analyzed. Additionally, MTT, wound healing and transwell assays were employed to investigate the biological function of CARLo-5. The results showed that CARLo-5 levels were significantly overexpressed in HCC tissues compared to ANLT. Besides, high expression of CARLo-5 was associated with liver cirrhosis (P = 0.001), tumor number (P < 0.001), vascular invasion (P = 0.001), capsular formation (P = 0.014) and Edmondson-Steiner grade (P < 0.001), which proved that CARLo-5 was an independent risk factor for overall survival and disease-free survival. In addition, in highly metastatic HCC cell lines (HCCLM3 and MHCC97-L), CARLo-5 was up-regulated, but in lowly metastatic HCC cell lines (HepG2, SNU387), it showed down-regulated. Besides, by using gain and loss of function experiments in HCC cell lines (HCCLM3 and HepG2), the results showed that CARLo-5 overexpression significantly enhanced cell proliferation, migration and invasion in vitro. Our study also revealed that CARLo-5 was prominently up-regulated in HCC specimens and its high expression was associated with poor prognosis of HCC patients. Totally, those findings together indicate that CARLo-5 promotes proliferation and metastasis of HCC and potentially emerged as a novel therapeutic target.
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177
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Sharma V, Khurana S, Kubben N, Abdelmohsen K, Oberdoerffer P, Gorospe M, Misteli T. A BRCA1-interacting lncRNA regulates homologous recombination. EMBO Rep 2015; 16:1520-34. [PMID: 26412854 DOI: 10.15252/embr.201540437] [Citation(s) in RCA: 115] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 08/25/2015] [Indexed: 12/17/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are important players in diverse biological processes. Upon DNA damage, cells activate a complex signaling cascade referred to as the DNA damage response (DDR). Using a microarray screen, we identify here a novel lncRNA, DDSR1 (DNA damage-sensitive RNA1), which is induced upon DNA damage. DDSR1 induction is triggered in an ATM-NF-κB pathway-dependent manner by several DNA double-strand break (DSB) agents. Loss of DDSR1 impairs cell proliferation and DDR signaling and reduces DNA repair capacity by homologous recombination (HR). The HR defect in the absence of DDSR1 is marked by aberrant accumulation of BRCA1 and RAP80 at DSB sites. In line with a role in regulating HR, DDSR1 interacts with BRCA1 and hnRNPUL1, an RNA-binding protein involved in DNA end resection. Our results suggest a role for the lncRNA DDSR1 in modulating DNA repair by HR.
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Affiliation(s)
- Vivek Sharma
- National Cancer Institute, NIH, Bethesda, MD, USA
| | | | - Nard Kubben
- National Cancer Institute, NIH, Bethesda, MD, USA
| | | | | | | | - Tom Misteli
- National Cancer Institute, NIH, Bethesda, MD, USA
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178
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Huang MD, Chen WM, Qi FZ, Sun M, Xu TP, Ma P, Shu YQ. Long non-coding RNA TUG1 is up-regulated in hepatocellular carcinoma and promotes cell growth and apoptosis by epigenetically silencing of KLF2. Mol Cancer 2015; 14:165. [PMID: 26336870 PMCID: PMC4558931 DOI: 10.1186/s12943-015-0431-0] [Citation(s) in RCA: 184] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 08/11/2015] [Indexed: 12/30/2022] Open
Abstract
Background Hepatocellular carcinoma (HCC) is one of the leading causes of cancer-related death worldwide, and the biology of this cancer remains poorly understood. Recent evidence indicates that long non-coding RNAs (lncRNAs) are found to be dysregulated in a variety of cancers, including HCC. Taurine Up-regulated Gene 1 (TUG1), a 7.1-kb lncRNA, recruiting and binding to polycomb repressive complex 2 (PRC2), is found to be disregulated in non-small cell lung carcinoma (NSCLC) and esophageal squamous cell carcinoma (ESCC). However, its clinical significance and potential role in HCC remain unclear. Methods and results In this study, expression of