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Wang YC, Chuang YH, Shao Q, Chen JF, Chen SY. Brain cytoplasmic RNA 1 suppresses smooth muscle differentiation and vascular development in mice. J Biol Chem 2018; 293:5668-5678. [PMID: 29467228 DOI: 10.1074/jbc.ra117.001578] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 02/17/2018] [Indexed: 02/04/2023] Open
Abstract
The cardiovascular system develops during the early stages of embryogenesis, and differentiation of smooth muscle cells (SMCs) is essential for that process. SMC differentiation is critically regulated by transforming growth factor (TGF)-β/SMAD family member 3 (SMAD3) signaling, but other regulators may also play a role. For example, long noncoding RNAs (lncRNAs) regulate various cellular activities and events, such as proliferation, differentiation, and apoptosis. However, whether long noncoding RNAs also regulate SMC differentiation remains largely unknown. Here, using the murine cell line C3H10T1/2, we found that brain cytoplasmic RNA 1 (BC1) is an important regulator of SMC differentiation. BC1 overexpression suppressed, whereas BC1 knockdown promoted, TGF-β-induced SMC differentiation, as indicated by altered cell morphology and expression of multiple SMC markers, including smooth muscle α-actin (αSMA), calponin, and smooth muscle 22α (SM22α). BC1 appeared to block SMAD3 activity and inhibit SMC marker gene transcription. Mechanistically, BC1 bound to SMAD3 via RNA SMAD-binding elements (rSBEs) and thus impeded TGF-β-induced SMAD3 translocation to the nucleus. This prevented SMAD3 from binding to SBEs in SMC marker gene promoters, an essential event in SMC marker transcription. In vivo, BC1 overexpression in mouse embryos impaired vascular SMC differentiation, leading to structural defects in the artery wall, such as random breaks in the elastic lamina, abnormal collagen deposition on SM fibers, and disorganized extracellular matrix proteins in the media of the neonatal aorta. Our results suggest that BC1 is a suppressor of SMC differentiation during vascular development.
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Affiliation(s)
- Yung-Chun Wang
- From the Department of Physiology and Pharmacology, University of Georgia, Athens, Georgia 30602
| | - Ya-Hui Chuang
- From the Department of Physiology and Pharmacology, University of Georgia, Athens, Georgia 30602
| | - Qiang Shao
- the Ostrow School of Dentistry, University of Southern California, Los Angeles, California 90089
| | - Jian-Fu Chen
- the Ostrow School of Dentistry, University of Southern California, Los Angeles, California 90089
| | - Shi-You Chen
- From the Department of Physiology and Pharmacology, University of Georgia, Athens, Georgia 30602, .,the Institute of Clinical Medicine and Department of Cardiology, Renmin Hospital, Hubei University of Medicine, Shiyan, Hubei 442000, China, and
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52
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Ren H, Yang X, Yang Y, Zhang X, Zhao R, Wei R, Zhang X, Zhang Y. Upregulation of LncRNA BCYRN1 promotes tumor progression and enhances EpCAM expression in gastric carcinoma. Oncotarget 2017; 9:4851-4861. [PMID: 29435146 PMCID: PMC5797017 DOI: 10.18632/oncotarget.23585] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 12/13/2017] [Indexed: 11/25/2022] Open
Abstract
Brain cytoplasmic RNA 1 (BCYRN1), along non-coding RNA, plays a critical role in various diseases, including some cancers. However, the expression of BCYRN1 and its roles in gastric carcinoma (GC) still remain unidentified. Thus, this study employed RT-qPCR to detect expression of BCYRN1 in 85 paired GC samples and adjacent normal tissues, and performed in vitro studies to explore effects of BCYRN1 in GC cells on cell proliferation, apoptosis and migration. We found BCYRN1 was significantly upregulated in GC samples, and its expression was positively correlated with advanced TNM stage (p = 0.0012) and tumor size (p = 0.027). Functionally, BCYRN1 knockdown by siRNA could inhibit cell proliferation, induce G1/G0 cell cycle arrest, increase apoptosis and impair migratory ability of AGS cells. Moreover, the results of RT-qPCR and western blotting indicated that knockdown of BCYRN1 notably decreased the expression of epithelial cell adhesion molecules (EpCAM). Otherwise, overexpression of BCYRN1 in GC cells (BGC-823 and SGC-7901) could reverse the effects of BCYRN1 knockdown. Taken together, our data indicate for the first time that BCYRN1 acts as an oncogenic lncRNA in GC progression and may be a potential therapeutic target in GC.
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Affiliation(s)
- Hao Ren
- Department of Clinical Laboratory, Qilu Hospital, Shandong University, Jinan, Shandong Province, China.,Department of Laboratory, Yuhuangding Hospital, Qingdao University Medical College, Yantai, Shandong Province, China
| | - Xiaomin Yang
- Department of Clinical Laboratory, The Affiliated Hospital of Qingdao University, Qingdao, Shandong Province, China
| | - Yongmei Yang
- Department of Clinical Laboratory, Qilu Hospital, Shandong University, Jinan, Shandong Province, China
| | - Xiaoyu Zhang
- Clinical Medicine of Undergraduate, Taishan Medical University, Taian, Shandong Province, China
| | - Rui Zhao
- Department of Clinical Laboratory, Qilu Hospital, Shandong University, Jinan, Shandong Province, China
| | - Ran Wei
- Wakayama Medical University, Wakayama, Wakayama, Japan
| | - Xin Zhang
- Department of Clinical Laboratory, Qilu Hospital, Shandong University, Jinan, Shandong Province, China
| | - Yi Zhang
- Department of Clinical Laboratory, Qilu Hospital, Shandong University, Jinan, Shandong Province, China
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53
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Chen X, Yan CC, Zhang X, You ZH. Long non-coding RNAs and complex diseases: from experimental results to computational models. Brief Bioinform 2017; 18:558-576. [PMID: 27345524 PMCID: PMC5862301 DOI: 10.1093/bib/bbw060] [Citation(s) in RCA: 295] [Impact Index Per Article: 42.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2016] [Indexed: 02/07/2023] Open
Abstract
LncRNAs have attracted lots of attentions from researchers worldwide in recent decades. With the rapid advances in both experimental technology and computational prediction algorithm, thousands of lncRNA have been identified in eukaryotic organisms ranging from nematodes to humans in the past few years. More and more research evidences have indicated that lncRNAs are involved in almost the whole life cycle of cells through different mechanisms and play important roles in many critical biological processes. Therefore, it is not surprising that the mutations and dysregulations of lncRNAs would contribute to the development of various human complex diseases. In this review, we first made a brief introduction about the functions of lncRNAs, five important lncRNA-related diseases, five critical disease-related lncRNAs and some important publicly available lncRNA-related databases about sequence, expression, function, etc. Nowadays, only a limited number of lncRNAs have been experimentally reported to be related to human diseases. Therefore, analyzing available lncRNA–disease associations and predicting potential human lncRNA–disease associations have become important tasks of bioinformatics, which would benefit human complex diseases mechanism understanding at lncRNA level, disease biomarker detection and disease diagnosis, treatment, prognosis and prevention. Furthermore, we introduced some state-of-the-art computational models, which could be effectively used to identify disease-related lncRNAs on a large scale and select the most promising disease-related lncRNAs for experimental validation. We also analyzed the limitations of these models and discussed the future directions of developing computational models for lncRNA research.
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Affiliation(s)
- Xing Chen
- School of Information and Electrical Engineering, China University of Mining and Technology, Xuzhou, China
- Corresponding authors. Xing Chen, School of Information and Electrical Engineering, China University of Mining and Technology, Xuzhou 221116, China. E-mail: ; Zhu-Hong You, School of Computer Science and Technology, China University of Mining and Technology, Xuzhou 221116, China. E-mail:
| | | | - Xu Zhang
- School of Mechanical, Electrical & Information Engineering, Shandong University, Weihai, China
- Corresponding authors. Xing Chen, School of Information and Electrical Engineering, China University of Mining and Technology, Xuzhou 221116, China. E-mail: ; Zhu-Hong You, School of Computer Science and Technology, China University of Mining and Technology, Xuzhou 221116, China. E-mail:
| | - Zhu-Hong You
- School of Computer Science and Technology, China University of Mining and Technology, Xuzhou, China
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54
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LncRNA MEG3 has anti-activity effects of cervical cancer. Biomed Pharmacother 2017; 94:636-643. [DOI: 10.1016/j.biopha.2017.07.056] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 06/30/2017] [Accepted: 07/11/2017] [Indexed: 01/19/2023] Open
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55
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Park JL, Lee YS, Kunkeaw N, Kim SY, Kim IH, Lee YS. Epigenetic regulation of noncoding RNA transcription by mammalian RNA polymerase III. Epigenomics 2017; 9:171-187. [PMID: 28112569 DOI: 10.2217/epi-2016-0108] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
RNA polymerase III (Pol III) synthesizes a range of medium-sized noncoding RNAs (collectively 'Pol III genes') whose early established biological roles were so essential that they were considered 'housekeeping genes'. Besides these fundamental functions, diverse unconventional roles of mammalian Pol III genes have recently been recognized and their expression must be exquisitely controlled. In this review, we summarize the epigenetic regulation of Pol III genes by chromatin structure, histone modification and CpG DNA methylation. We also recapitulate the association between dysregulation of Pol III genes and diseases such as cancer and neurological disorders. Additionally, we will discuss why in-depth molecular studies of Pol III genes have not been attempted and how nc886, a Pol III gene, may resolve this issue.
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Affiliation(s)
- Jong-Lyul Park
- Personalized Genomic Medicine Research Center, KRIBB, Daejeon 305-806, Korea.,Department of Functional Genomics, University of Science & Technology, Daejeon 305-806, Korea
| | - Yeon-Su Lee
- Cancer Genomics Branch, Research Institute, National Cancer Center, Goyang 10408, Korea
| | - Nawapol Kunkeaw
- Department of Biochemistry & Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555-1072, USA.,Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, 73170, Thailand
| | - Seon-Young Kim
- Personalized Genomic Medicine Research Center, KRIBB, Daejeon 305-806, Korea.,Department of Functional Genomics, University of Science & Technology, Daejeon 305-806, Korea
| | - In-Hoo Kim
- Graduate School of Cancer Science & Policy, National Cancer Center, Goyang 10408, Korea
| | - Yong Sun Lee
- Department of Biochemistry & Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555-1072, USA.,Graduate School of Cancer Science & Policy, National Cancer Center, Goyang 10408, Korea
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56
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Park JL, Lee YS, Song MJ, Hong SH, Ahn JH, Seo EH, Shin SP, Lee SJ, Johnson BH, Stampfer MR, Kim HP, Kim SY, Lee YS. Epigenetic regulation of RNA polymerase III transcription in early breast tumorigenesis. Oncogene 2017; 36:6793-6804. [PMID: 28846112 DOI: 10.1038/onc.2017.285] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2017] [Revised: 06/13/2017] [Accepted: 07/03/2017] [Indexed: 02/07/2023]
Abstract
RNA polymerase III (Pol III) transcribes medium-sized non-coding RNAs (collectively termed Pol III genes). Emerging diverse roles of Pol III genes suggest that individual Pol III genes are exquisitely regulated by transcription and epigenetic factors. Here we report global Pol III expression/methylation profiles and molecular mechanisms of Pol III regulation that have not been as extensively studied, using nc886 as a representative Pol III gene. In a human mammary epithelial cell system that recapitulates early breast tumorigenesis, the fraction of actively transcribed Pol III genes increases reaching a plateau during immortalization. Hyper-methylation of Pol III genes inhibits Pol III binding to DNA via inducing repressed chromatin and is a determinant for the Pol III repertoire. When Pol III genes are hypo-methylated, MYC amplifies their transcription, regardless of its recognition DNA motif. Thus, Pol III expression during tumorigenesis is delineated by methylation and magnified by MYC.
