251
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Investigation of long noncoding RNAs expression profile as potential serum biomarkers in patients with hepatocellular carcinoma. Transl Res 2016; 168:134-145. [PMID: 26551349 DOI: 10.1016/j.trsl.2015.10.002] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 09/26/2015] [Accepted: 10/06/2015] [Indexed: 12/30/2022]
Abstract
There is an increasing interest in using long noncoding RNAs (lncRNAs) as biomarkers in cancer. Predictive biomarkers in hepatocellular carcinoma (HCC) have great benefit in the choice of therapeutic modality for HCC. The aim of this study is to assess lncRNA-urothelial carcinoma associated-1 (lncRNA-UCA1) and WD repeat containing, antisense to TP53 (WRAP53) expression as novel noninvasive biomarkers for diagnosis of HCC in sera of HCC patients compared with chronic hepatitis C virus (HCV) patients and healthy volunteers and to analyze their relationship with respect to the clinicopathologic features. We retrieved HCC characteristic lncRNAs, lncRNA-UCA1 and lncRNA-WRAP53, based on the microarray signature profiling (released by LncRNADisease database). Quantitative reverse-transcriptase polymerase chain reaction assay (RT-qPCR) was then used to evaluate the expression of selected lncRNAs in the serum of 160 participants. Furthermore, in 20 of 82 HCC cases involved in the study, we examined the expression of lncRNA-UCA1 and lncRNA-WRAP53 in 20 HCC tissues and adjacent nontumor tissues and analyzed its correlation with the serum level of these lncRNAs. The prognostic significance of the investigated parameters in HCC patients was explored. We found that lncRNA-UCA1 and lncRNA-WRAP53 were significantly higher in sera of HCC than those with chronic HCV infection or healthy volunteers. Our data suggested that the increased expression of UCA1 and WRAP53 was associated with advanced clinical parameters in HCC. Of note, tissue levels of the chosen lncRNAs strongly correlate with their sera level. The combination of both lncRNAs with serum alpha fetoprotein resulted in improved sensitivity to 100%. The median follow-up period was 21.5 months. LncRNA-WRAP53 was significant independent prognostic markers in relapse-free survival. LncRNA-UCA1 and lncRNA-WRAP53 upregulation may serve as novel serum biomarkers for HCC diagnosis and prognosis.
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252
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Abstract
Recent investigations have highlighted the importance of the non-coding genome in regions of hypoxia in tumours. Such regions are frequently found in solid tumours, and are associated with worse patient survival and therapy resistance. Hypoxia stabilises the transcription factors, hypoxia inducible factors (HIF1α and HIF2α) which coordinate transcriptomic changes that occur in hypoxia. The changes in gene expression induced by HIF1α and HIF2α contribute to many of the hallmarks of cancer phenotypes and enable tumour growth, survival and invasion in the hypoxic tumour microenvironment. Non-coding RNAs, in particular microRNAs (miRNAs), which regulate mRNA stability and translation, and long-non-coding RNAs (lncRNAs), which have diverse functions including chromatin modification and transcriptional regulation, are also important in enabling the key hypoxia regulated processes. They have roles in the regulation of metabolism, angiogenesis, autophagy, invasion and metastasis in the hypoxic microenvironment. Furthermore, HIF1α and HIF2α expression and stabilisation are also regulated by both miRNAs and lncRNAs. Here we review the recent developments in the expression, regulation and functions of miRNAs, lncRNAs and other non-coding RNA classes in tumour hypoxia.
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Affiliation(s)
- Hani Choudhry
- Department of Biochemistry, Faculty of Science, Center of Innovation in Personalized Medicine, King Fahd Center for Medical Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Adrian L Harris
- Molecular Oncology Laboratories, Department of Oncology, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK.
| | - Alan McIntyre
- Cancer Biology, Division of Cancer and Stem Cells, QMC, University of Nottingham, Nottingham, NG7 2UH, UK.
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253
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Shen WJ, Zhang F, Zhao X, Xu J. LncRNAs and Esophageal Squamous Cell Carcinoma - Implications for Pathogenesis and Drug Development. J Cancer 2016; 7:1258-64. [PMID: 27390601 PMCID: PMC4934034 DOI: 10.7150/jca.14869] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2016] [Accepted: 04/26/2016] [Indexed: 02/05/2023] Open
Abstract
LncRNAs are a group of ncRNA species longer than 200 nt, which have fundamental regulatory roles in diverse cellular processes and diseases progression. Esophageal cancer is a serious malignancy with respect to prognosis and mortality rate. It is among the five leading cancer types for the cancer deaths in males of middle age in the United States. In China, esophageal cancer is the fourth most frequently diagnosed cancer and the fourth leading cause of cancer death. The molecular mechanisms of esophageal cancer development are not fully understood, but emerging studies point out that lncRNAs may actively associate with the pathogenesis. In this review, we first provided an introduction of lncRNAs classifications. Then we focused on the recent findings on lncRNA expression and function in esophageal cancer development. Implications for pathogenesis and potential drug developments will also be discussed.
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Affiliation(s)
- Wen-Jun Shen
- 2. Department of Bioinformatics, Shantou University Medical College, Shantou 515041, China
| | - Fan Zhang
- 2. Department of Bioinformatics, Shantou University Medical College, Shantou 515041, China
| | - Xing Zhao
- 2. Department of Bioinformatics, Shantou University Medical College, Shantou 515041, China
| | - Jianzhen Xu
- 1. Computational Systems Biology Lab, Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
- 2. Department of Bioinformatics, Shantou University Medical College, Shantou 515041, China
- ✉ Corresponding author: Jianzhen Xu. Ph.D. E-mail: or Phone: +86-754-88900491
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254
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Wang X, Gao Z, Liao J, Shang M, Li X, Yin L, Pu Y, Liu R. lncRNA UCA1 inhibits esophageal squamous-cell carcinoma growth by regulating the Wnt signaling pathway. JOURNAL OF TOXICOLOGY AND ENVIRONMENTAL HEALTH. PART A 2016; 79:407-418. [PMID: 27267823 DOI: 10.1080/15287394.2016.1176617] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Esophageal squamous-cell carcinoma (ESCC) is one of the most common tumors worldwide. Recent studies suggested that long noncoding RNAs (lncRNAs) might play a key role in regulating cellular processes and cancer progression. One of the lncRNAs, urothelial carcinoma associated 1 (UCA1), is known to be dysregulated in several cancers, including bladder carcinoma, colorectal, melanoma, breast, gastric, and ESCC. However, contributions of UCA1 to ESCC remain largely undiscovered. In order to understand the role and mechanisms underlying UCA1 in ESCC, the association of UCA1 expression with risk of esophageal cancer development was determined in 106 esophageal cancer tissues of ESCC patients and adjacent normal tissues using real-time reverse-transcription polymerase chain reaction (PCR). The relative expression of UCA1 was significantly reduced in cancer versus adjacent normal tissues suggesting an enhanced risk of esophageal cancer. To investigate the biological functions of UCA1 in ESCC, it was of interest to examine whether overexpression of UCA1 might influence cell proliferation, apoptosis, cell cycle distribution, migration, and invasion in vitro using EC109 cells. Our results demonstrated that UCA1 decreased cell proliferation, migration, invasion, and cell cycle progression of EC109 cells. Further, mRNA microarray analysis of overexpressed UCA1 in EC109 cells revealed that abnormal expression of UCA1 also inhibited the Wnt signaling pathway. Gene levels of DKK1 were elevated while C-myc fell significantly in overexpressed UCA1 EC109 cells. Interestingly, Western blot demonstrated no significant differences in relative expression of CTNNB1 (β-catenin) but marked reduction in β-catenin (active form) levels in both total and nuclear proteins. These results suggest that UCA1 may inhibit ESCC growth by regulating the Wnt signaling pathway. In conclusion, UCA1 may be a novel biomarker involved in ESCC development that may provide a potential therapeutic target for ESCC.
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Affiliation(s)
- Xianghu Wang
- a Key Laboratory of Environmental Medicine Engineering, Ministry of Education , School of Public Health, Southeast University , Nanjing , China
| | - Zhikui Gao
- a Key Laboratory of Environmental Medicine Engineering, Ministry of Education , School of Public Health, Southeast University , Nanjing , China
| | - Juan Liao
- a Key Laboratory of Environmental Medicine Engineering, Ministry of Education , School of Public Health, Southeast University , Nanjing , China
| | - Muhe Shang
- a Key Laboratory of Environmental Medicine Engineering, Ministry of Education , School of Public Health, Southeast University , Nanjing , China
| | - Xiajun Li
- a Key Laboratory of Environmental Medicine Engineering, Ministry of Education , School of Public Health, Southeast University , Nanjing , China
| | - Lihong Yin
- a Key Laboratory of Environmental Medicine Engineering, Ministry of Education , School of Public Health, Southeast University , Nanjing , China
| | - Yuepu Pu
- a Key Laboratory of Environmental Medicine Engineering, Ministry of Education , School of Public Health, Southeast University , Nanjing , China
| | - Ran Liu
- a Key Laboratory of Environmental Medicine Engineering, Ministry of Education , School of Public Health, Southeast University , Nanjing , China
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255
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Lo PK, Wolfson B, Zhou X, Duru N, Gernapudi R, Zhou Q. Noncoding RNAs in breast cancer. Brief Funct Genomics 2015; 15:200-21. [PMID: 26685283 DOI: 10.1093/bfgp/elv055] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The mammalian transcriptome has recently been revealed to encompass a large number of noncoding RNAs (ncRNAs) that play a variety of important regulatory roles in gene expression and other biological processes. MicroRNAs (miRNAs), the best studied of the short noncoding RNAs (sncRNAs), have been extensively characterized with regard to their biogenesis, function and importance in tumorigenesis. Another class of sncRNAs called piwi-interacting RNAs (piRNAs) has also gained attention recently in cancer research owing to their critical role in stem cell regulation. Long noncoding RNAs (lncRNAs) of >200 nucleotides in length have recently emerged as key regulators of developmental processes, including mammary gland development. lncRNA dysregulation has also been implicated in the development of various cancers, including breast cancer. In this review, we describe and discuss the roles of sncRNAs (including miRNAs and piRNAs) and lncRNAs in the initiation and progression of breast tumorigenesis, with a focus on outlining the molecular mechanisms of oncogenic and tumor-suppressor ncRNAs. Moreover, the current and potential future applications of ncRNAs to clinical breast cancer research are also discussed, with an emphasis on ncRNA-based diagnosis, prognosis and future therapeutics.