TUG1 was analyzed in 77 HCC tissues and matched normal tissues by using quantitative polymerase chain reaction (qPCR). TUG1 expression was up-regulated in HCC tissues and the higher expression of TUG1 was significantly correlated with tumor size and Barcelona Clinic Liver Cancer (BCLC) stage. Moreover, silencing of TUG1 expression inhibited HCC cell proliferation, colony formation, tumorigenicity and induced apoptosis in HCC cell lines. We also found that TUG1 overexpression was induced by nuclear transcription factor SP1 and TUG1 could epigeneticly repress Kruppel-like factor 2 (KLF2) transcription in HCC cells by binding with PRC2 and recruiting it to KLF2 promoter region. Conclusion Our results suggest that lncRNA TUG1, as a growth regulator, may serve as a new diagnostic biomarker and therapy target for HCC. Electronic supplementary material The online version of this article (doi:10.1186/s12943-015-0431-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ming-De Huang
- Department of Medical Oncology, Huai'an First People's Hospital, Nanjing Medical University, Huai'an City, Jiangsu Province, 223301, People's Republic of China
| | - Wen-Ming Chen
- Department of Oncology, Jining No.1 People's Hospital, No.6, Jiankang Road, Jining City, Shandong Province, 272011, People's Republic of China
| | - Fu-Zhen Qi
- Department of Hepatopancreatobiliary Surgery, Huai'an First People's Hospital, Nanjing Medical University, Huai'an City, Jiangsu Province, 223300, People's Republic of China
| | - Ming Sun
- Department of Biochemistry and Molecular Biology, Nanjing Medical University, Nanjing City, Jiangsu Province, People's Republic of China
| | - Tong-Peng Xu
- Department of Oncology, First Affiliated Hospital, Nanjing Medical University, Nanjing City, Jiangsu Province, People's Republic of China
| | - Pei Ma
- Department of Oncology, First Affiliated Hospital, Nanjing Medical University, Nanjing City, Jiangsu Province, People's Republic of China
| | - Yong-Qian Shu
- Department of Oncology, First Affiliated Hospital, Nanjing Medical University, Nanjing City, Jiangsu Province, People's Republic of China.
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179
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Chen X. Predicting lncRNA-disease associations and constructing lncRNA functional similarity network based on the information of miRNA. Sci Rep 2015; 5:13186. [PMID: 26278472 PMCID: PMC4538606 DOI: 10.1038/srep13186] [Citation(s) in RCA: 150] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 07/22/2015] [Indexed: 12/16/2022] Open
Abstract
Accumulating experimental studies have indicated that lncRNAs play important roles in various critical biological process and their alterations and dysregulations have been associated with many important complex diseases. Developing effective computational models to predict potential disease-lncRNA association could benefit not only the understanding of disease mechanism at lncRNA level, but also the detection of disease biomarkers for disease diagnosis, treatment, prognosis and prevention. However, known experimentally confirmed disease-lncRNA associations are still very limited. In this study, a novel model of HyperGeometric distribution for LncRNA-Disease Association inference (HGLDA) was developed to predict lncRNA-disease associations by integrating miRNA-disease associations and lncRNA-miRNA interactions. Although HGLDA didn't rely on any known disease-lncRNA associations, it still obtained an AUC of 0.7621 in the leave-one-out cross validation. Furthermore, 19 predicted associations for breast cancer, lung cancer, and colorectal cancer were verified by biological experimental studies. Furthermore, the model of LncRNA Functional Similarity Calculation based on the information of MiRNA (LFSCM) was developed to calculate lncRNA functional similarity on a large scale by integrating disease semantic similarity, miRNA-disease associations, and miRNA-lncRNA interactions. It is anticipated that HGLDA and LFSCM could be effective biological tools for biomedical research.
