51
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Richard JLC, Eichhorn PJA. Deciphering the roles of lncRNAs in breast development and disease. Oncotarget 2018; 9:20179-20212. [PMID: 29732012 PMCID: PMC5929455 DOI: 10.18632/oncotarget.24591] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Accepted: 02/21/2018] [Indexed: 02/06/2023] Open
Abstract
Breast cancer is the second leading cause of cancer related deaths in women. It is therefore important to understand the mechanisms underlying breast cancer development as well as raises the need for enhanced, non-invasive strategies for novel prognostic and diagnostic methods. The emergence of long non-coding RNAs (lncRNAs) as potential key players in neoplastic disease has received considerable attention over the past few years. This relatively new class of molecular regulators has been shown from ongoing research to act as critical players for key biological processes. Deregulated expression levels of lncRNAs have been observed in a number of cancers including breast cancer. Furthermore, lncRNAs have been linked to breast cancer initiation, progression, metastases and to limit sensitivity to certain targeted therapeutics. In this review we provide an update on the lncRNAs associated with breast cancer and mammary gland development and illustrate the versatility of such lncRNAs in gene control, differentiation and development both in normal physiological conditions and in diseased states. We also highlight the therapeutic and diagnostic potential of lncRNAs in cancer.
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Affiliation(s)
- John Lalith Charles Richard
- Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, 117597, Singapore
- Current Address: Genome Institute of Singapore, Agency for Science Technology and Research, 138672, Singapore
| | - Pieter Johan Adam Eichhorn
- Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, 117597, Singapore
- School of Pharmacy, Curtin University, Perth, 6845, Australia
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52
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Klinge CM. Non-coding RNAs: long non-coding RNAs and microRNAs in endocrine-related cancers. Endocr Relat Cancer 2018; 25:R259-R282. [PMID: 29440232 DOI: 10.1530/erc-17-0548] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 02/12/2018] [Indexed: 12/11/2022]
Abstract
The human genome is 'pervasively transcribed' leading to a complex array of non-coding RNAs (ncRNAs) that far outnumber coding mRNAs. ncRNAs have regulatory roles in transcription and post-transcriptional processes as well numerous cellular functions that remain to be fully described. Best characterized of the 'expanding universe' of ncRNAs are the ~22 nucleotide microRNAs (miRNAs) that base-pair to target mRNA's 3' untranslated region within the RNA-induced silencing complex (RISC) and block translation and may stimulate mRNA transcript degradation. Long non-coding RNAs (lncRNAs) are classified as >200 nucleotides in length, but range up to several kb and are heterogeneous in genomic origin and function. lncRNAs fold into structures that interact with DNA, RNA and proteins to regulate chromatin dynamics, protein complex assembly, transcription, telomere biology and splicing. Some lncRNAs act as sponges for miRNAs and decoys for proteins. Nuclear-encoded lncRNAs can be taken up by mitochondria and lncRNAs are transcribed from mtDNA. Both miRNAs and lncRNAs are dysregulated in endocrine cancers. This review provides an overview on the current understanding of the regulation and function of selected lncRNAs and miRNAs, and their interaction, in endocrine-related cancers: breast, prostate, endometrial and thyroid.