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256
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Xue M, Pang H, Li X, Li H, Pan J, Chen W. Long non-coding RNA urothelial cancer-associated 1 promotes bladder cancer cell migration and invasion by way of the hsa-miR-145-ZEB1/2-FSCN1 pathway. Cancer Sci 2015; 107:18-27. [PMID: 26544536 PMCID: PMC4724815 DOI: 10.1111/cas.12844] [Citation(s) in RCA: 138] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2015] [Revised: 10/08/2015] [Accepted: 11/01/2015] [Indexed: 12/14/2022] Open
Abstract
Numerous studies suggest that several long non‐coding RNAs (lncRNAs) play critical roles in bladder cancer development and progression. Long non‐coding RNA urothelial cancer‐associated 1 (lncRNA‐UCA1) is highly expressed in bladder cancer tissues and cells, and it has been shown to play an important role in regulating aggressive phenotypes of bladder cancer cells. However, little is known about the molecular mechanism of lncRNA‐UCA1‐mediated bladder cancer cell migration and invasion. Here, we show that overexpression of lncRNA‐UCA1 could induce EMT and increase the migratory and invasive abilities of bladder cancer cells. Mechanistically, lncRNA‐UCA1 induced EMT of bladder cancer cells by upregulating the expression levels of zinc finger E‐box binding homeobox 1 and 2 (ZEB1 and ZEB2), and regulated bladder cancer cell migration and invasion by tumor suppressive hsa‐miR‐145 and its target gene the actin‐binding protein fascin homologue 1 (FSCN1). Furthermore, we also observed a positive correlation between lncRNA‐UCA1 and ZEB1/2 expression, and a negative correlation between lncRNA‐UCA1 and hsa‐miR‐145 expression in bladder cancer specimens. Importantly, we found that lncRNA‐UCA1 repressed hsa‐miR‐145 expression to upregulate ZEB1/2, whereas the suppression of hsa‐miR‐145 could upregulate lncRNA‐UCA1 expression in bladder cancer cells. Moreover, the binding site for hsa‐miR‐145 within exons 2 and 3 of lncRNA‐UCA1 contributed to the reciprocal negative regulation of lncRNA‐UCA1 and hsa‐miR‐145. Taken together, our results identified that lncRNA‐UCA1 enhances bladder cancer cell migration and invasion in part through the hsa‐miR‐145/ZEB1/2/FSCN1 pathway. Therefore, lncRNA‐UCA1 might act as a promising therapeutic target for the invasion and metastasis of bladder cancer.
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Affiliation(s)
- Mei Xue
- Center for Translational Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Huan Pang
- Clinical Laboratory, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Xu Li
- Center for Translational Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Huijin Li
- Center for Translational Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Jingjing Pan
- Center for Translational Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Wei Chen
- Clinical Laboratory, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
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257
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Nicolai S, Pieraccioli M, Peschiaroli A, Melino G, Raschellà G. Neuroblastoma: oncogenic mechanisms and therapeutic exploitation of necroptosis. Cell Death Dis 2015; 6:e2010. [PMID: 26633716 PMCID: PMC4720889 DOI: 10.1038/cddis.2015.354] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Revised: 10/17/2015] [Accepted: 10/19/2015] [Indexed: 12/20/2022]
Abstract
Neuroblastoma (NB) is the most common extracranial childhood tumor classified in five stages (1, 2, 3, 4 and 4S), two of which (3 and 4) identify chemotherapy-resistant, highly aggressive disease. High-risk NB frequently displays MYCN amplification, mutations in ALK and ATRX, and genomic rearrangements in TERT genes. These NB subtypes are also characterized by reduced susceptibility to programmed cell death induced by chemotherapeutic drugs. The latter feature is a major cause of failure in the treatment of advanced NB patients. Thus, proper reactivation of apoptosis or of other types of programmed cell death pathways in response to treatment is relevant for the clinical management of aggressive forms of NB. In this short review, we will discuss the most relevant genomic rearrangements that define high-risk NB and the role that destabilization of p53 and p73 can have in NB aggressiveness. In addition, we will propose a strategy to stabilize p53 and p73 by using specific inhibitors of their ubiquitin-dependent degradation. Finally, we will introduce necroptosis as an alternative strategy to kill NB cells and increase tumor immunogenicity.
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Affiliation(s)
- S Nicolai
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Via Montpellier 1, Rome 00133, Italy
| | - M Pieraccioli
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Via Montpellier 1, Rome 00133, Italy
| | - A Peschiaroli
- Institute of Cell Biology and Neurobiology (IBCN), CNR, Via E. Ramarini 32, Rome 00015, Italy
| | - G Melino
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Via Montpellier 1, Rome 00133, Italy.,Medical Research Council, Toxicology Unit, Hodgkin Building, Leicester University, Lancaster Road, PO Box 138, Leicester LE1 9HN, UK
| | - G Raschellà
- ENEA Research Center Casaccia, Laboratory of Biosafety and Risk Assessment, Via Anguillarese, 301, Rome 00123, Italy
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258
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Abstract
Recent years have witnessed the discovery of several classes of noncoding RNAs (ncRNAs), which are indispensable for the regulation of cellular processes. Many of these RNAs are regulatory in nature with functions in gene expression regulation such as piwi-interacting RNAs, small interfering RNAs and micro RNAs. Long noncoding RNAs (lncRNAs) comprise the most recently characterized class. LncRNAs are involved in transcriptional regulation, chromatin remodeling, imprinting, splicing, and translation, among other critical functions in the cell. Recent studies have elucidated the importance of lncRNAs in hematopoietic development. Dysregulation of lncRNA expression is a feature of various diseases and cancers, and is also seen in hematopoietic malignancies. This article focuses on lncRNAs that have been implicated in the pathogenesis of hematopoietic malignancies.
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Affiliation(s)
- Norma I Rodríguez-Malavé
- Cellular and Molecular Pathology Program, Department of Pathology and Laboratory Medicine, University of California Los Angeles, Department of Pathology and Laboratory Medicine, Jonsson Comprehensive Cancer Center and Broad Stem Cell Research Center, University of California Los Angeles Cellular and Molecular Pathology Program, Department of Pathology and Laboratory Medicine, University of California Los Angeles, Department of Pathology and Laboratory Medicine, Jonsson Comprehensive Cancer Center and Broad Stem Cell Research Center, University of California Los Angeles
| | - Dinesh S Rao
- Cellular and Molecular Pathology Program, Department of Pathology and Laboratory Medicine, University of California Los Angeles, Department of Pathology and Laboratory Medicine, Jonsson Comprehensive Cancer Center and Broad Stem Cell Research Center, University of California Los Angeles Cellular and Molecular Pathology Program, Department of Pathology and Laboratory Medicine, University of California Los Angeles, Department of Pathology and Laboratory Medicine, Jonsson Comprehensive Cancer Center and Broad Stem Cell Research Center, University of California Los Angeles Cellular and Molecular Pathology Program, Department of Pathology and Laboratory Medicine, University of California Los Angeles, Department of Pathology and Laboratory Medicine, Jonsson Comprehensive Cancer Center and Broad Stem Cell Research Center, University of California Los Angeles
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259
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Wang G, Liu C, Deng S, Zhao Q, Li T, Qiao S, Shen L, Zhang Y, Lü J, Meng L, Liang C, Yu Z. Long noncoding RNAs in regulation of human breast cancer. Brief Funct Genomics 2015; 15:222-6. [PMID: 26582840 DOI: 10.1093/bfgp/elv049] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Less than 2% of the human genome DNA is composed of protein-coding genes, although the majority of the human genome is transcribed, indicating the transcripts mostly are noncoding RNAs. Those noncoding RNAs with length between 200 nt and 200 kb are categorized as long noncoding RNA (lncRNA). Around 30 000 lncRNAs have been predicted or identified, although little is known regarding the regulatory function for a vast majority of these sequences. Emerging evidence demonstrated that lncRNAs play crucial roles in regulation of many cancer types, including breast cancer, serving as oncogenes or tumor suppressors. Aberrant and differential expression of lncRNA in breast cancer has been frequently reported. Their regulation of breast cancer is still the beginning to be elucidated. This review collected those experimentally validated lncRNAs in human breast cancer, summarizing their biological function as well as the regulatory mechanism. In addition, the potential of lncRNAs as biomarkers for better diagnosis or therapeutic targets for cancer treatment was discussed.
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260
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Tao K, Yang J, Hu Y, Sun Y, Tan Z, Duan J, Zhang F, Yan H, Deng A. Clinical significance of urothelial carcinoma associated 1 in colon cancer. Int J Clin Exp Med 2015; 8:21854-21860. [PMID: 26885155 PMCID: PMC4724001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 10/27/2015] [Indexed: 06/05/2023]
Abstract
This study aimed to investigate the expression levels of urothelial carcinoma associated 1 (UCA1) in cancer tissues and plasma of colon cancer patients, and evaluate its clinical significance. Quantitative real-time PCR was used to determine the expression levels of UCA1 in 80 pairs of colon cancer and adjacent normal tissues, plasma samples from 20 healthy controls, 20 colon cancer patients before and after tumor removal. The relationships between UCA1 expression and clinical features and overall survival were analyzed. Compared with adjacent normal tissues, UCA1 was significantly upregulated in colon cancer tissues, especially in cases with LNM and advanced TNM stages (P < 0.05). High UCA1 expression was associated with LMN, higher pT category, and advanced TNM stages (P < 0.05). Patients with high UCA1 expression had worse survival time than those with low UCA1 expression (adjusted HR = 2.002, 95% CI 1.007-3.981, P = 0.048). Furthermore, plasma levels of UCA1 in colon cancer patients were significantly higher than those of controls (P = 0.016). There was significant difference in plasma level of UCA1 between samples taken before and after surgery (P = 0.048). In conclusion, tissue expression of UCA1 is related to prognosis in colon cancer. Plasma UCA1 may serve as a potential biomarker for early diagnosis and disease monitoring of colon cancer patients.