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Affiliation(s)
- Xing Chen
- National Center for Mathematics and Interdisciplinary Sciences, Chinese Academy of Sciences, Beijing, 100190, China
- Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, 100190, China
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180
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Zhou M, Guo M, He D, Wang X, Cui Y, Yang H, Hao D, Sun J. A potential signature of eight long non-coding RNAs predicts survival in patients with non-small cell lung cancer. J Transl Med 2015; 13:231. [PMID: 26183581 PMCID: PMC4504221 DOI: 10.1186/s12967-015-0556-3] [Citation(s) in RCA: 150] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 06/01/2015] [Indexed: 12/15/2022] Open
Abstract
Background Accumulated evidence suggests that dysregulated expression of long non-coding RNAs (lncRNAs) may play a critical role in tumorigenesis and prognosis of cancer, indicating the potential utility of lncRNAs as cancer prognostic or diagnostic markers. However, the power of lncRNA signatures in predicting the survival of patients with non-small cell lung cancer (NSCLC) has not yet been investigated. Methods We performed an array-based transcriptional analysis of lncRNAs in large patient cohorts with NSCLC by repurposing microarray probes from the gene expression omnibus database. A risk score model was constructed based on the expression data of these eight lncRNAs in the training dataset of NSCLC patients and was subsequently validated in other two independent NSCLC datasets. The biological implications of prognostic lncRNAs were also analyzed using the functional enrichment analysis. Results An expression pattern of eight lncRNAs was found to be significantly associated with overall survival (OS) of NSCLC patients in the training dataset. With the eight-lncRNA signature, patients of the training dataset could be classified into high- and low-risk groups with significantly different OS (median survival 1.67 vs. 6.06 years, log-rank test p = 4.33E−09). The prognostic power of eight-lncRNA signature was further validated in other two non-overlapping independent NSCLC cohorts, demonstrating good reproducibility and robustness of this eight-lncRNA signature in predicting OS of NSCLC patients. Multivariate regression and stratified analysis suggested that the prognostic power of the eight-lncRNA signature was independent of clinical and pathological factors. Functional enrichment analyses revealed potential functional roles of the eight prognostic lncRNAs in tumorigenesis. Conclusions These findings indicate that the eight-lncRNA signature may be an effective independent prognostic molecular biomarker in the prediction of NSCLC patient survival. Electronic supplementary material The online version of this article (doi:10.1186/s12967-015-0556-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Meng Zhou
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, People's Republic of China. .,School of Life Sciences, Jilin University, Changchun, 130012, People's Republic of China.
| | - Maoni Guo
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, People's Republic of China.
| | - Dongfeng He
- Department of Interventional Radiology, The Affiliated Tumor Hospital of Harbin Medical University, Harbin, Heilongjiang, 150040, People's Republic of China.
| | - Xiaojun Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, People's Republic of China.
| | - Yinqiu Cui
- School of Life Sciences, Jilin University, Changchun, 130012, People's Republic of China.
| | - Haixiu Yang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, People's Republic of China.
| | - Dapeng Hao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, People's Republic of China.
| | - Jie Sun
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, People's Republic of China.
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181
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Abstract
Long noncoding RNAs (lncRNAs) are pivotal regulators of genome structure and gene expression. LncRNAs can directly interact with chromatin-modifying enzymes and nucleosome-remodeling factors to control chromatin structure and accessibility of genetic information. Moreover, lncRNA expression can be controlled by chromatin-remodeling factors, suggesting a feedback circuit of regulation. Here, we discuss the recent advances of lncRNA studies, focusing on the function and mechanism of lncRNA-chromatin interactions.
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Affiliation(s)
- Pei Han
- a Krannert Institute of Cardiology and Division of Cardiology ; Department of Medicine; Indiana University School of Medicine ; Indianapolis , IN USA.,b Division of Cardiovascular Medicine; Stanford University School of Medicine ; Stanford , CA USA
| | - Ching-Pin Chang
- a Krannert Institute of Cardiology and Division of Cardiology ; Department of Medicine; Indiana University School of Medicine ; Indianapolis , IN USA.,c Department of Biochemistry and Molecular Biology ; Indiana University School of Medicine ; Indianapolis , IN USA.,d Department of Medical and Molecular Genetics ; Indiana University School of Medicine ; Indianapolis , IN USA
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182
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Chen X, Yan CC, Luo C, Ji W, Zhang Y, Dai Q. Constructing lncRNA functional similarity network based on lncRNA-disease associations and disease semantic similarity. Sci Rep 2015; 5:11338. [PMID: 26061969 PMCID: PMC4462156 DOI: 10.1038/srep11338] [Citation(s) in RCA: 150] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 05/21/2015] [Indexed: 12/28/2022] Open
Abstract
Increasing evidence has indicated that plenty of lncRNAs play important roles in many critical biological processes. Developing powerful computational models to construct lncRNA functional similarity network based on heterogeneous biological datasets is one of the most important and popular topics in the fields of both lncRNAs and complex diseases. Functional similarity network consturction could benefit the model development for both lncRNA function inference and lncRNA-disease association identification. However, little effort has been attempted to analysis and calculate lncRNA functional similarity on a large scale. In this study, based on the assumption that functionally similar lncRNAs tend to be associated with similar diseases, we developed two novel lncRNA functional similarity calculation models (LNCSIM). LNCSIM was evaluated by introducing similarity scores into the model of Laplacian Regularized Least Squares for LncRNA–Disease Association (LRLSLDA) for lncRNA-disease association prediction. As a result, new predictive models improved the performance of LRLSLDA in the leave-one-out cross validation of various known lncRNA-disease associations datasets. Furthermore, some of the predictive results for colorectal cancer and lung cancer were verified by independent biological experimental studies. It is anticipated that LNCSIM could be a useful and important biological tool for human disease diagnosis, treatment, and prevention.