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Affiliation(s)
- J-L Park
- Personalized Genomic Medicine Research Center, KRIBB, Daejeon, Korea.,Department of Functional Genomics, University of Science and Technology, Daejeon, Korea
| | - Y-S Lee
- Rare Cancer Branch, Research Institute, National Cancer Center, Goyang-si, Korea
| | - M-J Song
- Department of Environmental Medical Biology, Yonsei University College of Medicine, Seoul, Korea
| | - S-H Hong
- Rare Cancer Branch, Research Institute, National Cancer Center, Goyang-si, Korea
| | - J-H Ahn
- Department of Life and Nanopharmaceutical Sciences and Department of Oriental Pharmacy, Kyung Hee University, Seoul, Korea
| | - E-H Seo
- Personalized Genomic Medicine Research Center, KRIBB, Daejeon, Korea.,Department of Functional Genomics, University of Science and Technology, Daejeon, Korea
| | - S-P Shin
- Immunotherapeutics Branch, Research Institute, National Cancer Center, Goyang-si, Korea
| | - S-J Lee
- Immunotherapeutics Branch, Research Institute, National Cancer Center, Goyang-si, Korea
| | - B H Johnson
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, USA
| | - M R Stampfer
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - H-P Kim
- Department of Environmental Medical Biology, Yonsei University College of Medicine, Seoul, Korea.,Institute of Tropical Medicine, Yonsei University College of Medicine, Seoul, Korea.,Brain Korea 21 Plus Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - S-Y Kim
- Personalized Genomic Medicine Research Center, KRIBB, Daejeon, Korea.,Department of Functional Genomics, University of Science and Technology, Daejeon, Korea
| | - Y S Lee
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, USA.,Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Korea
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57
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Shi H, Liu Z, Pei D, Jiang Y, Zhu H, Chen B. Development and validation of nomogram based on lncRNA ZFAS1 for predicting survival in lymph node-negative esophageal squamous cell carcinoma patients. Oncotarget 2017; 8:59048-59057. [PMID: 28938617 PMCID: PMC5601713 DOI: 10.18632/oncotarget.19937] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 07/26/2017] [Indexed: 12/30/2022] Open
Abstract
Background There is increasing evidence of a relationship between long non-coding RNA (lncRNA) and cancer. This study aimed to examine the prognostic value of the lncRNA ZFAS1 in esophageal squamous cell carcinoma (ESCC). Results The results showed that ZFAS1 expression was significantly higher in ESCC tissues compared with the corresponding adjacent normal tissues (P < 0.001). ESCC patients with high ZFAS1 expression had a poor overall survival (OS). Histological grade, T stage and ZFAS1 expression were integrated to develop the nomogram. The nomogram showed a significantly better prediction of OS for patients with lymph node-negative ESCC. The ROC curve also showed higher specificity and sensitivity for predicting 3- and 5-year ESCC patient survival compared with the AJCC staging system. The decision curve analysis also indicated a greater potential for the nomogram in clinical application compared with the AJCC staging system. Importantly, our findings were supported by a validation cohort. Materials and Methods We retrospectively investigated 398 lymph node-negative ESCC patients. Data from the primary cohort (n = 246) were used to develop a multivariate nomogram. The nomogram was internally validated for discrimination and calibration with bootstrap samples and was externally validated with an independent patient cohort (n = 152). Conclusions Our proposed nomogram, which integrates clinicopathological factors and ZFAS1 expression, can accurately predict the prognosis of lymph node-negative ESCC patients without preoperative chemoradiotherapy.
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Affiliation(s)
- Hongtai Shi
- Department of Radiotherapy, The Third People's Hospital of Yancheng, Yancheng 224005, China
| | - Zhenhua Liu
- Department of Radiotherapy, Yancheng City No.1 People's Hospital, Yancheng 224000, China
| | - Dong Pei
- Department of Radiotherapy, The Third People's Hospital of Yancheng, Yancheng 224005, China
| | - Youqin Jiang
- Department of Radiotherapy, The Third People's Hospital of Yancheng, Yancheng 224005, China
| | - Haiwen Zhu
- Department of Radiotherapy, The Third People's Hospital of Yancheng, Yancheng 224005, China
| | - Bin Chen
- Department of Radiotherapy, The Third People's Hospital of Yancheng, Yancheng 224005, China
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58
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Kim Y, Lee J, Shin H, Jang S, Kim SC, Lee Y. Biosynthesis of brain cytoplasmic 200 RNA. Sci Rep 2017; 7:6884. [PMID: 28761139 PMCID: PMC5537265 DOI: 10.1038/s41598-017-05097-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 05/10/2017] [Indexed: 12/13/2022] Open
Abstract
Brain cytoplasmic 200 RNA (BC200 RNA), a neuron-specific non-coding RNA, is also highly expressed in a number of tumors of non-neuronal origin. However, the biosynthesis of BC200 RNA remains poorly understood. In this study, we show that the efficient transcription of BC200 RNA requires both internal and upstream promoter elements in cancer cells. The transcription complex seems to interact with a broad range of sequences within the upstream 100-bp region. The cellular levels and half-lives of BC200 RNA were found to differ across various cancer cell types, but there was no significant correlation between these parameters. Exogenously expressed BC200 RNA had a shorter half-life than that observed for the endogenous version in cancer cells, suggesting that BC200 RNA might be protected by some limiting factor(s) in cancer cells. Transient transfection experiments showed that the transcriptional activity of the exogenous BC200 RNA promoter element varied depending on the cancer cell type. However, the promoter activities together with the half-life data could not explain the differences in the levels of BC200 RNA among different cell types, suggesting that there is another level of transcriptional regulation beyond that detected by our transient transfection experiments.
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Affiliation(s)
- Youngmi Kim
- Department of Chemistry, KAIST, Daejeon, 34141, Korea
| | - Jungmin Lee
- Department of Chemistry, KAIST, Daejeon, 34141, Korea
| | - Heegwon Shin
- Department of Chemistry, KAIST, Daejeon, 34141, Korea
| | - Seonghui Jang
- Department of Chemistry, KAIST, Daejeon, 34141, Korea
| | - Sun Chang Kim
- Department of Biological Sciences, KAIST, Daejeon, 34141, Korea
| | - Younghoon Lee
- Department of Chemistry, KAIST, Daejeon, 34141, Korea.
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59
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lncRNAs and MYC: An Intricate Relationship. Int J Mol Sci 2017; 18:ijms18071497. [PMID: 28704924 PMCID: PMC5535987 DOI: 10.3390/ijms18071497] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 07/05/2017] [Accepted: 07/11/2017] [Indexed: 01/27/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are emerging as important regulators of gene expression networks, acting either at the transcriptional level, by influencing histone modifications, or at the post-transcriptional level, by controlling mRNA stability and translation. Among the gene expression networks known to influence the process of oncogenic transformation, the one controlled by the proto-oncogene MYC is one of the most frequently deregulated in cancer. In B-cell lymphomas, the MYC gene is subject to chromosomal rearrangements that result in MYC overexpression. In many other cancers, the region surrounding MYC is subject to gene amplification. MYC expression is also controlled at the level of protein and mRNA stability. Neoplastic lesions affecting MYC expression are responsible for a drastic change in the number and the type of genes that are transcriptionally controlled by MYC, depending on differential promoter affinities. Transcriptome profiling of tumor samples has shown that several lncRNAs can be found differentially regulated by MYC in different cancer types and many of them can influence cancer cell viability and proliferation. At the same time, lncRNAs have been shown to be able to control the expression of MYC itself, both at transcriptional and post-transcriptional levels. Given that targeting the MYC-dependent transcriptional program has the potential to reach broad anticancer activity, molecular dissection of the complex regulatory mechanisms governing MYC expression will be crucial in the future for the identification of novel therapeutic strategies.
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60
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Booy EP, McRae EK, Koul A, Lin F, McKenna SA. The long non-coding RNA BC200 (BCYRN1) is critical for cancer cell survival and proliferation. Mol Cancer 2017. [PMID: 28651607 PMCID: PMC5483959 DOI: 10.1186/s12943-017-0679-7] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND BC200 is a long non-coding RNA expressed at high levels in the brain and elevated in a variety of tumour types. BC200 has a hypothesized role in translational regulation; however, to date the functional role of BC200 in both normal and diseased states remains poorly characterized. METHODS Detailed BC200 expression analyses were performed in tumor cell lines, primary and non-tumorigenic cultured breast and lung cells, and a panel of normal human tissues by quantitative real-time PCR and confirmed by northern blot. Subcellular fractionation was performed to assess BC200 distribution and efficient knock-down of BC200 was established using both locked nucleic acid (LNA) GapmeRs and conventional siRNAs. Cell viability following BC200 knockdown and overexpression was assessed by MTT assay and induction of apoptosis was monitored by Annexin V/PI staining and flow cytometry. Cell cycle arrest and synchronization were performed using serum withdrawal as well as the specific inhibitors Lovastatin, Thymidine, RO3306 and Nocodazole. Synchronization was monitored by fluorescent analysis of cellular DNA content by flow cytometry RESULTS: BC200 expression was substantially upregulated in brain and elevated expression was also observed in testes, small intestine and ovary. Expression in cultured tumour cells was dramatically higher than corresponding normal tissue; however, expression in cultured primary cells was similar to that in immortalized and cancer cell lines. BC200 knockdown resulted in a dramatic loss of viability through growth arrest and induction of apoptosis that could be partially rescued by overexpression of wild-type BC200 but not an siRNA-resistant sequence mutant. A substantial decrease in BC200 expression was observed upon cell confluence or serum deprivation, as well as drug induced cell cycle arrest in G1 or G2 but not S- or M-phases. Upon release from cell cycle arrest, BC200 expression was recovered as cells entered S-phase, but did not follow a periodic expression pattern during synchronized progression through the cell cycle. This elevated expression was critical for the survival of proliferating cancerous and non-cancerous cells, but is dispensable upon senescence or cell cycle arrest. CONCLUSIONS BC200 expression is elevated in proliferating cultured cells regardless of origin. In primary cells, expression is dramatically reduced upon cell cycle arrest by confluence, serum deprivation or chemical inhibition. The lethality of BC200 knockdown is restricted to actively proliferating cells, making it a promising therapeutic target for a broad spectrum of cancers.