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Affiliation(s)
- Kun Tao
- Department of Pathology, Tongren Hospital, Shanghai Jiao Tong University School of MedicineShanghai 200336, China
- Department of Laboratory Diagnosis, Changhai Hospital, Second Military Medical UniversityShanghai 200433, China
| | - Jing Yang
- Department of Pathology, Tongren Hospital, Shanghai Jiao Tong University School of MedicineShanghai 200336, China
| | - Yuemei Hu
- Department of Pathology, Tongren Hospital, Shanghai Jiao Tong University School of MedicineShanghai 200336, China
| | - Yaohua Sun
- Department of Pathology, Tongren Hospital, Shanghai Jiao Tong University School of MedicineShanghai 200336, China
| | - Zhenyu Tan
- Department of Pathology, Tongren Hospital, Shanghai Jiao Tong University School of MedicineShanghai 200336, China
| | - Jinglin Duan
- Department of Pathology, Tongren Hospital, Shanghai Jiao Tong University School of MedicineShanghai 200336, China
| | - Feng Zhang
- Department of Pathology, Tongren Hospital, Shanghai Jiao Tong University School of MedicineShanghai 200336, China
| | - Hongli Yan
- Department of Laboratory Diagnosis, Changhai Hospital, Second Military Medical UniversityShanghai 200433, China
| | - Anmei Deng
- Department of Laboratory Diagnosis, Changhai Hospital, Second Military Medical UniversityShanghai 200433, China
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261
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Long non-coding RNA MVIH is associated with poor prognosis and malignant biological behavior in breast cancer. Tumour Biol 2015; 37:5257-64. [DOI: 10.1007/s13277-015-4360-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2015] [Accepted: 10/30/2015] [Indexed: 10/22/2022] Open
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262
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Fortes P, Morris KV. Long noncoding RNAs in viral infections. Virus Res 2015; 212:1-11. [PMID: 26454188 DOI: 10.1016/j.virusres.2015.10.002] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 10/01/2015] [Indexed: 01/11/2023]
Abstract
Viral infections induce strong modifications in the cell transcriptome. Among the RNAs whose expression is altered by infection are long noncoding RNAs (lncRNAs). LncRNAs are transcripts with potential to function as RNA molecules. Infected cells may express viral lncRNAs, cellular lncRNAs and chimeric lncRNAs formed by viral and cellular sequences. Some viruses express viral lncRNAs whose function is essential for viral viability. They are transcribed by polymerase II or III and some of them can be processed by unique maturation steps performed by host cell machineries. Some viral lncRNAs control transcription, stability or translation of cellular and viral genes. Surprisingly, similar functions can be exerted by cellular lncRNAs induced by infection. Expression of cellular lncRNAs may be altered in response to viral replication or viral protein expression. However, many cellular lncRNAs respond to the antiviral pathways induced by infection. In fact, many lncRNAs function as positive or negative regulators of the innate antiviral response. Our current knowledge about the identity and function of lncRNAs in infected cells is very limited. However, research into this field has already helped in the identification of novel cellular pathways and may help in the development of therapeutic tools for the treatment of viral infections, autoimmune diseases, neurological disorders and cancer.
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Affiliation(s)
- Puri Fortes
- Center for Applied Medical Research (CIMA) and Navarra Institute for Health Research (IdiSNA), Department of Gene Therapy and Hepatology, University of Navarra, Pamplona, Spain.
| | - Kevin V Morris
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, USA; School of Biotechnology and Biomedical Sciences, University of New South Wales, Kensington, NSW, Australia
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263
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Abstract
Viral infections induce strong modifications in the cell transcriptome. Among the RNAs whose expression is altered by infection are long noncoding RNAs (lncRNAs). LncRNAs are transcripts with potential to function as RNA molecules. Infected cells may express viral lncRNAs, cellular lncRNAs and chimeric lncRNAs formed by viral and cellular sequences. Some viruses express viral lncRNAs whose function is essential for viral viability. They are transcribed by polymerase II or III and some of them can be processed by unique maturation steps performed by host cell machineries. Some viral lncRNAs control transcription, stability or translation of cellular and viral genes. Surprisingly, similar functions can be exerted by cellular lncRNAs induced by infection. Expression of cellular lncRNAs may be altered in response to viral replication or viral protein expression. However, many cellular lncRNAs respond to the antiviral pathways induced by infection. In fact, many lncRNAs function as positive or negative regulators of the innate antiviral response. Our current knowledge about the identity and function of lncRNAs in infected cells is very limited. However, research into this field has already helped in the identification of novel cellular pathways and may help in the development of therapeutic tools for the treatment of viral infections, autoimmune diseases, neurological disorders and cancer.
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Affiliation(s)
- Puri Fortes
- Center for Applied Medical Research (CIMA) and Navarra Institute for Health Research (IdiSNA), Department of Gene Therapy and Hepatology, University of Navarra, Pamplona, Spain.
| | - Kevin V Morris
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, USA; School of Biotechnology and Biomedical Sciences, University of New South Wales, Kensington, NSW, Australia
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264
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Aparicio-Prat E, Arnan C, Sala I, Bosch N, Guigó R, Johnson R. DECKO: Single-oligo, dual-CRISPR deletion of genomic elements including long non-coding RNAs. BMC Genomics 2015; 16:846. [PMID: 26493208 PMCID: PMC4619085 DOI: 10.1186/s12864-015-2086-z] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 10/15/2015] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND CRISPR genome-editing technology makes it possible to quickly and cheaply delete non-protein-coding regulatory elements. We present a vector system adapted for this purpose called DECKO (Double Excision CRISPR Knockout), which applies a simple two-step cloning to generate lentiviral vectors expressing two guide RNAs (gRNAs) simultaneously. The key feature of DECKO is its use of a single 165 bp starting oligonucleotide carrying the variable sequences of both gRNAs, making it fully scalable from single-locus studies to complex library cloning. RESULTS We apply DECKO to deleting the promoters of one protein-coding gene and two oncogenic lncRNAs, UCA1 and the highly-expressed MALAT1, focus of many previous studies employing RNA interference approaches. DECKO successfully deleted genomic fragments ranging in size from 100 to 3000 bp in four human cell lines. Using a clone-derivation workflow lasting approximately 20 days, we obtained 9 homozygous and 17 heterozygous promoter knockouts in three human cell lines. Frequent target region inversions were observed. These clones have reductions in steady-state MALAT1 RNA levels of up to 98 % and display reduced proliferation rates. CONCLUSIONS We present a dual CRISPR tool, DECKO, which is cloned using a single starting oligonucleotide, thereby affording simplicity and scalability to CRISPR knockout studies of non-coding genomic elements, including long non-coding RNAs.
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Affiliation(s)
- Estel Aparicio-Prat
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain.
- Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Dr. Aiguader 88, 08003, Barcelona, Spain.
| | - Carme Arnan
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain.
- Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Dr. Aiguader 88, 08003, Barcelona, Spain.
| | - Ilaria Sala
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain.
- Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Dr. Aiguader 88, 08003, Barcelona, Spain.
| | - Núria Bosch
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain.
- Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Dr. Aiguader 88, 08003, Barcelona, Spain.
| | - Roderic Guigó
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain.
- Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Dr. Aiguader 88, 08003, Barcelona, Spain.
| | - Rory Johnson
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain.
- Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Dr. Aiguader 88, 08003, Barcelona, Spain.
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Liu ZJ, Semenza GL, Zhang HF. Hypoxia-inducible factor 1 and breast cancer metastasis. J Zhejiang Univ Sci B 2015; 16:32-43. [PMID: 25559953 DOI: 10.1631/jzus.b1400221] [Citation(s) in RCA: 152] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Accumulating evidence has shown that the hypoxic microenvironment, which is critical during cancer development, plays a key role in regulating breast cancer progression and metastasis. The effects of hypoxia-inducible factor 1 (HIF-1), a master regulator of the hypoxic response, have been extensively studied during these processes. In this review, we focus on the roles of HIF-1 in regulating breast cancer cell metastasis, specifically its effects on multiple key steps of metastasis, such as epithelial-mesenchymal transition (EMT), invasion, extravasation, and metastatic niche formation. We also discuss the roles of HIF-1-regulated non-coding RNAs in breast cancer metastasis, and therapeutic opportunities for breast cancer through targeting the HIF-1 pathway.
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Affiliation(s)
- Zhao-Ji Liu
- CAS Key Laboratory of Innate Immunity and Chronic Disease, Innovation Center for Cell Biology, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China; Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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266
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Carnero E, Fortes P. HCV infection, IFN response and the coding and non-coding host cell genome. Virus Res 2015; 212:85-102. [PMID: 26454190 DOI: 10.1016/j.virusres.2015.10.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 10/01/2015] [Indexed: 02/07/2023]
Abstract
HCV is an ideal model to study how the infected cell is altered to allow the establishment of a chronic infection. After infection, the transcriptome of the cell changes in response to the virus or to the antiviral pathways induced by infection. The cell has evolved to sense HCV soon after infection and to activate antiviral pathways. In turn, HCV has evolved to block the antiviral pathways induced by the cell and, at the same time, to use some for its own benefit. In this review, we summarize the proviral and antiviral factors induced in HCV infected cells. These factors can be proteins and microRNAs, but also long noncoding RNAs (lncRNAs) that are induced by infection. Interestingly, several of the lncRNAs upregulated after HCV infection have oncogenic functions, suggesting that upregulation of lncRNAs could explain, at least in part, the increased rate of liver tumors observed in HCV-infected patients. Other lncRNAs induced by HCV infection may regulate the expression of coding genes required for replication or control genes involved in the cellular antiviral response. Given the evolutionary pressure imposed by viral infections and that lncRNAs are specially targeted by evolution, we believe that the study of proviral and antiviral lncRNAs may lead to unexpected discoveries that may have a strong impact on basic science and translational research.
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Affiliation(s)
- Elena Carnero
- Center for Applied Medical Research (CIMA) and Navarra Institute for Health Research (IdiSNA), Department of Gene Therapy and Hepatology, University of Navarra, Pamplona, Spain
| | - Puri Fortes
- Center for Applied Medical Research (CIMA) and Navarra Institute for Health Research (IdiSNA), Department of Gene Therapy and Hepatology, University of Navarra, Pamplona, Spain.
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267
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Sarkar D, Leung EY, Baguley BC, Finlay GJ, Askarian-Amiri ME. Epigenetic regulation in human melanoma: past and future. Epigenetics 2015; 10:103-21. [PMID: 25587943 PMCID: PMC4622872 DOI: 10.1080/15592294.2014.1003746] [Citation(s) in RCA: 206] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The development and progression of melanoma have been attributed to independent or combined genetic and epigenetic events. There has been remarkable progress in understanding melanoma pathogenesis in terms of genetic alterations. However, recent studies have revealed a complex involvement of epigenetic mechanisms in the regulation of gene expression, including methylation, chromatin modification and remodeling, and the diverse activities of non-coding RNAs. The roles of gene methylation and miRNAs have been relatively well studied in melanoma, but other studies have shown that changes in chromatin status and in the differential expression of long non-coding RNAs can lead to altered regulation of key genes. Taken together, they affect the functioning of signaling pathways that influence each other, intersect, and form networks in which local perturbations disturb the activity of the whole system. Here, we focus on how epigenetic events intertwine with these pathways and contribute to the molecular pathogenesis of melanoma.