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Affiliation(s)
- Xing Chen
- 1] National Center for Mathematics and Interdisciplinary Sciences, Chinese Academy of Sciences, Beijing, 100190, China [2] Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, 100190, China
| | | | - Cai Luo
- Department of Automation, Tsinghua University, Beijing, 100084, China
| | - Wen Ji
- Institute of Computing Technology, Chinese Academy of Sciences, Beijing, 100190, China
| | - Yongdong Zhang
- Key Lab of Intelligent Information Processing of Chinese Academy of Sciences, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, 100190, China
| | - Qionghai Dai
- Department of Automation, Tsinghua University, Beijing, 100084, China
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183
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Yang ZG, Gao L, Guo XB, Shi YL. Roles of long non-coding RNAs in gastric cancer metastasis. World J Gastroenterol 2015; 21:5220-5230. [PMID: 25954095 PMCID: PMC4419062 DOI: 10.3748/wjg.v21.i17.5220] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 01/18/2015] [Accepted: 03/27/2015] [Indexed: 02/06/2023] Open
Abstract
Gastric cancer is the second leading cause of cancer-related deaths. Metastasis, which is an important element of gastric cancer, leads to a high mortality rate and to a poor prognosis. Gastric cancer metastasis has a complex progression that involves multiple biological processes. The comprehensive mechanisms of metastasis remain unclear, though traditional regulation modulates the molecular functions associated with metastasis. Long non-coding RNAs (lncRNAs) have a role in different gene regulatory pathways by epigenetic modification and by transcriptional and post-transcription regulation. lncRNAs participate in various diseases, including Alzheimer’s disease, cardiovascular disease, and cancer. The altered expressions of certain lncRNAs are linked to gastric cancer metastasis and invasion, as with tumor suppressor genes or oncogenes. Studies have partly elucidated the roles of lncRNAs as biomarkers and in therapies, as well as their gene regulatory mechanisms. However, comprehensive knowledge regarding the functional mechanisms of gene regulation in metastatic gastric cancer remains scarce. To provide a theoretical basis for therapeutic intervention in metastatic gastric cancer, we reviewed the functions of lncRNAs and their regulatory roles in gastric cancer metastasis.
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184
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Aberrant expression of UCA1 in gastric cancer and its clinical significance. Clin Transl Oncol 2015; 17:640-6. [PMID: 25903045 DOI: 10.1007/s12094-015-1290-2] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Accepted: 04/08/2015] [Indexed: 12/22/2022]
Abstract
Long noncoding RNAs (lncRNAs) have been shown to regulate tumor biology and might be used for cancer diagnosis, prognosis and potential therapeutic targets. Although up-regulation of lncRNA UCA1 (urothelial carcinoma-associated 1) in several cancers has been found, its role in gastric cancer remains elusive. The aim of this study was to detect the expression of lncRNA UCA1 in gastric cancer and its clinical association. The expression of UCA1 was detected in 112 pairs of tumorous and adjacent normal tissues from patients with gastric cancer, as well as in four gastric cancer cell lines and a human normal gastric epithelium cell line using RT-qPCR. Results showed that UCA1 expression was remarkably increased in gastric cancer tissues and cell lines compared with that in the normal control. Clinicopathologic analysis revealed that high UCA1 expression correlated with worse differentiation, tumor size, invasion depth and TNM stage in gastric cancer. Kaplan-Meier analysis showed that increased UCA1 expression contributed to poor overall survival (p = 0.017) and disease-free survival (p = 0.024) of patients. A multivariate survival analysis also indicated that UCA1 could be an independent prognostic marker. The levels of UCA1 in gastric juice from gastric patients were significantly higher than those from normal subjects (p = 0.016). Moreover, validation analysis showed that UCA1 levels were robust in differentiating gastric cancer patients from control subjects [area under the curve (AUC) = 0.721; 95 % confidence interval (CI) = 0.655-0.788, p < 0.01]. These results suggested that UCA1 might serve as a promising biomarker for early detection and prognosis prediction of gastric cancer.