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Affiliation(s)
- Evan P Booy
- Department of Chemistry, University of Manitoba, Room 380 Parker Building, 144 Dysart Road, Winnipeg, MB, R3T 2N2, Canada
| | - Ewan Ks McRae
- Department of Chemistry, University of Manitoba, Room 380 Parker Building, 144 Dysart Road, Winnipeg, MB, R3T 2N2, Canada
| | - Amit Koul
- Department of Chemistry, University of Manitoba, Room 380 Parker Building, 144 Dysart Road, Winnipeg, MB, R3T 2N2, Canada
| | - Francis Lin
- Department of Immunology, University of Manitoba, 750 McDermot Ave, Winnipeg, R3E 0T5, MB, Canada.,Department of Physics & Astronomy, University of Manitoba, Allen Building, Winnipeg, R3T 2N2, MB, Canada
| | - Sean A McKenna
- Department of Chemistry, University of Manitoba, Room 380 Parker Building, 144 Dysart Road, Winnipeg, MB, R3T 2N2, Canada. .,Department of Biochemistry & Medical Genetics, University of Manitoba, 745 Bannatyne Ave, Winnipeg, R3E 0J9, MB, Canada.
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61
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Zhang K, Luo Z, Zhang Y, Song X, Zhang L, Wu L, Liu J. Long non-coding RNAs as novel biomarkers for breast cancer invasion and metastasis. Oncol Lett 2017; 14:1895-1904. [PMID: 28789424 DOI: 10.3892/ol.2017.6462] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 04/26/2017] [Indexed: 02/07/2023] Open
Abstract
Breast cancer (BC) is now the most common malignancy worldwide, with high prevalence and lethality among women. Invasion and metastasis are the major reasons for breast cancer-associated mortality. However, the underlying mechanism of invasion and metastasis has not been entirely elucidated. Long non-coding RNAs (lncRNAs) are a large class of non-coding transcripts that are >200 bases in length and cannot encode proteins. Evidence has indicated that lncRNAs regulate gene expression at the levels of epigenetic modification, transcription and post-transcription. In addition, they are involved in diverse tumor biological processes, including cell proliferation, apoptosis, invasion, metastasis and angiogenesis. The present review focuses on the recent progress of lncRNAs in breast cancer invasion and metastasis, aiming to provide novel strategies for the clinical prevention, diagnosis and treatment of breast cancer.
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Affiliation(s)
- Kaijiong Zhang
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Zhenglian Luo
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Yi Zhang
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Xiaoyu Song
- Department of Laboratory Medicine, Sichuan Cancer Hospital, Chengdu, Sichuan 610041, P.R. China
| | - Li Zhang
- Department of Laboratory Medicine, Sichuan Cancer Hospital, Chengdu, Sichuan 610041, P.R. China
| | - Lichun Wu
- Department of Laboratory Medicine, Sichuan Cancer Hospital, Chengdu, Sichuan 610041, P.R. China
| | - Jinbo Liu
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
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62
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Shin H, Lee J, Kim Y, Jang S, Lee Y, Kim S, Lee Y. Knockdown of BC200 RNA expression reduces cell migration and invasion by destabilizing mRNA for calcium-binding protein S100A11. RNA Biol 2017; 14:1418-1430. [PMID: 28277927 DOI: 10.1080/15476286.2017.1297913] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Although BC200 RNA is best known as a neuron-specific non-coding RNA, it is overexpressed in various cancer cells. BC200 RNA was recently shown to contribute to metastasis in several cancer cell lines, but the underlying mechanism was not understood in detail. To examine this mechanism, we knocked down BC200 RNA in cancer cells, which overexpress the RNA, and examined cell motility, profiling of ribosome footprints, and the correlation between cell motility changes and genes exhibiting altered ribosome profiles. We found that BC200 RNA knockdown reduced cell migration and invasion, suggesting that BC200 RNA promotes cell motility. Our ribosome profiling analysis identified 29 genes whose ribosomal occupations were altered more than 2-fold by BC200 RNA knockdown. Many (> 30%) of them were directly or indirectly related to cancer progression. Among them, we focused on S100A11 (which showed a reduced ribosome footprint) because its expression was previously shown to increase cellular motility. S100A11 was decreased at both the mRNA and protein levels following knockdown of BC200 RNA. An actinomycin-chase experiment showed that BC200 RNA knockdown significantly decreased the stability of the S100A11 mRNA without changing its transcription rate, suggesting that the downregulation of S100A11 was mainly caused by destabilization of its mRNA. Finally, we showed that the BC200 RNA-knockdown-induced decrease in cell motility was mainly mediated by S100A11. Together, our results show that BC200 RNA promotes cell motility by stabilizing S100A11 transcripts.
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Affiliation(s)
- Heegwon Shin
- a Department of Chemistry , KAIST , Daejeon , Korea
| | - Jungmin Lee
- a Department of Chemistry , KAIST , Daejeon , Korea
| | - Youngmi Kim
- a Department of Chemistry , KAIST , Daejeon , Korea
| | | | - Yunhee Lee
- a Department of Chemistry , KAIST , Daejeon , Korea.,b Korea Research Institute of Bioscience and Biotechnology (KRIBB) , Daejeon , Korea
| | - Semi Kim
- a Department of Chemistry , KAIST , Daejeon , Korea.,b Korea Research Institute of Bioscience and Biotechnology (KRIBB) , Daejeon , Korea
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63
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Ye N, Wang B, Quan ZF, Cao SJ, Wen XT, Huang Y, Huang XB, Wu R, Ma XP, Yan QG. Functional roles of long non-coding RNA in human breast cancer. Asian Pac J Cancer Prev 2017; 15:5993-7. [PMID: 25124562 DOI: 10.7314/apjcp.2014.15.15.5993] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
The discovery of long noncoding RNA (LncRNA) changes our view of transcriptional and posttranscriptional regulation of gene expression. With application of new research techniques such as high-throughput sequencing, the biological functions of LncRNAs are gradually becoming to be understood. Multiple studies have shown that LncRNAs serve as carcinogenic factors or tumor suppressors in breast cancer with abnormal expression, prompts the question of whether they have potential value in predicting the stages and survival rate of breast cancer patients, and also as therapeutic targets. Focusing on the latest research data, this review mainly summarizes the tumorigenic mechanisms of certain LncRNAs in breast cancer, in order to provide a theoretical basis for finding safer, more effective treatment of breast cancer at the LncRNA molecular level.
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Affiliation(s)
- Ni Ye
- College of Veterinary Medicine, Sichuan Agricultural University, Yaan, Sichuan, China E-mail :
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Gallo A, Vella S, Miele M, Timoneri F, Di Bella M, Bosi S, Sciveres M, Conaldi PG. Global profiling of viral and cellular non-coding RNAs in Epstein-Barr virus-induced lymphoblastoid cell lines and released exosome cargos. Cancer Lett 2016; 388:334-343. [PMID: 27956246 DOI: 10.1016/j.canlet.2016.12.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 12/01/2016] [Accepted: 12/02/2016] [Indexed: 01/01/2023]
Abstract
The human EBV-transformed lymphoblastoid cell line (LCL), obtained by infecting peripheral blood monocular cells with Epstein-Barr Virus, has been extensively used for human genetic, pharmacogenomic, and immunologic studies. Recently, the role of exosomes has also been indicated as crucial in the crosstalk between EBV and the host microenvironment. Because the role that the LCL and LCL exosomal cargo might play in maintaining persistent infection, and since little is known regarding the non-coding RNAs of LCL, the aim of our work was the comprehensive characterization of this class of RNA, cellular and viral miRNAs, and cellular lncRNAs, in LCL compared with PBMC derived from the same donors. In this study, we have demonstrated, for the first time, that all the viral miRNAs expressed by LCL are also packaged in the exosomes, and we found that two miRNAs, ebv-miR-BART3 and ebv-miR-BHRF1-1, are more abundant in the exosomes, suggesting a microvescicular viral microRNA transfer. In addition, lncRNA profiling revealed that LCLs were enriched in lncRNA H19 and H19 antisense, and released these through exosomes, suggesting a leading role in the regulation of the tumor microenvironment.
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Affiliation(s)
- Alessia Gallo
- Department of Laboratory Medicine and Advanced Biotechnologies, IRCCS-ISMETT (Istituto Mediterraneo per i Trapianti e Terapie ad alta specializzazione), Italy.
| | - Serena Vella
- Department of Laboratory Medicine and Advanced Biotechnologies, IRCCS-ISMETT (Istituto Mediterraneo per i Trapianti e Terapie ad alta specializzazione), Italy
| | | | | | | | | | - Marco Sciveres
- Pediatric Hepatology and Liver Transplantation, IRCCS ISMETT, University of Pittsburgh Medical Center, Palermo, Italy
| | - Pier Giulio Conaldi
- Department of Laboratory Medicine and Advanced Biotechnologies, IRCCS-ISMETT (Istituto Mediterraneo per i Trapianti e Terapie ad alta specializzazione), Italy; Fondazione Ri.MED, Italy
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65
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Endothelial dysfunction and cardiometabolic diseases: Role of long non-coding RNAs. Life Sci 2016; 167:6-11. [DOI: 10.1016/j.lfs.2016.11.005] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 11/02/2016] [Accepted: 11/07/2016] [Indexed: 12/19/2022]
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66
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Wang J, Zhao S, Wei Y, Zhou Y, Shore P, Deng W. Cytoskeletal Filamin A Differentially Modulates RNA Polymerase III Gene Transcription in Transformed Cell Lines. J Biol Chem 2016; 291:25239-25246. [PMID: 27738102 DOI: 10.1074/jbc.m116.735886] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 10/11/2016] [Indexed: 11/06/2022] Open
Abstract
Cytoskeletal filamin A (FLNA) is an important protein involved in multiple cellular processes. Previous studies have shown that FLNA can promote or inhibit cancer growth and development; however, the mechanisms underlying these events are not fully understood. Here we show that, in both 293T and SaOS2 cells, knockdown of FLNA significantly enhanced transcription of RNA polymerase (pol) III-transcribed genes except for a subset of tRNA genes. In contrast, re-expression of FLNA in an FLNA-deficient melanoma cell line (A7) repressed transcription of all pol III-transcribed genes, suggesting that FLNA inhibits pol III transcription in a cell type-specific manner. Chromatin immunoprecipitation assays revealed that the repression of pol III gene transcription by FLNA correlates with the decreased occupancy of the RNA pol III transcription machinery at promoters. Immunofluorescence microscopy and coimmunoprecipitation assays revealed that FLNA can associate with the RNA pol III transcription machinery through its actin-binding domain within nuclei. Mechanistic analysis revealed that FLNA suppresses pol III gene transcription by confining the recruitment of the RNA pol III transcription machinery at the promoters of the genes that are sensitive to the alteration of FLNA expression. These findings not only extend the understanding of FLNA function in cells but also provide novel insights into the mechanism by which FLNA represses cell proliferation.