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Key Words
- 5hmC, 5-hydroxymethylcytosine
- 5mC, 5-methylcytosine
- ACE, angiotensin converting enzyme
- ANCR, anti-differentiation non-coding RNA
- ANRIL, antisense noncoding RNA in INK4 locus
- ASK1, apoptosis signal-regulating kinase 1
- ATRA, all-trans retinoic acid
- BANCR, BRAF-activated non-coding RNA
- BCL-2, B-cell lymphoma 2
- BRAF, B-Raf proto-oncogene, serine/threonine kinase
- BRG1, ATP-dependent helicase SMARCA4
- CAF-1, chromatin assembly factor-1
- CBX7, chromobox homolog 7
- CCND1, cyclin D1
- CD28, cluster of differentiation 28
- CDK, cyclin-dependent kinase
- CDKN2A/B, cyclin-dependent kinase inhibitor 2A/B
- CHD8, chromodomain-helicase DNA-binding protein 8
- CREB, cAMP response element-binding protein
- CUDR, cancer upregulated drug resistant
- Cdc6, cell division cycle 6
- DNA methylation/demethylation
- DNMT, DNA methyltransferase
- EMT, epithelial-mesenchymal transition
- ERK, extracellular signal-regulated kinase
- EZH2, enhancer of zeste homolog 2
- GPCRs, G-protein coupled receptors
- GSK3a, glycogen synthase kinase 3 α
- GWAS, genome-wide association study
- HDAC, histone deacetylase
- HOTAIR, HOX antisense intergenic RNA
- IAP, inhibitor of apoptosis
- IDH2, isocitrate dehydrogenase
- IFN, interferon, interleukin 23
- JNK, Jun N-terminal kinase
- Jak/STAT, Janus kinase/signal transducer and activator of transcription
- MAFG, v-maf avian musculoaponeurotic fibrosarcoma oncogene homolog G
- MALAT1, metastasis-associated lung adenocarcinoma transcript 1
- MAPK, mitogen-activated protein kinase
- MC1R, melanocortin-1 receptor
- MGMT, O6-methylguanine-DNA methyltransferase
- MIF, macrophage migration inhibitory factor
- MITF, microphthalmia-associated transcription factor
- MRE, miRNA recognition element
- MeCP2, methyl CpG binding protein 2
- NF-κB, nuclear factor kappa-light-chain-enhancer of activated B cells
- NOD, nucleotide-binding and oligomerization domain
- PBX, pre-B-cell leukemia homeobox
- PEDF, pigment epithelium derived factor
- PI3K, phosphatidylinositol-4, 5-bisphosphate 3-kinase
- PIB5PA, phosphatidylinositol-4, 5-biphosphate 5-phosphatase A
- PKA, protein kinase A
- PRC, polycomb repressor complex
- PSF, PTB associated splicing factor
- PTB, polypyrimidine tract-binding
- PTEN, phosphatase and tensin homolog
- RARB, retinoic acid receptor-β2
- RASSF1A, Ras association domain family 1A
- SETDB1, SET Domain, bifurcated 1
- SPRY4, Sprouty 4
- STAU1, Staufen1
- SWI/SNF, SWItch/Sucrose Non-Fermentable
- TCR, T-cell receptor
- TET, ten eleven translocase
- TGF β, transforming growth factor β
- TINCR, tissue differentiation-inducing non-protein coding RNA
- TOR, target of rapamycin
- TP53, tumor protein 53
- TRAF6, TNF receptor-associated factor 6
- UCA1, urothelial carcinoma-associated 1
- ceRNA, competitive endogenous RNAs
- chromatin modification
- chromatin remodeling
- epigenetics
- gene regulation
- lncRNA, long ncRNA
- melanoma
- miRNA, micro RNA
- ncRNA, non-coding RNA
- ncRNAs
- p14ARF, p14 alternative reading frame
- p16INK4a, p16 inhibitor of CDK4
- pRB, retinoblastoma protein
- snoRNA, small nucleolar RNA
- α-MSHm, α-melanocyte stimulating hormone
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Affiliation(s)
- Debina Sarkar
- a Auckland Cancer Society Research Center ; University of Auckland ; Auckland , New Zealand
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268
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Gupta SC, Singh R, Pochampally R, Watabe K, Mo YY. Acidosis promotes invasiveness of breast cancer cells through ROS-AKT-NF-κB pathway. Oncotarget 2015; 5:12070-82. [PMID: 25504433 PMCID: PMC4322981 DOI: 10.18632/oncotarget.2514] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Accepted: 09/24/2014] [Indexed: 01/24/2023] Open
Abstract
It is well known that acidic microenvironment promotes tumorigenesis, however, the underlying mechanism remains largely unknown. In the present study, we show that acidosis promotes invasiveness of breast cancer cells through a series of signaling events. First, our study indicates that NF-κB is a key factor for acidosis-induced cell invasion. Acidosis activates NF-κB without affecting STAT3 activity; knockdown of NF-κB p65 abrogates the acidosis-induced invasion activity. Next, we show that the activation of NF-κB is mediated through phosphorylation and degradation of IκBα; and phosphorylation and nuclear translocation of p65. Upstream to NF-κB signaling, AKT is activated under acidic conditions. Moreover, acidosis induces generation of reactive oxygen species (ROS) which can be suppressed by ROS scavengers, reversing the acidosis-induced activation of AKT and NF-κB, and invasiveness. As a negative regulator of AKT, PTEN is oxidized and inactivated by the acidosis-induced ROS. Finally, inhibition of NADPH oxidase (NOX) suppresses acidosis-induced ROS production, suggesting involvement of NOX in acidosis-induced signaling cascade. Of considerable interest, acidosis-induced ROS production and activation of AKT and NF-κB can be only detected in cancer cells, but not in non-malignant cells. Together, these results demonstrate a cancer specific acidosis-induced signaling cascade in breast cancer cells, leading to cell invasion.
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Affiliation(s)
- Subash C Gupta
- Cancer Institute, University of Mississippi Medical Center, Jackson, MS. Department of Biochemistry, University of Mississippi Medical Center, Jackson, MS
| | - Ramesh Singh
- Cancer Institute, University of Mississippi Medical Center, Jackson, MS. Department of Biochemistry, University of Mississippi Medical Center, Jackson, MS
| | - Radhika Pochampally
- Cancer Institute, University of Mississippi Medical Center, Jackson, MS. Department of Biochemistry, University of Mississippi Medical Center, Jackson, MS
| | - Kounosuke Watabe
- Cancer Institute, University of Mississippi Medical Center, Jackson, MS. Department of Microbiology, University of Mississippi Medical Center, Jackson, MS
| | - Yin-Yuan Mo
- Cancer Institute, University of Mississippi Medical Center, Jackson, MS. Department of Pharmacology and Toxicology, University of Mississippi Medical Center, Jackson, MS
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269
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Expression analysis of four long noncoding RNAs in breast cancer. Tumour Biol 2015; 37:2933-40. [PMID: 26409453 DOI: 10.1007/s13277-015-4135-2] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 09/21/2015] [Indexed: 10/23/2022] Open
Abstract
Breast cancer is a molecularly heterogeneous disease which necessitates a search for markers to provide a more specific classification of this disorder. Long noncoding RNAs as the important subset of noncoding transcripts have been shown to be involved in tumorigenic processes. So, they may be used as markers for early detection of cancer and evaluation of cancer prognosis. In addition, they can be applied as therapeutic targets. In this study, we analyzed expression of four long noncoding RNAs (lncRNAs) namely SOX2OT, PTPRG-AS1, ANRASSF1, and ANRIL in 38 breast cancer tissues and their adjacent noncancerous tissues (ANCTs). ANRASSF1 expression was not detected in any noncancerous tissue. All lncRNAs showed significant overexpression in tumor tissues compared with ANCTs. No association was found between gene expressions and individual clinical data such as tumor stage, grade, size and hormone receptor status except for ANRASSF1 expression and Her2/neu status. In addition, ANRASSF1 and ANRIL expressions were significantly higher in triple negative samples. This study suggests a putative role for these lncRNAs in breast cancer and implies that they can be used as potential cancer biomarkers.
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270
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Hu W, Wang T, Yang Y, Zheng S. Tumor heterogeneity uncovered by dynamic expression of long noncoding RNA at single-cell resolution. Cancer Genet 2015; 208:581-6. [PMID: 26556691 DOI: 10.1016/j.cancergen.2015.09.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Revised: 09/09/2015] [Accepted: 09/18/2015] [Indexed: 11/27/2022]
Abstract
The expression of long noncoding RNA (lncRNA) is thought to be more cell-type specific than the expression of protein-coding genes. However, the expression profile of individual cells regarding lncRNA remains to be elucidated. Here, we comprehensively investigated the pattern of lncRNA expression across five glioblastoma tumors (414 cells) and two cell lines (GBM6 and GBM8, 127 cells). We found that there were more than 1,000 lncRNAs that varied between any two cells and that there was frequent gain and loss of lncRNA expression during tumor cell proliferation, suggesting a great heterogeneity in lncRNA expression across different single cells in glioblastoma.
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Affiliation(s)
- Wangxiong Hu
- Cancer Institute, Second Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | | | - Yanmei Yang
- Key Laboratory of Reproductive Genetics, Ministry of Education, Women's Hospital, Zhejiang University, Hangzhou, China
| | - Shu Zheng
- Cancer Institute, Second Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.
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271
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Cai Y, He J, Zhang D. Long noncoding RNA CCAT2 promotes breast tumor growth by regulating the Wnt signaling pathway. Onco Targets Ther 2015; 8:2657-64. [PMID: 26442763 PMCID: PMC4590572 DOI: 10.2147/ott.s90485] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
In addition to protein-coding genes, the human genome makes a large amount of noncoding RNAs, including microRNAs and long noncoding RNAs (lncRNAs). Emerging evidence indicates that lncRNAs could have a critical role in the regulation of cellular processes such as cell growth and apoptosis as well as cancer progression and metastasis. The lncRNA CCAT2 is dysregulated in several cancers such as colon cancer, non-small cell lung cancer, esophageal squamous cell carcinoma, gastric cancer, and breast cancer; however, the contributions of CCAT2 to breast cancer remain largely unknown. In the current paper, we first confirmed the high expression level of CCAT2 in breast cancer tissues and breast cancer cell lines by reverse transcription quantitative polymerase chain reaction (RT-qPCR) assay, and we further analyzed the relationship between CCAT2 expression and clinical prognostic factors. Also, the biological function of CCAT2 was explored and the results showed silencing of CCAT2 could suppress cell growth in vitro and tumor formation in vivo. Finally, our results revealed that the abnormal expression of CCAT2 could influence the Wnt signaling pathway. In conclusion, lncRNA CCAT2 might be considered as a novel molecule involved in breast cancer development, which provides a potential therapeutic target for breast cancer.