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185
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Kong R, Zhang EB, Yin DD, You LH, Xu TP, Chen WM, Xia R, Wan L, Sun M, Wang ZX, De W, Zhang ZH. Long noncoding RNA PVT1 indicates a poor prognosis of gastric cancer and promotes cell proliferation through epigenetically regulating p15 and p16. Mol Cancer 2015; 14:82. [PMID: 25890171 PMCID: PMC4399399 DOI: 10.1186/s12943-015-0355-8] [Citation(s) in RCA: 264] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2014] [Accepted: 03/31/2015] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Mounting evidence indicates that long noncoding RNAs (lncRNAs) could play a pivotal role in cancer biology. However, the overall biological role and clinical significance of PVT1 in gastric carcinogenesis remains largely unknown. METHODS Expression of PVT1 was analyzed in 80 GC tissues and cell lines by qRT-PCR. The effect of PVT1 on proliferation was evaluated by MTT and colony formation assays, and cell apoptosis was evaluated by Flow-cytometric analysis. GC cells transfected with shPVT1 were injected into nude mice to study the effect of PVT1 on tumorigenesis in vivo. RIP was performed to confirm the interaction between PVT1 and EZH2. ChIP was used to study the promoter region of related genes. RESULTS The higher expression of PVT1 was significantly correlated with deeper invasion depth and advanced TNM stage. Multivariate analyses revealed that PVT1 expression served as an independent predictor for overall survival (p = 0.031). Further experiments demonstrated that PVT1 knockdown significantly inhibited the proliferation both in vitro and in vivo. Importantly, we also showed that PVT1 played a key role in G1 arrest. Moreover, we further confirmed that PVT1 was associated with enhancer of zeste homolog 2 (EZH2) and that this association was required for the repression of p15 and p16. To our knowledge, this is the first report showed that the role and the mechanism of PVT1 in the progression of gastric cancer. CONCLUSIONS Together, these results suggest that lncRNA PVT1 may serve as a candidate prognostic biomarker and target for new therapies in human gastric cancer.
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Affiliation(s)
- Rong Kong
- Clinical Medical Examination Center, Northern Jiangsu People's Hospital, Yangzhou, Jiangsu, PR China. .,Department of Biochemistry and Molecular Biology, Nanjing Medical University, Nanjing, Jiangsu, PR China.
| | - Er-bao Zhang
- Department of Biochemistry and Molecular Biology, Nanjing Medical University, Nanjing, Jiangsu, PR China.
| | - Dan-dan Yin
- Cancer Research and Therapy Center, The Second Affiliated Hospital of Southeast University, Nanjing, 210029, Jiangsu, PR China.
| | - Liang-hui You
- Nanjing Maternity and Child Health Care Institute, Nanjing Maternity and Child Health Care Hospital Affiliated with Nanjing Medical University, Nanjing, 210029, China.
| | - Tong-peng Xu
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, PR China.
| | - Wen-ming Chen
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, PR China.
| | - Rui Xia
- Department of Biochemistry and Molecular Biology, Nanjing Medical University, Nanjing, Jiangsu, PR China.
| | - Li Wan
- Department of Oncology, Second Affiliated Hospital of Nanjing Medical University, Jiangjiayuan Road, Nanjing, 210011, Jiangsu, PR China.
| | - Ming Sun
- Department of Biochemistry and Molecular Biology, Nanjing Medical University, Nanjing, Jiangsu, PR China.
| | - Zhao-xia Wang
- Department of Oncology, Second Affiliated Hospital of Nanjing Medical University, Jiangjiayuan Road, Nanjing, 210011, Jiangsu, PR China.
| | - Wei De
- Department of Biochemistry and Molecular Biology, Nanjing Medical University, Nanjing, Jiangsu, PR China.
| | - Zhi-hong Zhang
- Departments of Pathology, First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, PR China.
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186
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Piccoli MT, Gupta SK, Thum T. Noncoding RNAs as regulators of cardiomyocyte proliferation and death. J Mol Cell Cardiol 2015; 89:59-67. [PMID: 25665459 DOI: 10.1016/j.yjmcc.2015.02.002] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Revised: 01/15/2015] [Accepted: 02/01/2015] [Indexed: 11/27/2022]
Abstract
Cardiovascular diseases are currently the main cause of morbidity and mortality worldwide. Ischemic heart disease, in particular, is responsible for the majority of cardiac-related deaths. Given the negligible regenerative potential of the human myocardium, there is a strong need for therapeutic strategies aiming at enhancing cardiomyocyte survival and proliferation following injury or at inhibiting their death. MicroRNAs (miRNAs) are small non-coding RNA molecules regulating gene expression at a post-transcriptional level with important functions in cardiovascular physiology and disease. It has been demonstrated that miRNAs can influence the ability of cardiomyocytes to enter the cell cycle and/or escape from death pathways. Additionally, long non coding-RNAs could be involved in such pathways. This review summarizes recent evidences on noncoding RNAs regulating proliferation and death of cardiomyocytes representing a future therapeutic for the treatment of heart diseases. This article is part of a Special Issue entitled SI: Non-coding RNAs.