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53
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Lefever S, Anckaert J, Volders PJ, Luypaert M, Vandesompele J, Mestdagh P. decodeRNA- predicting non-coding RNA functions using guilt-by-association. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2018; 2017:3866795. [PMID: 29220434 PMCID: PMC5502368 DOI: 10.1093/database/bax042] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 05/01/2017] [Indexed: 12/23/2022]
Abstract
Although the long non-coding RNA (lncRNA) landscape is expanding rapidly, only a small number of lncRNAs have been functionally annotated. Here, we present decodeRNA (http://www.decoderna.org), a database providing functional contexts for both human lncRNAs and microRNAs in 29 cancer and 12 normal tissue types. With state-of-the-art data mining and visualization options, easy access to results and a straightforward user interface, decodeRNA aims to be a powerful tool for researchers in the ncRNA field. Database URL:http://www.decoderna.org
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Affiliation(s)
- Steve Lefever
- Center for Medical Genetics Ghent (CMGG), Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
| | - Jasper Anckaert
- Center for Medical Genetics Ghent (CMGG), Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
| | - Pieter-Jan Volders
- Center for Medical Genetics Ghent (CMGG), Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
| | - Manuel Luypaert
- Center for Medical Genetics Ghent (CMGG), Ghent University, Ghent, Belgium
| | - Jo Vandesompele
- Center for Medical Genetics Ghent (CMGG), Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium.,Biogazelle, Zwijnaarde, Belgium
| | - Pieter Mestdagh
- Center for Medical Genetics Ghent (CMGG), Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium.,Biogazelle, Zwijnaarde, Belgium
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54
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Chen X, Yang C, Xie S, Cheung E. Long non-coding RNA GAS5 and ZFAS1 are prognostic markers involved in translation targeted by miR-940 in prostate cancer. Oncotarget 2018; 9:1048-1062. [PMID: 29416676 PMCID: PMC5787418 DOI: 10.18632/oncotarget.23254] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 12/03/2017] [Indexed: 12/30/2022] Open
Abstract
Identification of prognostic biomarkers helps facilitate the prediction of patient outcomes as well as guide treatments. Accumulating evidence now suggests that long non-coding RNAs (lncRNAs) play key roles in tumor progression with diagnostic and prognostic values. However, little is known about the biological functions of lncRNAs and how they contribute to the pathogenesis of cancer. Herein, we performed weighted correlation network analysis (WGCNA) on 380 RNA-seq samples from prostate cancer patients to create networks comprising of microRNAs, lncRNAs, and protein-coding genes. Our analysis revealed expression modules that associated with pathological parameters. More importantly, we identified a gene module that is involved in protein translation and is associated with patient survival. In this gene module, we explored the regulation axis involving GAS5, ZFAS1, and miR-940. We show that GAS5, ZFAS1, and miR-940 are up-regulated in tumors relative to normal prostate tissues, and high expression of either lncRNA is an indicator of poor patient outcome. Finally, we constructed a co-expression network involving GAS5, ZFAS1, and miR-940, as well as the targets of miR-940. Our results show that GAS5 and ZFAS1 are targeted by miR-940 via NAA10 and RPL28. Taken together, co-expression analysis of gene expression profiling from RNA-seq can accelerate the identification and functional characterization of novel prognostic markers in prostate cancer.
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Affiliation(s)
- Xin Chen
- Guangdong Key Laboratory of IoT Information Technology, School of Automation, Guangdong University of Technology, Guangzhou, China
- Faculty of Health Sciences, University of Macau, Macau, China
| | - Chao Yang
- Guangdong Key Laboratory of IoT Information Technology, School of Automation, Guangdong University of Technology, Guangzhou, China
| | - Shengli Xie
- Guangdong Key Laboratory of IoT Information Technology, School of Automation, Guangdong University of Technology, Guangzhou, China
| | - Edwin Cheung
- Faculty of Health Sciences, University of Macau, Macau, China
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55
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Latgé G, Poulet C, Bours V, Josse C, Jerusalem G. Natural Antisense Transcripts: Molecular Mechanisms and Implications in Breast Cancers. Int J Mol Sci 2018; 19:ijms19010123. [PMID: 29301303 PMCID: PMC5796072 DOI: 10.3390/ijms19010123] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 12/07/2017] [Accepted: 12/29/2017] [Indexed: 12/13/2022] Open
Abstract
Natural antisense transcripts are RNA sequences that can be transcribed from both DNA strands at the same locus but in the opposite direction from the gene transcript. Because strand-specific high-throughput sequencing of the antisense transcriptome has only been available for less than a decade, many natural antisense transcripts were first described as long non-coding RNAs. Although the precise biological roles of natural antisense transcripts are not known yet, an increasing number of studies report their implication in gene expression regulation. Their expression levels are altered in many physiological and pathological conditions, including breast cancers. Among the potential clinical utilities of the natural antisense transcripts, the non-coding|coding transcript pairs are of high interest for treatment. Indeed, these pairs can be targeted by antisense oligonucleotides to specifically tune the expression of the coding-gene. Here, we describe the current knowledge about natural antisense transcripts, their varying molecular mechanisms as gene expression regulators, and their potential as prognostic or predictive biomarkers in breast cancers.
