201
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Sattarifard H, Hashemi M, Hassanzarei S, Narouie B, Bahari G. Association between genetic polymorphisms of long non-coding RNA PRNCR1 and prostate cancer risk in a sample of the Iranian population. Mol Clin Oncol 2017; 7:1152-1158. [PMID: 29285392 DOI: 10.3892/mco.2017.1462] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 10/18/2017] [Indexed: 12/19/2022] Open
Abstract
The aim of the present study was to determine whether there is an association between the long non-coding RNA (lncRNA) prostate cancer-associated non-coding RNA 1 (PRNCR1) polymorphisms and prostate cancer (PCa) risk in a sample of the Iranian population. This case-control study was performed on 178 patients with PCa and 180 subjects with benign prostatic hyperplasia (BPH). Genotyping assay was performed by polymerase chain reaction-restriction fragment length polymorphism. The findings indicated that the GG genotype of the rs13252298 A>G variant significantly increased the risk of PCa (odds ratio=3.49, 95% confidence interval: 1.79-6.81, P=0.0001) compared with AA+AG. As regards the rs1456315 G>A polymorphism, the AG genotype and G allele significantly increased the risk of PCa. As regards the rs7841060 T>G variant, the findings demonstrated that this TG genotype and the G allele significantly increased the risk of PCa. The rs7007694 T>C variant was not found to be associated with the risk of PCa. Haplotype analysis indicated that GTGA and GTGG significantly increased the risk of PCa compared with rs1456315A/rs7007694T/rs7841060T/rs13252298G (ATTG). The PRNCR1 variants were not found to be significantly associated with the clinicopathological characteristics of PCa patients. In conclusion, our findings support an association between PRNCR1 variants and the risk of PCa in a sample of the Iranian population.
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Affiliation(s)
- Hedieh Sattarifard
- Cellular and Molecular Research Center, School of Medicine, Zahedan University of Medical Sciences, Zahedan 98167-43181, Iran.,Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan 98167-43181, Iran
| | - Mohammad Hashemi
- Cellular and Molecular Research Center, School of Medicine, Zahedan University of Medical Sciences, Zahedan 98167-43181, Iran.,Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan 98167-43181, Iran
| | - Shekoofeh Hassanzarei
- Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan 98167-43181, Iran
| | - Behzad Narouie
- Urology and Nephrology Research Center, Department of Urology, Shahid Labbafinejad Medical Center, Shahid Beheshti University of Medical Sciences, Tehran 198396-3113, Iran
| | - Gholamreza Bahari
- Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan 98167-43181, Iran
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202
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Zhou J, Wang R, Zhang J, Zhu L, Liu W, Lu S, Chen P, Li H, Yin B, Yuan J, Qiang B, Shu P, Peng X. Conserved expression of ultra-conserved noncoding RNA in mammalian nervous system. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2017; 1860:1159-1168. [PMID: 29055695 DOI: 10.1016/j.bbagrm.2017.10.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 10/08/2017] [Accepted: 10/11/2017] [Indexed: 02/07/2023]
Abstract
T-UCRs, a class of long non-coding RNAs that are transcribed from ultra-conserved regions (UCRs), might play an important role in development and diseases. However, the amount of T-UCRs that are conservatively expressed in the developing nervous systems of mice, monkeys and humans is still unknown. In this study, we screened the RNA sequence signals of 481 identified UCRs in an E14.5 mouse brain from the ENCODE database and found 76 UCRs that may be transcribed into T-UCRs. To verify the expression of these potential T-UCRs, we used an RT-PCR experiment and identified that 60 T-UCRs can be expressed in the E14.5 mouse brain. Furthermore, we detected the expression conservation of 76 potential T-UCRs in two comparisons: postnatal day 0 brains of a mouse and a rhesus monkey and neural stem cells of mouse and human by RT-PCR experimentation. It was found that up to 65% of these T-UCRs were expressed in mouse, rhesus monkey and human nervous systems. Next, by testing the spatiotemporal expression pattern of these T-UCRs expressed in mouse, rhesus monkey and human nervous systems, we found that approximately 30% of the T-UCRs showed a relatively high and dynamical expression during mouse brain development. Finally, through biological process and molecular function gene ontology analysis of the host genes of intronic or exonic-antisense T-UCRs, it was discovered that most of the genes were involved in RNA splicing or RNA binding. These results suggest that T-UCRs are likely to participate in nervous system development through RNA processing.