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Affiliation(s)
- Maria-Teresa Piccoli
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS), IFB-Tx, Hannover Medical School, Hannover, Germany; Excellence Cluster REBIRTH, Hannover Medical School, Hannover, Germany
| | - Shashi Kumar Gupta
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS), IFB-Tx, Hannover Medical School, Hannover, Germany
| | - Thomas Thum
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS), IFB-Tx, Hannover Medical School, Hannover, Germany; Excellence Cluster REBIRTH, Hannover Medical School, Hannover, Germany; National Heart and Lung Institute, Imperial College London, UK.
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187
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Abstract
Idiopathic pulmonary fibrosis (IPF) is a lethal chronic lung disorder with no effective treatment and a prognosis worse than that of lung cancer. Despite extensive research efforts, its etiology and pathogenesis still remain largely unknown. Current experimental evidence has shifted the disease paradigm from chronic inflammation towards the premise of abnormal epithelial wound repair in response to repeated epigenetic injurious stimuli in genetically predisposed individuals. Epigenetics is defined as the study of heritable changes in gene function by factors other than an individual's DNA sequence, providing valuable information regarding adaption of genes to environmental changes. Although cancer is the most studied disease with relevance to epigenetic modifications, recent data support the idea that epigenomic alterations may lead to variable disease phenotypes, including fibroproliferative lung disorders such as IPF. This review article summarizes the latest experimental and translational epigenetic studies in the research field of chronic lung disorders, mainly focusing on IPF, highlights current methodology limitations, and underlines future directions and perspectives.
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Affiliation(s)
- Argyrios Tzouvelekis
- Department of Internal Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, 300 Cedar St., TAC-441 South, P.O. Box 208057, New Haven, CT 06520, USA
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188
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Role of epigenetic mechanisms in epithelial-to-mesenchymal transition of breast cancer cells. Transl Res 2015; 165:126-42. [PMID: 24768944 DOI: 10.1016/j.trsl.2014.04.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Revised: 03/26/2014] [Accepted: 04/03/2014] [Indexed: 02/06/2023]
Abstract
The epithelial-to-mesenchymal transition (EMT) is a crucial process during normal development that allows dynamic and reversible shifts between epithelial and mesenchymal cell states. Cancer cells take advantage of the complex, interrelated cellular networks that regulate EMT to promote their migratory and invasive capabilities. During the past few years, evidence has accumulated that indicates that genetic mutations and changes to epigenetic mechanisms are key drivers of EMT in cancer cells. Recent studies have begun to shed light on the epigenetic reprogramming in cancer cells that enables them to switch from a noninvasive form to an invasive, metastatic form. The authors review the current knowledge of alterations of epigenetic machinery, including DNA methylation, histone modifications, nucleosome remodeling and expression of microRNAs, associated with EMT and tumor progression of breast cancer cells. Last, existing and upcoming drug therapies targeting epigenetic regulators and their potential benefit for developing novel treatment strategies are discussed.