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Affiliation(s)
- Guillaume Latgé
- Laboratory of Human Genetics, GIGA-Institute, University of Liège, 4500 Liège, Belgium.
| | - Christophe Poulet
- Laboratory of Human Genetics, GIGA-Institute, University of Liège, 4500 Liège, Belgium.
| | - Vincent Bours
- Laboratory of Human Genetics, GIGA-Institute, University of Liège, 4500 Liège, Belgium.
- Center of Genetics, University Hospital (CHU), 4500 Liège, Belgium.
| | - Claire Josse
- Laboratory of Human Genetics, GIGA-Institute, University of Liège, 4500 Liège, Belgium.
- Department of Medical Oncology, University Hospital (CHU), 4500 Liège, Belgium.
- Laboratory of Medical Oncology, GIGA-Institute, University of Liège, 4500 Liège, Belgium.
| | - Guy Jerusalem
- Department of Medical Oncology, University Hospital (CHU), 4500 Liège, Belgium.
- Laboratory of Medical Oncology, GIGA-Institute, University of Liège, 4500 Liège, Belgium.
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56
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Li LJ, Leng RX, Fan YG, Pan HF, Ye DQ. Translation of noncoding RNAs: Focus on lncRNAs, pri-miRNAs, and circRNAs. Exp Cell Res 2017; 361:1-8. [PMID: 29031633 DOI: 10.1016/j.yexcr.2017.10.010] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 09/17/2017] [Accepted: 10/11/2017] [Indexed: 02/06/2023]
Abstract
Mammalian genome is pervasively transcribed, producing large number of noncoding RNAs (ncRNAs), including long noncoding RNAs (lncRNAs), primary miRNAs (pri-miRNA), and circular RNAs (circRNAs). The translation of these ncRNAs has long been overlooked. Increasing studies, however, based on ribosome profiling in various organisms provide important clues to unanticipated translation potential of lncRNAs. Moreover, a few functional peptides encoded by lncRNAs and pri-miRNAs underline the significance of their translation. Recently, several novel researches also evidence the translation of endogenous circRNAs. Given the functional significance exemplified by peptides translated by some ncRNAs and their pervasive translation, it is not too far-fetched to image that abnormal translation of ncRNAs may contribute to human diseases. Through challenging, deciphering ncRNA translation is required for comprehensive understanding of biology and medicine. In this review, we firstly present evidence concerning translation potential of lncRNAs and go on to introduce a few functional short peptides encoded by lncRNAs. Then, salient observations showing translation of pri-miRNAs and circRNAs are described in detail. We end by discussing the impact of ncRNA translation beyond producing peptides and referring briefly to the potential role of abnormal ncRNA translation in human diseases.
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Affiliation(s)
- Lian-Ju Li
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, 81 Meishan Road, Hefei 230032, Anhui, China; Anhui Province Key Laboratory of Major Autoimmune Diseases, Hefei 230032, Anhui, China
| | - Rui-Xue Leng
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, 81 Meishan Road, Hefei 230032, Anhui, China; Anhui Province Key Laboratory of Major Autoimmune Diseases, Hefei 230032, Anhui, China
| | - Yin-Guang Fan
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, 81 Meishan Road, Hefei 230032, Anhui, China; Anhui Province Key Laboratory of Major Autoimmune Diseases, Hefei 230032, Anhui, China
| | - Hai-Feng Pan
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, 81 Meishan Road, Hefei 230032, Anhui, China; Anhui Province Key Laboratory of Major Autoimmune Diseases, Hefei 230032, Anhui, China
| | - Dong-Qing Ye
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, 81 Meishan Road, Hefei 230032, Anhui, China; Anhui Province Key Laboratory of Major Autoimmune Diseases, Hefei 230032, Anhui, China.