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Affiliation(s)
- Juan Wang
- From the Institute of Biology and Medicine, Wuhan University of Science and Technology, Wuhan, Hubei Province 430065, China and
| | - Shasha Zhao
- From the Institute of Biology and Medicine, Wuhan University of Science and Technology, Wuhan, Hubei Province 430065, China and
| | - Yun Wei
- From the Institute of Biology and Medicine, Wuhan University of Science and Technology, Wuhan, Hubei Province 430065, China and
| | - Ying Zhou
- From the Institute of Biology and Medicine, Wuhan University of Science and Technology, Wuhan, Hubei Province 430065, China and
| | - Paul Shore
- the Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, United Kingdom
| | - Wensheng Deng
- From the Institute of Biology and Medicine, Wuhan University of Science and Technology, Wuhan, Hubei Province 430065, China and
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67
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Wei MM, Zhou GB. Long Non-coding RNAs and Their Roles in Non-small-cell Lung Cancer. GENOMICS, PROTEOMICS & BIOINFORMATICS 2016; 14:280-288. [PMID: 27397102 PMCID: PMC5093404 DOI: 10.1016/j.gpb.2016.03.007] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 02/24/2016] [Accepted: 03/01/2016] [Indexed: 12/25/2022]
Abstract
As a leading cause of cancer deaths worldwide, lung cancer is a collection of diseases with diverse etiologies which can be broadly classified into small-cell lung cancer (SCLC) and non-small-cell lung cancer (NSCLC). Lung cancer is characterized by genomic and epigenomic alterations; however, mechanisms underlying lung tumorigenesis remain to be elucidated. Long non-coding RNAs (lncRNAs) are a group of non-coding RNAs that consist of ⩾200 nucleotides but possess low or no protein-coding potential. Accumulating evidence indicates that abnormal expression of lncRNAs is associated with tumorigenesis of various cancers, including lung cancer, through multiple biological mechanisms involving epigenetic, transcriptional, and post-transcriptional alterations. In this review, we highlight the expression and roles of lncRNAs in NSCLC and discuss their potential clinical applications as diagnostic or prognostic biomarkers, as well as therapeutic targets.
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Affiliation(s)
- Ming-Ming Wei
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guang-Biao Zhou
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
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68
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Nikpayam E, Tasharrofi B, Sarrafzadeh S, Ghafouri-Fard S. The Role of Long Non-Coding RNAs in Ovarian Cancer. IRANIAN BIOMEDICAL JOURNAL 2016; 21:3-15. [PMID: 27132108 PMCID: PMC5141250 DOI: 10.6091/.21.1.24] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Background: Mesenchymal stem cells (MSCs) are important candidates for MSC-based cellular therapy. Current paradigm states that MSCs support local progenitor cells in damaged tissue through paracrine signaling. Therefore, the study of paracrine effects and secretome of MSCs could lead to the appreciation of mechanisms and molecules associated with the therapeutic effects of these cells. This study analyzed anti-inflammatory and immune-modulatory effects of MSC secretomes derived from embryonic stem cells (ESCs) and bone marrow cells after hypoxia and normoxia preconditioning. Methods: ESCs differentiated into MSCs and characterized by flow cytometry as well as by differentiation into adipocytes and osteoblasts. The experimental groups were consisted of individual groups of ESC-MSCs and BM-MSCs (bone marrow-derived mesenchymal stromal cells), which were preconditioned with either hypoxia or normoxia for 24, 48 and 72 h. After collecting the cell-free medium from each treatment, secretomes were concentrated by centrifugal filters. Using a peripheral blood mononuclear cell (PBMC) assay and ELISA, IL-10 concentration in PBMCs was evaluated after their incubation with different secretomes from preconditioned and non-preconditioned MSCs. Results: A significant difference was observed between ESC-MSC normoxia and ESC-MSC hypoxia in IL-10 concentration, and normoxia secretomes increased IL-10 secretion from PBMCs. Moreover, the strongest IL-10 secretion from PBMCs could be detected after the stimulation by ESC-MSC conditioned secretomes, but not BM-MSC conditioned medium. Conclusions: Human hypoxia preconditioned ESC-MSC secretome indicated stronger immune-modulatory effects compared to BM-MSC conditioned medium. It could be suggested that induced MSCs confer less immune-modulatory effects but produce more inflammatory molecules such as tumor necrosis factor α, which needs further investigation.
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Affiliation(s)
- Elahe Nikpayam
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Behnoosh Tasharrofi
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Shaghayegh Sarrafzadeh
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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69
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Genome-wide profiling of transfer RNAs and their role as novel prognostic markers for breast cancer. Sci Rep 2016; 6:32843. [PMID: 27604545 PMCID: PMC5015097 DOI: 10.1038/srep32843] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 08/11/2016] [Indexed: 11/25/2022] Open
Abstract
Transfer RNAs (tRNAs, key molecules in protein synthesis) have not been investigated as potential prognostic markers in breast cancer (BC), despite early findings of their dysregulation and diagnostic potential. We aim to comprehensively profile tRNAs from breast tissues and to evaluate their role as prognostic markers (Overall Survival, OS and Recurrence Free Survival, RFS). tRNAs were profiled from 11 normal breast and 104 breast tumor tissues using next generation sequencing. We adopted a Case-control (CC) and Case-Only (CO) association study designs. Risk scores constructed from tRNAs were subjected to univariate and multivariate Cox-proportional hazards regression to investigate their prognostic value. Of the 571 tRNAs profiled, 76 were differentially expressed (DE) and three were significant for OS in the CC approach. We identified an additional 11 tRNAs associated with OS and 14 tRNAs as significant for RFS in the CO approach, indicating that CC alone may not capture all discriminatory tRNAs in prognoses. In both the approaches, the risk scores were significant in the multivariate analysis as independent prognostic factors, and patients belonging to high-risk group were associated with poor prognosis. Our results confirmed global up-regulation of tRNAs in BC and identified tRNAs as potential novel prognostic markers for BC.
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70
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Kieckhaefer JE, Lukovac S, Ye DZ, Lee D, Beetler DJ, Pack M, Kaestner KH. The RNA polymerase III subunit Polr3b is required for the maintenance of small intestinal crypts in mice. Cell Mol Gastroenterol Hepatol 2016; 2:783-795. [PMID: 28090567 PMCID: PMC5235342 DOI: 10.1016/j.jcmgh.2016.08.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
BACKGROUND & AIMS The continuously self-renewing mammalian intestinal epithelium, with high cellular turnover, depends on adequate protein synthesis for its proliferative capacity. RNA polymerase III activity is closely related to cellular growth and proliferation. Here, we studied the role of Polr3b, a large RNA polymerase III subunit, in the mammalian intestinal epithelium. METHODS We derived mice with an intestinal epithelium-specific hypomorphic mutation of the Polr3b gene, using VillinCre-mediated gene ablation. Phenotypic consequences of the Polr3b mutation on the intestinal epithelium in mice were assessed using histological and molecular methodologies, including genetic lineage tracing. RESULTS The Polr3b mutation severely reduced survival and growth in mice during the first postnatal week, the period when the expansion of the intestinal epithelium, and thus the requirement for protein synthesis, are highest. The neonatal intestinal epithelium of Polr3bloxP/loxP;VillinCre mice was characterized by areas with reduced proliferation, abnormal epithelial architecture, loss of Wnt signaling and a dramatic increase in apoptotic cells in crypts. Genetic lineage tracing using Polr3bLoxP/LoxP;Rosa26-lox-stop-lox-YFP;VillinCre mice demonstrated that in surviving mutant mice, Polr3b-deficient dying crypts were progressively replaced by 'Cre-escaper' cells that had retained wild type Polr3b function. In addition, enteroids cultured from Polr3bloxP/loxP;VillinCre mice show reduced proliferative activity and increased apoptosis. CONCLUSIONS We provide evidence for an essential role of the Pol III subunit Polr3b in orchestrating the maintenance of the intestinal crypt during early postnatal development in mice.
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Affiliation(s)
- Julia E. Kieckhaefer
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania,Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Sabina Lukovac
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania,Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Diana Z. Ye
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania,Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Dolim Lee
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania,Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Danielle J. Beetler
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Michael Pack
- Department of Cell and Developmental Biology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania,Michael Pack, MD, University of Pennsylvania, Perelman School of Medicine, 1212 Biomedical Research Building II/III, 421 Curie Boulevard, Philadelphia, Pennsylvania 19104. fax: (215) 898-9871.University of PennsylvaniaPerelman School of Medicine1212 Biomedical Research Building II/III421 Curie BoulevardPhiladelphiaPennsylvania 19104
| | - Klaus H. Kaestner
- Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania,Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania,Correspondence Address correspondence to: Klaus H. Kaestner, PhD, 12-126 Smilow Center for Translational Research, University of Pennsylvania, Perelman School of Medicine, 3400 Civic Center Boulevard, Philadelphia, Pennsylvania 19104. fax: (215) 573-5892.12-126 Smilow Center for Translational ResearchUniversity of PennsylvaniaPerelman School of Medicine3400 Civic Center BoulevardPhiladelphiaPennsylvania 19104
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71
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Wang T, Ma S, Qi X, Tang X, Cui D, Wang Z, Chi J, Li P, Zhai B. Long noncoding RNA ZNFX1-AS1 suppresses growth of hepatocellular carcinoma cells by regulating the methylation of miR-9. Onco Targets Ther 2016; 9:5005-14. [PMID: 27574442 PMCID: PMC4990377 DOI: 10.2147/ott.s103329] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Many long noncoding RNAs have been reported to play pivotal roles in cancer biology. Among them, the long noncoding RNA ZNFX1-AS1 has been confirmed to function in breast cancer progression, but the role of ZNFX1-AS1 in hepatocellular carcinoma (HCC) growth and the related molecular mechanisms still remains unknown. In the present study, we first identified the expression of ZNFX1-AS1 in HCC patients' specimens and HCC cell lines through quantitative reverse transcription polymerase chain reaction. Next, the effects of ZNFX1-AS1 on HCC cell growth and apoptosis were analyzed. MTT assay was used to measure the cell numbers, and fluorescence-activated cell sorting analysis was performed to evaluate cell apoptosis. Finally, the relationship between ZNFX1-AS1 and miR-9 in HCC was studied. Our results suggest that ZNFX1-AS1 was markedly downregulated in HCC samples and cell lines. Overexpression of ZNFX1-AS1 inhibited the cell proliferation and colony formation in HCC cell lines and also induced HCC cell apoptosis. Additionally, miR-9 was lowly expressed in HCC tissues and positively correlated with ZNFX1-AS1 expression. Meanwhile, significant upregulation of miR-9 and downregulation of the methylation of miR-9 promoter CpG island were observed when ZNFX1-AS1 was overexpressed. In summary, our results indicate that ZNFX1-AS1 plays a vital role in HCC progression via regulating the methylation of miR-9 and may be a potential tumor suppressor.
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Affiliation(s)
- Tao Wang
- Department of Interventional Oncology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Sicong Ma
- Department of Interventional Oncology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Xingxing Qi
- Department of Interventional Oncology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Xiaoyin Tang
- Department of Interventional Oncology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Dan Cui
- Department of Interventional Oncology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Zhi Wang
- Department of Interventional Oncology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Jiachang Chi
- Department of Interventional Oncology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Ping Li
- Department of Interventional Oncology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Bo Zhai
- Department of Interventional Oncology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People's Republic of China
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Abstract
Despite great progress in research and treatment options, lung cancer remains the leading cause of cancer-related deaths worldwide. Oncogenic driver mutations in protein-encoding genes were defined and allow for personalized therapies based on genetic diagnoses. Nonetheless, diagnosis of lung cancer mostly occurs at late stages, and chronic treatment is followed by a fast onset of chemoresistance. Hence, there is an urgent need for reliable biomarkers and alternative treatment options. With the era of whole genome and transcriptome sequencing technologies, long noncoding RNAs emerged as a novel class of versatile, functional RNA molecules. Although for most of them the mechanism of action remains to be defined, accumulating evidence confirms their involvement in various aspects of lung tumorigenesis. They are functional on the epigenetic, transcriptional, and posttranscriptional level and are regulators of pathophysiological key pathways including cell growth, apoptosis, and metastasis. Long noncoding RNAs are gaining increasing attention as potential biomarkers and a novel class of druggable molecules. It has become clear that we are only beginning to understand the complexity of tumorigenic processes. The clinical integration of long noncoding RNAs in terms of prognostic and predictive biomarker signatures and additional cancer targets could provide a chance to increase the therapeutic benefit. Here, we review the current knowledge about the expression, regulation, biological function, and clinical relevance of long noncoding RNAs in lung cancer.
