351
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Biscarini S, Capauto D, Peruzzi G, Lu L, Colantoni A, Santini T, Shneider NA, Caffarelli E, Laneve P, Bozzoni I. Characterization of the lncRNA transcriptome in mESC-derived motor neurons: Implications for FUS-ALS. Stem Cell Res 2018; 27:172-179. [PMID: 29449089 DOI: 10.1016/j.scr.2018.01.037] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 12/22/2017] [Accepted: 01/15/2018] [Indexed: 12/26/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are currently recognized as crucial players in nervous system development, function and pathology. In Amyotrophic Lateral Sclerosis (ALS), identification of causative mutations in FUS and TDP-43 or hexanucleotide repeat expansion in C9ORF72 point to the essential role of aberrant RNA metabolism in neurodegeneration. In this study, by taking advantage of an in vitro differentiation system generating mouse motor neurons (MNs) from embryonic stem cells, we identified and characterized the long non-coding transcriptome of MNs. Moreover, by using mutant mouse MNs carrying the equivalent of one of the most severe ALS-associated FUS alleles (P517L), we identified lncRNAs affected by this mutation. Comparative analysis with human MNs derived in vitro from induced pluripotent stem cells indicated that candidate lncRNAs are conserved between mouse and human. Our work provides a global view of the long non-coding transcriptome of MN, as a prerequisite toward the comprehension of the still poorly characterized non-coding side of MN physiopathology.
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Affiliation(s)
- Silvia Biscarini
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Rome, Italy.
| | - Davide Capauto
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Rome, Italy.
| | - Giovanna Peruzzi
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Rome, Italy.
| | - Lei Lu
- Department of Neurology, Center for Motor Neuron Biology and Disease, Columbia University, New York, NY, USA.
| | - Alessio Colantoni
- Department of Biology and Biotechnology, Sapienza University of Rome, Italy.
| | - Tiziana Santini
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Rome, Italy.
| | - Neil A Shneider
- Department of Neurology, Center for Motor Neuron Biology and Disease, Columbia University, New York, NY, USA.
| | - Elisa Caffarelli
- Institute of Molecular Biology and Pathology of CNR, Rome, Italy.
| | - Pietro Laneve
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Rome, Italy.
| | - Irene Bozzoni
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Rome, Italy; Department of Biology and Biotechnology, Sapienza University of Rome, Italy; Institute of Molecular Biology and Pathology of CNR, Rome, Italy; Institute Pasteur Fondazione Cenci-Bolognetti, Sapienza University of Rome, Italy.
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352
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Hu H, Wang Y, Ding X, He Y, Lu Z, Wu P, Tian L, Yuan H, Liu D, Shi G, Xia T, Yin J, Cai B, Miao Y, Jiang K. Long non-coding RNA XLOC_000647 suppresses progression of pancreatic cancer and decreases epithelial-mesenchymal transition-induced cell invasion by down-regulating NLRP3. Mol Cancer 2018; 17:18. [PMID: 29386037 PMCID: PMC5793431 DOI: 10.1186/s12943-018-0761-9] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 01/05/2018] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) play an important role in the development and progression of various tumors, including pancreatic cancer (PC). Recent studies have shown that lncRNAs can 'act in cis' to regulate the expression of its neighboring genes. Previously, we used lncRNAs microarray to identify a novel lncRNA termed XLOC_000647 that was down-regulated in PC tissues. However, the expression and function of XLOC_000647 in PC remain unclear. METHODS The expression of XLOC_000647 and NLRP3 in PC specimens and cell lines were detected by quantitative real-time PCR. Transwell assays were used to determine migration and invasion of PC cells. Western blot was carried out for detection of epithelial-mesenchymal transition (EMT) markers in PC cells. The effect of XLOC_000647 on PC cells was assessed in vitro and in vivo. The function of NOD-like receptor family pyrin domain-containing 3 (NLRP3) in PC was investigated in vitro. In addition, the regulation of NLRP3 by XLOC_000647 in PC was examined in vitro. RESULTS Here, XLOC_000647 expression was down-regulated in PC tissues and cell lines. The expression level of XLOC_000647 was significantly correlated to tumor stage, lymph node metastasis, and overall survival. Overexpression of XLOC_000647 attenuated cell proliferation, invasion, and EMT in vitro and impaired tumor growth in vivo. Further, a significantly negative correlation was observed between XLOC_000647 levels and its genomic nearby gene NLRP3 in vitro and in vivo. Moreover, XLOC_000647 decreased NLRP3 by inhibiting its promoter activity. Knockdown of NLRP3 decreased proliferation of cancer cells, invasion, and EMT in vitro. Importantly, after XLOC_000647 was overexpressed, the corresponding phenotypes of cells invasion and EMT were reversed by overexpression of NLRP3. CONCLUSIONS Together, these results indicate that XLOC_000647 functions as a novel tumor suppressor of lncRNA and acts as an important regulator of NLRP3, inhibiting cell proliferation, invasion, and EMT in PC.
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Affiliation(s)
- Hao Hu
- Pancreas Center, Nanjing Medical University, 300 Guangzhou Rd, Gulou District, Nanjing, Jiangsu Province, 210029, China.,Department of Hepatopancreatobiliary Center, The Third Hospital Affiliated to Nantong University, Wuxi, 214041, China
| | - Yandong Wang
- Pancreas Center, Nanjing Medical University, 300 Guangzhou Rd, Gulou District, Nanjing, Jiangsu Province, 210029, China.,Department of General Surgery, The Second People's Hospital of Wuhu, Wuhu, 241000, China
| | - Xiangya Ding
- Department of Microbiology, Nanjing Medical University, Nanjing, 211166, China
| | - Yuan He
- Pancreas Center, Nanjing Medical University, 300 Guangzhou Rd, Gulou District, Nanjing, Jiangsu Province, 210029, China.,Department of General Surgery, Huai'an Hospital Affiliated to Xuzhou Medical University, Huai'an, 223001, China
| | - Zipeng Lu
- Pancreas Center, Nanjing Medical University, 300 Guangzhou Rd, Gulou District, Nanjing, Jiangsu Province, 210029, China.,Pancreas Institute, Nanjing Medical University, Nanjing, 210029, China
| | - Pengfei Wu
- Pancreas Center, Nanjing Medical University, 300 Guangzhou Rd, Gulou District, Nanjing, Jiangsu Province, 210029, China.,Pancreas Institute, Nanjing Medical University, Nanjing, 210029, China
| | - Lei Tian
- Pancreas Center, Nanjing Medical University, 300 Guangzhou Rd, Gulou District, Nanjing, Jiangsu Province, 210029, China.,Pancreas Institute, Nanjing Medical University, Nanjing, 210029, China
| | - Hao Yuan
- Pancreas Center, Nanjing Medical University, 300 Guangzhou Rd, Gulou District, Nanjing, Jiangsu Province, 210029, China.,Pancreas Institute, Nanjing Medical University, Nanjing, 210029, China
| | - Dongfang Liu
- Pancreas Center, Nanjing Medical University, 300 Guangzhou Rd, Gulou District, Nanjing, Jiangsu Province, 210029, China.,Pancreas Institute, Nanjing Medical University, Nanjing, 210029, China
| | - Guodong Shi
- Pancreas Center, Nanjing Medical University, 300 Guangzhou Rd, Gulou District, Nanjing, Jiangsu Province, 210029, China.,Pancreas Institute, Nanjing Medical University, Nanjing, 210029, China
| | - Tianfang Xia
- Pancreas Center, Nanjing Medical University, 300 Guangzhou Rd, Gulou District, Nanjing, Jiangsu Province, 210029, China.,Department of General Surgery, Huai'an First Hospital Affiliated to Nanjing Medical University, Huai'an, 223001, China
| | - Jie Yin
- Pancreas Center, Nanjing Medical University, 300 Guangzhou Rd, Gulou District, Nanjing, Jiangsu Province, 210029, China.,Pancreas Institute, Nanjing Medical University, Nanjing, 210029, China
| | - Baobao Cai
- Pancreas Center, Nanjing Medical University, 300 Guangzhou Rd, Gulou District, Nanjing, Jiangsu Province, 210029, China.,Pancreas Institute, Nanjing Medical University, Nanjing, 210029, China
| | - Yi Miao
- Pancreas Center, Nanjing Medical University, 300 Guangzhou Rd, Gulou District, Nanjing, Jiangsu Province, 210029, China. .,Pancreas Institute, Nanjing Medical University, Nanjing, 210029, China.
| | - Kuirong Jiang
- Pancreas Center, Nanjing Medical University, 300 Guangzhou Rd, Gulou District, Nanjing, Jiangsu Province, 210029, China. .,Pancreas Institute, Nanjing Medical University, Nanjing, 210029, China.
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353
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Guo Y, Ma Y, Hu X, Song R, Zhu L, Zhong M. Long non-coding RNA CEBPA-AS1 correlates with poor prognosis and promotes tumorigenesis via CEBPA/Bcl2 in oral squamous cell carcinoma. Cancer Biol Ther 2018; 19:205-213. [PMID: 29281558 DOI: 10.1080/15384047.2017.1416276] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Abstract
Oral squamous cell carcinoma (OSCC) is one of the most aggressive and lethal malignancies affecting the head and neck region with a general 5-year survival rate about 50%. Long non-coding RNAs (lncRNAs) are believed to participate in diverse biological processes and are emerging as convenient and minimally invasive diagnostic/prognostic/therapeutic markers. The aim of this study was to explore CEBPA-AS1 role and mechanism in OSCC tumorigenesis. In this study, CEBPA-AS1 localized in the cytoplasm and the peri-nuclear cellular compartment functioning as a potential oncogene up-regulated in OSCC was correlated with poor differentiation, lymph node metastasis and high clinical stage, which made it considered to be a prognostic biomarker. Silence of CEBPA-AS1 inhibited OSCC cells proliferation and induced cells apoptosis, migration and invasion by targeting CEBPA and via a novel pathway CEBPA/Bcl2. Our findings provided the first evidence for the lncRNA CEBPA-AS1 regulatory network in OSCC tumorigenesis, which might be helpful to improve the effects of clinical treatment in OSCC.
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Affiliation(s)
- Yan Guo
- a Department of Central Laboratory , School of Stomatology, China Medical University , Shenyang , Liaoning , China.,b Key laboratory of Oral Disease Liaoning Province , Shenyang , Liaoning , China.,c Department of Oral Biology , School of Stomatology, China Medical University , Shenyang , Liaoning , China
| | - Yuji Ma
- a Department of Central Laboratory , School of Stomatology, China Medical University , Shenyang , Liaoning , China.,b Key laboratory of Oral Disease Liaoning Province , Shenyang , Liaoning , China.,c Department of Oral Biology , School of Stomatology, China Medical University , Shenyang , Liaoning , China
| | - Xuanhao Hu
- d Department of Neurobiology , China Medical University , Shenyang , Liaoning , China
| | - Rongbo Song
- a Department of Central Laboratory , School of Stomatology, China Medical University , Shenyang , Liaoning , China.,b Key laboratory of Oral Disease Liaoning Province , Shenyang , Liaoning , China.,c Department of Oral Biology , School of Stomatology, China Medical University , Shenyang , Liaoning , China
| | - Li Zhu
- a Department of Central Laboratory , School of Stomatology, China Medical University , Shenyang , Liaoning , China.,b Key laboratory of Oral Disease Liaoning Province , Shenyang , Liaoning , China.,c Department of Oral Biology , School of Stomatology, China Medical University , Shenyang , Liaoning , China
| | - Ming Zhong
- a Department of Central Laboratory , School of Stomatology, China Medical University , Shenyang , Liaoning , China.,b Key laboratory of Oral Disease Liaoning Province , Shenyang , Liaoning , China
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354
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Tao F, Tian X, Zhang Z. The PCAT3/PCAT9-miR-203-SNAI2 axis functions as a key mediator for prostate tumor growth and progression. Oncotarget 2018; 9:12212-12225. [PMID: 29552304 PMCID: PMC5844740 DOI: 10.18632/oncotarget.24198] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 12/05/2017] [Indexed: 11/25/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) have been reported to be of great importance in the formation and progression of a wide range of human carcinomas including prostate cancer (PCa). Among them, PCAT3 and PCAT9 have been identified as two prostate tissue-specific lncRNAs and are up-regulated in PCa. However, their roles in the biological characteristics of PCa have not been fully elucidated. In the present study, our data revealed that knockdown of PCAT3 and PCAT9 suppressed cellular proliferation, invasion, migration, angiogenesis and stemness in androgen-dependent LNCaP and 22Rv1 cells. Strikingly, bioinformatics analysis predicted that both PCAT3 and PCAT9 transcripts had two conserved binding sties for miR-203. Meanwhile, dual luciferase report assays revealed that miR-203 could suppress the luciferase activities of reporter plasmids carrying the binding site of miR-203 on the mRNA of PCAT3 or PCAT9. Quantitative RT-PCR (qRT-PCR) and RNA fluorescence in situ hybridization (RNA-FISH) showed that miR-203 mimic reduced the expression of PCAT3 and PCAT9 both in LNCaP and 22Rv1 cells. We also noted that both PCAT3 and PCAT9 inhibited miR-203 expression and alleviated repression on the expression of SNAI2, a critical regulator of epithelial-mesenchymal transition directly targeted by miR-203. Functionally, silence of miR-203 or ectopic expression of SNAI2 attenuated the inhibitory effect of PCAT3 and PCAT9 knockdown on cell proliferation and migration in vitro, and xenograft growth in vivo. Taken together, our data suggested that the PCAT3/PCAT9-miR-203-SNAI2 axis may serve as a promising diagnostic and therapeutic target for PCa.