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Affiliation(s)
- Yi Cai
- Department of Geriatric Oncology, The General Hospital of Chinese People's Liberation Army, Beijing City, People's Republic of China
| | - Jing He
- Department of Geriatric Integrated Surgery, The General Hospital of Chinese People's Liberation Army, Beijing City, People's Republic of China
| | - Dong Zhang
- Department of Geriatric Oncology, The General Hospital of Chinese People's Liberation Army, Beijing City, People's Republic of China
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272
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Lin CY, Xu HM. Novel perspectives of long non-coding RNAs in esophageal carcinoma. Carcinogenesis 2015; 36:1255-62. [PMID: 26392258 DOI: 10.1093/carcin/bgv136] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 09/12/2015] [Indexed: 12/16/2022] Open
Abstract
Esophageal carcinoma (EC) is one of the most aggressive cancer types worldwide. However, the underlying genomic events of EC are not fully understood. It is becoming evident that long non-coding RNAs (lncRNAs) play vital roles in tumorgenesis, metastasis, prognosis and diagnosis. Accumulating EC-related lncRNAs have been verified to involve in various biological processes through diverse functions including signal, decoy, scaffold and guide. However, the molecular mechanism of lncRNAs in EC has not been fully explored. In this review, we outline the functions and underlying mechanism of EC-related lncRNAs to pave the way for identification of novel potential biomarkers for EC.
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Affiliation(s)
- Chen-Yu Lin
- Department of The Engineering Research Center of Peptide Drug Discovery and Development and Department of State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Han-Mei Xu
- Department of The Engineering Research Center of Peptide Drug Discovery and Development and Department of State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, P. R. China
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273
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Long Noncoding RNAs as New Architects in Cancer Epigenetics, Prognostic Biomarkers, and Potential Therapeutic Targets. BIOMED RESEARCH INTERNATIONAL 2015; 2015:320214. [PMID: 26448935 PMCID: PMC4584070 DOI: 10.1155/2015/320214] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2014] [Accepted: 05/06/2015] [Indexed: 12/27/2022]
Abstract
Recent advances in genome-wide analysis have revealed that 66% of the genome is actively transcribed into noncoding RNAs (ncRNAs) while less than 2% of the sequences encode proteins. Among ncRNAs, high-resolution microarray and massively parallel sequencing technologies have identified long ncRNAs (>200 nucleotides) that lack coding protein function. LncRNAs abundance, nuclear location, and diversity allow them to create in association with protein interactome, a complex regulatory network orchestrating cellular phenotypic plasticity via modulation of all levels of protein-coding gene expression. Whereas lncRNAs biological functions and mechanisms of action are still not fully understood, accumulating data suggest that lncRNAs deregulation is pivotal in cancer initiation and progression and metastatic spread through various mechanisms, including epigenetic effectors, alternative splicing, and microRNA-like molecules. Mounting data suggest that several lncRNAs expression profiles in malignant tumors are associated with prognosis and they can be detected in biological fluids. In this review, we will briefly discuss characteristics and functions of lncRNAs, their role in carcinogenesis, and their potential usefulness as diagnosis and prognosis biomarkers and novel therapeutic targets.
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274
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Ding J, Lu B, Wang J, Wang J, Shi Y, Lian Y, Zhu Y, Wang J, Fan Y, Wang Z, De W, Wang K. Long non-coding RNA Loc554202 induces apoptosis in colorectal cancer cells via the caspase cleavage cascades. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2015; 34:100. [PMID: 26362196 PMCID: PMC4567799 DOI: 10.1186/s13046-015-0217-7] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Accepted: 09/02/2015] [Indexed: 01/17/2023]
Abstract
Background Aberrant expression of long noncoding RNAs (lncRNAs) has frequently been reported in cancer studies, including those of colorectal cancer (CRC). Increasing evidence suggests that lncRNAs are significantly correlated with the pathogenesis, development and metastasis of cancer. Loc554202 is a 2166-bp transcript on human chromosome 9p21.3, the expression of which is dysregulated in breast and lung cancer cells. However, its role in CRC remains under investigation. Methods Quantitative real-time polymerase chain reaction (qRT-PCR) was carried out to assess the relative expression of Loc554202 in CRC cell lines and tissues. Gain and/or loss of function approaches were used to investigate the potential functional roles in cell proliferation and apoptosis in vitro and in vivo. qRT-PCR, western-blotting and immunohistochemistry were used to evaluate the mRNA and protein expression of apoptosis-related factors. Results Loc554202 was significantly downregulated in cancerous tissues and CRC cell lines compared with adjacent normal tissue and a normal human intestinal epithelial cell line. Low Loc554202 expression was closely associated with advanced pathologic stage and a larger tumor size. The overexpression of Loc554202 decreased the cell proliferation and induced apoptosis in vitro and hindered tumorigenesis in vivo. Loc554202 regulated cell apoptosis partly through the activation of specific caspase cleavage cascades. Conclusion Our results suggest that Loc554202 may play an important role in the progression of CRC and could be a candidate prognostic biomarker or a target for new cancer therapies. Electronic supplementary material The online version of this article (doi:10.1186/s13046-015-0217-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jie Ding
- Department of Oncology, Second Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu, PR China
| | - Binbin Lu
- Department of Oncology, Second Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu, PR China
| | - Jianping Wang
- Department of clinical laboratory, Second Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu, PR China
| | - Juan Wang
- Department of Oncology, Second Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu, PR China
| | - Yongguo Shi
- Department of Oncology, Second Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu, PR China
| | - Yifan Lian
- Department of Oncology, Second Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu, PR China
| | - Ya Zhu
- Department of Oncology, Second Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu, PR China
| | - Jirong Wang
- Department of Oncology, Second Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu, PR China
| | - Yingrui Fan
- Department of Oncology, Second Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu, PR China
| | - Zhaoxia Wang
- Department of Oncology, Second Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu, PR China
| | - Wei De
- Department of Biochemistry and Molecular Biology, Nanjing Medical University, Nanjing, Jiangsu, 210029, PR China
| | - Keming Wang
- Department of Oncology, Second Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu, PR China.
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275
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Long Noncoding RNA CUDR Regulates HULC and β-Catenin to Govern Human Liver Stem Cell Malignant Differentiation. Mol Ther 2015; 23:1843-53. [PMID: 26347501 DOI: 10.1038/mt.2015.166] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 09/01/2015] [Indexed: 12/14/2022] Open
Abstract
Long noncoding RNA cancer upregulated drug resistant (CUDR) is overexpressed in many tumors and promotes tumorigenesis. Herein, we demonstrate CUDR could enhance the human embryonic stem cells (ESC) differentiation into hepatocyte-like cells by reducing trimethylation on histone H3 twenty-seventh lysine (H3K27me3). On the other hand, excessive CUDR triggers hepatocyte-like cells malignant transformation. Mechanistically, we identify CUDR causes highly upregulated in liver cancer (HULC) and β-catenin abnormal expression by inhibiting HULC promoter methylation and promoting β-catenin promoter-enhancer chromatin looping formation mediated by CUDR-ccctc-binding factor (CTCF) complex, which recruits more RNA polII and P300. Strikingly, HULC and β-catenin activity are crucial for CUDR oncogenic function. These findings provide the first demonstration that CUDR plays a positive potential role in liver cancer stem cell through the cascade of CUDR-HULC/CUDR-β-catenin signaling, and offer insights into a novel link between long noncoding RNA (lncRNA) and the epigenetic modification in cancer stem cells.
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276
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Xue M, Chen W, Li X. Urothelial cancer associated 1: a long noncoding RNA with a crucial role in cancer. J Cancer Res Clin Oncol 2015; 142:1407-19. [PMID: 26341664 DOI: 10.1007/s00432-015-2042-y] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 08/27/2015] [Indexed: 02/06/2023]
Abstract
BACKGROUND Urothelial cancer associated 1 (UCA1) is a long noncoding RNA (lncRNA) which has gained more attention in recent years due to its aberrant expression in embryogenesis and a broad range of cancer tissues and cells. Importantly, multiple studies have shown that UCA1 plays oncogenic roles in tumor growth and metastasis, and it may act as a potential biomarker and therapeutic target for human cancers. However, the molecular mechanism of UCA1 in cancer initiation, progression and metastasis remains incompletely understood. Thus, gaining a better understanding of the functional mechanism of UCA1 in cancer onset and progression is of the utmost significance for evaluating the potential application of UCA1. RESULTS AND DISCUSSION In this review, we discuss UCA1 expression profiling, isoform, expression regulation, biological role and mechanism for UCA1 tumor-promoting effect. We further discuss the potential clinical application of UCA1 as a promising diagnostic biomarker or therapeutic target for human cancers. CONCLUSION UCA1 functions as an oncogenic lncRNA in several malignancies, and it might become a potential biomarker or therapeutic target for human cancers.
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Affiliation(s)
- Mei Xue
- Center for Translational Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, 277 West Yanta Road, Xi'an, 710061, People's Republic of China
| | - Wei Chen
- Clinical Laboratory, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, People's Republic of China
| | - Xu Li
- Center for Translational Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, 277 West Yanta Road, Xi'an, 710061, People's Republic of China.
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277
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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: 62] [Impact Index Per Article: 6.9] [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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278
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Pei J, Wang B. Notch-1 promotes breast cancer cells proliferation by regulating LncRNA GAS5. Int J Clin Exp Med 2015; 8:14464-14471. [PMID: 26550436 PMCID: PMC4613121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 08/11/2015] [Indexed: 06/05/2023]
Abstract
BACKGROUND Notch signaling is indicated as novel therapeutic targets to prevent recurrence of breast cancer. LncRNAs were identified as downstream target of Notch pathway. However, the exact mechanisms involved in Notch signaling, lncRNAs and breast cancer remain to be explained. OBJECTIVE This original research aimed to determine the prognostic implications of Notch-1 for breast cancer, and explain mechanisms involved in regulation of lnRNA GAS5 by Notch-1, and identify the function of this mechanism on breast cancer. METHOD Thirty breast cancer patients were included from The First Affiliated Hospital of Anhui Medical University (China) since January 2006 in this study. The mRNA level by RT-PCR and protein level of Notch-1 by western blot in tumor tissues and adjacent normal tissues were evaluated and 5-year survival analysis was applied to examine the significance of Notch-1. The levels of ten reported lncRNAs were determined by RT-PCR, and subsequently linear analysis was applied to analyze the relationship between these four unique lncRNAs and protein level of Notch-1, which identified the most relevant lncRNA GAS5 with Notch-1 in breast cancer. Subsequently, Notch1-siRNA was applied to influence the expression of Notch-1 in T47D, then the level of RSA5 was measured by RT-PCR, and CCK-8 assay was applied to measure the proliferation of T47D cells. RESULTS High level of Notch-1 provided a poor prognosis in breast cancer. Interference of Notch-1 significantly suppressed proliferation of T47D cell (P < 0.05), and significantly increased the level of GAS5. CONCLUSION Notch-1 promotes breast cancer cells proliferation by regulating LncRNA GAS5.