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Affiliation(s)
- Anna Roth
- Division of RNA Biology and Cancer, German Cancer Research Center (DKFZ) and Institute of Pathology, University Hospital Heidelberg, Im Neuenheimer Feld 280 (B150), 69120, Heidelberg, Germany
| | - Sven Diederichs
- Division of RNA Biology and Cancer, German Cancer Research Center (DKFZ) and Institute of Pathology, University Hospital Heidelberg, Im Neuenheimer Feld 280 (B150), 69120, Heidelberg, Germany.
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Noncoding RNAs Regulating p53 and c-Myc Signaling. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 927:337-65. [DOI: 10.1007/978-981-10-1498-7_13] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Singh R, Gupta SC, Peng WX, Zhou N, Pochampally R, Atfi A, Watabe K, Lu Z, Mo YY. Regulation of alternative splicing of Bcl-x by BC200 contributes to breast cancer pathogenesis. Cell Death Dis 2016; 7:e2262. [PMID: 27277684 PMCID: PMC5143396 DOI: 10.1038/cddis.2016.168] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 05/29/2016] [Accepted: 05/12/2016] [Indexed: 01/06/2023]
Abstract
BC200 is a long non-coding RNA (lncRNA) that has been implicated in the regulation of protein synthesis, yet whether dysregulation of BC200 contributes to the pathogenesis of human diseases remains elusive. In this study, we show that BC200 is upregulated in breast cancer; among breast tumor specimens there is a higher level of BC200 in estrogen receptor (ER) positive than in ER-negative tumors. Further experiments show that activation of estrogen signaling induces expression of BC200. To determine the significance of ER-regulated BC200 expression, we knockout (KO) BC200 by CRISPR/Cas9. BC200 KO suppresses tumor cell growth in vitro and in vivo by expression of the pro-apoptotic Bcl-xS isoform. Mechanistically, BC200 contains a 17-nucleotide sequence complementary to Bcl-x pre-mRNA, which may facilitate its binding to Bcl-x pre-mRNA and recruitment of heterogeneous nuclear ribonucleoprotein (hnRNP) A2/B1, a known splicing factor. Consequently, hnRNP A2/B1 interferes with association of Bcl-x pre-mRNA with the Bcl-xS-promoting factor Sam68, leading to a blockade of Bcl-xS expression. Together, these results suggest that BC200 plays an oncogenic role in breast cancer. Thus, BC200 may serve as a prognostic marker and possible target for attenuating deregulated cell proliferation in estrogen-dependent breast cancer.
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Affiliation(s)
- R Singh
- Department of Biochemistry, Cancer Institute, University of Mississippi Medical Center, Jackson, MS, USA
| | - S C Gupta
- Department of Biochemistry, Cancer Institute, University of Mississippi Medical Center, Jackson, MS, USA
| | - W-X Peng
- Department of Biochemistry, Cancer Institute, University of Mississippi Medical Center, Jackson, MS, USA.,Department of Cell Biology, School of Medicine, Jiangsu University, Zhenjiang, China
| | - N Zhou
- System Biosciences, Mountain View, CA, USA
| | - R Pochampally
- Department of Biochemistry, Cancer Institute, University of Mississippi Medical Center, Jackson, MS, USA
| | - A Atfi
- Department of Biochemistry, Cancer Institute, University of Mississippi Medical Center, Jackson, MS, USA
| | - K Watabe
- Cancer Biology, Wake Forest School of Medicine, Bermuda Run, NC, USA
| | - Z Lu
- Department of Endocrinology, PLA General Hospital, Beijing, China
| | - Y-Y Mo
- Department of Pharmacology/Toxicology and Cancer Institute, University of Mississippi Medical Center, Jackson, MS, USA
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75
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Zhao RH, Zhu CH, Li XK, Cao W, Zong H, Cao XG, Hu HY. BC200 LncRNA a potential predictive marker of poor prognosis in esophageal squamous cell carcinoma patients. Onco Targets Ther 2016; 9:2221-6. [PMID: 27143917 PMCID: PMC4846077 DOI: 10.2147/ott.s99401] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
OBJECTIVE To explore the expression and prognosis significance of BC200 in esophageal squamous cell carcinoma (ESCC) patients who received radical resection. METHODS We used quantitative real-time polymerase chain reaction to detect the expression level of BC200 in cancer tissue and paired adjacent normal tissue samples from 70 ESCC patients who received radical surgical resection and analyzed the correlation of the relative expression level of BC200 with clinical-pathological features and prognosis. RESULTS We found that the relative expression of BC200 was significantly higher in ESCC tissues compared with adjacent normal tissue samples (P=0.023). But the expression of BC200 were not related to clinical-pathological features, such as age, TNM stages, and histological grade (P>0.05). Kaplan-Meier analysis showed that high expression levels of BC200 were correlated with poor prognosis in ESCC patients. Patients with a high level of BC200 had a shorter disease-free survival and overall survival than those with low BC200 expression (P=0.034 and P=0.031, respectively). On multivariate analysis, the hazard ratio (HR) of BC200 expression was 2.17 (95% confidence interval [CI]=1.12-4.19, P=0.022) for disease-free survival and 2.24 (95% CI=1.12-4.49, P=0.023) for overall survival. CONCLUSION Our results indicate that high expression of BC200 reflects poor prognosis and could serve as a novel predictive marker for ESCC patients who received radical resection.
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Affiliation(s)
- Rui-Hua Zhao
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - Cai-Hua Zhu
- Department of General Surgery, The Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - Xiang-Ke Li
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - Wei Cao
- Department of Translational Medicine Center, Zhengzhou Center Hospital, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - Hong Zong
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - Xin-Guang Cao
- Department of General Surgery, The Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, Henan, People's Republic of China; Department of Digestive Disease, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - Hai-Yan Hu
- Oncology Department, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, People's Republic of China
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Abstract
Long noncoding RNAs (lncRNAs) are dysregulated in many cancer types and are believed to play crucial roles in regulating several hallmarks of cancer biology. Currently, most studies support the concept that lncRNAs are involved in either transcriptional or post-transcriptional processes via binding/targeting epigenetic modifiers or hRNP complexes. The discovery of new biological functions of lncRNA and novel RNA binding proteins suggests that lncRNAs may be implicated in a broad spectrum of biological processes such as signal transduction, allosteric regulation of cytoplasmic enzymatic activities, among other potential processes. In a recent report that we have made, based on open-ended lncRNA pulldown technology and a series of systematic analyses, we suggest that lncRNAs also play critical roles in the regulation of noncanonical Hedgehog/GLI 2 signal transduction pathways in cancer cells, which further broadens the scope of known lncRNA functions and aids in the discovery and design of more effective and evidence-based therapeutic targets for the treatment of human cancers and other diseases.
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Affiliation(s)
- Zhen Xing
- a Department of Molecular and Cellular Oncology; MD Anderson Cancer Center; The University of Texas ; Houston , TX , USA
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Széll M, Danis J, Bata-Csörgő Z, Kemény L. PRINS, a primate-specific long non-coding RNA, plays a role in the keratinocyte stress response and psoriasis pathogenesis. Pflugers Arch 2016; 468:935-43. [PMID: 26935426 PMCID: PMC4893059 DOI: 10.1007/s00424-016-1803-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 02/23/2016] [Indexed: 12/30/2022]
Abstract
In the last few years with the recent emergence of high-throughput technologies, thousands of long non-coding RNAs (lncRNAs) have been identified in the human genome. However, assigning functional annotation and determining cellular contexts for these RNAs are still in its infancy. As information gained about lncRNA structure, interacting partners, and roles in human diseases may be helpful in the characterization of novel lncRNAs, we review our knowledge on a selected group of lncRNAs that were identified serendipitously years ago by large-scale gene expression methods used to study human diseases. In particular, we focus on the Psoriasis-susceptibility-Related RNA Gene Induced by Stress (PRINS) lncRNA, first identified by our research group as a transcript highest expressed in psoriatic non-lesional epidermis. Results gathered for PRINS in the last 10 years indicate that it is conserved in primates and plays a role in keratinocyte stress response. Elevated levels of PRINS expression in psoriatic non-lesional keratinocytes alter the stress response of non-lesional epidermis and contribute to disease pathogenesis. Finally, we propose a categorization for the PRINS lncRNA based on a recently elaborated system for lncRNA classification.
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Affiliation(s)
- Márta Széll
- Department of Medical Genetics, Faculty of Medicine, University of Szeged, Szeged, Somogyi B. u. 4, 6720, Hungary. .,MTA-SZTE Dermatological Research Group, Szeged, Korányi fasor 6, 6720, Hungary.
| | - Judit Danis
- Department of Dermatology and Allergology, Faculty of Medicine, University of Szeged, Szeged, Korányi fasor 6, 6720, Hungary
| | - Zsuzsanna Bata-Csörgő
- MTA-SZTE Dermatological Research Group, Szeged, Korányi fasor 6, 6720, Hungary.,Department of Dermatology and Allergology, Faculty of Medicine, University of Szeged, Szeged, Korányi fasor 6, 6720, Hungary
| | - Lajos Kemény
- MTA-SZTE Dermatological Research Group, Szeged, Korányi fasor 6, 6720, Hungary.,Department of Dermatology and Allergology, Faculty of Medicine, University of Szeged, Szeged, Korányi fasor 6, 6720, Hungary
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Booy EP, McRae EKS, Howard R, Deo SR, Ariyo EO, Dzananovic E, Meier M, Stetefeld J, McKenna SA. RNA Helicase Associated with AU-rich Element (RHAU/DHX36) Interacts with the 3'-Tail of the Long Non-coding RNA BC200 (BCYRN1). J Biol Chem 2016; 291:5355-72. [PMID: 26740632 DOI: 10.1074/jbc.m115.711499] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Indexed: 12/14/2022] Open
Abstract
RNA helicase associated with AU-rich element (RHAU) is an ATP-dependent RNA helicase that demonstrates high affinity for quadruplex structures in DNA and RNA. To elucidate the significance of these quadruplex-RHAU interactions, we have performed RNA co-immunoprecipitation screens to identify novel RNAs bound to RHAU and characterize their function. In the course of this study, we have identified the non-coding RNA BC200 (BCYRN1) as specifically enriched upon RHAU immunoprecipitation. Although BC200 does not adopt a quadruplex structure and does not bind the quadruplex-interacting motif of RHAU, it has direct affinity for RHAU in vitro. Specifically designed BC200 truncations and RNase footprinting assays demonstrate that RHAU binds to an adenosine-rich region near the 3'-end of the RNA. RHAU truncations support binding that is dependent upon a region within the C terminus and is specific to RHAU isoform 1. Tests performed to assess whether BC200 interferes with RHAU helicase activity have demonstrated the ability of BC200 to act as an acceptor of unwound quadruplexes via a cytosine-rich region near the 3'-end of the RNA. Furthermore, an interaction between BC200 and the quadruplex-containing telomerase RNA was confirmed by pull-down assays of the endogenous RNAs. This leads to the possibility that RHAU may direct BC200 to bind and exert regulatory functions at quadruplex-containing RNA or DNA sequences.