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189
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Richard JLC, Ogawa Y. Understanding the Complex Circuitry of lncRNAs at the X-inactivation Center and Its Implications in Disease Conditions. Curr Top Microbiol Immunol 2015; 394:1-27. [PMID: 25982976 DOI: 10.1007/82_2015_443] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Balanced gene expression is a high priority in order to maintain optimal functioning since alterations and variations could result in acute consequences. X chromosome inactivation (X-inactivation) is one such strategy utilized by mammalian species to silence the extra X chromosome in females to uphold a similar level of expression between the two sexes. A functionally versatile class of molecules called long noncoding RNA (lncRNA) has emerged as key regulators of gene expression and plays important roles during development. An lncRNA that is indispensable for X-inactivation is X-inactive specific transcript (Xist), which induces a repressive epigenetic landscape and creates the inactive X chromosome (Xi). With recent advents in the field of X-inactivation, novel positive and negative lncRNA regulators of Xist such as Jpx and Tsix, respectively, have broadened the regulatory network of X-inactivation. Xist expression failure or dysregulation has been implicated in producing developmental anomalies and disease states. Subsequently, reactivation of the Xi at a later stage of development has also been associated with certain tumors. With the recent influx of information about lncRNA biology and advancements in methods to probe lncRNA, we can now attempt to understand this complex network of Xist regulation in development and disease. It has become clear that the presence of an extra set of genes could be fatal for the organism. Only by understanding the precise ways in which lncRNAs function can treatments be developed to bring aberrations under control. This chapter summarizes our current understanding and knowledge with regard to how lncRNAs are orchestrated at the X-inactivation center (Xic), with a special focus on how genetic diseases come about as a consequence of lncRNA dysregulation.
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Affiliation(s)
- John Lalith Charles Richard
- Division of Reproductive Sciences, Cincinnati Children's Hospital Medical Center; Department of Pediatrics, University of Cincinnati College of Medicine, 3333 Burnet Avenue, Cincinnati, OH, 45229, USA
| | - Yuya Ogawa
- Division of Reproductive Sciences, Cincinnati Children's Hospital Medical Center; Department of Pediatrics, University of Cincinnati College of Medicine, 3333 Burnet Avenue, Cincinnati, OH, 45229, USA.
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190
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Focusing on long noncoding RNA dysregulation in gastric cancer. Tumour Biol 2014; 36:129-41. [DOI: 10.1007/s13277-014-2894-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Accepted: 11/26/2014] [Indexed: 12/16/2022] Open
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191
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Ma L, Li A, Zou D, Xu X, Xia L, Yu J, Bajic VB, Zhang Z. LncRNAWiki: harnessing community knowledge in collaborative curation of human long non-coding RNAs. Nucleic Acids Res 2014; 43:D187-92. [PMID: 25399417 PMCID: PMC4383965 DOI: 10.1093/nar/gku1167] [Citation(s) in RCA: 103] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) perform a diversity of functions in numerous important biological processes and are implicated in many human diseases. In this report we present lncRNAWiki (http://lncrna.big.ac.cn), a wiki-based platform that is open-content and publicly editable and aimed at community-based curation and collection of information on human lncRNAs. Current related databases are dependent primarily on curation by experts, making it laborious to annotate the exponentially accumulated information on lncRNAs, which inevitably requires collective efforts in community-based curation of lncRNAs. Unlike existing databases, lncRNAWiki features comprehensive integration of information on human lncRNAs obtained from multiple different resources and allows not only existing lncRNAs to be edited, updated and curated by different users but also the addition of newly identified lncRNAs by any user. It harnesses community collective knowledge in collecting, editing and annotating human lncRNAs and rewards community-curated efforts by providing explicit authorship based on quantified contributions. LncRNAWiki relies on the underling knowledge of scientific community for collective and collaborative curation of human lncRNAs and thus has the potential to serve as an up-to-date and comprehensive knowledgebase for human lncRNAs.
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Affiliation(s)
- Lina Ma
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Ang Li
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Dong Zou
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xingjian Xu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lin Xia
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jun Yu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Vladimir B Bajic
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Zhang Zhang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
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192
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Heward JA, Lindsay MA. Long non-coding RNAs in the regulation of the immune response. Trends Immunol 2014; 35:408-19. [PMID: 25113636 PMCID: PMC7106471 DOI: 10.1016/j.it.2014.07.005] [Citation(s) in RCA: 326] [Impact Index Per Article: 32.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Revised: 07/13/2014] [Accepted: 07/16/2014] [Indexed: 11/23/2022]
Abstract
Widespread changes in lncRNA expresssion are associated with the immune response. lncRNAs regulate the inflammatory response following activation of innate immunity. lncRNAs regulate T cell differentiation and migration. The action of long non-coding RNAs is mediated via diverse mechanisms.
It is increasingly clear that long non-coding RNAs (lncRNAs) regulate a variety biological responses, and that they do so by a diverse range of mechanisms. In the field of immunology, recent publications have shown widespread changes in the expression of lncRNAs during the activation of the innate immune response and T cell development, differentiation, and activation. These lncRNAs control important aspects of immunity such as production of inflammatory mediators, differentiation, and cell migration through regulating protein–protein interactions or via their ability to basepair with RNA and DNA. We review the current understanding of the mechanism of action of these immune-related lncRNAs, discuss their impact on physiological and pathological processes, and highlight important areas of inquiry at the intersection between immunology and lncRNA biology.