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57
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Tang Y, Zhou T, Yu X, Xue Z, Shen N. The role of long non-coding RNAs in rheumatic diseases. Nat Rev Rheumatol 2017; 13:657-669. [PMID: 28978995 DOI: 10.1038/nrrheum.2017.162] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Long non-coding RNAs (lncRNAs) have emerged as key epigenetic regulators that govern gene expression and influence multiple biological processes. Accumulating evidence demonstrates that lncRNAs have critical roles in immune cell development and function. In this Review, the molecular mechanisms of gene expression regulation by lncRNAs are described and current knowledge of the role of lncRNAs in immune regulation and inflammation are presented, highlighting strategies for defining the roles of lncRNAs in the pathogenesis of multiple rheumatic diseases. Finally, research progress in understanding the role of lncRNAs in rheumatic diseases is discussed.
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Affiliation(s)
- Yuanjia Tang
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 145 Shan Dong Road (c), Shanghai 200001, China.,Institute of Health Sciences, Shanghai Jiao Tong University School of Medicine and Shanghai Institutes for Biological Sciences (SIBS), University of Chinese Academy of Sciences, Chinese Academy of Sciences (CAS), 320 Yueyang Road, Shanghai, China
| | - Tian Zhou
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 145 Shan Dong Road (c), Shanghai 200001, China
| | - Xiang Yu
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 145 Shan Dong Road (c), Shanghai 200001, China
| | - Zhixin Xue
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 145 Shan Dong Road (c), Shanghai 200001, China
| | - Nan Shen
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 145 Shan Dong Road (c), Shanghai 200001, China.,Institute of Health Sciences, Shanghai Jiao Tong University School of Medicine and Shanghai Institutes for Biological Sciences (SIBS), University of Chinese Academy of Sciences, Chinese Academy of Sciences (CAS), 320 Yueyang Road, Shanghai, China.,State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, 2200 Lane 25 Xietu Road, Shanghai, China.,Collaborative Innovation Centre for Translational Medicine, Shanghai Jiao Tong University School of Medicine, 197 Rui Jin Er Road, Shanghai, China.,Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, Ohio, USA
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58
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Song W, Tian C, Zhang RJ, Zou SB, Wang K. Meta-analysis of the prognostic value of lncRNA ZFAS1 in patients with solid tumors. Oncotarget 2017; 8:90301-90307. [PMID: 29163829 PMCID: PMC5685750 DOI: 10.18632/oncotarget.19566] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 07/18/2017] [Indexed: 01/11/2023] Open
Abstract
Expression of ZFAS1, a newly identified long noncoding RNA (lncRNA), is dysregulated in several types of cancer. Here we assessed the prognostic value of ZFAS1 in solid tumors. A comprehensive literature search was performed by screening the PubMed, EMBASE, MEDLINE, Cochrane Library, CNKI, and Wanfang databases. A total of 874 patients from 10 studies were included. The pooled analysis demonstrated that patients with high ZFAS1 expression had a significantly shorter overall survival (OS) (HR, 1.58; 95% CI, 1.28–1.97; P < 0.001) and recurrence-free survival (RFS) (HR, 1.90; 95% CI, 1.29–2.79; P = 0.001). Moreover, elevated ZFAS1 expression correlated with tumor size, tumor-node-metastasis (TNM) stage, and lymph node metastasis (LNM). These results demonstrate that increased ZFAS1 expression correlates with a poor prognosis in cancer patients, which suggests ZFAS1 might be useful as a potential prognostic biomarker in patients with solid tumors.