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Affiliation(s)
| | | | | | | | | | | | | | - Jörg Stetefeld
- From the Departments of Chemistry and Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Sean A McKenna
- From the Departments of Chemistry and Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
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79
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Li Y, Wang X. Role of long noncoding RNAs in malignant disease (Review). Mol Med Rep 2015; 13:1463-9. [PMID: 26708950 DOI: 10.3892/mmr.2015.4711] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 11/24/2015] [Indexed: 11/06/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are endogenous transcribed RNA molecules without protein-coding potential, ranging between 200 and 100,000 nt in length. LncRNAs regulate the expression of specific genes in several ways, including guiding chromatin-remodeling, and affecting splicing, transcription or translation. The mutations and dysregulation of lncRNAs have been found to be important in various human diseases, but particularly in human cancer. Previous studies have demonstrated that changes to lncRNAs are closely associated with tumorigenesis, metastasis, prognosis and diagnosis. The current review aims to present a brief overview of the associated reports of lncRNAs in malignant neoplasms, including breast cancer, prostate cancer and hematological malignancies. LncRNAs may be evaluated as novel markers in disease diagnosis, and as prospective therapeutic targets for the prevention and treatment of human diseases.
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Affiliation(s)
- Ying Li
- Department of Hematology, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, Shandong 250021, P.R. China
| | - Xin Wang
- Department of Hematology, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, Shandong 250021, P.R. China
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80
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Downregulation of BC200 in ovarian cancer contributes to cancer cell proliferation and chemoresistance to carboplatin. Oncol Lett 2015; 11:1189-1194. [PMID: 26893717 DOI: 10.3892/ol.2015.3983] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2015] [Accepted: 10/28/2015] [Indexed: 12/27/2022] Open
Abstract
Previous studies have demonstrated that long non-coding RNAs (lncRNAs) serve an important role in carcinogenesis. BC200 is a lncRNA that is reportedly associated with ovarian cancer. The aim of the present study was to investigate this potential association between BC200 and ovarian cancer, and to subsequently analyze the biological function of BC200 in the disease. BC200 expression was compared in ovarian cancer tissue and normal ovarian tissue samples through the use of quantitative polymerase chain reaction. To allow the biological function of BC200 in ovarian cancer to be analyzed, small interfering RNA was used to knock down the expression of BC200 in SKOV3 and A2780 ovarian cancer cells. The proliferative, invasive and migratory abilities of the cells were identified by means of cell counting kits and Transwell assays. Carboplatin was also used to treat the ovarian cancer cells, and a luminescent cell viability assay was subsequently used to detect the sensitivity of the cells to the carboplatin. The results demonstrated that BC200 expression was reduced in ovarian cancer compared with normal ovarian tissue samples. In the SKOV3 and A2780 cells, BC200 exerted no effect on invasive or migratory ability, however, the inhibition of BC200 was demonstrated to promote cell proliferation. Additionally, it was observed that carboplatin induced BC200 expression in the cell lines, and that the inhibition of BC200 decreased the sensitivity of the cells to the drug. BC200 is therefore likely to have a tumor suppressive function in ovarian cancer by affecting cell proliferation. Furthermore, BC200 appears to serve a role in the mediation of carboplatin-induced ovarian cancer cell death.
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81
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Role of Exosomal Noncoding RNAs in Lung Carcinogenesis. BIOMED RESEARCH INTERNATIONAL 2015; 2015:125807. [PMID: 26583084 PMCID: PMC4637011 DOI: 10.1155/2015/125807] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 07/05/2015] [Accepted: 07/16/2015] [Indexed: 12/28/2022]
Abstract
Lung cancer is the major cause of cancer death worldwide. Novel, recently discovered classes of noncoding RNAs (ncRNAs) have diverse functional and regulatory activities and increasing evidence suggests crucial roles for deregulated ncRNAs in the onset and progression of cancer, including lung cancer. Exosomes are small extracellular membrane vesicles of endocytic origin that are released by many cells and are found in most body fluids. Tumor-derived exosomes mediate tumorigenesis by facilitating tumor growth and metastasis. MicroRNAs (miRNAs) are a subclass of ncRNAs that are present in exosomes. miRNAs are taken up by neighboring or distant cells and modulate various functions of recipient cells. Here, we review exosome-derived ncRNAs with a focus on miRNAs and their role in lung cancer biology.
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82
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Sosińska P, Mikuła-Pietrasik J, Książek K. The double-edged sword of long non-coding RNA: The role of human brain-specific BC200 RNA in translational control, neurodegenerative diseases, and cancer. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2015; 766:58-67. [DOI: 10.1016/j.mrrev.2015.08.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 07/29/2015] [Accepted: 08/28/2015] [Indexed: 12/14/2022]
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83
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Abdelmohsen K, Gorospe M. Noncoding RNA control of cellular senescence. WILEY INTERDISCIPLINARY REVIEWS-RNA 2015; 6:615-29. [PMID: 26331977 DOI: 10.1002/wrna.1297] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Revised: 07/19/2015] [Accepted: 07/20/2015] [Indexed: 12/23/2022]
Abstract
Senescent cells accumulate in normal tissues with advancing age and arise by long-term culture of primary cells. Senescence develops following exposure to a range of stress-causing agents and broadly influences the physiology and pathology of tissues, organs, and systems in the body. While many proteins are known to control senescence, numerous noncoding (nc)RNAs are also found to promote or repress the senescent phenotype. Here, we review the regulatory ncRNAs (primarily microRNAs and lncRNAs) identified to-date as key modulators of senescence. We highlight the major senescent pathways (p53/p21 and pRB/p16), as well as the senescence-associated secretory phenotype (SASP) and other senescence-associated events governed by ncRNAs, and discuss the importance of understanding comprehensively the ncRNAs implicated in cell senescence.
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Affiliation(s)
- Kotb Abdelmohsen
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, National Institutes of Health, Baltimore, MD, USA
| | - Myriam Gorospe
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, National Institutes of Health, Baltimore, MD, USA
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84
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Grammatikakis I, Panda AC, Abdelmohsen K, Gorospe M. Long noncoding RNAs(lncRNAs) and the molecular hallmarks of aging. Aging (Albany NY) 2015; 6:992-1009. [PMID: 25543668 PMCID: PMC4298369 DOI: 10.18632/aging.100710] [Citation(s) in RCA: 149] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
During aging, progressive deleterious changes increase the risk of disease and death. Prominent molecular hallmarks of aging are genomic instability, telomere attrition, epigenetic alterations, loss of proteostasis, cellular senescence, stem cell exhaustion, and altered intercellular communication. Long noncoding RNAs (lncRNAs) play important roles in a wide range of biological processes, including age-related diseases like cancer, cardiovascular pathologies, and neurodegenerative disorders. Evidence is emerging that lncRNAs influence the molecular processes that underlie age-associated phenotypes. Here, we review our current understanding of lncRNAs that control the development of aging traits.
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Affiliation(s)
- Ioannis Grammatikakis
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, NIH, Baltimore, MD 21224, USA
| | - Amaresh C Panda
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, NIH, Baltimore, MD 21224, USA
| | - Kotb Abdelmohsen
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, NIH, Baltimore, MD 21224, USA
| | - Myriam Gorospe
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, NIH, Baltimore, MD 21224, USA
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85
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Kim J, Kim KM, Noh JH, Yoon JH, Abdelmohsen K, Gorospe M. Long noncoding RNAs in diseases of aging. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1859:209-21. [PMID: 26141605 DOI: 10.1016/j.bbagrm.2015.06.013] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 06/13/2015] [Accepted: 06/24/2015] [Indexed: 12/22/2022]
Abstract
Aging is a process during which progressive deteriorating of cells, tissues, and organs over time lead to loss of function, disease, and death. Towards the goal of extending human health span, there is escalating interest in understanding the mechanisms that govern aging-associated pathologies. Adequate regulation of expression of coding and noncoding genes is critical for maintaining organism homeostasis and preventing disease processes. Long noncoding RNAs (lncRNAs) are increasingly recognized as key regulators of gene expression at all levels--transcriptional, post-transcriptional and post-translational. In this review, we discuss our emerging understanding of lncRNAs implicated in aging illnesses. We focus on diseases arising from age-driven impairment in energy metabolism (obesity, diabetes), the declining capacity to respond homeostatically to proliferative and damaging stimuli (cancer, immune dysfunction), and neurodegeneration. We identify the lncRNAs involved in these ailments and discuss the rising interest in lncRNAs as diagnostic and therapeutic targets to ameliorate age-associated pathologies and prolong health. This article is part of a Special Issue entitled: Clues to long noncoding RNA taxonomy1, edited by Dr. Tetsuro Hirose and Dr. Shinichi Nakagawa.
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Affiliation(s)
- Jiyoung Kim
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Kyoung Mi Kim
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Ji Heon Noh
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Je-Hyun Yoon
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Kotb Abdelmohsen
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA.
| | - Myriam Gorospe
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA.
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86
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Fatima R, Akhade VS, Pal D, Rao SM. Long noncoding RNAs in development and cancer: potential biomarkers and therapeutic targets. MOLECULAR AND CELLULAR THERAPIES 2015; 3:5. [PMID: 26082843 PMCID: PMC4469312 DOI: 10.1186/s40591-015-0042-6] [Citation(s) in RCA: 203] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 05/19/2015] [Indexed: 02/07/2023]
Abstract
Long noncoding RNAs are emerging as key players in various fundamental biological processes. We highlight the varied molecular mechanisms by which lncRNAs modulate gene expression in diverse cellular contexts and their role in early mammalian development in this review. Furthermore, it is being increasingly recognized that altered expression of lncRNAs is specifically associated with tumorigenesis, tumor progression and metastasis. We discuss various lncRNAs implicated in different cancer types with a focus on their clinical applications as potential biomarkers and therapeutic targets in the pathology of diverse cancers.