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Affiliation(s)
- James A Heward
- Department of Pharmacy and Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Mark A Lindsay
- Department of Pharmacy and Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, UK.
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193
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Zane L, Sharma V, Misteli T. Common features of chromatin in aging and cancer: cause or coincidence? Trends Cell Biol 2014; 24:686-94. [PMID: 25103681 DOI: 10.1016/j.tcb.2014.07.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Revised: 06/30/2014] [Accepted: 07/01/2014] [Indexed: 02/06/2023]
Abstract
Age is a major risk factor for cancer. Alterations in DNA methylation, histone modifications, chromatin structure, and epigenetic regulatory mechanisms are prominent hallmarks of both the aging process and cancer. Intriguingly--or possibly coincidentally--several chromatin features are common between aging and cancer. Here we ask whether, and if so how, aging-associated chromatin modifications contribute to tumor susceptibility and tumorigenesis.
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Affiliation(s)
- Linda Zane
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Vivek Sharma
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tom Misteli
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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Kameswaran V, Kaestner KH. The Missing lnc(RNA) between the pancreatic β-cell and diabetes. Front Genet 2014; 5:200. [PMID: 25071830 PMCID: PMC4077016 DOI: 10.3389/fgene.2014.00200] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Accepted: 06/15/2014] [Indexed: 01/15/2023] Open
Abstract
Diabetes mellitus represents a group of complex metabolic diseases that result in impaired glucose homeostasis, which includes destruction of β-cells or the failure of these insulin-secreting cells to compensate for increased metabolic demand. Despite a strong interest in characterizing the transcriptome of the different human islet cell types to understand the molecular basis of diabetes, very little attention has been paid to the role of long non-coding RNAs (lncRNAs) and their contribution to this disease. Here we summarize the growing evidence for the potential role of these lncRNAs in β-cell function and dysregulation in diabetes, with a focus on imprinted genomic loci.
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Affiliation(s)
- Vasumathi Kameswaran
- Department of Genetics and Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania Philadelphia, PA, USA
| | - Klaus H Kaestner
- Department of Genetics and Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania Philadelphia, PA, USA
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González-Ramírez I, Soto-Reyes E, Sánchez-Pérez Y, Herrera LA, García-Cuellar C. Histones and long non-coding RNAs: the new insights of epigenetic deregulation involved in oral cancer. Oral Oncol 2014; 50:691-5. [PMID: 24844984 DOI: 10.1016/j.oraloncology.2014.04.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Revised: 04/04/2014] [Accepted: 04/20/2014] [Indexed: 01/24/2023]
Abstract
Oral squamous cell carcinoma (OSCC) is a category of aggressive malignancies that represent clinically, molecularly, and etiologically heterogeneous tumors. The majority of OSCCs are associated with tobacco and alcohol use, acting both independently and synergistically, which suggests that the environment plays an important role in carcinogenesis; however, the mechanisms associated with the development of OSCC are not well understood. It has been proposed that the epigenetic components could be implicated in the initiation and progression of OSCC. Primarily, aberrant DNA methylation patterns have been widely addressed in the study of OSCC. Diverse studies have proposed that other epigenetic processes such as post-translational histone modification, the deposition of histone variants, histone chaperones, and recently non-coding RNA, can be also involved in the development of oral cancer. In this review we focus on describing the new insights of the epigenetics processes that are related with OSCC as histones variants and long non-coding RNAs.
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Affiliation(s)
- I González-Ramírez
- Instituto Nacional de Cancerología, Subdirección de Investigación Básica, San Fernando No. 22, Tlalpan, 14080 México City, Mexico
| | - E Soto-Reyes
- Instituto Nacional de Cancerología, Subdirección de Investigación Básica, San Fernando No. 22, Tlalpan, 14080 México City, Mexico
| | - Y Sánchez-Pérez
- Instituto Nacional de Cancerología, Subdirección de Investigación Básica, San Fernando No. 22, Tlalpan, 14080 México City, Mexico
| | - L A Herrera
- Unidad de Investigación Biomédica en Cáncer, INCan; Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM)
| | - C García-Cuellar
- Instituto Nacional de Cancerología, Subdirección de Investigación Básica, San Fernando No. 22, Tlalpan, 14080 México City, Mexico.
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