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Affiliation(s)
- Jing Pei
- The Department of Breast Surgery, The First Affiliated Hospital of Anhui Medical University Jixi Road 218, Hefei 230022, Anhui, China
| | - Benzhong Wang
- The Department of Breast Surgery, The First Affiliated Hospital of Anhui Medical University Jixi Road 218, Hefei 230022, Anhui, China
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279
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Lisitsyn NA, Chernyi AA, Karpov VL, Beresten SF. A role of long noncoding RNAs in carcinogenesis. Mol Biol 2015. [DOI: 10.1134/s002689331504010x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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280
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Chen S, Shao C, Xu M, Ji J, Xie Y, Lei Y, Wang X. Macrophage infiltration promotes invasiveness of breast cancer cells via activating long non-coding RNA UCA1. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2015; 8:9052-9061. [PMID: 26464647 PMCID: PMC4583879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 07/21/2015] [Indexed: 06/05/2023]
Abstract
There is now considerable evidence supporting the view that macrophage infiltration is playing a critical role in the proliferation and progression of breast cancer but the underlying molecular mechanisms remain largely unknown. To this end, using long non-coding RNA (lncRNA) expression profiling, we examined changes in lncRNA expression in breast cancer cells treated with conditioned medium (CM) from cultured human THP-1 macrophages. We found that treatment with macrophage CM induced the expression of numerous lncRNAs, including urothelial cancer associated 1 (UCA1). Knockdown of UCA1 using shRNA inhibited AKT phosphorylation and abolished invasiveness of tumor cells induced by macrophage CM. Consistent with these results; we further showed that UCA1 level was significantly enhanced in human primary breast tumors and correlated with advanced clinical stage, supporting its role in promoting carcinogenesis and progression of breast cancer. Together, these results suggest that macrophage could promote invasiveness of breast cancer cells by enhancing expression of lncRNA UCA1.
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Affiliation(s)
- Shuzheng Chen
- Lishui Central Hospital & Zhejiang University Lishui HospitalLishui, Zhejiang, China
| | - Chuxiao Shao
- Lishui Central Hospital & Zhejiang University Lishui HospitalLishui, Zhejiang, China
| | - Min Xu
- Lishui Central Hospital & Zhejiang University Lishui HospitalLishui, Zhejiang, China
| | - Jiansong Ji
- Lishui Central Hospital & Zhejiang University Lishui HospitalLishui, Zhejiang, China
| | - Yanru Xie
- Lishui Central Hospital & Zhejiang University Lishui HospitalLishui, Zhejiang, China
| | - Yongliang Lei
- Lishui Center for Disease Control and PreventionLishui, Zhejiang, China
| | - Xiaoguang Wang
- Lishui Center for Disease Control and PreventionLishui, Zhejiang, China
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281
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Increased urothelial cancer associated 1 is associated with tumor proliferation and metastasis and predicts poor prognosis in colorectal cancer. Int J Oncol 2015; 47:1329-38. [PMID: 26238511 DOI: 10.3892/ijo.2015.3109] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 06/26/2015] [Indexed: 01/16/2023] Open
Abstract
Long non-coding RNA, urothelial cancer associated 1 (UCA1), is reported to play a critical role in progression of carcinogenesis. In the present study, we identified differential expression of UCA1 in colorectal cancer (CRC) and paired peritumoral tissues using gene expression microarray analyses. qPCR analysis confirmed that UCA1 was upregulated in CRC (p<0.001) and the expression of UCA1 was statistically correlated with lymph node metastasis (P=0.040), distant metastasis (P=0.043) and tumor stage (P=0.010). Kaplan-Meier analysis indicated that patients with high UCA1 expression had a poor prognosis. Moreover, multivariate analysis identified UCA1 overexpression as an independent predictor for CRC. We also found that knockdown of UCA1 significantly suppressed cell proliferation and metastasis in CRC cells. Flow cytometry assays showed UCA1 silencing induced G0/G1 growth arrest and apoptosis of CRC cells. To further investigate the regulatory mechanisms of UCA1, we identified that Ets-2 bound to the UCA1 core promoter using luciferase assays. Collectively, our findings suggested that UCA1 might be an important prognostic indicator in CRC and may be a potential target for diagnosis and gene therapy.
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282
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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: 146] [Impact Index Per Article: 16.2] [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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283
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Milowich D, Le Mercier M, De Neve N, Sandras F, Roumeguere T, Decaestecker C, Salmon I, Rorive S. Diagnostic value of the UCA1 test for bladder cancer detection: a clinical study. SPRINGERPLUS 2015; 4:349. [PMID: 26191476 PMCID: PMC4502048 DOI: 10.1186/s40064-015-1092-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 06/09/2015] [Indexed: 01/03/2023]
Abstract
Purpose To evaluate the efficiency of the UCA1 test as a diagnostic tool for the detection of bladder cancer. Methods Between October 2009 and December 2011 the UCA1 test was performed on collected urine samples from 162 patients divided into screening and follow-up groups, based on the absence or presence of prior bladder cancer. The test performance was then evaluated in each group and compared to cystoscopy and urinary cytology. Results The overall sensitivity, specificity and positive and negative predictive values for the UCA1 test were 70, 70.7, 75.6 and 64.5%, respectively. We observed no difference in performance for tumours of higher grade or stage, but sensitivity was increased in the screening population compared to patients under follow-up (83.9 vs. 59%). The UCA1 test successfully detected all 7 cases of isolated carcinoma in situ and was more sensitive in this particular setting than cystoscopy or urinary cytology. Conclusion The efficiency of the UCA1 test for the detection of primary and recurring bladder cancer in our study was lower than previously reported. We confirmed the role of UCA1 as a possible adjunct to cystoscopy and cytology when a primary bladder cancer is suspected, but its role in the follow-up of recurring tumours remains limited. Further studies are needed to investigate the role of the UCA1 test in the early detection of carcinoma in situ lesions.
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Affiliation(s)
- Dina Milowich
- Department of Pathology, Erasme University Hospital, Université Libre de Bruxelles, 808 Route de Lennik, 1070 Brussels, Belgium ; Department of Pathology, Jules Bordet Institute, Université Libre de Bruxelles, Brussels, Belgium
| | - Marie Le Mercier
- Department of Pathology, Erasme University Hospital, Université Libre de Bruxelles, 808 Route de Lennik, 1070 Brussels, Belgium
| | - Nancy De Neve
- Department of Pathology, Erasme University Hospital, Université Libre de Bruxelles, 808 Route de Lennik, 1070 Brussels, Belgium
| | - Flavienne Sandras
- Department of Pathology, Erasme University Hospital, Université Libre de Bruxelles, 808 Route de Lennik, 1070 Brussels, Belgium
| | - Thierry Roumeguere
- Department of Urology, Erasme University Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Christine Decaestecker
- Laboratory of Image Synthesis and Analysis (LISA), Brussels School of Engineering/École Polytechnique de Bruxelles, Université Libre de Bruxelles, Brussels, Belgium ; DIAPath, Center for Microscopy and Molecular Imaging (CMMI), Académie Universitaire Wallonie-Bruxelles, Gosselies, Belgium
| | - Isabelle Salmon
- Department of Pathology, Erasme University Hospital, Université Libre de Bruxelles, 808 Route de Lennik, 1070 Brussels, Belgium ; DIAPath, Center for Microscopy and Molecular Imaging (CMMI), Académie Universitaire Wallonie-Bruxelles, Gosselies, Belgium
| | - Sandrine Rorive
- Department of Pathology, Erasme University Hospital, Université Libre de Bruxelles, 808 Route de Lennik, 1070 Brussels, Belgium ; DIAPath, Center for Microscopy and Molecular Imaging (CMMI), Académie Universitaire Wallonie-Bruxelles, Gosselies, Belgium
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284
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Downregulation of the long noncoding RNA EGOT correlates with malignant status and poor prognosis in breast cancer. Tumour Biol 2015; 36:9807-12. [PMID: 26159853 DOI: 10.1007/s13277-015-3746-y] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 06/30/2015] [Indexed: 01/22/2023] Open
Abstract
Eosinophil granule ontogeny transcript (EGOT) is a long noncoding RNA involved in the regulation of eosinophil granule protein transcript expression. However, little is known about the role of EGOT in malignant disease. This study aimed to assess the potential role of EGOT in the pathogenesis of breast cancer. Quantitative real-time polymerase chain reaction was performed to detect the expression levels of EGOT in 250 breast cancerous tissues and 50 adjacent noncancerous tissues. The correlation of EGOT expression with clinicopathological features and prognosis was also analyzed. EGOT expression was lower in breast cancer compared with the adjacent noncancerous tissues (P < 0.001), and low levels of EGOT expression were significantly correlated with larger tumor size (P = 0.022), more lymph node metastasis (P = 0.020), and higher Ki-67 expression (P = 0.017). Moreover, patients with low levels of EGOT expression showed significantly worse prognosis for overall survival (P = 0.040), and this result was further validated in a larger cohort from a public database. Multivariate analysis suggested that low levels of EGOT were a poor independent prognostic predictor for breast cancer patients (HR = 1.857, 95 % CI = 1.032-3.340, P = 0.039). In conclusion, EGOT may play an important role in breast cancer progression and prognosis and may serve as a new potential prognostic target in breast cancer patients.
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285
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Liz J, Esteller M. lncRNAs and microRNAs with a role in cancer development. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1859:169-76. [PMID: 26149773 DOI: 10.1016/j.bbagrm.2015.06.015] [Citation(s) in RCA: 405] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 06/03/2015] [Accepted: 06/30/2015] [Indexed: 12/12/2022]
Abstract
Most diseases, including human cancer, are frequently associated with an altered transcription pattern. The alteration of the transcriptome is not restricted to the production of aberrant levels of protein-coding RNAs, but also refers to the dysregulation of the expression of the multiple noncoding members that comprise the human genome. Unexpectedly, recent RNA-seq data of the human transcriptome have revealed that less than 2% of the genome encodes protein-coding transcripts, even though the vast majority of the genome is actively transcribed into non-coding RNAs (ncRNAs) under different conditions. In this review, we present an updated version of the mechanistic aspects of some long non-coding RNAs (lncRNAs) that play critical roles in human cancer. Most importantly, we focus on the interplay between lncRNAs and microRNAs, and the importance of such interactions during the tumorigenic process, providing new insight into the regulatory mechanisms underlying several ncRNA classes of importance in cancer, particularly transcribed ultraconserved regions (T-UCRs). 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)
- Julia Liz
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, Barcelona, Catalonia, Spain
| | - Manel Esteller
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, Barcelona, Catalonia, Spain; Department of Physiological Sciences II, School of Medicine, University of Barcelona, Barcelona, Catalonia, Spain; Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain.