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Affiliation(s)
- Fangfang Tao
- Department of Immunology and Microbiology, Basic Medical College, Zhejiang Chinese Medical University, Hangzhou 310053, Zhejiang, People's Republic of China
| | - Xinxin Tian
- Department of Biochemistry and Biophysics, Texas A and M University and Texas AgriLife Research, College Station, TX 77843-2128, USA.,Tianjin International Joint Academy of Biomedicine (TJAB), Tianjin 300457, People's Republic of China
| | - Zhiqian Zhang
- Tianjin International Joint Academy of Biomedicine (TJAB), Tianjin 300457, People's Republic of China.,State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, People's Republic of China
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355
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Abstract
With a progressively growing elderly population, aging-associated cardiovascular diseases and other pathologies have brought great burden to the economy, society, and individuals. Therefore, identifying therapeutic targets and developing effective strategies to prevent from cardiovascular aging are highly needed. Accumulating evidences suggest that noncoding RNAs (ncRNAs) such as microRNAs and long noncoding RNAs (lncRNAs) play important roles in regulating gene expression, which contributes to many pathophysiological processes of cellular senescence, aging, and aging-related diseases in cardiovascular systems. Here we provided a general overview of ncRNAs as well as the underlying mechanisms involved in cardiovascular aging. Although the importance of ncRNAs in cardiovascular aging has been reported and commonly acknowledged, further studies are still necessary to elucidate the underlying molecular mechanisms.
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Affiliation(s)
- Yongqin Li
- Cardiac Regeneration and Ageing Lab, Institute of Cardiovascular Sciences, School of Life Science, Shanghai University, Shanghai, China
| | - Yujiao Zhu
- Cardiac Regeneration and Ageing Lab, Institute of Cardiovascular Sciences, School of Life Science, Shanghai University, Shanghai, China
| | - Guoping Li
- Cardiovascular Division of the Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Junjie Xiao
- Cardiac Regeneration and Ageing Lab, Institute of Cardiovascular Sciences, School of Life Science, Shanghai University, Shanghai, China.
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356
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Gao JR, Qin XJ, Jiang H, Gao YC, Guo MF, Jiang NN. Potential role of lncRNAs in contributing to pathogenesis of chronic glomerulonephritis based on microarray data. Gene 2017; 643:46-54. [PMID: 29199037 DOI: 10.1016/j.gene.2017.11.075] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 11/04/2017] [Accepted: 11/29/2017] [Indexed: 02/06/2023]
Abstract
BACKGROUND Chronic glomerulonephritis (CGN) is the most common form of primary glomerular disease with unclear molecular mechanisms, which related to immune-mediated inflammatory diseases. Our study intended to identify potential long non-coding RNAs (lncRNAs) and genes, and to determine the potential molecular mechanisms of CGN pathogenesis. METHODS The microarray of GSE64265 and GSE46295 were downloaded from the Gene Expression Omnibus database, GSE64265 including 3 rats control kidney tissues and 5 rats model kidney tissues, GSE46295 including 3 rats control kidney tissues and 3 rats model kidney tissues, which was on the basis of GPL1355 platform. Identification of differentially expressed lncRNAs and mRNAs were performed between the 2 groups. Gene ontology (GO) and pathway enrichment analyses were performed to analyze the biological functions and pathways for the differentially expressed mRNAs. LncRNA-mRNA weighted co-expression network was constructed using the WGCNA package to analyses for the genes in the modules. The protein-protein interaction (PPI) network was visualized. RESULTS A total of 40 significantly up-regulated and 24 down-regulated lncRNAs, 653 up-regulated and 128 down-regulated mRNAs were identified. Additionally, Cdk1, with the highest connectivity degree in PPI network, was noteworthy enriched in cell cycle. Seven lncRNAs: NONRATT026650, LOC102547664, NONRATT77021989, NONRATT012453, LOC102551856, LOC102553536 and NONRATT7047175 were observed in the modules of lncRNA-mRNA weighted co-expression network. CONCLUSIONS LncRNAs NONRATT026650, LOC102547664, NONRATT77021989, NONRATT012453, LOC102551856, LOC102553536 and NONRATT7047175 were differentially expressed and might play important roles in the development of CGN. Key genes, such as Cd44, Rftn1, Runx1, may be crucial biomarkers for CGN.
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Affiliation(s)
- Jia-Rong Gao
- Department of Pharmacy, The first affiliated hospital of Anhui university of Chinese medicine, 117 Meishan Road, Hefei, China.
| | - Xiu-Juan Qin
- Department of Pharmacy, The first affiliated hospital of Anhui university of Chinese medicine, 117 Meishan Road, Hefei, China
| | - Hui Jiang
- Department of Pharmacy, The first affiliated hospital of Anhui university of Chinese medicine, 117 Meishan Road, Hefei, China
| | - Ya-Chen Gao
- Department of Nephrology, The first affiliated hospital of Anhui university of Chinese medicine, 117 Meishan Road, Hefei, China
| | - Ming-Fei Guo
- Department of Pharmacy, The first affiliated hospital of Anhui university of Chinese medicine, 117 Meishan Road, Hefei, China
| | - Nan-Nan Jiang
- Department of Pharmacy, The first affiliated hospital of Anhui university of Chinese medicine, 117 Meishan Road, Hefei, China
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357
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Liu J, Li Q, Zhang KS, Hu B, Niu X, Zhou SM, Li SG, Luo YP, Wang Y, Deng ZF. Downregulation of the Long Non-Coding RNA Meg3 Promotes Angiogenesis After Ischemic Brain Injury by Activating Notch Signaling. Mol Neurobiol 2017; 54:8179-8190. [PMID: 27900677 PMCID: PMC5684256 DOI: 10.1007/s12035-016-0270-z] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 10/30/2016] [Indexed: 12/29/2022]
Abstract
Angiogenesis after ischemic brain injury contributes to the restoration of blood supply in the ischemic zone. Strategies to improve angiogenesis may facilitate the function recovery after stroke. Recent researches have demonstrated that dysfunction of long non-coding RNAs are associated with angiogenesis. We have previously reported that long non-coding RNAs (lncRNAs) are aberrantly expressed in ischemic stroke. However, little is known about long non-coding RNAs and theirs role in angiogenesis after stroke. In this study, we identified a rat lncRNAs, Meg3, and found that Meg3 was significantly decreased after ischemic stroke. Overexpression of Meg3 suppressed functional recovery and decreased capillary density after ischemic stroke. Downregulation of Meg3 ameliorated brain lesion and increased angiogenesis after ischemic stroke. Silencing of Meg3 resulted in a proangiogenic effect evidenced by increased endothelial cell migration, proliferation, sprouting, and tube formation. Mechanistically, we showed that Meg3 negatively regulated notch pathway both in vivo and in vitro. Inhibition of notch signaling in endothelial cells reversed the proangiogenic effect induced by Meg3 downregulation. This study revealed the function of Meg3 in ischemic stroke and elucidated its mechanism in angiogenesis after ischemic stroke.
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Affiliation(s)
- Juan Liu
- Department of Neurosurgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Qing Li
- Institute of Microsurgery on Extremities, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China.
| | - Kun-Shan Zhang
- Stem Cell Translational Research Center, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Bin Hu
- Institute of Microsurgery on Extremities, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Xin Niu
- Institute of Microsurgery on Extremities, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Shu-Min Zhou
- Institute of Microsurgery on Extremities, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Si-Guang Li
- Stem Cell Translational Research Center, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yu-Ping Luo
- Stem Cell Translational Research Center, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yang Wang
- Institute of Microsurgery on Extremities, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China.
| | - Zhi-Feng Deng
- Department of Neurosurgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China.
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358
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Pandey AD, Goswami S, Shukla S, Das S, Ghosal S, Pal M, Bandyopadhyay B, Ramachandran V, Basu N, Sood V, Pandey P, Chakrabarti J, Vrati S, Banerjee A. Correlation of altered expression of a long non-coding RNA, NEAT1, in peripheral blood mononuclear cells with dengue disease progression. J Infect 2017; 75:541-554. [PMID: 29031635 DOI: 10.1016/j.jinf.2017.09.016] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Revised: 09/16/2017] [Accepted: 09/19/2017] [Indexed: 02/01/2023]
Abstract
The association of long non-coding RNAs (lncRNAs) with dengue disease progression is currently unknown. Therefore, the present study aimed to identify lncRNAs in different categories of dengue patients and evaluate their association with dengue disease progression. Herein, we examined the expression profiles of lncRNAs and protein-coding genes between other febrile illness (OFI) and different grade of dengue patients through high-throughput RNA sequencing. We identified Nuclear Enriched Abundant Transcript 1 (NEAT1) as one of the differentially expressed lncRNAs (adjusted P ≤ 0.05 and log-fold change ≥ 2) and subsequently validated the expression by qRT-PCR. The co-expression analysis further revealed that NEAT1 and the coding gene IFI27 were highly co-expressed and negatively correlated with dengue severity. Using regression analysis, we observed that NEAT1 expression was significantly dependent on disease progression (Coefficient = -0.27750, SE Coefficient = 0.07145, and t = -3.88).Further, receiver operating characteristic (ROC) curve revealed that NEAT1 expression could discriminate DI from DS (sensitivity and specificity of 100% (95%CI: 85.69 - 97.22) and area under the curve (AUC) = 0.97). Overall, the results of this study offer the first experimental evidence demonstrating the correlation between lncRNAs and severe dengue phenotype. Monitoring NEAT1and IFI27 expression in PBMC may be useful in understanding dengue virus-induced disease progression.
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Affiliation(s)
- Abhay Deep Pandey
- Vaccine and Infectious Disease Research Center (VIDRC), Translational Health Science and Technology Institute (THSTI), Faridabad 121001, India
| | - Saptamita Goswami
- Calcutta School of Tropical Medicine (STM), Kolkata, West Bengal 700073, India
| | - Shweta Shukla
- University College of Medical Sciences (UCMS) & Guru Teg Bahadur (GTB) Hospital, Delhi 110095, India
| | - Shaoli Das
- Indian Association for the Cultivation of Science, Jadavpur, Kolkata, India
| | - Suman Ghosal
- Indian Association for the Cultivation of Science, Jadavpur, Kolkata, India
| | - Manisha Pal
- Department of Statistics, Calcutta University, Kolkata 700019, India
| | | | | | - Nandita Basu
- Calcutta School of Tropical Medicine (STM), Kolkata, West Bengal 700073, India
| | - Vikas Sood
- Vaccine and Infectious Disease Research Center (VIDRC), Translational Health Science and Technology Institute (THSTI), Faridabad 121001, India
| | - Priyanka Pandey
- National Institute of Biomedical Genomics (NIBMG), Kalyani, West Bengal 741251, India
| | | | - Sudhanshu Vrati
- Vaccine and Infectious Disease Research Center (VIDRC), Translational Health Science and Technology Institute (THSTI), Faridabad 121001, India; Regional Center for Biotechnology (RCB), Faridabad, India
| | - Arup Banerjee
- Vaccine and Infectious Disease Research Center (VIDRC), Translational Health Science and Technology Institute (THSTI), Faridabad 121001, India.
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359
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Abstract
Long non-coding RNAs (LncRNAs) are a class of endogenous RNA molecules, which have a transcribing length of over 200 nt, lack a complete functional open reading frame (ORF), and rarely encode a functional short peptide. Recent studies have revealed that disruption of LncRNAs levels correlates with several human diseases, including diabetes mellitus (DM), a complex multifactorial metabolic disorder affecting more than 400 million people worldwide. LncRNAs are emerging as pivotal regulators in various biological processes, in the progression of DM and its associated complications, involving pancreatic β-cell disorder, insulin resistance, and epigenetic regulation, etc. Further investigation into the mechanisms of action of LncRNAs in DM will be of great value in the thorough understanding of pathogenesis. However, prior to successful application of LncRNAs, further search for molecular biomarkers and drug targets to provide a new strategy for DM prevention, early diagnosis, and therapy is warranted.
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Affiliation(s)
- Xiaoyun He
- Department of Endocrinology, Affiliated Hospital of Guilin Medical University, Guilin 541001, China
- Department of Endocrinology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Chunlin Ou
- Cancer Research Institute, Central South University, Changsha 410078, China
| | - Yanhua Xiao
- Department of Endocrinology, Affiliated Hospital of Guilin Medical University, Guilin 541001, China
| | - Qing Han
- Department of Endocrinology, Affiliated Hospital of Guilin Medical University, Guilin 541001, China
| | - Hao Li
- Department of Neurology, Affiliated Hospital of Guilin Medical University, Guilin 541001, China
| | - Suxian Zhou
- Department of Endocrinology, Affiliated Hospital of Guilin Medical University, Guilin 541001, China
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360
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Drak Alsibai K, Meseure D. Tumor microenvironment and noncoding RNAs as co-drivers of epithelial-mesenchymal transition and cancer metastasis. Dev Dyn 2017; 247:405-431. [PMID: 28691356 DOI: 10.1002/dvdy.24548] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 05/31/2017] [Accepted: 06/29/2017] [Indexed: 12/13/2022] Open
Abstract
Reciprocal interactions between cancer cells and tumor microenvironment (TME) are crucial events in tumor progression and metastasis. Pervasive stromal reprogramming of TME modifies numerous cellular functions, including extracellular matrix (ECM) stiffness, inflammation, and immunity. These environmental factors allow selection of more aggressive cells that develop adaptive strategies associating plasticity and epithelial-mesenchymal transition (EMT), stem-like phenotype, invasion, immunosuppression, and resistance to therapies. EMT is a morphomolecular process that endows epithelial tumor cells with mesenchymal properties, including reduced adhesion and increased motility. Numerous studies have demonstrated involvement of noncoding RNAs (ncRNAs), such as miRNAs and lncRNAs, in tumor initiation, progression, and metastasis. NcRNAs regulate every hallmark of cancer and have now emerged as new players in induction and regulation of EMT. The reciprocal regulatory interactions between ncRNAs, TME components, and cancer cells increase the complexity of gene expression and protein translation in cancer. Thus, deeper understanding of molecular mechanisms controlling EMT will not only shed light on metastatic processes of cancer cells, but enhance development of new therapies targeting metastasis. In this review, we will provide recent findings on the role of known ncRNAs relevant to EMT and cancer metastasis and discuss the role of the interaction between ncRNAs and TME as co-drivers of EMT. Developmental Dynamics 247:405-431, 2018. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
| | - Didier Meseure
- Platform of Investigative Pathology, Curie Institute, Paris, France.,Department of Pathology, Curie Institute, Paris, France
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361
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Ren W, Chen S, Liu G, Wang X, Ye H, Xi Y. TUSC7 acts as a tumor suppressor in colorectal cancer. Am J Transl Res 2017; 9:4026-4035. [PMID: 28979678 PMCID: PMC5622247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Accepted: 05/05/2017] [Indexed: 06/07/2023]
Abstract
Increasing studies showed that long non-coding RNAs (lncRNAs) played important roles in the development and progression of tumors. Previous evidences suggested that Tumor suppressor candidate 7 (TUSC7) was involved in several tumors initiation. However, the role of TUSC7 in colorectal cancer is still unknown. In this study, we indicated that the expression of TUSC7 was downregulated in colorectal cancer cell lines and tissues. Moreover, the expression of TUSC7 was lower in the high-grade (Dukes C and D) colorectal cancer patients compared to that in the low-grade colorectal cancer patients (Dukes A and B). Colorectal cancer patients with a lower level of TUSC7 expression had worse overall survival rate. Elevated expression of TUSC7 suppressed SW480 and HT29 cell proliferation and invasion. In addition, we demonstrated that overexpression of TUSC7 inhibited the expression of miR-10a and enhanced the expression of PTEN and EphA8, which were the direct target genes of miR-10a. Furthermore, the expression of miR-10a was upregulated in colorectal cancer cell lines and tissues. TUSC7 suppressed colorectal cancer cell proliferation and invasion partly through targeting miR-10a. These results suggested that TUSC7 played as a tumor suppressor gene in colorectal cancer partly through inhibiting miR-10a expression.