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Affiliation(s)
- Wei Song
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Chuan Tian
- Department of Nuclear Medicine, Guizhou Provincial People's Hospital, Guiyang, China
| | - Run-Jin Zhang
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Shu-Bing Zou
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Kai Wang
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
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59
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Ye Y, Gao X, Yang N. LncRNA ZFAS1 promotes cell migration and invasion of fibroblast-like synoviocytes by suppression of miR-27a in rheumatoid arthritis. Hum Cell 2017; 31:14-21. [PMID: 28721682 DOI: 10.1007/s13577-017-0179-5] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 07/01/2017] [Indexed: 02/05/2023]
Abstract
Rheumatoid arthritis (RA) is a systemic and chronic inflammatory disease. Synoviocyte migration and invasion were found to be essential to the pathology of RA. Upregulation of long noncoding RNA ZFAS1 has been observed in cancers and promotes cell migration and invasion. To date, the functions and mechanisms of ZFAS1 in RA have not been revealed. In this study, we analyzed expression pattern of ZFAS1 in RA patients and found that ZFAS1 expression was increased in synovial tissue and fibroblast-like synoviocytes (FLS) from RA patients (RA-FLS) compared with that in healthy donors. Functional assays showed that silence of ZFAS1 suppressed RA-FLS migration and invasion, while overexpression of ZFAS1 showed the opposite effect. Further investigation demonstrated that ZFAS1 directly interacted with miR-27a and decreased miR-27a expression. ZFAS1 promotes RA-FLS migration and invasion in an miR-27a-dependent manner. Taken together, the present study provides the first evidence that ZFAS1 promotes cell migration and invasion through miR-27a in RA-FLS, suggesting that ZFAS1 may be an effective therapeutic target for RA patients.
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Affiliation(s)
- Yang Ye
- Immunology Department, Affiliated Hospital of Southwest Medical University, No. 25, Taiping Street, Jiangyang District, Luzhou, Sichuan, China.
| | - Xiaomei Gao
- Immunology Department, Affiliated Hospital of Southwest Medical University, No. 25, Taiping Street, Jiangyang District, Luzhou, Sichuan, China
| | - Nanping Yang
- Immunology Department, West China Hospital of Sichuan University, Chengdu, China
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60
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Lee J, Park HY, Kim WW, Lee SJ, Jeong JH, Kang SH, Jung JH, Chae YS. Biological function of long noncoding RNA snaR in HER2-positive breast cancer cells. Tumour Biol 2017; 39:1010428317707374. [PMID: 28653903 DOI: 10.1177/1010428317707374] [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: 12/14/2022] Open
Abstract
PURPOSE Long noncoding RNA, snaR (small NF90-associated RNA), has been reported to be upregulated in various cancer cell lines. We evaluated the additional role of snaR in HER2-positive breast cancer cell lines. METHODS We explored changes of expression of snaR among the selected long noncoding RNAs which have a potential in cancer proliferation or progression. The proliferation, migration, and invasion of HER2-positive breast cancer cells (SK-BR3) were evaluated by snaR with RNA interruption in 3-(4,5-dimethylthiazol-2yl)-2,5-diphenyltetrazolium bromide, wound-healing assay, and Transwell assay. RESULTS The expression of snaR was remarkably upregulated in SK-BR3 cell lines together with ANRIL, while the SFMBT2 was downregulated in SK-BR3 cell lines. Although Nespas, 7SK, PSF inhibiting RNA, mascRNA, Hoxa11as, NRON, AK023948, MER11C, p53 mRNA, CAR Intergenic 10, HUC 1 and 2, ZFAS1, SCA8, and SNHG5 were also upregulated and UCA1 was downregulated, the differences were not dominent. Based on the expression result, we explored the functional role of snaR in HER2-positive breast cancer. Downregulation of snaR with small interfering RNA was identified to significanlty inhibit migration as well as proliferation of SK-BR3 cells. CONCLUSION In this study, snaR was identified as upregulated and to play a role in cancer progression of HER2-positive breast cancer cells. These results suggest snaR as a potential biomarker for HER2-positive breast cancer.