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286
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Khorkova O, Hsiao J, Wahlestedt C. Basic biology and therapeutic implications of lncRNA. Adv Drug Deliv Rev 2015; 87:15-24. [PMID: 26024979 PMCID: PMC4544752 DOI: 10.1016/j.addr.2015.05.012] [Citation(s) in RCA: 245] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 05/11/2015] [Accepted: 05/21/2015] [Indexed: 12/11/2022]
Abstract
Long non-coding RNAs (lncRNA), a class of non-coding RNA molecules recently identified largely due to the efforts of FANTOM, and later GENCODE and ENCODE consortia, have been a subject of intense investigation in the past decade. Extensive efforts to get deeper understanding of lncRNA biology have yielded evidence of their diverse structural and regulatory roles in protecting chromosome integrity, maintaining genomic architecture, X chromosome inactivation, imprinting, transcription, translation and epigenetic regulation. Here we will briefly review the recent studies in the field of lncRNA biology focusing mostly on mammalian species and discuss their therapeutic implications.
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MESH Headings
- Animals
- Chromosomal Instability
- Epigenesis, Genetic
- Evolution, Molecular
- Gene Expression Regulation/drug effects
- Gene Expression Regulation/genetics
- Genetic Diseases, Inborn/diagnosis
- Genetic Diseases, Inborn/genetics
- Genetic Diseases, Inborn/therapy
- Humans
- Neoplasms/diagnosis
- Neoplasms/genetics
- Neoplasms/therapy
- Oligonucleotides, Antisense/administration & dosage
- Oligonucleotides, Antisense/therapeutic use
- RNA Processing, Post-Transcriptional
- RNA, Long Noncoding/blood
- RNA, Long Noncoding/genetics
- RNA, Long Noncoding/urine
- Species Specificity
- Telomere/genetics
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Affiliation(s)
- O Khorkova
- OPKO Health Inc., 10320 USA Today Way, Miramar, FL 33025, USA
| | - J Hsiao
- OPKO Health Inc., 10320 USA Today Way, Miramar, FL 33025, USA
| | - C Wahlestedt
- Center for Therapeutic Innovation and the Department of Psychiatry and Behavioral Sciences, University of Miami Miller School of Medicine, 1501 NW 10th Avenue, Miami 33136, FL, USA.
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287
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Zhang D, Hou XL, Wu B, Li DD. Long non-coding RNAs in esophageal cancer. Shijie Huaren Xiaohua Zazhi 2015; 23:2744-2753. [DOI: 10.11569/wcjd.v23.i17.2744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are RNA transcripts which are longer than 200 nucleotides and have no protein-coding capacity. Studies have shown that lncRNAs can regulate gene expression at multiple levels and play roles in cell proliferation, differentiation, metabolism, and apoptosis. Abnormal expression of lncRNAs has close relationships to tumor development, invasion, metastasis and prognosis. Esophageal cancer is one of the most deadly gastrointestinal cancers, and lncRNAs play important roles in the pathogenesis of esophageal cancer. In this paper, we review the current progress in research on lncRNAs in esophageal cancer, hoping to provide new ideas and strategies for early diagnosis, treatment and prognostic evaluation of esophageal cancer.
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288
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Fatima R, Akhade VS, Pal D, Rao SMR. Long noncoding RNAs in development and cancer: potential biomarkers and therapeutic targets. MOLECULAR AND CELLULAR THERAPIES 2015; 3:5. [PMID: 26082843 PMCID: PMC4469312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 05/19/2015] [Indexed: 11/21/2023]
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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289
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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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290
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Abstract
Recent systematic genomic studies have revealed a broad spectrum of lncRNAs that are involved in a variety of disease (diseases), including tumor progression, by regulating gene expression at epigenetic, transcriptional and post-transcriptional levels. However, their exact roles of physiological function and the mechanism (mechanisms) of action are yet to be clarified. In breast cancer research, several lncRNAs are identified as tumor driving oncogenic lncRNAs and few are identified as tumor suppressive lncRNAs. They are involved in cell growth, apoptosis, cell migration and invasiveness as well as cancer cell stemness. Therefore, this new class of RNAs may serve as biomarkers for diagnostic and prognostic purpose and also as potential therapeutic targets. This review summarizes the current information about lncRNAs that are particularly involved in breast cancer progression and also discusses the potential translational application of these newly discovered nucleic acids.
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Affiliation(s)
| | - Sambad Sharma
- 2500 N. State, Jackson MS 39216, University of Mississippi Medical Center, Cancer Institute
| | - Kounosuke Watabe
- Pathology Unit, Istituto Nazionale Tumori Fondazione "G. Pascale", via Mariano Semmola 80131, Napoli, Italy,
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291
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Shi Y, Liu Y, Wang J, Jie D, Yun T, Li W, Yan L, Wang K, Feng J. Downregulated Long Noncoding RNA BANCR Promotes the Proliferation of Colorectal Cancer Cells via Downregualtion of p21 Expression. PLoS One 2015; 10:e0122679. [PMID: 25928067 PMCID: PMC4415816 DOI: 10.1371/journal.pone.0122679] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 02/24/2015] [Indexed: 12/20/2022] Open
Abstract
BRAF activated non-coding RNA (BANCR), a long non-coding RNA (lncRNA), is crucial for cell migration in melanoma cells and non-small cell lung cancer (NSCLC) cells. However, little is known regarding the role of this gene in the proliferation of colorectal cancer. Therefore, we investigated the involvement of BANCR in the proliferation of colorectal cancer cells. In this study, we show that BANCR expression was significantly down-regulated in colorectal cancer tissues compared with normal tissues, and overexpression of BANCR suppressed colorectal cancer cell growth in vitro and in vivo. We also determined that pCDNA-BANCR-mediated colorectal cancer cell proliferation was associated with induction of G0/G1 cell-cycle arrest and apoptosis enhancement through regulation of p21, and its effects were most likely posttranscriptional. Taken together, our findings suggest that down-regulation of BANCR contributes to the proliferation of colorectal cancer cells, at least in part, through the regulation of p21 protein.
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Affiliation(s)
- Yongguo Shi
- Department of Oncology, Second Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu, PR China
- Taixing People's Hospital, Taixing, Jiangsu, PR China
| | - Yangchen Liu
- Taixing People's Hospital, Taixing, Jiangsu, PR China
| | - Jirong Wang
- Department of Oncology, Second Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu, PR China
| | - Ding Jie
- Department of Oncology, Second Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu, PR China
| | - Tian Yun
- Department of Oncology, Second Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu, PR China
| | - Wang Li
- Department of Oncology, Second Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu, PR China
| | - Lin Yan
- Department of Oncology, Second Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu, PR China
| | - Keming Wang
- Department of Oncology, Second Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu, PR China
- * E-mail: (KW); (JF)
| | - Jifeng Feng
- Cancer Hospital of Jiangsu Province, Nanjing, Jiangsu, PR China
- * E-mail: (KW); (JF)
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292
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Carvajal-Hausdorf D, Schalper KA, Neumeister V, Rimm DL. Quantitative measurement of cancer tissue biomarkers in the lab and in the clinic. J Transl Med 2015; 95:385-96. [PMID: 25502176 PMCID: PMC4383674 DOI: 10.1038/labinvest.2014.157] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 11/18/2014] [Indexed: 02/06/2023] Open
Abstract
Detection of biomolecules in tissues provides contextual information and the possibility to assess the interaction of different cell types and markers. Routine qualitative assessment of immune- and oligonucleotide-based methods in research and the clinic has been associated with assay variability because of lack of stringent validation and subjective interpretation of results. As a result, the vast majority of in situ assays in clinical usage are nonquantitative and, although useful, often of questionable scientific validity. Here, we revisit the reporters and methods used for single- and multiplexed in situ visualization of protein and RNA. Then we examine methods for the use of quantitative platforms for in situ measurement of protein and mRNA levels. Finally, we discuss the challenges of the transition of these methods to the clinic and their potential role as tools for development of companion diagnostic tests.
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Affiliation(s)
| | - Kurt A. Schalper
- Department of Pathology, Yale University School of Medicine, New Haven, CT
| | | | - David L. Rimm
- Department of Pathology, Yale University School of Medicine, New Haven, CT
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293
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Kabacik S, Manning G, Raffy C, Bouffler S, Badie C. Time, Dose and Ataxia Telangiectasia Mutated (ATM) Status Dependency of Coding and Noncoding RNA Expression after Ionizing Radiation Exposure. Radiat Res 2015; 183:325-37. [DOI: 10.1667/rr13876.1] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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294
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Cao C, Sun J, Zhang D, Guo X, Xie L, Li X, Wu D, Liu L. The long intergenic noncoding RNA UFC1, a target of MicroRNA 34a, interacts with the mRNA stabilizing protein HuR to increase levels of β-catenin in HCC cells. Gastroenterology 2015; 148:415-26.e18. [PMID: 25449213 DOI: 10.1053/j.gastro.2014.10.012] [Citation(s) in RCA: 199] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Revised: 09/24/2014] [Accepted: 10/16/2014] [Indexed: 12/15/2022]
Abstract
BACKGROUND & AIMS Altered activities of long noncoding RNAs (lncRNAs) have been associated with cancer development. We investigated the mechanisms by which the long intergenic noncoding RNA UFC1 (lincRNA-UFC1) promotes progression of hepatocellular carcinoma (HCC), using human tissues and cell lines. METHODS We used microarrays to compare expression profiles of lncRNAs in HCC samples and adjacent nontumor tissues (controls) from 7 patients. HCC and nontumor tissues were collected from 2006 through 2012 from patients in Guangzhou, China. We used quantitative real-time polymerase chain reaction to measure levels of lincRNA-UFC1 in tissues from 49 patients, and in situ hybridization to measure levels in samples from 131 patients; clinical data were collected from patients for up to 5 years. The lincRNA-UFC1 was expressed transgenically, or knocked down with short hairpin RNAs, in BEL-7402, SK-Hep1, Huh7, and MHCC-97H HCC cell lines; luciferase reporter and RNA immunoprecipitation and pull-down assays were performed. We also analyzed growth of xenograft tumors from these cells in BALB/c nude mice. RESULTS Levels of the lincRNA-UFC1 were increased in HCC tissues compared with controls, and associated with tumor size, Barcelona Clinic Liver Cancer stage, and patient outcomes. Transgenic expression of the lincRNA-UFC1 in HCC cells promoted their proliferation and cell-cycle progression and inhibited apoptosis, whereas short hairpin RNA knockdown of lincRNA-UFC1 had opposite effects. Xenograft tumors grown from cells overexpressing lincRNA-UFC1 had larger mean volumes and weights, and formed more rapidly, than tumors grown from control cells. Tumors grown from lincRNA-UFC1 knockdown were smaller than controls. The lincRNA-UFC1 interacted directly with the messenger RNA (mRNA) stabilizing protein HuR (encoded by ELAVL1) to increase levels of β-catenin mRNA (encoded by CTNNB1) and protein. Levels of lincRNA-UFC1 correlated with those of β-catenin in HCC tissues. In contrast, there was a negative correlation between levels of microRNA 34a and lincRNA-UFC1 in HCC tissues; microRNA 34a reduced the stability of lincRNA-UFC1. CONCLUSIONS The lincRNA-UFC1, a target of microRNA 34a, promotes proliferation and reduces apoptosis in HCC cells to promote growth of xenograft tumors in mice. It interacts directly with the mRNA stabilizing protein HuR to regulate levels of β-catenin in HCC cells.