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Affiliation(s)
- Weidan Ren
- Department of Anorectal Surgery, Cang Zhou Central HospitalCang Zhou, Hebei, China
| | - Shuo Chen
- Department of Colorectal Surgery, Tianjin Union Medical Center (TUMC), Tianjin People’s HospitalTianjin 300121, China
| | - Guiwei Liu
- Department of Anorectal Surgery, Cang Zhou Central HospitalCang Zhou, Hebei, China
| | - Xuesong Wang
- Department of Anorectal Surgery, Cang Zhou Central HospitalCang Zhou, Hebei, China
| | - Haopeng Ye
- Department of Anorectal Surgery, Cang Zhou Central HospitalCang Zhou, Hebei, China
| | - Yanguo Xi
- Department of Neurosurgery, Cang Zhou Central HospitalCang Zhou, Hebei, China
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362
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Chi HC, Tsai CY, Tsai MM, Yeh CT, Lin KH. Roles of Long Noncoding RNAs in Recurrence and Metastasis of Radiotherapy-Resistant Cancer Stem Cells. Int J Mol Sci 2017; 18:ijms18091903. [PMID: 28872613 PMCID: PMC5618552 DOI: 10.3390/ijms18091903] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 08/29/2017] [Accepted: 08/30/2017] [Indexed: 12/14/2022] Open
Abstract
Radiotherapy is a well-established therapeutic regimen applied to treat at least half of all cancer patients worldwide. Radioresistance of cancers or failure to treat certain tumor types with radiation is associated with enhanced local invasion, metastasis and poor prognosis. Elucidation of the biological characteristics underlying radioresistance is therefore critical to ensure the development of effective strategies to resolve this issue, which remains an urgent medical problem. Cancer stem cells (CSCs) comprise a small population of tumor cells that constitute the origin of most cancer cell types. CSCs are virtually resistant to radiotherapy, and consequently contribute to recurrence and disease progression. Metastasis is an increasing problem in resistance to cancer radiotherapy and closely associated with the morbidity and mortality rates of several cancer types. Accumulating evidence has demonstrated that radiation induces epithelial–mesenchymal transition (EMT) accompanied by increased cancer recurrence, metastasis and CSC generation. CSCs are believed to serve as the basis of metastasis. Previous studies indicate that CSCs contribute to the generation of metastasis, either in a direct or indirect manner. Moreover, the heterogeneity of CSCs may be responsible for organ specificity and considerable complexity of metastases. Long noncoding RNAs (lncRNAs) are a class of noncoding molecules over 200 nucleotides in length involved in the initiation and progression of several cancer types. Recently, lncRNAs have attracted considerable attention as novel critical regulators of cancer progression and metastasis. In the current review, we have discussed lncRNA-mediated regulation of CSCs following radiotherapy, their association with tumor metastasis and significance in radioresistance of cancer.
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Affiliation(s)
- Hsiang-Cheng Chi
- Radiation Biology Research Center, Institute for Radiological Research, Chang Gung University/Chang Gung Memorial Hospital, Linkou, Taoyuan 333, Taiwan.
| | - Chung-Ying Tsai
- Kidney Research Center and Department of Nephrology, Chang Gung Immunology Consortium, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan 333, Taiwan.
| | - Ming-Ming Tsai
- Department of Nursing, Chang-Gung University of Science and Technology, Taoyuan 333, Taiwan.
- Department of General Surgery, Chang Gung Memorial Hospital, Chiayi 613, Taiwan.
| | - Chau-Ting Yeh
- Liver Research Center, Chang Gung Memorial Hospital, Linkou, Taoyuan 333, Taiwan.
| | - Kwang-Huei Lin
- Liver Research Center, Chang Gung Memorial Hospital, Linkou, Taoyuan 333, Taiwan.
- Department of Biochemistry, College of Medicine, Chang-Gung University, Taoyuan 333, Taiwan.
- Research Center for Chinese Herbal Medicine, College of Human Ecology, Chang Gung University of Science and Technology, Taoyuan 333, Taiwan.
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363
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Zheng ZK, Pang C, Yang Y, Duan Q, Zhang J, Liu WC. Serum long noncoding RNA urothelial carcinoma-associated 1: A novel biomarker for diagnosis and prognosis of hepatocellular carcinoma. J Int Med Res 2017; 46:348-356. [PMID: 28856933 PMCID: PMC6011314 DOI: 10.1177/0300060517726441] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Objective Long noncoding RNAs (lncRNAs) offer great potential as cancer biomarkers. This study was performed to assess the applicability of serum lncRNA urothelial carcinoma-associated 1 (UCA1) as a diagnostic and/or prognostic biomarker for hepatocellular carcinoma (HCC). Methods We examined UCA1 expression in serum samples from 105 patients with HCC, 105 patients with benign liver disease (BLD), and 105 healthy volunteers using reverse-transcription polymerase chain reaction and analyzed the relationship between serum UCA1 and clinicopathological parameters of HCC as well as survival. Results Expression of serum UCA1 was significantly higher in patients with HCC and allowed for discrimination of HCC from BLD and healthy controls. High expression of serum UCA1 was significantly associated with a high tumor grade, large tumor size, positive vascular invasion, and advanced TNM stage. Multivariate analysis revealed that a high serum UCA1 level was an independent unfavorable prognostic factor for HCC. Conclusions Our results confirm the upregulation of serum UCA1 expression in HCC and indicate its clinical value as a noninvasive biomarker for HCC screening and prognostic prediction.
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Affiliation(s)
- Zhi-Kun Zheng
- 1 Department of Oncology, Xijing Hospital, The Fourth Military Medical University, Xi'an, China
| | - Cui Pang
- 1 Department of Oncology, Xijing Hospital, The Fourth Military Medical University, Xi'an, China
| | - Yang Yang
- 1 Department of Oncology, Xijing Hospital, The Fourth Military Medical University, Xi'an, China
| | - Qiong Duan
- 1 Department of Oncology, Xijing Hospital, The Fourth Military Medical University, Xi'an, China
| | - Ju Zhang
- 2 Institute of Gene Diagnosis, School of Pharmacology, The Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Wen-Chao Liu
- 1 Department of Oncology, Xijing Hospital, The Fourth Military Medical University, Xi'an, China
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364
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Zheng J, Yi D, Liu Y, Wang M, Zhu Y, Shi H. Long nonding RNA UCA1 regulates neural stem cell differentiation by controlling miR-1/Hes1 expression. Am J Transl Res 2017; 9:3696-3704. [PMID: 28861160 PMCID: PMC5575183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 03/21/2017] [Indexed: 06/07/2023]
Abstract
Neural stem cells are able to self-renew and generate glial and neuronal lineages. Neural stem cell may serve as therapeutic method for neurological disorders including spinal cord injuries, Parkinson's disease, Huntington's disease and Alzheimer's disease. Long noncoding RNAs (lncRNAs) are longer than 200 nucleotides with limited protein-coding capacity. Recent studies have demonstreated that lncRNAs play an important role in several cellular processes including cell differentiation, cell development, proliferation, apoptosis, invasion and migration. However, the role of lncRNA human urothelial carcinoma associated 1 (UCA1) in the development of neural stem cells remains unknown. In this study, we showed that the expression of UCA1 was upregulated in the neural stem cell in a time-dependent manner. Knockdown of UCA1 suppressed the neural stem cell proliferation. Inhibition of UCA1 decreased the expression of nestin and the formation of neurosphere. Moreover, knockdown of UCA1 suppressed the neural stem cell differentiation to astrocyte and promoted the neural stem cell differentiation to neuron. Furthermore, we demonstrated that knockdown of UCA1 increased the expression of miR-1 in the neural stem cell and suppressed the expresion of Hes1, which is one target gene of miR-1. In addition, ectopic expression of Hes1 could impair siUCA1-induced neural stem cells proliferation. Overexpression of Hes1 suppressed siUCA1-induced β-tubulin expression and promoted siUCA1-inhibited GFAP expression in the neural stem cell. These results suggested that UCA1 regulated the neural stem cell proliferation and differentiation through regulating Hes1 expression.
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Affiliation(s)
- Jiaolin Zheng
- Department of Neruology, The Second Hospital of Harbin Medical UniversityHarbin 150086, Heilong Jiang, China
| | - Dan Yi
- Department of Pharmacology, Rush University Medical CenterChicago IL 60612, USA
| | - Yu Liu
- Department of Neruology, The Second Hospital of Harbin Medical UniversityHarbin 150086, Heilong Jiang, China
| | - Mingqiu Wang
- Department of Neruology, The Second Hospital of Harbin Medical UniversityHarbin 150086, Heilong Jiang, China
| | - Yulan Zhu
- Department of Neruology, The Second Hospital of Harbin Medical UniversityHarbin 150086, Heilong Jiang, China
| | - Huaizhang Shi
- Department of Neurosurgery, The First Hospital of Harbin Medical UniversityHarbin 150001, Heilong Jiang, China
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365
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Fan C, Tang Y, Wang J, Xiong F, Guo C, Wang Y, Zhang S, Gong Z, Wei F, Yang L, He Y, Zhou M, Li X, Li G, Xiong W, Zeng Z. Role of long non-coding RNAs in glucose metabolism in cancer. Mol Cancer 2017; 16:130. [PMID: 28738810 PMCID: PMC5525357 DOI: 10.1186/s12943-017-0699-3] [Citation(s) in RCA: 145] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 07/11/2017] [Indexed: 02/06/2023] Open
Abstract
Long-noncoding RNAs (lncRNAs) are a group of transcripts that are longer than 200 nucleotides and do not code for proteins. However, this class of RNAs plays pivotal regulatory roles. The mechanism of their action is highly complex. Mounting evidence shows that lncRNAs can regulate cancer onset and progression in a variety of ways. They can not only regulate cancer cell proliferation, differentiation, invasion and metastasis, but can also regulate glucose metabolism in cancer cells through different ways, such as by directly regulating the glycolytic enzymes and glucose transporters (GLUTs), or indirectly modulating the signaling pathways. In this review, we summarized the role of lncRNAs in regulating glucose metabolism in cancer, which will help understand better the pathogenesis of malignant tumors. The understanding of the role of lncRNAs in glucose metabolism may help provide new therapeutic targets and novel diagnostic and prognosis markers for human cancer.
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Affiliation(s)
- Chunmei Fan
- The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health, Xiangya Hospital, Central South University, Changsha, Hunan, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan, China
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Disease Genome Research Center, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yanyan Tang
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan, China
| | - Jinpeng Wang
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan, China
| | - Fang Xiong
- The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Can Guo
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan, China
| | - Yumin Wang
- The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health, Xiangya Hospital, Central South University, Changsha, Hunan, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan, China
| | - Shanshan Zhang
- The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Zhaojian Gong
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan, China
| | - Fang Wei
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan, China
| | - Liting Yang
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan, China
| | - Yi He
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan, China
| | - Ming Zhou
- The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health, Xiangya Hospital, Central South University, Changsha, Hunan, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan, China
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Disease Genome Research Center, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xiaoling Li
- The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health, Xiangya Hospital, Central South University, Changsha, Hunan, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan, China
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Disease Genome Research Center, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Guiyuan Li
- The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health, Xiangya Hospital, Central South University, Changsha, Hunan, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan, China
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Disease Genome Research Center, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Wei Xiong
- The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health, Xiangya Hospital, Central South University, Changsha, Hunan, China.
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan, China.
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Disease Genome Research Center, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China.
| | - Zhaoyang Zeng
- The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health, Xiangya Hospital, Central South University, Changsha, Hunan, China.
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan, China.
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Disease Genome Research Center, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China.
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Abstract
Background Few long noncoding RNAs (lncRNAs) that act as oncogenic genes in breast cancer have been identified. Methods Oncogenic lncRNAs associated with tumourigenesis and worse survival outcomes were examined and validated in Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA), respectively. Then, the potential biological functions and expression regulation of these lncRNAs were studied via bioinformatics and genome data analysis. Moreover, progressive breast cancer subtype-specific lncRNAs were investigated via high-throughput sequencing in our cohort and TCGA validation. To elucidate the mechanisms of the regulation of these lncRNAs, genomic alterations from the TCGA, Broad, Sanger and BCCRC data, as well as epigenetic modifications from GEO data, were then applied and examined to meet this objective. Finally, cell proliferation assays, flow cytometry analyses and TUNEL assays were applied to validate the oncogenic roles of these lncRNAs in vitro. Results A cluster of oncogenic lncRNAs that was upregulated in breast cancer tissue and was associated with worse survival outcomes was identified. These oncogenic lncRNAs are involved in regulating immune system activation and the TGF-beta and Jak-STAT signalling pathways. Moreover, TINCR, LINC00511, and PPP1R26-AS1 were identified as subtype-specific lncRNAs associated with HER-2, triple-negative and luminal B subtypes of breast cancer, respectively. The up-regulation of these oncogenic lncRNAs is mainly caused by gene amplification in the genome in breast cancer and other solid tumours. Finally, the knockdown of TINCR, DSCAM-AS1 or HOTAIR inhibited breast cancer cell proliferation, increased apoptosis and inhibited cell cycle progression in vitro. Conclusions These findings enhance the landscape of known oncogenic lncRNAs in breast cancer and provide insights into their roles. This understanding may potentially aid in the comprehensive management of breast cancer. Electronic supplementary material The online version of this article (doi:10.1186/s12943-017-0696-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shouping Xu
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150081, China
| | - Dejia Kong
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150081, China
| | - Qianlin Chen
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150081, China
| | - Yanyan Ping
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Da Pang
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150081, China. .,Heilongjiang Academy of Medical Sciences, 157 Baojian Road, Harbin, 150086, China.