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Affiliation(s)
- Roshan Fatima
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Center for Advanced Scientific Research, Jakkur, Bangalore 560064 India
| | - Vijay Suresh Akhade
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Center for Advanced Scientific Research, Jakkur, Bangalore 560064 India
| | - Debosree Pal
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Center for Advanced Scientific Research, Jakkur, Bangalore 560064 India
| | - Satyanarayana Mr Rao
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Center for Advanced Scientific Research, Jakkur, Bangalore 560064 India
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87
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Abstract
Background Terpenoids are abundant in the foliage of Eucalyptus, providing the characteristic smell as well as being valuable economically and influencing ecological interactions. Quantitative and qualitative inter- and intra- specific variation of terpenes is common in eucalypts. Results The genome sequences of Eucalyptus grandis and E. globulus were mined for terpene synthase genes (TPS) and compared to other plant species. We investigated the relative expression of TPS in seven plant tissues and functionally characterized five TPS genes from E. grandis. Compared to other sequenced plant genomes, Eucalyptus grandis has the largest number of putative functional TPS genes of any sequenced plant. We discovered 113 and 106 putative functional TPS genes in E. grandis and E. globulus, respectively. All but one TPS from E. grandis were expressed in at least one of seven plant tissues examined. Genomic clusters of up to 20 genes were identified. Many TPS are expressed in tissues other than leaves which invites a re-evaluation of the function of terpenes in Eucalyptus. Conclusions Our data indicate that terpenes in Eucalyptus may play a wider role in biotic and abiotic interactions than previously thought. Tissue specific expression is common and the possibility of stress induction needs further investigation. Phylogenetic comparison of the two investigated Eucalyptus species gives insight about recent evolution of different clades within the TPS gene family. While the majority of TPS genes occur in orthologous pairs some clades show evidence of recent gene duplication, as well as loss of function. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1598-x) contains supplementary material, which is available to authorized users.
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88
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Külheim C, Padovan A, Hefer C, Krause ST, Köllner TG, Myburg AA, Degenhardt J, Foley WJ. The Eucalyptus terpene synthase gene family. BMC Genomics 2015. [PMID: 26062733 DOI: 10.1186/s.12864-015-1598] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/24/2023] Open
Abstract
BACKGROUND Terpenoids are abundant in the foliage of Eucalyptus, providing the characteristic smell as well as being valuable economically and influencing ecological interactions. Quantitative and qualitative inter- and intra- specific variation of terpenes is common in eucalypts. RESULTS The genome sequences of Eucalyptus grandis and E. globulus were mined for terpene synthase genes (TPS) and compared to other plant species. We investigated the relative expression of TPS in seven plant tissues and functionally characterized five TPS genes from E. grandis. Compared to other sequenced plant genomes, Eucalyptus grandis has the largest number of putative functional TPS genes of any sequenced plant. We discovered 113 and 106 putative functional TPS genes in E. grandis and E. globulus, respectively. All but one TPS from E. grandis were expressed in at least one of seven plant tissues examined. Genomic clusters of up to 20 genes were identified. Many TPS are expressed in tissues other than leaves which invites a re-evaluation of the function of terpenes in Eucalyptus. CONCLUSIONS Our data indicate that terpenes in Eucalyptus may play a wider role in biotic and abiotic interactions than previously thought. Tissue specific expression is common and the possibility of stress induction needs further investigation. Phylogenetic comparison of the two investigated Eucalyptus species gives insight about recent evolution of different clades within the TPS gene family. While the majority of TPS genes occur in orthologous pairs some clades show evidence of recent gene duplication, as well as loss of function.
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Affiliation(s)
- Carsten Külheim
- Research School of Biology, College of Medicine, Biology and the Environment, Australian National University, Canberra, 0200, Australia.
| | - Amanda Padovan
- Research School of Biology, College of Medicine, Biology and the Environment, Australian National University, Canberra, 0200, Australia.
| | - Charles Hefer
- Department of Botany, University of British Columbia, Vancouver, BC, V6T1Z4, Canada.
| | - Sandra T Krause
- Institut für Pharmazie, Martin-Luther Universität Halle-Wittenberg, 06120, Halle, (Saale), Germany.
| | - Tobias G Köllner
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, 07745, Jena, Germany.
| | - Alexander A Myburg
- Department of Genetics, Forestry and Agricultural Biotechnology Institute, Private Bag X20, Pretoria, 0028, South Africa.
| | - Jörg Degenhardt
- Institut für Pharmazie, Martin-Luther Universität Halle-Wittenberg, 06120, Halle, (Saale), Germany.
| | - William J Foley
- Research School of Biology, College of Medicine, Biology and the Environment, Australian National University, Canberra, 0200, Australia.
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89
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Chen X, Yan CC, Luo C, Ji W, Zhang Y, Dai Q. Constructing lncRNA functional similarity network based on lncRNA-disease associations and disease semantic similarity. Sci Rep 2015; 5:11338. [PMID: 26061969 PMCID: PMC4462156 DOI: 10.1038/srep11338] [Citation(s) in RCA: 150] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 05/21/2015] [Indexed: 12/28/2022] Open
Abstract
Increasing evidence has indicated that plenty of lncRNAs play important roles in many critical biological processes. Developing powerful computational models to construct lncRNA functional similarity network based on heterogeneous biological datasets is one of the most important and popular topics in the fields of both lncRNAs and complex diseases. Functional similarity network consturction could benefit the model development for both lncRNA function inference and lncRNA-disease association identification. However, little effort has been attempted to analysis and calculate lncRNA functional similarity on a large scale. In this study, based on the assumption that functionally similar lncRNAs tend to be associated with similar diseases, we developed two novel lncRNA functional similarity calculation models (LNCSIM). LNCSIM was evaluated by introducing similarity scores into the model of Laplacian Regularized Least Squares for LncRNA–Disease Association (LRLSLDA) for lncRNA-disease association prediction. As a result, new predictive models improved the performance of LRLSLDA in the leave-one-out cross validation of various known lncRNA-disease associations datasets. Furthermore, some of the predictive results for colorectal cancer and lung cancer were verified by independent biological experimental studies. It is anticipated that LNCSIM could be a useful and important biological tool for human disease diagnosis, treatment, and prevention.
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Affiliation(s)
- Xing Chen
- 1] National Center for Mathematics and Interdisciplinary Sciences, Chinese Academy of Sciences, Beijing, 100190, China [2] Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, 100190, China
| | | | - Cai Luo
- Department of Automation, Tsinghua University, Beijing, 100084, China
| | - Wen Ji
- Institute of Computing Technology, Chinese Academy of Sciences, Beijing, 100190, China
| | - Yongdong Zhang
- Key Lab of Intelligent Information Processing of Chinese Academy of Sciences, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, 100190, China
| | - Qionghai Dai
- Department of Automation, Tsinghua University, Beijing, 100084, China
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90
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Matouk IJ, Halle D, Gilon M, Hochberg A. The non-coding RNAs of the H19-IGF2 imprinted loci: a focus on biological roles and therapeutic potential in Lung Cancer. J Transl Med 2015; 13:113. [PMID: 25884481 PMCID: PMC4397711 DOI: 10.1186/s12967-015-0467-3] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Accepted: 03/18/2015] [Indexed: 12/15/2022] Open
Abstract
Since it was first described, the imprinted cluster 11p15.5 has been reported to be deregulated in a variety of pediatric and adult cancers including that of the lung. Both protein coding and non-coding genes functioning as oncogenes or as tumor suppressor genes reside within this cluster. Oncomirs that can function as oncogenes or as tumor suppressors have also been reported. While a complete account of the role played by the 11p15.5 imprinted cluster in lung cancer is beyond the scope of this review, we will focus on the role of the non-coding RNAs processed from the H19-IGF2 loci. A special emphasis will be given to the H19/miR-675 gene locus. Their potential diagnostic and therapeutic use in lung cancer will be described.
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Affiliation(s)
- Imad J Matouk
- Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel.
| | - David Halle
- Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel.
| | - Michal Gilon
- Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel.
| | - Abraham Hochberg
- Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel.
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91
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Hu T, Lu YR. BCYRN1, a c-MYC-activated long non-coding RNA, regulates cell metastasis of non-small-cell lung cancer. Cancer Cell Int 2015; 15:36. [PMID: 25866480 PMCID: PMC4392634 DOI: 10.1186/s12935-015-0183-3] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 03/16/2015] [Indexed: 12/20/2022] Open
Abstract
Background Long non-coding RNAs (lncRNAs) are increasingly implicated in the regulation of the progression of malignancy. Aim To clarify the relations among BCYRN1 (brain cytoplasmic RNA 1, a long non-coding RNA), c-MYC and cell metastasis of non-small-cell lung cancer (NSCLC). Methods Real-time PCR was used to measure expression of BCYRN1 in NSCLC. Knockdown and overexpression of c-MYC were respectively performed using shRNA and lentivirus to investigate its effect on BCYRN1 expression. BCYRN1 was respectively knockdown and overexpressed by siRNA and BCYRN1 mimics to investigate its role in regulating cell metastasis in vitro. ChIP (chromatin immunoprecipitation) assay was performed to confirm the binding of c-MYC to the promoter of BCYRN1. Expression levels of matrix metalloproteinases (MMP9 and MMP13) were determined using real-time PCR and Western blotting. Results BCYRN1 is upregulated and targeted by c-MYC in NSCLC, leading to the increase of cell motility and invasiveness. RNA interference and lentivirus infection showed a positive correlation between the expressions of c-MYC and BCYRN1. ChIP assay confirmed the binding of c-MYC to the promoter region of BCYRN1 gene. In-vitro cell metastasis experiments demonstrated that BCYRN1 was necessary in the c-MYC-regulated cell migration and invasion. The mRNA and protein expression levels of MMP9 and MMP13 descended with the decreasing BCYRN1 level and ascended with the upregulation of BCYRN1. Conclusion These findings uncover a regulatory mechanism in NSCLC cells involving the metastasis-promoting lncRNA BCYRN1 that improves expressions of the key metastasis-supporting proteins MMP9 and MMP13.
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Affiliation(s)
- Tao Hu
- Sichuan Provincial People's Hospital, No. 32, Section 2, 1st Ring Road (West), Chengdu City, 610072 China
| | - Yu-Run Lu
- Sichuan Provincial People's Hospital, No. 32, Section 2, 1st Ring Road (West), Chengdu City, 610072 China
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92
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Abstract
In recent years, long non-coding RNAs (lncRNAs) are emerging as either oncogenes or tumor suppressor genes. Recent evidences suggest that lncRNAs play a very important role in digestive system carcinomas. However, the biological function of lncRNAs in the vast majority of digestive system carcinomas remains unclear. Recently, increasing studies has begun to explore their molecular mechanisms and regulatory networks that they are implicated in tumorigenesis. In this review, we highlight the emerging functional role of lncRNAs in digestive system carcinomas. It is becoming clear that lncRNAs will be exciting and potentially useful for diagnosis and treatment of digestive system carcinomas, some of these lncRNAs might function as both diagnostic markers and the treatment targets of digestive system carcinomas.
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93
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Altered expression of long non-coding RNAs during genotoxic stress-induced cell death in human glioma cells. J Neurooncol 2015; 122:283-92. [PMID: 25645334 DOI: 10.1007/s11060-015-1718-0] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Accepted: 01/03/2015] [Indexed: 12/30/2022]
Abstract
Long non-coding RNAs (lncRNAs), a recently discovered class of non-coding genes, are transcribed throughout the genome. Emerging evidence suggests that lncRNAs may be involved in modulating various aspects of tumor biology, including regulating gene activity in response to external stimuli or DNA damage. No data are available regarding the expression of lncRNAs during genotoxic stress-induced apoptosis and/or necrosis in human glioma cells. In this study, we detected a change in the expression of specific candidate lncRNAs (neat1, GAS5, TUG1, BC200, Malat1, MEG3, MIR155HG, PAR5, and ST7OT1) during DNA damage-induced apoptosis in human glioma cell lines (U251 and U87) using doxorubicin (DOX) and resveratrol (RES). We also detected the expression pattern of these lncRNAs in human glioma cell lines under necrosis induced using an increased dose of DOX. Our results reveal that the lncRNA expression patterns are distinct between genotoxic stress-induced apoptosis and necrosis in human glioma cells. The sets of lncRNA expressed during genotoxic stress-induced apoptosis were DNA-damaging agent-specific. Generally, MEG3 and ST7OT1 are up-regulated in both cell lines under apoptosis induced using both agents. The induction of GAS5 is only clearly detected during DOX-induced apoptosis, whereas the up-regulation of neat1 and MIR155HG is only found during RES-induced apoptosis in both cell lines. However, TUG1, BC200 and MIR155HG are down regulated when necrosis is induced using a high dose of DOX in both cell lines. In conclusion, our findings suggest that the distinct regulation of lncRNAs may possibly involve in the process of cellular defense against genotoxic agents.