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Affiliation(s)
- Jeeyeon Lee
- 1 Department of Surgery, Kyungpook National University School of Medicine, Daegu, Republic of Korea
| | - Ho Yong Park
- 1 Department of Surgery, Kyungpook National University School of Medicine, Daegu, Republic of Korea
| | - Wan Wook Kim
- 1 Department of Surgery, Kyungpook National University School of Medicine, Daegu, Republic of Korea
| | - Soo Jung Lee
- 2 Department of Hemato-Oncology, Kyungpook National University School of Medicine, Daegu, Republic of Korea
| | - Jae-Hwan Jeong
- 3 Cell and Matrix Research Institute, Kyungpook National University School of Medicine, Daegu, Republic of Korea
| | - Seung Hee Kang
- 3 Cell and Matrix Research Institute, Kyungpook National University School of Medicine, Daegu, Republic of Korea
| | - Jin Hyang Jung
- 1 Department of Surgery, Kyungpook National University School of Medicine, Daegu, Republic of Korea.,4 Breast Cancer Center, Kyungpook National University School of Medicine, Daegu, Republic of Korea
| | - Yee Soo Chae
- 2 Department of Hemato-Oncology, Kyungpook National University School of Medicine, Daegu, Republic of Korea.,4 Breast Cancer Center, Kyungpook National University School of Medicine, Daegu, Republic of Korea
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61
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Mas-Ponte D, Carlevaro-Fita J, Palumbo E, Hermoso Pulido T, Guigo R, Johnson R. LncATLAS database for subcellular localization of long noncoding RNAs. RNA (NEW YORK, N.Y.) 2017; 23:1080-1087. [PMID: 28386015 PMCID: PMC5473142 DOI: 10.1261/rna.060814.117] [Citation(s) in RCA: 203] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 03/31/2017] [Indexed: 05/04/2023]
Abstract
The subcellular localization of long noncoding RNAs (lncRNAs) holds valuable clues to their molecular function. However, measuring localization of newly discovered lncRNAs involves time-consuming and costly experimental methods. We have created "lncATLAS," a comprehensive resource of lncRNA localization in human cells based on RNA-sequencing data sets. Altogether, 6768 GENCODE-annotated lncRNAs are represented across various compartments of 15 cell lines. We introduce relative concentration index (RCI) as a useful measure of localization derived from ensemble RNA-seq measurements. LncATLAS is accessible through an intuitive and informative webserver, from which lncRNAs of interest are accessed using identifiers or names. Localization is presented across cell types and organelles, and may be compared to the distribution of all other genes. Publication-quality figures and raw data tables are automatically generated with each query, and the entire data set is also available to download. LncATLAS makes lncRNA subcellular localization data available to the widest possible number of researchers. It is available at lncatlas.crg.eu.
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Affiliation(s)
- David Mas-Ponte
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain
| | - Joana Carlevaro-Fita
- Department of Clinical Research, University of Bern, 3008 Bern, Switzerland
- Department of Medical Oncology, Inselspital, University Hospital and University of Bern, 3010 Bern, Switzerland
| | - Emilio Palumbo
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain
| | - Toni Hermoso Pulido
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain
| | - Roderic Guigo
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain
- Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), 08003 Barcelona, Catalonia, Spain
| | - Rory Johnson
- Department of Clinical Research, University of Bern, 3008 Bern, Switzerland
- Department of Medical Oncology, Inselspital, University Hospital and University of Bern, 3010 Bern, Switzerland
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62
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Insights from Global Analyses of Long Noncoding RNAs in Breast Cancer. CURRENT PATHOBIOLOGY REPORTS 2017; 5:23-34. [PMID: 28616363 DOI: 10.1007/s40139-017-0122-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
PURPOSE OF REVIEW The goal of this review was to compare and contrast the results and implications from several recent transcriptomic studies that analyzed the expression of lncRNAs in breast cancer. How many lncRNAs are dysregulated in breast cancer? Do dysregulated lncRNAs contribute to breast cancer etiology? Are lncRNAs viable biomarkers in breast cancer? RECENT FINDINGS Transcriptomic profiling of breast cancer tissues, mostly from The Cancer Genome Atlas, identified thousands of long noncoding RNAs that are expressed and dysregulated in breast cancer. The expression of lncRNAs alone can divide patients into molecular subtypes. Subsequent functional studies demonstrated that several of these lncRNAs have important roles in breast cancer cell biology. SUMMARY Thousands of lncRNAs are dysregulated in breast cancer that can be developed as biomarkers for prognostic or therapeutic purposes. The reviewed reports provide a roadmap to guide functional studies to discover lncRNAs with critical biological functions relating to breast cancer development and progression.
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