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367
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Wu Z, He Y, Li D, Fang X, Shang T, Zhang H, Zheng X. Long noncoding RNA MEG3 suppressed endothelial cell proliferation and migration through regulating miR-21. Am J Transl Res 2017; 9:3326-3335. [PMID: 28804550 PMCID: PMC5553882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 01/10/2017] [Indexed: 06/07/2023]
Abstract
Long non-coding RNAs (lncRNAs) act critical roles in many biological processes, including cell proliferation, apoptosis, development, invasion and migration. LncRNA maternally expressed gene 3 (MEG3) is found to be downregulated in several tumors; however, its role in the atherosclerosis is still unknown. In the present study, we demonstrated that MEG3 expression level was downregulated in the coronary artery disease (CAD) tissues compared to in the control tissues. We also showed that TNF-α enhanced EC cell proliferation. In addition, the expression of MEG3 was increased in EC after treated with TNF-α. Overexpression of MEG3 suppressed EC cell proliferation and inhibited the expression of cyclin D1, ki-67 and PCNA. Elevated expression of MEG3 suppressed the type I collagen, type V collagen and proteoglycan expression. In addition, we showed that elevated expression of MEG3 suppressed the miR-21 expression in the EC and promoted the expression of RhoB and PTEN, which were the direct target genes of miR-21. We demonstrated that miR-21 expression level was upregulated in the CAD tissues compared to in the control tissues. Moreover, miR-21 expression was reversely correlated with MEG3 expression in the CAD tissues. Overexpression of MEG3 suppressed EC cell proliferation and type I collagen, type V collagen and proteoglycan expression through inhibiting miR-21 expression. These results suggested that MEG3 played a critical role in regulating EC proliferation and type I collagen, type V collagen and proteoglycan expression partly through suppressing miR-21 expression.
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Affiliation(s)
- Ziheng Wu
- Department of Vascular Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang UniversityHangzhou 310000, Zhejiang, People’s Republic of China
| | - Yangyan He
- Department of Vascular Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang UniversityHangzhou 310000, Zhejiang, People’s Republic of China
| | - Donglin Li
- Department of Vascular Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang UniversityHangzhou 310000, Zhejiang, People’s Republic of China
| | - Xin Fang
- Department of Vascular Surgery, Hangzhou First People’s HospitalHangzhou 310000, People’s Republic of China
| | - Tao Shang
- Department of Vascular Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang UniversityHangzhou 310000, Zhejiang, People’s Republic of China
| | - Hongkun Zhang
- Department of Vascular Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang UniversityHangzhou 310000, Zhejiang, People’s Republic of China
| | - Xiangtao Zheng
- Department of Vascular Surgery, The First Affiliated Hospital of Wenzhou Medical UniversityWenzhou 325015, People’s Republic of China
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368
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Xu T, Hu XX, Liu XX, Wang HJ, Lin K, Pan YQ, Sun HL, Peng HX, Chen XX, Wang SK, He BS. Association between SNPs in Long Non-coding RNAs and the Risk of Female Breast Cancer in a Chinese Population. J Cancer 2017; 8:1162-1169. [PMID: 28607590 PMCID: PMC5463430 DOI: 10.7150/jca.18055] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 12/19/2016] [Indexed: 12/11/2022] Open
Abstract
Long non-coding RNAs (LncRNAs) have been reported to be involved in tumorigenesis and tumor progression. Single nucleotide polymorphisms (SNPs) in the lncRNAs also play a vital role in carcinogenesis. The aim of this study was to assess the relationships between the four selected tagSNPs (rs944289, rs3787016, rs1456315, rs7463708) in the lncRNAs and the risk of female breast cancer in a Chinese population. A case-control study was carried out involving in a total of 439 breast cancer patients and 439 age-matched healthy controls. The genotyping was performed with Sequenom MassARRAY and the expression of estrogen receptor (ER), progesterone receptor (PR) and human epidermal growth factor receptor-2 (HER-2) in tumor tissues was measured by the immunohistochemistry (IHC) assay. We found that rs3787016 TT genotype (adjusted odds ratio (OR) = 1.62, 95% confidence interval (CI) = 1.09-2.41, P = 0.018) was associated with an increased risk of female breast cancer, especially among the patients with premenopausal status (adjusted OR = 2.55, 95% CI = 1.30-4.97, P = 0.006). Moreover, a statistically significant increased risk of the rs3787016 TT genotype was observed among the patients with advanced tumor stage (Ⅲ and Ⅳ), poor histological grade (G3-G4), positive lymph node involvement, positive expression of ER and PR and negative expression of HER-2; rs7463708 GT and GT/GG genotype were associated with decreased risk of breast cancer in the subgroup of patients with postmenopausal status (GT versus (vs.) TT: adjusted OR = 0.67, 95% CI = 0.46-0.99, P = 0.043; GT/GG vs. TT: adjusted OR = 0.68, 95% CI = 0.47-0.98, P = 0.041) and tumor late-stage (GT vs. TT: adjusted OR = 0.65, 95% CI = 0.43-0.97, P = 0.037; GT/GG vs. TT: adjusted OR = 0.65, 95% CI = 0.44-0.96, P = 0.029). In short, rs3787016 TT genotype was associated with increased breast cancer risk and clinicopathologic features of the tumor, especially among premenopausal women.
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Affiliation(s)
- Tao Xu
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Xiu-Xiu Hu
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing, China.,Medical college, Southeast University, Nanjing, China
| | - Xiang-Xiang Liu
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Han-Jin Wang
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Kang Lin
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Yu-Qin Pan
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Hui-Ling Sun
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Hong-Xin Peng
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing, China.,Medical college, Southeast University, Nanjing, China
| | - Xiao-Xiang Chen
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing, China.,Medical college, Southeast University, Nanjing, China
| | - Shu-Kui Wang
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Bang-Shun He
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
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369
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Khandelwal A, Malhotra A, Jain M, Vasquez KM, Jain A. The emerging role of long non-coding RNA in gallbladder cancer pathogenesis. Biochimie 2016; 132:152-160. [PMID: 27894946 DOI: 10.1016/j.biochi.2016.11.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 11/24/2016] [Indexed: 02/08/2023]
Abstract
Gallbladder cancer (GBC) is the most common and aggressive form of biliary tract carcinoma with an alarmingly low 5-year survival rate. Despite its high mortality rate, the underlying mechanisms of GBC pathogenesis are not completely understood. Recently, from a growing volume of literature, long non-coding RNAs (lncRNAs) have emerged as key regulators of gene expression and appear to play vital roles in many human cancers. To date, a number of lncRNAs have been implicated in GBC, but their potential roles in GBC have not been systematically examined. Thus, in this review, we critically discuss the emerging roles of lncRNAs in GBC, and the pathways involved. Specifically, we note that some lncRNAs show greater expression in T1 and T2 tumor stages compared to T3 and T4 tumor stages and that their dysregulation leads to alterations in cell cycle progression and can cause an increase in GBC cell proliferation or apoptosis. In addition, some lncRNAs control the epithelial-mesenchymal transition process, while others take part in the regulation of ERK/MAPK and Ras cancer-associated signaling pathways. We also present their potential utility in diagnosis, prognosis, and/or treatment of GBC. The overall goal of this review is to stimulate interest in the role of lncRNAs in GBC, which may open new avenues in the determination of GBC pathogenesis and may lead to the development of new preventive and therapeutic strategies for GBC.
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Affiliation(s)
- Akanksha Khandelwal
- Centre for Animal Sciences, Central University of Punjab, Bathinda, Punjab, India; Centre for Biochemistry and Microbial Sciences, Central University of Punjab, Bathinda, Punjab, India
| | - Akshay Malhotra
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, HP, India
| | - Manju Jain
- Centre for Biochemistry and Microbial Sciences, Central University of Punjab, Bathinda, Punjab, India
| | - Karen M Vasquez
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, 1400 Barbara Jordan Blvd, Austin, TX, 78723, USA
| | - Aklank Jain
- Centre for Animal Sciences, Central University of Punjab, Bathinda, Punjab, India.
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370
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Hou M, Tang X, Tian F, Shi F, Liu F, Gao G. AnnoLnc: a web server for systematically annotating novel human lncRNAs. BMC Genomics 2016; 17:931. [PMID: 27852242 PMCID: PMC5112684 DOI: 10.1186/s12864-016-3287-9] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2016] [Accepted: 11/10/2016] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Long noncoding RNAs (lncRNAs) have been shown to play essential roles in almost every important biological process through multiple mechanisms. Although the repertoire of human lncRNAs has rapidly expanded, their biological function and regulation remain largely elusive, calling for a systematic and integrative annotation tool. RESULTS Here we present AnnoLnc ( http://annolnc.cbi.pku.edu.cn ), a one-stop portal for systematically annotating novel human lncRNAs. Based on more than 700 data sources and various tool chains, AnnoLnc enables a systematic annotation covering genomic location, secondary structure, expression patterns, transcriptional regulation, miRNA interaction, protein interaction, genetic association and evolution. An intuitive web interface is available for interactive analysis through both desktops and mobile devices, and programmers can further integrate AnnoLnc into their pipeline through standard JSON-based Web Service APIs. CONCLUSIONS To the best of our knowledge, AnnoLnc is the only web server to provide on-the-fly and systematic annotation for newly identified human lncRNAs. Compared with similar tools, the annotation generated by AnnoLnc covers a much wider spectrum with intuitive visualization. Case studies demonstrate the power of AnnoLnc in not only rediscovering known functions of human lncRNAs but also inspiring novel hypotheses.
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Affiliation(s)
- Mei Hou
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Center for Bioinformatics, Peking University, Beijing, 100871, P.R. China
| | - Xing Tang
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Center for Bioinformatics, Peking University, Beijing, 100871, P.R. China.,Present address: Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Feng Tian
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Center for Bioinformatics, Peking University, Beijing, 100871, P.R. China.,Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, P.R. China
| | - Fangyuan Shi
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Center for Bioinformatics, Peking University, Beijing, 100871, P.R. China
| | - Fenglin Liu
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Center for Bioinformatics, Peking University, Beijing, 100871, P.R. China
| | - Ge Gao
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Center for Bioinformatics, Peking University, Beijing, 100871, P.R. China.
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371
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Lu C, Yang L, Chen H, Shan Z. Upregulated long non-coding RNA BC032469 enhances carcinogenesis and metastasis of esophageal squamous cell carcinoma through regulating hTERT expression. Tumour Biol 2016; 37:10.1007/s13277-016-5428-9. [PMID: 27726103 DOI: 10.1007/s13277-016-5428-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 09/23/2016] [Indexed: 01/19/2023] Open
Abstract
Currently, long non-coding RNAs (lncRNAs) have been shown to have critical regulatory roles in various cancers. However, its role in esophageal squamous cell carcinoma (ESCC) remains largely unknown. Here, we focused on lncRNA BC032469, one of the lncRNAs involved in the development of ESCC. The levels of a specific differentially expressed lncRNA (termed lncRNA-BC032469) were measured in 45 paired esophageal squamous cell carcinoma tissue samples by quantitative real-time RT-PCR and then subjected to correlation analysis with clinical parameters and prognosis. The functions of lncRNA-BC032469 were evaluated by silencing and overexpressing the lncRNA in vitro and in vivo. The expression level of BC032469 in esophageal squamous cell carcinoma tissues was higher than that in the corresponding non-cancerous tissues. High BC032469 levels were correlated with lymph node metastasis, TNM stage, and tumor size and lower overall survival. Knockdown of BC032469 in TE13 and Eca109 cells inhibited cell proliferation, migration, and invasion; induced cell cycle arrest in the G0/G1 phase; and promoted apoptosis. Western blot analysis revealed that BC032469 regulated the expression of human telomerase reverse transcriptase (hTERT), which is important for cell proliferation and metastasis. Moreover, the restored expression of hTERT protein in BC032469-knockdown cells attenuated the suppressive effects of BC032469 on ESCC cells. Collectively, these results indicated that lncRNA-BC032469 is an oncogenic lncRNA that promotes tumor progression and leads us to propose that lncRNAs may serve as key regulatory hubs in ESCC development.