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94
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Zhong Q, Shi G, Zhang Y, Lu L, Levy D, Zhong S. Alteration of BRCA1 expression affects alcohol-induced transcription of RNA Pol III-dependent genes. Gene 2015; 556:74-9. [PMID: 25447904 PMCID: PMC4272617 DOI: 10.1016/j.gene.2014.11.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Revised: 11/04/2014] [Accepted: 11/06/2014] [Indexed: 02/05/2023]
Abstract
Emerging evidence has indicated that alcohol consumption is an established risk factor for breast cancer. Deregulation of RNA polymerase III (Pol III) transcription enhances cellular Pol III gene production, leading to an increase in translational capacity to promote cell transformation and tumor formation. We have reported that alcohol intake increases Pol III gene transcription to promote cell transformation and tumor formation in vitro and in vivo. Studies revealed that tumor suppressors, pRb, p53, PTEN and Maf1 repress the transcription of Pol III genes. BRCA1 is a tumor suppressor and its mutation is tightly related to breast cancer development. However, it is not clear whether BRCA1 expression affects alcohol-induced transcription of Pol III genes. At the present studies, we report that restoring BRCA1 in HCC 1937 cells, which is a BRCA1 deficient cell line, represses Pol III gene transcription. Expressing mutant or truncated BRCA1 in these cells does not affect the ability of repression on Pol III genes. Our analysis has demonstrated that alcohol induces Pol III gene transcription. More importantly, overexpression of BRCA1 in estrogen receptor positive (ER+) breast cancer cells (MCF-7) decreases the induction of tRNA(Leu) and 5S rRNA genes by alcohol, whereas reduction of BRCA1 by its siRNA slightly increases the transcription of the class of genes. This suggests that BRCA1 is associated with alcohol-induced deregulation of Pol III genes. These studies for the first time demonstrate the role of BRCA1 in induction of Pol III genes by alcohol and uncover a novel mechanism of alcohol-associated breast cancer.
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Affiliation(s)
- Qian Zhong
- Department of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, China
| | - Ganggang Shi
- Shantou University Medical College, Shantou, Guangdong, China
| | - Yanmei Zhang
- Shantou University Medical College, Shantou, Guangdong, China
| | - Lei Lu
- Department of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Daniel Levy
- Department of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Shuping Zhong
- Department of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Shantou University Medical College, Shantou, Guangdong, China.
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95
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Fang TT, Sun XJ, Chen J, Zhao Y, Sun RX, Ren N, Liu BB. Long Non-coding RNAs are Differentially Expressed in Hepatocellular Carcinoma Cell Lines with Differing Metastatic Potential. Asian Pac J Cancer Prev 2015; 15:10513-24. [DOI: 10.7314/apjcp.2014.15.23.10513] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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96
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Non Coding RNA Molecules as Potential Biomarkers in Breast Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 867:263-75. [PMID: 26530371 DOI: 10.1007/978-94-017-7215-0_16] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The pursuit of minimally invasive biomarkers is a challenging but exciting area of research. Clearly, such markers would need to be sensitive and specific enough to aid in the detection of breast cancer at an early stage, would monitor progression of the disease, and could predict the individual patient's response to treatment. Unfortunately, to date, markers with such characteristics have not made it to the clinic for breast cancer. Past years, many studies indicated that the non-coding part of our genome (the so called 'junk' DNA), may be an ideal source for these biomarkers. In this chapter, the potential use of microRNAs and long non-coding RNAs as biomarkers will be discussed.
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97
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Hansji H, Leung EY, Baguley BC, Finlay GJ, Askarian-Amiri ME. Keeping abreast with long non-coding RNAs in mammary gland development and breast cancer. Front Genet 2014; 5:379. [PMID: 25400658 PMCID: PMC4215690 DOI: 10.3389/fgene.2014.00379] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Accepted: 10/13/2014] [Indexed: 12/18/2022] Open
Abstract
The majority of the human genome is transcribed, even though only 2% of transcripts encode proteins. Non-coding transcripts were originally dismissed as evolutionary junk or transcriptional noise, but with the development of whole genome technologies, these non-coding RNAs (ncRNAs) are emerging as molecules with vital roles in regulating gene expression. While shorter ncRNAs have been extensively studied, the functional roles of long ncRNAs (lncRNAs) are still being elucidated. Studies over the last decade show that lncRNAs are emerging as new players in a number of diseases including cancer. Potential roles in both oncogenic and tumor suppressive pathways in cancer have been elucidated, but the biological functions of the majority of lncRNAs remain to be identified. Accumulated data are identifying the molecular mechanisms by which lncRNA mediates both structural and functional roles. LncRNA can regulate gene expression at both transcriptional and post-transcriptional levels, including splicing and regulating mRNA processing, transport, and translation. Much current research is aimed at elucidating the function of lncRNAs in breast cancer and mammary gland development, and at identifying the cellular processes influenced by lncRNAs. In this paper we review current knowledge of lncRNAs contributing to these processes and present lncRNA as a new paradigm in breast cancer development.
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Affiliation(s)
- Herah Hansji
- Auckland Cancer Society Research Centre, University of Auckland Auckland, New Zealand
| | - Euphemia Y Leung
- Auckland Cancer Society Research Centre, University of Auckland Auckland, New Zealand
| | - Bruce C Baguley
- Auckland Cancer Society Research Centre, University of Auckland Auckland, New Zealand
| | - Graeme J Finlay
- Auckland Cancer Society Research Centre, University of Auckland Auckland, New Zealand ; Department of Molecular Medicine and Pathology, University of Auckland Auckland, New Zealand
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98
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Chen H, Xin Y, Zhou L, Huang JM, Tao L, Cheng L, Tian J. Cisplatin and paclitaxel target significant long noncoding RNAs in laryngeal squamous cell carcinoma. Med Oncol 2014; 31:246. [PMID: 25257554 DOI: 10.1007/s12032-014-0246-7] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 09/12/2014] [Indexed: 01/25/2023]
Abstract
The objectives of this study were to identify specific long noncoding RNAs (lncRNAs) in laryngeal squamous cell carcinoma (LSCC) and to clarify the function of cisplatin and paclitaxel on the confirmed laryngeal cancer lncRNAs. Fifty-four pairs of laryngeal tumor and adjacent normal tissue were collected. Candidate lncRNAs were searched in authorized databases. The significant lncRNAs were identified and confirmed through high-output real-time PCR. Chemotherapy assay evaluated the influences of cisplatin and paclitaxel on the significant lncRNAs. Thirty-seven cancer-related candidate lncRNAs were selected. Three up-expressed and two down-expressed significant lncRNAs were identified and confirmed. The expressions of lncRNA CDKN2B-AS1, HOTAIR and MALAT1 were dramatically reduced with the increasing concentration of cisplatin and paclitaxel and also lengthening of the treatment duration. Cisplatin and paclitaxel have target function on significant lncRNAs in LSCC, which presents novel molecular targets to cure LSCC patients and also leads an orientation for developing new drugs.
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Affiliation(s)
- Hui Chen
- Department of Otolaryngology-Head and Neck Surgery, Affiliated Eye and ENT Hospital of Fudan University, #83, Fenyang Road, Shanghai, 200031, China
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99
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Mohanty V, Gökmen-Polar Y, Badve S, Janga SC. Role of lncRNAs in health and disease-size and shape matter. Brief Funct Genomics 2014; 14:115-29. [PMID: 25212482 DOI: 10.1093/bfgp/elu034] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Most of the mammalian genome including a large fraction of the non-protein coding transcripts has been shown to be transcribed. Studies related to these non-coding RNA molecules have predominantly focused on smaller molecules like microRNAs. In contrast, long non-coding RNAs (lncRNAs) have long been considered to be transcriptional noise. Accumulating evidence suggests that lncRNAs are involved in key cellular and developmental processes. Several critical questions regarding functions and properties of lncRNAs and their circular forms remain to be answered. Increasing evidence from high-throughput sequencing screens also suggests the involvement of lncRNAs in diseases such as cancer, although the underlying mechanisms still need to be elucidated. Here, we discuss the current state of research in the field of lncRNAs, questions that need to be addressed in light of recent genome-wide studies documenting the landscape of lncRNAs, their functional roles and involvement in diseases. We posit that with the availability of high-throughput data sets it is not only possible to improve methods for predicting lncRNAs but will also facilitate our ability to elucidate their functions and phenotypes by using integrative approaches.
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100
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Abdelmohsen K, Panda AC, Kang MJ, Guo R, Kim J, Grammatikakis I, Yoon JH, Dudekula DB, Noh JH, Yang X, Martindale JL, Gorospe M. 7SL RNA represses p53 translation by competing with HuR. Nucleic Acids Res 2014; 42:10099-111. [PMID: 25123665 PMCID: PMC4150789 DOI: 10.1093/nar/gku686] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Noncoding RNAs (ncRNAs) and RNA-binding proteins are potent post-transcriptional regulators of gene expression. The ncRNA 7SL is upregulated in cancer cells, but its impact upon the phenotype of cancer cells is unknown. Here, we present evidence that 7SL forms a partial hybrid with the 3'-untranslated region (UTR) of TP53 mRNA, which encodes the tumor suppressor p53. The interaction of 7SL with TP53 mRNA reduced p53 translation, as determined by analyzing p53 expression levels, nascent p53 translation and TP53 mRNA association with polysomes. Silencing 7SL led to increased binding of HuR to TP53 mRNA, an interaction that led to the promotion of p53 translation and increased p53 abundance. We propose that the competition between 7SL and HuR for binding to TP53 3'UTR contributes to determining the magnitude of p53 translation, in turn affecting p53 levels and the growth-suppressive function of p53. Our findings suggest that targeting 7SL may be effective in the treatment of cancers with reduced p53 levels.
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Affiliation(s)
- Kotb Abdelmohsen
- Laboratory of Genetics, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Amaresh C Panda
- Laboratory of Genetics, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Min-Ju Kang
- Laboratory of Genetics, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Rong Guo
- Laboratory of Genetics, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Jiyoung Kim
- Laboratory of Genetics, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Ioannis Grammatikakis
- Laboratory of Genetics, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Je-Hyun Yoon
- Laboratory of Genetics, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Dawood B Dudekula
- Laboratory of Genetics, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Ji Heon Noh
- Laboratory of Genetics, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Xiaoling Yang
- Laboratory of Genetics, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Jennifer L Martindale
- Laboratory of Genetics, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Myriam Gorospe
- Laboratory of Genetics, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
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