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Affiliation(s)
- Chuanhui Cao
- Hepatology Unit and Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China; Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Jingyuan Sun
- Hepatology Unit and Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China; Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Dongyan Zhang
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xuejun Guo
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Liwei Xie
- Center of Molecular Medicine, University of Georgia, Athens, Georgia; Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia
| | - Xin Li
- Cancer Research Institute, Southern Medical University, Guangzhou, China
| | - Dehua Wu
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China.
| | - Li Liu
- Hepatology Unit and Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China.
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295
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Hsa-miR-1 downregulates long non-coding RNA urothelial cancer associated 1 in bladder cancer. Tumour Biol 2015; 35:10075-84. [PMID: 25015192 DOI: 10.1007/s13277-014-2321-2] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Accepted: 07/06/2014] [Indexed: 02/07/2023] Open
Abstract
MicroRNAs (miRNAs) are known to mainly target protein-coding genes at post-transcriptional level, resulting in mRNA destabilization and/or translational repression. Long non-coding RNAs (lncRNAs) are emerging as a novel set of targets for miRNAs. Here, we report that downregulated hsa-miR-1 and upregulated lncRNA urothelial cancer associated 1 (UCA1) were inversely expressed in bladder cancer. Hsa-miR-1 decreased the expression of UCA1 in bladder cancer cells in an Ago2-slicer-dependent manner. The binding site between UCA1 and hsa-miR-1 was confirmed. Overexpression of hsa-miR-1 inhibited bladder cancer cell growth, induced apoptosis, and decreased cell motility. Knockdown of UCA1 expression phenocopied the effects of upregulation of hsa-miR-1. Transfection of UCA1 expression vector partly reversed the changes caused by transfection of pre-miR-1 plasmids. This study provides evidence for hsa-miR-1 to play tumor suppressive roles via downregulating lncRNA UCA1 in bladder cancer, which may have potential therapeutic significance.
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296
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Yang Z, Lu Y, Xu Q, Tang B, Park CK, Chen X. HULC and H19 Played Different Roles in Overall and Disease-Free Survival from Hepatocellular Carcinoma after Curative Hepatectomy: A Preliminary Analysis from Gene Expression Omnibus. DISEASE MARKERS 2015; 2015:191029. [PMID: 26136615 PMCID: PMC4475561 DOI: 10.1155/2015/191029] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 05/28/2015] [Indexed: 02/06/2023]
Abstract
OBJECTIVE This study aimed to evaluate the relationships between long noncoding RNAs (lncRNAs) in tumor tissues and hepatocellular carcinoma (HCC) aggressiveness and survival. METHODS We correlated the lncRNAs in tumor tissues with HCC survival and clinicopathological features based on Gene Expression Omnibus expression profile GSE36376. RESULTS Eight lncRNAs and 240 HCC patients were included. Cox regression analysis indicated that HULC was a positive factor for HCC overall survival (HR = 0.885, 95% CI = 0.797-0.983, and P = 0.023) and disease-free survival time (HR = 0.913, 95% CI = 0.835-0.998, and P = 0.045). H19 and UCA1 were both demonstrated to be risk factors of HCC disease-free survival in multivariate Cox model (HR = 1.071, 95% CI = 1.01-1.137, and P = 0.022 and HR = 2.4, 95% CI = 1.092-5.273, and P = 0.029, resp.). But Kaplan-Meier method showed no significant association between UCA1 and HCC disease-free survival (log rank P = 0.616). Logistic regression demonstrated that H19 was overexpressed in HBV-infected patients (OR = 1.14, 95% CI = 1.008-1.29, and P = 0.037). HULC had a significant association with vascular invasion (OR = 0.648, 95% CI = 0.523-0.803, and P < 0.001). H19 and MEG3 were both considered to be risk factors for high AFP level (OR = 1.45, 95% CI = 1.277-1.646, and P < 0.001 and OR = 1.613, 95% CI = 1.1-2.365, and P = 0.014, resp.). CONCLUSIONS Contributing to decreased susceptibility to vascular invasion, upregulation of HULC in tumor tissues was positively associated with HCC survival. In contrast, H19 overexpression might be risk factor for HCC aggressiveness and poor outcomes.
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Affiliation(s)
- Zongguo Yang
- 1Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Yunfei Lu
- 1Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Qingnian Xu
- 1Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Bozong Tang
- 1Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Cheol-Keun Park
- 2Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 135-710, Republic of Korea
- *Cheol-Keun Park: and
| | - Xiaorong Chen
- 1Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
- *Xiaorong Chen:
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297
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Ho TT, Zhou N, Huang J, Koirala P, Xu M, Fung R, Wu F, Mo YY. Targeting non-coding RNAs with the CRISPR/Cas9 system in human cell lines. Nucleic Acids Res 2014; 43:e17. [PMID: 25414344 PMCID: PMC4330338 DOI: 10.1093/nar/gku1198] [Citation(s) in RCA: 184] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The CRISPR/Cas has been recently shown to be a powerful genome-editing tool in a variety of organisms. However, these studies are mainly focused on protein-coding genes. The present study aims to determine whether this technology can be applied to non-coding genes. One of the challenges for knockout of non-coding genes is that a small deletion or insertion generated by the standard CRISPR/Cas system may not necessarily lead to functional loss of a given non-coding gene because of lacking an open reading frame, especially in polyploidy human cell lines. To overcome this challenge, we adopt a selection system that allows for marker genes to integrate into the genome through homologous recombination (HR). Moreover, we construct a dual guide RNA vector that can make two cuts simultaneously at designated sites such that a large fragment can be deleted. With these approaches, we are able to successfully generate knockouts for miR-21, miR-29a, lncRNA-21A, UCA1 and AK023948 in various human cell lines. Finally, we show that the HR-mediated targeting efficiency can be further improved by suppression of the non-homologous end joining pathway. Together, these results demonstrate the feasibility of knockout for non-coding genes by the CRISPR/Cas system in human cell lines.
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Affiliation(s)
- Tsui-Ting Ho
- Department of Pharmacology/Toxicology and Cancer Institute, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Nanjiang Zhou
- Department of Pharmacology/Toxicology and Cancer Institute, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Jianguo Huang
- Department of Pharmacology/Toxicology and Cancer Institute, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Pratirodh Koirala
- Department of Pharmacology/Toxicology and Cancer Institute, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Min Xu
- Department of Gastroenterology, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu 212001, China
| | - Roland Fung
- System Biosciences, Mountain View, CA 94043, USA
| | - Fangting Wu
- System Biosciences, Mountain View, CA 94043, USA
| | - Yin-Yuan Mo
- Department of Pharmacology/Toxicology and Cancer Institute, University of Mississippi Medical Center, Jackson, MS 39216, USA
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298
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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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299
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Li JY, Ma X, Zhang CB. Overexpression of long non-coding RNA UCA1 predicts a poor prognosis in patients with esophageal squamous cell carcinoma. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2014; 7:7938-7944. [PMID: 25550835 PMCID: PMC4270573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Accepted: 10/18/2014] [Indexed: 06/04/2023]
Abstract
INTRODUCTION Long non-coding RNAs (lncRNAs) have been shown to have important regulatory roles in cancer biology, and the lncRNA UCA1 is upregulated in several cancers such as bladder cancer, breast cancer and colorectal cancer, however, the contributions of UCA1 to esophageal cancer remain largely unknown. METHODS Expression levels of lncRNA UCA1 in esophageal squamous cell carcinoma (ESCC) patients and esophageal cancer cell lines were evaluated by quantitative real-time PCR (qRT-PCR), and its association with overall survival of patients was analyzed by statistical analysis. Small interfering RNA was used to suppress UCA1 expression in esophageal cancer cell line. In vitro assays were conducted to further explore its underlying roles in tumor progression. RESULTS The relative level of UCA1 was significantly higher in ESCC tissues compared to the adjacent non-tumor tissues, and remarkably higher expression of UCA1 was found in esophageal cancer cell lines compared with the immortalized esophageal epithelial cell line NE1. The ESCC patients with higher UCA1 expression had an advanced clinical stage and a poorer prognosis than those with lower expression. In vitro assays, our data indicated that downregulation of UCA1 decrease cell proliferation, migration, and invasion ability. CONCLUSIONS lncRNA UCA1 might be considered as a novel molecule involved in ESCC progression, which provides a potential prognostic biomarker and therapeutic target.
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Affiliation(s)
- Ji-Yuan Li
- Department of Thoracic Surgery, The First Affiliated Hospital of Henan University of Science and TechnologyLuoyang 471000, China
| | - Xin Ma
- Department of Rheumatology, The First Affiliated Hospital of Henan University of Science and TechnologyLuoyang 471000, China
| | - Can-Bin Zhang
- Department of Thoracic Surgery, The First Affiliated Hospital of Henan University of Science and TechnologyLuoyang 471000, China
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300
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Abstract
Long non-coding RNAs (lncRNAs) are series of transcripts with important biological functions. Various diseases have been associated with aberrant expression of lncRNAs and the related dysregulation of mRNAs. In this review, we highlight the mechanisms of dynamic lncRNA expression. The chromatin state contributes to the low and specific expression of lncRNAs. The transcription of non-coding RNA genes is regulated by many core transcription factors applied to protein-coding genes. However, specific DNA sequences may allow their unsynchronized transcription with their location-associated mRNAs. Additionally, there are multiple mechanisms involved in the post-transcriptional regulation of lncRNAs. Among these, microRNAs might have indispensible regulatory effects on lncRNAs, based on recent discoveries.
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