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Affiliation(s)
- Chaojing Lu
- Department of Thoracic Surgery, Changhai Hospital, Second Military Medical University, No 168, Changhai Rd, Shanghai, China
| | - Lixin Yang
- Department of Thoracic Surgery, Changhai Hospital, Second Military Medical University, No 168, Changhai Rd, Shanghai, China.
| | - Hezhong Chen
- Department of Thoracic Surgery, Changhai Hospital, Second Military Medical University, No 168, Changhai Rd, Shanghai, China
| | - Zhengxiang Shan
- Department of Thoracic Surgery, Changhai Hospital, Second Military Medical University, No 168, Changhai Rd, Shanghai, China
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372
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Chen X, Zhou X, Lu D, Yang X, Zhou Z, Chen X, Chen Y, He W, Feng X. Aberrantly expressed long noncoding RNAs are involved in sevoflurane-induced developing hippocampal neuronal apoptosis: a microarray related study. Metab Brain Dis 2016; 31:1031-40. [PMID: 27234990 DOI: 10.1007/s11011-016-9838-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 05/16/2016] [Indexed: 12/23/2022]
Abstract
The commonly used volatile anesthetic sevoflurane has been shown to induce widespread apoptosis in the developing brain, yet the underlying molecular mechanisms are not fully understood. Accumulating research has demonstrated that long noncoding RNAs (lncRNAs) regulate multiple biological processes, including neural development, differentiation and apoptosis. They are aberrantly expressed in multiple neurodegenerative diseases. In this study, we employed a lncRNA-mRNA microarray analysis to determine whether and how lncRNAs are involved in sevoflurane-induced hippocampal neuronal apoptosis in neonatal mice. Our data showed that a single 6-h sevoflurane exposure of P7 mice resulted in significant morphological changes and apoptosis in the hippocampus. Moreover, the microarray simultaneously revealed 817 lncRNAs and 856 of their potential coding targets that related to apoptosis, of which 31 lncRNAs (19 up and 12 down) and 25 mRNAs were significantly differentially expressed (P < 0.05) after sevoflurane exposure. Importantly, we found that Bcl2l11 (BIM), which potentiates mitochondria-dependent apoptosis and its nearby enhancer-like lncRNA ENSMUST00000136025, were both more highly expressed in sevoflurane-treated samples compared with control samples. Subsequent qRT-PCR results confirmed the changes. Further CNC network indicated that lncRNA ENSMUST00000136025 was positively correlated with Bim. Moreover, sevoflurane induced a significant increase of pro-apoptotic protein BIM and Bax but a reduction of anti-apoptotic proteins Bcl-2 in the hippocampus. Our study first demonstrates that aberrantly expressed lncRNAs play a role in sevoflurane-induced hippocampal apoptosis. We noted that up-regulated ENSMUST00000136025 highly likely induced the over-expression of BIM, which eventually promoted mitochondria-mediated apoptosis. Such findings further broaden the understanding of molecular mechanisms responsible for sevoflurane-induced neurotoxicity.
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Affiliation(s)
- Xiaohui Chen
- Department of Anesthesiology, Fujian Provincial Hospital, Fujian Provincial Clinical Medical College, Fujian Medical University, Fuzhou, 350001, China
- Department of Anesthesiology, The First Affiliated Hospital of Sun Yat-Sen University, No 58 zhongshan Road 2, Guangzhou, 510080, China
| | - Xue Zhou
- Department of Anesthesiology, The First Affiliated Hospital of Sun Yat-Sen University, No 58 zhongshan Road 2, Guangzhou, 510080, China
| | - Dihan Lu
- Department of Anesthesiology, The First Affiliated Hospital of Sun Yat-Sen University, No 58 zhongshan Road 2, Guangzhou, 510080, China
| | - Xiaoyu Yang
- Department of Anesthesiology, The First Affiliated Hospital of Sun Yat-Sen University, No 58 zhongshan Road 2, Guangzhou, 510080, China
| | - Zhibin Zhou
- Department of Anesthesiology, The First Affiliated Hospital of Sun Yat-Sen University, No 58 zhongshan Road 2, Guangzhou, 510080, China
| | - Xi Chen
- Department of Anesthesiology, The First Affiliated Hospital of Sun Yat-Sen University, No 58 zhongshan Road 2, Guangzhou, 510080, China
| | - Yanqing Chen
- Department of Anesthesiology, Fujian Provincial Hospital, Fujian Provincial Clinical Medical College, Fujian Medical University, Fuzhou, 350001, China
| | - Wen He
- Department of Cardiology, The First Affiliated Hospital of Sun Yat-Sen University, No 58 zhongshan Road 2, Guangzhou, 510080, China
| | - Xia Feng
- Department of Anesthesiology, The First Affiliated Hospital of Sun Yat-Sen University, No 58 zhongshan Road 2, Guangzhou, 510080, China.
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373
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Zhu X, Tian X, Yu C, Shen C, Yan T, Hong J, Wang Z, Fang JY, Chen H. A long non-coding RNA signature to improve prognosis prediction of gastric cancer. Mol Cancer 2016; 15:60. [PMID: 27647437 PMCID: PMC5029104 DOI: 10.1186/s12943-016-0544-0] [Citation(s) in RCA: 139] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 09/07/2016] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Increasing evidence suggests long non-coding RNAs (lncRNAs) are frequently aberrantly expressed in cancers, however, few related lncRNA signatures have been established for prediction of cancer prognosis. We aimed at developing alncRNA signature to improve prognosis prediction of gastric cancer (GC). METHODS Using a lncRNA-mining approach, we performed lncRNA expression profiling in large GC cohorts from Gene Expression Ominus (GEO), including GSE62254 data set (N = 300) and GSE15459 data set (N = 192). We established a set of 24-lncRNAs that were significantly associated with the disease free survival (DFS) in the test series. RESULTS Based on this 24-lncRNA signature, the test series patients could be classified into high-risk or low-risk subgroup with significantly different DFS (HR = 1.19, 95 % CI = 1.13-1.25, P < 0.0001). The prognostic value of this 24-lncRNA signature was confirmed in the internal validation series and another external validation series, respectively. Further analysis revealed that the prognostic value of this signature was independent of lymph node ratio (LNR) and postoperative chemotherapy. Gene set enrichment analysis (GSEA) indicated that high risk score group was associated with several cancer recurrence and metastasis associated pathways. CONCLUSIONS The identification of the prognostic lncRNAs indicates the potential roles of lncRNAs in GC biogenesis. Our results may provide an efficient classification tool for clinical prognosis evaluation of GC.
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Affiliation(s)
- Xiaoqiang Zhu
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai JiaoTong University, Shanghai Institute of Digestive Disease, 145 Middle Shandong Road, Shanghai, 200001 China
| | - Xianglong Tian
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai JiaoTong University, Shanghai Institute of Digestive Disease, 145 Middle Shandong Road, Shanghai, 200001 China
| | - Chenyang Yu
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai JiaoTong University, Shanghai Institute of Digestive Disease, 145 Middle Shandong Road, Shanghai, 200001 China
| | - Chaoqin Shen
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai JiaoTong University, Shanghai Institute of Digestive Disease, 145 Middle Shandong Road, Shanghai, 200001 China
| | - Tingting Yan
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai JiaoTong University, Shanghai Institute of Digestive Disease, 145 Middle Shandong Road, Shanghai, 200001 China
| | - Jie Hong
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai JiaoTong University, Shanghai Institute of Digestive Disease, 145 Middle Shandong Road, Shanghai, 200001 China
| | - Zheng Wang
- Department of gastrointestinal surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
| | - Jing-Yuan Fang
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai JiaoTong University, Shanghai Institute of Digestive Disease, 145 Middle Shandong Road, Shanghai, 200001 China
| | - Haoyan Chen
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai JiaoTong University, Shanghai Institute of Digestive Disease, 145 Middle Shandong Road, Shanghai, 200001 China
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374
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Sun L, Sun P, Zhou QY, Gao X, Han Q. Long noncoding RNA MALAT1 promotes uveal melanoma cell growth and invasion by silencing of miR-140. Am J Transl Res 2016; 8:3939-3946. [PMID: 27725873 PMCID: PMC5040691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 02/19/2016] [Indexed: 06/06/2023]
Abstract
Increasing evidences have demonstrated that long noncoding RNAs (LncRNAs) play a significant role in the development of tumor. However, the role of metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) in uveal melanoma remains unknown. In this study, we demonstrated that the expression of MALAT1 was upregulated in the uveal melanoma tissues compared to normal tissues. Among them, MALAT1 was upregulated in 72% (18/25) uveal melanoma tissues compared to their paired normal tissues. Knockdown of MALAT1 suppressed uveal melanoma cell proliferation, colony information, invasion and migration. Moreover, we showed that knockdown of MALAT1 promoted miR-140 expression and suppressed Slug and ADAM10 expression in the MUM-2C cell. In addition, we demonstrated that miR-140 was downregulated in the uveal melanoma tissues compared to normal tissues and cell lines. The expression level of MALAT1 was inversely correlated with the expression level of miR-140 in uveal melanoma tissues. These results suggested that MALAT1 served as an oncogenic LncRNA in the development of uveal melanoma.
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Affiliation(s)
- Lei Sun
- Department of Ophthalmology, The Fourth Hospital of Harbin Medical UniversityHarbin 150001, Heilongjiang, China
| | - Peng Sun
- Department of Ophthalmology, The First Affiliated Hospital of Jiamusi UniversityJiamusi 154002, Heilongjiang, China
| | - Qi-ying Zhou
- College of Computer Science and Technology (Network and Information Security) of Jilin UniversityChangchun 130012, Jilin, China
| | - Xiangchun Gao
- Department of Ophthalmology, The Fourth Hospital of Harbin Medical UniversityHarbin 150001, Heilongjiang, China
| | - Qing Han
- Department of Ophthalmology, The Fourth Hospital of Harbin Medical UniversityHarbin 150001, Heilongjiang, China
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375
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He A, Liu Y, Chen Z, Li J, Chen M, Liu L, Liao X, Lv Z, Zhan Y, Zhuang C, Lin J, Huang W, Mei H. Over-expression of long noncoding RNA BANCR inhibits malignant phenotypes of human bladder cancer. J Exp Clin Cancer Res 2016; 35:125. [PMID: 27514530 PMCID: PMC4981950 DOI: 10.1186/s13046-016-0397-9] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 07/14/2016] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Accumulating evidences indicated that lncRNAs play crucial regulatory roles in oncogenesis and progression of cancers. BRAF activated non-coding RNA (BANCR) has been identified to contribute to the progression of some human cancers. However, the relationship between BANCR and bladder cancer (BC) is largely unclear. METHODS BANCR expression levels in BC, paired non-cancer tissues and BC cell lines were detected by real-time quantitative RT-PCR (qRT-PCR). The relationships between BANCR expression levels and the clinical characteristics were evaluated. BANCR expression was enhanced by transfecting a pcDNA-BANCR vector. We used both CCK-8 assay and Edu assay to detect cell proliferation. We also detect cell apoptosis and migration by using ELISA assay, Flow cytometry and transwell assay, respectively. All statistical analyses were executed by using the SPSS 20.0 software. RESULTS BANCR expression levels were remarkably decreased in BC tissues compared with adjacent noncancerous tissues. BANCR expression levels in two BC cell lines were also significantly down-regulated. Clinicopathologic analysis revealed that low BANCR expression was positively correlated with TNM stage, but not associated with other clinicopathological characteristics. BANCR has been successfully overexpressed in BC cell lines (T24 and SW780) by transfecting a pcDNA-BANCR vector. Cell proliferation inhibition, apoptosis induction and migration suppression were also observed in pCDNA-BANCR-transfected T24 and SW780 cells. CONCLUSIONS These data suggested that BANCR represents a tumor suppressor player in bladder cancer, contributes to tumor proliferation, apoptosis and migration, and may serve as a new candidate biomarker and a potential therapeutic target for patients with BC.
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Affiliation(s)
- Anbang He
- Shenzhen Second People’s Hospital, Clinical Medicine College of Anhui Medical University, Shenzhen, 518039 Guangdong China
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People’s Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, 518035 China
| | - Yuchen Liu
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People’s Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, 518035 China
| | - Zhicong Chen
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People’s Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, 518035 China
- Shantou University Medical College, Shantou, 515041 China
| | - Jianfa Li
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People’s Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, 518035 China
- Shantou University Medical College, Shantou, 515041 China
| | - Mingwei Chen
- Shenzhen Second People’s Hospital, Clinical Medicine College of Anhui Medical University, Shenzhen, 518039 Guangdong China
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People’s Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, 518035 China
| | - Li Liu
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People’s Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, 518035 China
- Shantou University Medical College, Shantou, 515041 China
| | - Xinhui Liao
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People’s Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, 518035 China
| | - Zhaojie Lv
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People’s Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, 518035 China
| | - Yonghao Zhan
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People’s Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, 518035 China
- Shantou University Medical College, Shantou, 515041 China
| | - Chengle Zhuang
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People’s Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, 518035 China
- Shantou University Medical College, Shantou, 515041 China
| | - Junhao Lin
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People’s Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, 518035 China
- Shantou University Medical College, Shantou, 515041 China
| | - Weiren Huang
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People’s Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, 518035 China
| | - Hongbing Mei
- Shenzhen Second People’s Hospital, Clinical Medicine College of Anhui Medical University, Shenzhen, 518039 Guangdong China
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People’s Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, 518035 China
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376
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Jiang H, Qin XJ, Li WP, Ma R, Wang T, Li ZQ. LncRNAs expression in adjuvant-induced arthritis rats reveals the potential role of LncRNAs contributing to rheumatoid arthritis pathogenesis. Gene 2016; 593:131-142. [PMID: 27511374 DOI: 10.1016/j.gene.2016.08.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 07/28/2016] [Accepted: 08/05/2016] [Indexed: 01/16/2023]
Abstract
BACKGROUND Long non-coding RNAs (LncRNAs) are an important class of widespread molecules involved in diverse biological functions, which are exceptionally expressed in numerous types of diseases. Currently, limited study on LncRNA in rheumatoid arthritis (RA) is available. In this study, we aimed to identify the specifically expressed LncRNA that are relevant to adjuvant-induced arthritis (AA) in rats, and to explore the possible molecular mechanisms of RA pathogenesis. METHODS To identify LncRNAs specifically expressed in rheumatoid arthritis, the expression of LncRNAs in synoviums of rats from the model group (n=3) was compared with that in the control group (n=3) using Arraystar Rat LncRNA/mRNA microarray and real-time polymerase chain reaction (RT-PCR). RESULTS Up to 260 LncRNAs were found to be differentially expressed (≥1.5-fold-change) in the synoviums between AA model and the normal rats (170 up-regulated and 90 down-regulated LncRNAs in AA rats compared with normal rats). Coding-non-coding gene co-expression networks (CNC network) were drawn based on the correlation analysis between the differentially expressed LncRNAs and mRNAs. Six LncRNAs, XR_008357, U75927, MRAK046251, XR_006457, DQ266363 and MRAK003448, were selected to analyze the relationship between LncRNAs and RA via the CNC network and GO analysis. Real-time PCR result confirmed that the six LncRNAs were specifically expressed in the AA rats. CONCLUSIONS These results revealed that clusters of LncRNAs were uniquely expressed in AA rats compared with controls, which manifests that these differentially expressed LncRNAs in AA rats might play a vital role in RA development. Up-regulation or down-regulation of the six LncRNAs might contribute to the molecular mechanism underlying RA. To sum up, our study provides potential targets for treatment of RA and novel profound understanding of the pathogenesis of RA.
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Affiliation(s)
- Hui Jiang
- College of Basic Medicine, Anhui Medical University, 81 Meishan Road, Hefei, China; Department of Pharmacy, The first affiliated hospital of Anhui university of Chinese medicine, 117 Meishan Road, Hefei, China.
| | - Xiu-Juan Qin
- Department of Pharmacy, The first affiliated hospital of Anhui university of Chinese medicine, 117 Meishan Road, Hefei, China.
| | - Wei-Ping Li
- College of Basic Medicine, Anhui Medical University, 81 Meishan Road, Hefei, China.
| | - Rong Ma
- Department of Integrative Physiology and Cardiovascular Research Institute, University of North Texas Health Sciences Center, 3500 Camp Bowie Boulevard, Fort Worth, TX 76107, USA.
| | - Ting Wang
- Department of Pharmacy, The first affiliated hospital of Anhui university of Chinese medicine, 117 Meishan Road, Hefei, China.
| | - Zhu-Qing Li
- College of Basic Medicine, Anhui Medical University, 81 Meishan Road, Hefei, China.
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Abstract
OBJECTIVE In this study, we examined the relationships between the expression level of long non-coding RNA MIR31HG in bladder cancer and the clinical characteristics. METHODS A total of 55 tissue samples from patients with bladder cancer were collected, and the lncRNA MIR31HG levels in cancer, paired non-cancer tissues and BC cell lines were detected by real-time quantitative RT-PCR (qRT-PCR). The relationships between MIR31HG level and the clinical characteristics were evaluated. RESULTS MIR31HG expression was remarkably decreased in bladder cancer tissues compared with adjacent noncancerous tissues (P < 0.05). MIR31HG expression was also significantly down-regulated in four bladder cancer cell lines (P < 0.001). Clinicopathologic analysis revealed that MIR31HG expression was negatively associated with TNM stage (P = 0.010), but not with other clinicopathological characteristics. CONCLUSIONS These findings revealed that MIR31HG may function as a cancer-suppressor gene to participate in the bladder cancer carcinogenesis and development.
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Affiliation(s)
- Anbang He
- Shenzhen Second People's Hospital, Clinical Medicine College of Anhui Medical University, Shenzhen, Guangdong, China
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University Shenzhen, Guangdong, China
- Shenzhen Second People's Hospital, Clinical Medicine College of Anhui Medical University, Shenzhen, Guangdong, China
| | - Zhicong Chen
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University Shenzhen, Guangdong, China
- Shantou University Medical College, Shantou, Guangdong, China
- Shenzhen Second People's Hospital, Clinical Medicine College of Anhui Medical University, Shenzhen, Guangdong, China
| | - Hongbing Mei
- Shenzhen Second People's Hospital, Clinical Medicine College of Anhui Medical University, Shenzhen, Guangdong, China
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University Shenzhen, Guangdong, China
| | - Yuchen Liu
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University Shenzhen, Guangdong, China
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Chen M, Zhuang C, Liu Y, Li J, Dai F, Xia M, Zhan Y, Lin J, Chen Z, He A, Xu W, Zhao G, Guo Y, Cai Z, Huang W. Tetracycline-inducible shRNA targeting antisense long non-coding RNA HIF1A-AS2 represses the malignant phenotypes of bladder cancer. Cancer Lett 2016; 376:155-64. [PMID: 27018306 DOI: 10.1016/j.canlet.2016.03.037] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 03/21/2016] [Accepted: 03/21/2016] [Indexed: 02/05/2023]
Abstract
Various studies have indicated that long non-coding RNAs (lncRNAs) play vital roles in the cancer development and progression. LncRNA hypoxia inducible factor 1alpha antisense RNA-2 (HIF1A-AS2) is upregulated in gastric carcinomas and knockdown of HIF1A-AS2 expression by siRNA could inhibit cell proliferation in vitro and tumorigenesis in vivo. Inspired by these observations, we hypothesized that HIF1A-AS2 possibly plays the analogous roles in bladder cancer. In our study, we first reported that HIF1A-AS2 was up-regulated in bladder cancer tissues and cells, and HIF1A-AS2 expression level in bladder cancer tissues is positively associated with advanced clinical pathologic grade and TNM phase. Cell proliferation inhibition, cell migration suppression and apoptosis induction were observed by silencing HIF1A-AS2 in bladder cancer T24 and 5637 cells. Overexpression of HIF1A-AS2 in SV-HUC-1 cells could promote cell proliferation, cell migration and anti-apoptosis. Besides, we utilized the emerging technology of medical synthetic biology to design tetracycline-inducible small hairpin RNA (shRNA) vector which specifically silenced HIF1A-AS2 in a dosage-dependent manner to inhibit the progression of human bladder cancer. In conclusion, our data suggested that HIF1A-AS2 plays oncogenic roles and can be used as a therapeutic target for treating human bladder cancer. Synthetic "tetracycline-on" switch system that quantitatively controlled the expression of HIF1A-AS2 in bladder cancer can inhibit the progression of bladder cancer cells in a dosage-dependent manner. Our findings provide new insights into the role of the lncRNA HIF1A-AS2 in the bladder cancer.
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Affiliation(s)
- Mingwei Chen
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People's Hospital, Clinical Institute of Anhui Medical University, The First Affiliated Hospital of Shenzhen University, Shenzhen 518039, Guangdong Province, China; Department of Urology, The Fourth Affiliated Hospital of Zhejiang University School of Medicine, Yiwu 322000, Zhejiang Province, China; Anhui Medical University, Hefei 230032, Anhui Province, China
| | - Chengle Zhuang
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People's Hospital, Clinical Institute of Anhui Medical University, The First Affiliated Hospital of Shenzhen University, Shenzhen 518039, Guangdong Province, China; Shantou University Medical College, Shantou 515041, Guangdong Province, China
| | - Yuchen Liu
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People's Hospital, Clinical Institute of Anhui Medical University, The First Affiliated Hospital of Shenzhen University, Shenzhen 518039, Guangdong Province, China
| | - Jianfa Li
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People's Hospital, Clinical Institute of Anhui Medical University, The First Affiliated Hospital of Shenzhen University, Shenzhen 518039, Guangdong Province, China; Shantou University Medical College, Shantou 515041, Guangdong Province, China
| | - Fen Dai
- Anhui Medical University, Hefei 230032, Anhui Province, China
| | - Ming Xia
- Department of Urology, The Third Affiliated Hospital of Southen Medical University, Guangzhou 510630, Guangdong Province, China
| | - Yonghao Zhan
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People's Hospital, Clinical Institute of Anhui Medical University, The First Affiliated Hospital of Shenzhen University, Shenzhen 518039, Guangdong Province, China; Shantou University Medical College, Shantou 515041, Guangdong Province, China
| | - Junhao Lin
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People's Hospital, Clinical Institute of Anhui Medical University, The First Affiliated Hospital of Shenzhen University, Shenzhen 518039, Guangdong Province, China; Shantou University Medical College, Shantou 515041, Guangdong Province, China
| | - Zhicong Chen
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People's Hospital, Clinical Institute of Anhui Medical University, The First Affiliated Hospital of Shenzhen University, Shenzhen 518039, Guangdong Province, China; Shantou University Medical College, Shantou 515041, Guangdong Province, China
| | - Anbang He
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People's Hospital, Clinical Institute of Anhui Medical University, The First Affiliated Hospital of Shenzhen University, Shenzhen 518039, Guangdong Province, China; Anhui Medical University, Hefei 230032, Anhui Province, China
| | - Wen Xu
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People's Hospital, Clinical Institute of Anhui Medical University, The First Affiliated Hospital of Shenzhen University, Shenzhen 518039, Guangdong Province, China
| | - Guoping Zhao
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People's Hospital, Clinical Institute of Anhui Medical University, The First Affiliated Hospital of Shenzhen University, Shenzhen 518039, Guangdong Province, China; Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai 200000, China
| | - Yinglu Guo
- Department of Urology, Peking University First Hospital, Institute of Urology, Peking University, National Urological Cancer Center, Beijing 100034, China
| | - Zhiming Cai
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People's Hospital, Clinical Institute of Anhui Medical University, The First Affiliated Hospital of Shenzhen University, Shenzhen 518039, Guangdong Province, China; Anhui Medical University, Hefei 230032, Anhui Province, China; Shantou University Medical College, Shantou 515041, Guangdong Province, China; Department of Urology, Peking University First Hospital, Institute of Urology, Peking University, National Urological Cancer Center, Beijing 100034, China.
| | - Weiren Huang
- Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People's Hospital, Clinical Institute of Anhui Medical University, The First Affiliated Hospital of Shenzhen University, Shenzhen 518039, Guangdong Province, China; Anhui Medical University, Hefei 230032, Anhui Province, China; Shantou University Medical College, Shantou 515041, Guangdong Province, China; Department of Urology, Peking University First Hospital, Institute of Urology, Peking University, National Urological Cancer Center, Beijing 100034, China.
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379
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Wu Q, Zhou X, Han X, Zhuo Y, Zhu S, Zhao Y, Wang D. Genome-wide identification and functional analysis of long noncoding RNAs involved in the response to graphene oxide. Biomaterials 2016; 102:277-91. [PMID: 27348851 DOI: 10.1016/j.biomaterials.2016.06.041] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 06/16/2016] [Accepted: 06/19/2016] [Indexed: 11/23/2022]
Abstract
Long noncoding RNAs (lncRNAs), which are defined as noncoding RNAs having at least 200 nucleotides, can potentially regulate various biological processes. However, the roles of lncRNAs in regulating cellular response to engineered nanomaterials (ENMs) are still unclear. Using Hiseq 2000 sequencing technique, we performed a genome-wide screen to identify lncRNAs involved in the control of toxicity of graphene oxide (GO) using in vivo Caenorhabditis elegans assay system. HiSeq 2000 sequencing, followed by quantitative analysis, identified only 34 dysregulated lncRNAs in GO exposed nematodes. Bioinformatics analysis implies the biological processes and signaling pathways mediated by candidate lncRNAs involved in the control of GO toxicity. A lncRNAs-miRNAs network possibly involved in the control of GO toxicity was further raised. Moreover, we identified the shared lncRNAs based on the molecular regulation basis for chemical surface modifications and/or genetic mutations in reducing GO toxicity. We further provide direct evidence that these shared lncRNAs, linc-37 and linc-14, were involved in the control of chemical surface modifications and genetic mutations in reducing GO toxicity. linc-37 binding to transcriptional factor FOXO/DAF-16 might be important for the control of GO toxicity. Our whole-genome identification and functional analysis of lncRNAs highlights the important roles of lncRNAs based molecular mechanisms for cellular responses to ENMs in organisms.
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380
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Huang S, Qing C, Huang Z, Zhu Y. The long non-coding RNA CCAT2 is up-regulated in ovarian cancer and associated with poor prognosis. Diagn Pathol 2016; 11:49. [PMID: 27283598 PMCID: PMC4901397 DOI: 10.1186/s13000-016-0499-x] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Accepted: 06/03/2016] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Ovarian cancer is a malignant tumor with a poor prognosis. Accumulating evidence demonstrates that long non-coding RNAs (lncRNAs) are emerging regulators in cancer biology, and can be used as potential biomarkers for cancer diagnosis, prognosis and targeted therapy. The lncRNA CCAT2 (colon cancer associated transcript 2) was recently shown to be involved in several cancers; however, its role in ovarian cancer remains unknown. METHODS Expression levels of the lncRNA CCAT2 in ovarian cancer tissues, adjacent normal tissues, and cell lines were assessed by quantitative real-time PCR. Then, the associations of CCAT2 expression levels with clinicopathological features and prognosis were evaluated. In addition, CCAT2 functions in tumor progression and invasion were further determined by siRNA-induced CCAT2 silencing in vitro. RESULTS Expression levels of the lncRNA CCAT2 in ovarian cancer tissues and cell lines were significantly higher compared with values obtained for adjacent non-tumor tissues and normal ovarian epithelial cells. Interestingly, higher CCAT2 expression levels were associated with a shorter overall survival (P = 0.006) and disease-free survival (P = 0.001) in ovarian cancer patients. In addition, CCAT2 expression was positively correlated with FIGO stage (P = 0.002), tumor grade (P = 0.006) and distant metastasis (P < 0.001). Moreover, CCAT2 knockdown in ovarian cancer cells markedly suppressed cell proliferation, migration, and invasion. CONCLUSIONS The lncRNA CCAT2 is a novel factor involved in ovarian cancer progression, and constitutes a potential prognostic biomarker and therapeutic target for patients with ovarian cancer.
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Affiliation(s)
- Shuying Huang
- Department of Obstetrics and Gynecology, the First Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, China
| | - Cheng Qing
- Intensive Care Unit, the First Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, China
| | - Zikun Huang
- Department of Clinical Laboratory, the First Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, China
| | - Yuanfang Zhu
- Department of Obstetrics and Gynecology, the First Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, China. .,Department of Obstetrics and Gynecology, Shenzhen Baoan Matemal and Chlid Health Hospital, Shenzhen, 518133, Guangdong, China.
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381
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Lopez-Pajares V. Long non-coding RNA regulation of gene expression during differentiation. Pflugers Arch 2016; 468:971-81. [PMID: 26996975 DOI: 10.1007/s00424-016-1809-6] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 03/03/2016] [Accepted: 03/14/2016] [Indexed: 12/13/2022]
Abstract
Transcriptome analysis of mammalian genomes has revealed widespread transcription, much of which does not encode protein. Long non-coding RNAs (lncRNAs) are a subset of the non-coding transcriptome that are emerging as critical regulators of various cellular processes. Differentiation of stem and progenitor cells requires a careful execution of specific genetic programs, and recent studies have revealed that lncRNA expression contributes to specification of cell identity. LncRNAs participate in regulating differentiation at multiple levels of gene expression through various mechanisms of action. In this review, functional roles of lncRNAs in regulating cellular differentiation of blood, muscle, skin, cardiomyocytes, adipocytes, and neurons are discussed.
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Affiliation(s)
- Vanessa Lopez-Pajares
- Program in Epithelial Biology, Stanford University, 269 Campus Drive, Room 2150, Stanford, CA, 94305, USA.
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382
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Abstract
Aging is the universal, intrinsic, genetically-controlled, evolutionarily-conserved and time-dependent intricate biological process characterised by the cumulative decline in the physiological functions and their coordination in an organism after the attainment of adulthood resulting in the imbalance of neurological, immunological and metabolic functions of the body. Various biological processes and mechanisms along with altered levels of mRNAs and proteins have been reported to be involved in the progression of aging. It is one of the major risk factors in the patho-physiology of various diseases and disorders. Recently, the discovery of pervasive transcription of a vast pool of heterogeneous regulatory noncoding RNAs (ncRNAs), including small ncRNAs (sncRNAs) and long ncRNAs (lncRNAs), in the mammalian genome have provided an alternative way to study and explore the missing links in the aging process, its mechanism(s) and related diseases in a whole new dimension. The involvement of small noncoding RNAs in aging and age-related diseases have been extensively studied and recently reviewed. However, lncRNAs, whose function is far less explored in relation to aging, have emerged as a class of major regulators of genomic functions. Here, we have described some examples of known as well as novel lncRNAs that have been implicated in the progression of the aging process and age-related diseases. This may further stimulate research on noncoding RNAs and the aging process.
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Affiliation(s)
- Sukhleen Kour
- Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Pramod C Rath
- Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India.
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383
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Wu R, Su Y, Wu H, Dai Y, Zhao M, Lu Q. Characters, functions and clinical perspectives of long non-coding RNAs. Mol Genet Genomics 2016; 291:1013-33. [PMID: 26885843 DOI: 10.1007/s00438-016-1179-y] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2015] [Accepted: 01/26/2016] [Indexed: 02/07/2023]
Abstract
It is well established that most of the human genome and those of other mammals and plants are transcribed into RNA without protein-coding capacity, which we define as non-coding RNA. From siRNA to microRNA, whose functions and features have been well characterized, non-coding RNAs have been a popular topic in life science research over the last decade. Long non-coding RNAs (lncRNAs), however, as a novel class of transcripts, are distinguished from these other small RNAs. Recent studies have revealed a diverse population of lncRNAs with different sizes and functions across different species. These populations are expressed dynamically and act as important regulators in a variety of biological processes, especially in gene expression. Nevertheless, the functions and mechanisms of most lncRNAs remain unclear. In this review, we present recent progress in the identification of lncRNAs, their functions and molecular mechanisms, their roles in human diseases, their potential diagnostic and therapeutic applications as well as newer technologies for identifying deregulated lncRNAs in disease tissues.
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Affiliation(s)
- Ruifang Wu
- Hunan Key Laboratory of Medical Epigenomics, Department of Dermatology, The Second Xiangya Hospital, Central South University, #139 Renmin Middle Road, Changsha, 410011, Hunan, China
| | - Yuwen Su
- Hunan Key Laboratory of Medical Epigenomics, Department of Dermatology, The Second Xiangya Hospital, Central South University, #139 Renmin Middle Road, Changsha, 410011, Hunan, China
| | - Haijing Wu
- Hunan Key Laboratory of Medical Epigenomics, Department of Dermatology, The Second Xiangya Hospital, Central South University, #139 Renmin Middle Road, Changsha, 410011, Hunan, China
| | - Yong Dai
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University (Shenzhen People's Hospital), Shenzhen, 518020, Guangdong, China
| | - Ming Zhao
- Hunan Key Laboratory of Medical Epigenomics, Department of Dermatology, The Second Xiangya Hospital, Central South University, #139 Renmin Middle Road, Changsha, 410011, Hunan, China.
| | - Qianjin Lu
- Hunan Key Laboratory of Medical Epigenomics, Department of Dermatology, The Second Xiangya Hospital, Central South University, #139 Renmin Middle Road, Changsha, 410011, Hunan, China.
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384
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Mirsafian H, Manda SS, Mitchell CJ, Sreenivasamurthy S, Ripen AM, Mohamad SB, Merican AF, Pandey A. Long non-coding RNA expression in primary human monocytes. Genomics 2016; 108:37-45. [PMID: 26778813 DOI: 10.1016/j.ygeno.2016.01.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 12/27/2015] [Accepted: 01/01/2016] [Indexed: 12/23/2022]
Abstract
Long non-coding RNAs (lncRNAs) have been shown to possess a wide range of functions in both cellular and developmental processes including cancers. Although some of the lncRNAs have been implicated in the regulation of the immune response, the exact function of the large majority of lncRNAs still remains unknown. In this study, we characterized the lncRNAs in human primary monocytes, an essential component of the innate immune system. We performed RNA sequencing of monocytes from four individuals and combined our data with eleven other publicly available datasets. Our analysis led to identification of ~8000 lncRNAs of which >1000 have not been previously reported in monocytes. PCR-based validation of a subset of the identified novel long intergenic noncoding RNAs (lincRNAs) revealed distinct expression patterns. Our study provides a landscape of lncRNAs in monocytes, which could facilitate future experimental studies to characterize the functions of these molecules in the innate immune system.
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Affiliation(s)
- Hoda Mirsafian
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Srinivas Srikanth Manda
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India; McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Centre of Bioinformatics, Bioinformatics Centre, School of Life Sciences, Pondicherry University, Puducherry 605 014, India
| | - Christopher J Mitchell
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Sreelakshmi Sreenivasamurthy
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India; McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Adiratna Mat Ripen
- Allergy and Immunology Research Centre, Institute for Medical Research, Jalan Pahang, 50588 Kuala Lumpur, Malaysia
| | - Saharuddin Bin Mohamad
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia; Centre of Research for Computational Sciences and Informatics in Biology, Bioindustry, Environment, Agriculture and Healthcare (CRYSTAL), University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Amir Feisal Merican
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia; Centre of Research for Computational Sciences and Informatics in Biology, Bioindustry, Environment, Agriculture and Healthcare (CRYSTAL), University of Malaya, 50603 Kuala Lumpur, Malaysia.
| | - Akhilesh Pandey
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India; McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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385
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Zheng S, Chen H, Wang Y, Gao W, Fu Z, Zhou Q, Jiang Y, Lin Q, Tan L, Ye H, Zhao X, Luo Y, Li G, Ye L, Liu Y, Li W, Li Z, Chen R. Long non-coding RNA LOC389641 promotes progression of pancreatic ductal adenocarcinoma and increases cell invasion by regulating E-cadherin in a TNFRSF10A-related manner. Cancer Lett 2016; 371:354-65. [PMID: 26708505 DOI: 10.1016/j.canlet.2015.12.010] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 12/05/2015] [Accepted: 12/07/2015] [Indexed: 02/07/2023]
Abstract
Long non-coding RNAs (lncRNAs) are important regulators in pathological processes, yet their potential roles in pancreatic ductal adenocarcinoma (PDAC) are poorly understood. Here, we found that a novel lncRNA, LOC389641, was upregulated in PDAC tissues and cell lines. The expression of LOC389641 was significantly correlated with staging, lymph node metastasis and overall survival. Knockdown of LOC389641 impaired cell proliferation and invasion and induced cell apoptosis in vitro, whereas overexpression of LOC389641 had the opposite effect. The growth promoting effect of LOC389641 was also demonstrated in vivo. Further, a significant negative correlation was observed between E-cadherin levels and LOC389641 levels in vivo. Knockdown of LOC389641 upregulated E-cadherin expression, but knockdown of E-cadherin had a limited influence on LOC389641. Importantly, after E-cadherin was inhibited, the enhancement of LOC389641 on cell invasion was hindered. Moreover, the expression of LOC389641 was closely associated with its genomic neighboring gene TNFRSF10A. Lastly, knockdown experiments showed that TNFRSF10A might be a connection between LOC389641and E-cadherin. We conclude that LOC389641 promotes PDAC progression and increases cell invasion by regulating E-cadherin with the possible involvement of TNFRSF10A.
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386
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Abstract
Non-coding RNAs (ncRNAs) have evolved in eukaryotes as epigenetic regulators of gene expression. The most abundant regulatory ncRNAs are the 20-24 nt small microRNAs (miRNAs) and long non-coding RNAs (lncRNAs, <200 nt). Each class of ncRNAs operates through distinct mechanisms, but their pathways to regulating gene expression are interrelated in ways that are just being recognized. While the importance of lncRNAs in epigenetic control of transcription, developmental processes and human traits is emerging, the identity of lncRNAs in skeletal biology is scarcely known. However, since the first profiling studies of miRNA at stages during osteoblast and osteoclast differentiation, over 1100 publications related to bone biology and pathologies can be found, as well as many recent comprehensive reviews summarizing miRNA in skeletal cells. Delineating the activities and targets of specific miRNAs regulating differentiation of osteogenic and resorptive bone cells, coupled with in vivo gain- and loss-of-function studies, discovered unique mechanisms that support bone development and bone homeostasis in adults. We present here "guiding principles" for addressing biological control of bone tissue formation by ncRNAs. This review emphasizes recent advances in understanding regulation of the process of miRNA biogenesis that impact on osteogenic lineage commitment, transcription factors and signaling pathways. Also discussed are the approaches to be pursued for an understanding of the role of lncRNAs in bone and the challenges in addressing their multiple and complex functions. Based on new knowledge of epigenetic control of gene expression to be gained for ncRNA regulation of the skeleton, new directions for translating the miRNAs and lncRNAs into therapeutic targets for skeletal disorders are possible. This article is part of a Special Issue entitled Epigenetics and Bone.
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Affiliation(s)
- Mohammad Q Hassan
- Department of Oral & Maxillofacial Surgery, School of Dentistry, The University of Alabama at Birmingham, Birmingham, AL, USA.
| | - Coralee E Tye
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont College of Medicine, Burlington, VT, USA.
| | - Gary S Stein
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont College of Medicine, Burlington, VT, USA.
| | - Jane B Lian
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont College of Medicine, Burlington, VT, USA.
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387
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Tao H, Yang JJ, Zhou X, Deng ZY, Shi KH, Li J. Emerging role of long noncoding RNAs in lung cancer: Current status and future prospects. Respir Med 2015; 110:12-9. [PMID: 26603340 DOI: 10.1016/j.rmed.2015.10.006] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Revised: 10/08/2015] [Accepted: 10/09/2015] [Indexed: 01/01/2023]
Abstract
Lung cancer is the leading cause of cancer-related death worldwide with a 5-year survival rate of less than 15%, despite significant advances in both diagnostic and therapeutic approaches. Combined genomic and transcriptomic sequencing studies have identified numerous genetic driver mutations that are responsible for the development of lung cancer. Importantly, these approaches have also uncovered the widespread expression of "noncoding RNAs" including long noncoding RNAs (LncRNAs), which impact biologic responses through the regulation of mRNA transcription or translation. To date, most studies of the role of noncoding RNAs have focused on LncRNAs, which regulate mRNA translation via the RNA interference pathway. Although many of their attributes, such as patterns of expression, remain largely unknown, LncRNAs have key functions in transcriptional, post-transcriptional, and epigenetic gene regulation. Recent research showed that LncRNAs regulate flowering time in the lung cancer. In this review, we discuss these investigations into long noncoding RNAs were performed almost exclusively in lung cancer. Future work will need to extend these into lung cancer and to analyze how LncRNAs interact to regulate mRNA expression. From a clinical perspective, the targeting of LncRNAs as a novel therapeutic approach will require a deeper understanding of their function and mechanism of action.
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Affiliation(s)
- Hui Tao
- Department of Cardiothoracic Surgery, The Second Hospital of Anhui Medical University, Hefei 230601, China
| | - Jing-Jing Yang
- Department of Pharmacology, The Second Hospital of Anhui Medical University, Hefei 230601, China
| | - Xiao Zhou
- Department of Cardiothoracic Surgery, The Second Hospital of Anhui Medical University, Hefei 230601, China.
| | - Zi-Yu Deng
- Department of Scientific and Educational, The Second Hospital of Anhui Medical University, China
| | - Kai-Hu Shi
- Department of Cardiothoracic Surgery, The Second Hospital of Anhui Medical University, Hefei 230601, China.
| | - Jun Li
- School of Pharmacy, Anhui Medical University, Hefei 230032, China
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388
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Pei J, Wang B. Notch-1 promotes breast cancer cells proliferation by regulating LncRNA GAS5. Int J Clin Exp Med 2015; 8:14464-14471. [PMID: 26550436 PMCID: PMC4613121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 08/11/2015] [Indexed: 06/05/2023]
Abstract
BACKGROUND Notch signaling is indicated as novel therapeutic targets to prevent recurrence of breast cancer. LncRNAs were identified as downstream target of Notch pathway. However, the exact mechanisms involved in Notch signaling, lncRNAs and breast cancer remain to be explained. OBJECTIVE This original research aimed to determine the prognostic implications of Notch-1 for breast cancer, and explain mechanisms involved in regulation of lnRNA GAS5 by Notch-1, and identify the function of this mechanism on breast cancer. METHOD Thirty breast cancer patients were included from The First Affiliated Hospital of Anhui Medical University (China) since January 2006 in this study. The mRNA level by RT-PCR and protein level of Notch-1 by western blot in tumor tissues and adjacent normal tissues were evaluated and 5-year survival analysis was applied to examine the significance of Notch-1. The levels of ten reported lncRNAs were determined by RT-PCR, and subsequently linear analysis was applied to analyze the relationship between these four unique lncRNAs and protein level of Notch-1, which identified the most relevant lncRNA GAS5 with Notch-1 in breast cancer. Subsequently, Notch1-siRNA was applied to influence the expression of Notch-1 in T47D, then the level of RSA5 was measured by RT-PCR, and CCK-8 assay was applied to measure the proliferation of T47D cells. RESULTS High level of Notch-1 provided a poor prognosis in breast cancer. Interference of Notch-1 significantly suppressed proliferation of T47D cell (P < 0.05), and significantly increased the level of GAS5. CONCLUSION Notch-1 promotes breast cancer cells proliferation by regulating LncRNA GAS5.
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Affiliation(s)
- Jing Pei
- The Department of Breast Surgery, The First Affiliated Hospital of Anhui Medical University Jixi Road 218, Hefei 230022, Anhui, China
| | - Benzhong Wang
- The Department of Breast Surgery, The First Affiliated Hospital of Anhui Medical University Jixi Road 218, Hefei 230022, Anhui, China
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389
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Liu X, Yang J, Wu N, Song R, Zhu H. Evolution and Coevolution of PRC2 Genes in Vertebrates and Mammals. Adv Protein Chem Struct Biol 2015; 101:125-48. [PMID: 26572978 DOI: 10.1016/bs.apcsb.2015.06.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Recruited by noncoding RNAs (ncRNAs) to specific genomic sites, polycomb repressive complexes 2 (PRC2) modify chromatin states in nearly all eukaryotes. The limited ncRNAs in Drosophila but abundant in mammals should have made PRC2 genes evolved significantly in Deuterostomia to adapt to the much increased ncRNAs. This study analyzes the evolution and coevolution of seven PRC2 genes in 29 Deuterostomia. These genes, previously assumed highly conserved, are found to have obtained multiple insertions in vertebrates and mammals and undergone significant positive selections in marsupials and prosimians, indicating adaptions to substantially increased lncRNAs (long noncoding RNAs) in mammals and in primates. Some insertions occur notably in homologous sequences of human nonsense-mediated decay (NMD) transcripts. Moreover, positive selections and signals of convergent evolution imply the independent increase of lncRNAs in mammals and in primates. Coevolutionary analysis reveals that patterns of interaction between PRC2 proteins have also much evolved from vertebrates to mammals, indicating adaptation at the protein complex level. The potential functions of mammalian-specific insertions and NMD transcripts deserve further experimental examination.
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390
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Abstract
Hematopoiesis is characterized by a lifelong balance between hematopoietic stem cell (HSC) self-renewal and differentiation into mature blood populations. Proper instruction of cell fate decisions requires tight homeostatic regulation of transcriptional programs through a combination of epigenetic modifications, management of cis-regulatory elements, and transcription factor activity. Recent work has focused on integrating biochemical, genetic, and evolutionary data sets to gain further insight into these regulatory components. Long noncoding RNA (lncRNA), post-translational modifications of transcription factors, and circadian rhythm add additional layers of complexity. These analyses have provided a wealth of information, much of which has been made available through public databases. Elucidating the regulatory processes that govern hematopoietic transcriptional programs is expected to provide useful insights into hematopoiesis that may be applied broadly across tissue types while enabling the discovery and implementation of therapeutics to treat human disease.
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Affiliation(s)
- David E Muench
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - H Leighton Grimes
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
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391
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Liu X, Che L, Xie YK, Hu QJ, Ma CJ, Pei YJ, Wu ZG, Liu ZH, Fan LY, Wang HQ. Noncoding RNAs in human intervertebral disc degeneration: An integrated microarray study. Genom Data 2015; 5:80-1. [PMID: 26484230 DOI: 10.1016/j.gdata.2015.05.027] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 05/25/2015] [Indexed: 11/23/2022]
Abstract
Accumulating evidence indicates that noncoding RNAs play important roles in a multitude of biological processes. The striking findings of miRNAs (microRNAs) and lncRNAs (long noncoding RNAs) as members of noncoding RNAs open up an exciting era in the studies of gene regulation. More recently, the reports of circRNAs (circular RNAs) add fuel to the noncoding RNAs research. Human intervertebral disc degeneration (IDD) is a main cause of low back pain as a disabling spinal disease. We have addressed the expression profiles if miRNAs, lncRNAs and mRNAs in IDD (Wang et al., J Pathology, 2011 and Wan et al., Arthritis Res Ther, 2014). Furthermore, we thoroughly analysed noncoding RNAs, including miRNAs, lncRNAs and circRNAs in IDD using the very same samples. Here we delineate in detail the contents of the aforementioned microarray analyses. Microarray and sample annotation data were deposited in GEO under accession number GSE67567 as SuperSeries. The integrated analyses of these noncoding RNAs will shed a novel light on coding-noncoding regulatory machinery.
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392
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Affiliation(s)
- Linlin Mai
- Department of Cardiology, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080, China; Department of Cardiology, the First People's Hospital of Shunde, Foshan, 528300 China
| | - Lin Xiao
- Department of Internal Medicine, the Xingtan Affiliated Hospital of the First People's Hospital of Shunde, Foshan 528300, China
| | - Yuli Huang
- Department of Cardiology, the First People's Hospital of Shunde, Foshan, 528300 China
| | - Weiyi Mai
- Department of Cardiology, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080, China.
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393
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Abstract
INTRODUCTION Hepatocellular carcinoma (HCC) is the most common form of primary liver cancer with an estimated over half a million new cases diagnosed annually. Due to the difficulty in early diagnosis and lack of effective treatment options, HCC is currently ranked as the second highest neoplastic-related mortality in the world, with an extremely low 5-year survival rate of between 6 and 11%. Long noncoding RNAs (lncRNAs), are genes lacking protein coding ability, have recently emerged as pivotal participants in biological processes, often dysregulated in a range of cancers, including HCC. AREAS COVERED In this review, we highlight the recent findings of lncRNAs in HCC pathogenesis, with particular attention on epigenetic events. In silico analysis was utilized to emphasize intrinsic linkages within the ncRNA families associated with hepatocarcinogenesis. EXPERT OPINION While our understanding of lncRNAs in the onset and progression of HCC is still in its infancy, there is no doubt that understanding the activities of ncRNAs will certainly secure strong biomarkers and improve treatment options for HCC patients.
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Affiliation(s)
- Jun Zhao
- Experimental Medicine, UCD School of Medicine and Medical Science, Mater Misericordiae University Hospital, Catherine McAuley Centre, Nelson Street , Dublin 7 , Ireland
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394
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Zhang XQ, Leung GKK. Long non-coding RNAs in glioma: functional roles and clinical perspectives. Neurochem Int 2014; 77:78-85. [PMID: 24887176 DOI: 10.1016/j.neuint.2014.05.008] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 05/20/2014] [Accepted: 05/24/2014] [Indexed: 12/19/2022]
Abstract
Long non-coding RNAs (lncRNAs) are a new class of non-coding gene regulators. But unlike their smaller counterparts, microRNAs, relatively less is known about the roles and functions of lncRNAs. Current evidence suggests that lncRNAs may play important roles in a wide range of biological processes in human cancers, including glioma. By acting as oncogenes or tumor suppressors, lncRNAs may contribute to glioma initiation, progression and other malignant phenotypes. Their expression profiles may also have important clinical implications in glioma subclassification and patients' prognostication. Here, we review current evidence related to the functional roles of lncRNAs in glioma. We will discuss the aberrant lncRNA expression signatures associated with glioma initiation and progression, as well as the potential mechanisms underlying lncRNA dysregulation. We also discuss the functional roles of lncRNAs in glioma biological behavior. Finally, the potentials and prospects of employing lncRNAs as novel biomarkers and therapeutic targets for glioma clinical practice will also be addressed.
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Affiliation(s)
- Xiao-Qin Zhang
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Queen Mary Hospital, Hong Kong
| | - Gilberto Ka-Kit Leung
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Queen Mary Hospital, Hong Kong.
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395
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Tao HB, Wan YX, Deng AM, Yan HL. Long noncoding RNAs in colorectal cancer. Shijie Huaren Xiaohua Zazhi 2014; 22:901-906. [DOI: 10.11569/wcjd.v22.i7.901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) are broadly defined as RNA molecules greater than 200 bp in length and lacking an open reading frame. Recent studies have demonstrated that lncRNAs are widely involved in the regulation of gene expression network at epigenetic, transcriptional and post-transcriptional levels, which may affect cell growth, proliferation, differentiation, metabolism, apoptosis and other important physiological processes. Abnormal expression of lncRNAs is closely associated with the tumor development, invasion, metastasis and prognosis. The development of colorectal cancer is a multi-factor, multi-step process, and abnormal gene expression may play an important role in this process. This review focuses on the current advances in research of lncRNAs in colorectal cancer, with an aim to provide new clues to clinical prevention, diagnosis and treatment of this malignancy.
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396
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Hu P, Yang J, Hou Y, Zhang H, Zeng Z, Zhao L, Yu T, Tang X, Tu G, Cui X, Liu M. LncRNA expression signatures of twist-induced epithelial-to-mesenchymal transition in MCF10A cells. Cell Signal 2013; 26:83-93. [PMID: 24113349 DOI: 10.1016/j.cellsig.2013.10.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Accepted: 10/02/2013] [Indexed: 11/19/2022]
Abstract
The epithelial-to-mesenchymal transient (EMT) is associated with tumor metastasis. Twist is one of the key transcription factors for EMT and relates to tumor cell migration. Long non-coding RNAs (lncRNAs) have recently emerged as important regulatory molecules involved in a broad range of biological processes and complicated diseases. However, it is unknown whether a signal network and lncRNAs are involved in Twist-induced EMT program. Taking MCF10A/Twist as a model, more than 99 lncRNAs and 3164 genes are regulated in the Twist-induced EMT process using lncRNA-array and cDNA micro-array. We establish a downstream signal network associated with EMT induced by Twist using bioinformatic analysis (Gene Ontology, pathway analysis) and experimental data. A set of multiple canonical signal pathways (such as WNT, MAPK, JAK/STAT, TGF-β, mTOR, Hedgehog and P53 signaling pathways) and several lncRNAs [such as lncRNA (chr6, 26124411-26139312, +), lncRNA (chr1, 41944445-41949874, -), lncRNA (chr17, 44833874-44834830, +)] are altered in MCF10A/Twist cells. More interestingly, lncRNA (chr17, 44833874-44834830, +), lncRNA (chr17, 21142183-21156578, -), lncRNA (chr6, 26124411-26139312, +) and lncRNA (chr19, 438420-2083745, -) may be involved in regulation or activation of WNT signaling pathway in the Twist-induced EMT process. These findings first determine that Twist contributes to invasion and metastasis by inducing wide-ranging transcriptional and functional changes of lncRNAs and signal pathways in our study.
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Affiliation(s)
- Ping Hu
- Key Laboratory of Laboratory Medical Diagnostics, Chinese Ministry of Education, Chongqing Medical University, Chongqing 400016, China
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397
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Shi X, Sun M, Liu H, Yao Y, Song Y. Long non-coding RNAs: a new frontier in the study of human diseases. Cancer Lett 2013; 339:159-66. [PMID: 23791884 DOI: 10.1016/j.canlet.2013.06.013] [Citation(s) in RCA: 912] [Impact Index Per Article: 82.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Revised: 06/05/2013] [Accepted: 06/08/2013] [Indexed: 02/07/2023]
Abstract
With the development of whole genome and transcriptome sequencing technologies, long noncoding RNAs (lncRNAs) have received increased attention. Multiple studies indicate that lncRNAs act not only as the intermediary between DNA and protein but also as important protagonists of cellular functions. LncRNAs can regulate gene expression in many ways, including chromosome remodeling, transcription and post-transcriptional processing. Moreover, the dysregulation of lncRNAs has increasingly been linked to many human diseases, especially in cancers. Here, we reviewed the rapidly advancing field of lncRNAs and described the relationship between the dysregulation of lncRNAs and human diseases, highlighting the specific roles of lncRNAs in human diseases.
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Affiliation(s)
- Xuefei Shi
- Department of Respiratory Medicine, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China.
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398
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Abstract
With the development of whole genome and transcriptome sequencing technologies, long noncoding RNAs (lncRNAs) have received increased attention. Multiple studies indicate that lncRNAs act not only as the intermediary between DNA and protein but also as important protagonists of cellular functions. LncRNAs can regulate gene expression in many ways, including chromosome remodeling, transcription and post-transcriptional processing. Moreover, the dysregulation of lncRNAs has increasingly been linked to many human diseases, especially in cancers. Here, we reviewed the rapidly advancing field of lncRNAs and described the relationship between the dysregulation of lncRNAs and human diseases, highlighting the specific roles of lncRNAs in human diseases.
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Affiliation(s)
- Xuefei Shi
- Department of Respiratory Medicine, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China.
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399
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Zhang XQ, Sun S, Lam KF, Kiang KMY, Pu JKS, Ho ASW, Lui WM, Fung CF, Wong TS, Leung GKK. A long non-coding RNA signature in glioblastoma multiforme predicts survival. Neurobiol Dis 2013; 58:123-31. [PMID: 23726844 DOI: 10.1016/j.nbd.2013.05.011] [Citation(s) in RCA: 157] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Revised: 05/08/2013] [Accepted: 05/20/2013] [Indexed: 12/19/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) represent the leading edge of cancer research, and have been implicated in cancer biogenesis and prognosis. We aimed to identify lncRNA signatures that have prognostic values in glioblastoma multiforme (GBM). Using a lncRNA-mining approach, we performed lncRNA expression profiling in 213 GBM tumors from The Cancer Genome Atlas (TCGA), randomly divided into a training (n=107) and a testing set (n=106). We analyzed the associations between lncRNA signatures and clinical outcome in the training set, and validated the findings in the testing set. We also validated the identified lncRNA signature in another two independent GBM data sets from Gene Expression Omnibus (GEO), which contained specimens from 68 and 101 patients, respectively. We identified a set of six lncRNAs that were significantly associated with the overall survival in the training set (P≤0.01). Based on this six-lncRNA signature, the training-set patients could be classified into high-risk and low-risk subgroups with significantly different survival (HR=2.13, 95% CI=1.38-3.29; P=0.001). The prognostic value of this six-lncRNA signature was confirmed in the testing set and the two independent data sets. Further analysis revealed that the prognostic value of this signature was independent of age and O-6-methylguanine-DNA methyltransferase (MGMT) promoter methylation status. The identification of the prognostic lncRNAs indicates the potential roles of lncRNAs in GBM pathogenesis. This six-lncRNA signature may have clinical implications in the subclassification of GBM.
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Affiliation(s)
- Xiao-Qin Zhang
- Department of Surgery, The University of Hong Kong, Hong Kong
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