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Affiliation(s)
- Junjie Zhou
- State Key Laboratory of Medical Molecular Biology, Medical Primate Research Center, Neuroscience Center, and Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China; Medical Primate Research Center, Chinese Academy of Medical Science, Peking Union Medical College, Beijing 100005, China
| | - Ruiyu Wang
- State Key Laboratory of Medical Molecular Biology, Medical Primate Research Center, Neuroscience Center, and Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China; Medical Primate Research Center, Chinese Academy of Medical Science, Peking Union Medical College, Beijing 100005, China
| | - Jing Zhang
- State Key Laboratory of Medical Molecular Biology, Medical Primate Research Center, Neuroscience Center, and Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China; Medical Primate Research Center, Chinese Academy of Medical Science, Peking Union Medical College, Beijing 100005, China
| | - Liyuan Zhu
- State Key Laboratory of Medical Molecular Biology, Medical Primate Research Center, Neuroscience Center, and Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China; Medical Primate Research Center, Chinese Academy of Medical Science, Peking Union Medical College, Beijing 100005, China
| | - Wei Liu
- Department of Anatomy and Histology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China; Medical Primate Research Center, Chinese Academy of Medical Science, Peking Union Medical College, Beijing 100005, China
| | - Shuaiyao Lu
- Institute of Medical Biology Chinese Academy of Medical Sciences, Chinese Academy of Medical Science and Peking Union Medical College, Kunming 650118, China; Medical Primate Research Center, Chinese Academy of Medical Science, Peking Union Medical College, Beijing 100005, China
| | - Pan Chen
- State Key Laboratory of Medical Molecular Biology, Medical Primate Research Center, Neuroscience Center, and Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China; Medical Primate Research Center, Chinese Academy of Medical Science, Peking Union Medical College, Beijing 100005, China
| | - Hanlu Li
- State Key Laboratory of Medical Molecular Biology, Medical Primate Research Center, Neuroscience Center, and Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China; Medical Primate Research Center, Chinese Academy of Medical Science, Peking Union Medical College, Beijing 100005, China
| | - Bin Yin
- State Key Laboratory of Medical Molecular Biology, Medical Primate Research Center, Neuroscience Center, and Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China; Medical Primate Research Center, Chinese Academy of Medical Science, Peking Union Medical College, Beijing 100005, China
| | - Jiangang Yuan
- State Key Laboratory of Medical Molecular Biology, Medical Primate Research Center, Neuroscience Center, and Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China; Medical Primate Research Center, Chinese Academy of Medical Science, Peking Union Medical College, Beijing 100005, China
| | - Boqin Qiang
- State Key Laboratory of Medical Molecular Biology, Medical Primate Research Center, Neuroscience Center, and Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China; Medical Primate Research Center, Chinese Academy of Medical Science, Peking Union Medical College, Beijing 100005, China
| | - Pengcheng Shu
- State Key Laboratory of Medical Molecular Biology, Medical Primate Research Center, Neuroscience Center, and Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China; Medical Primate Research Center, Chinese Academy of Medical Science, Peking Union Medical College, Beijing 100005, China.
| | - Xiaozhong Peng
- State Key Laboratory of Medical Molecular Biology, Medical Primate Research Center, Neuroscience Center, and Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China; Medical Primate Research Center, Chinese Academy of Medical Science, Peking Union Medical College, Beijing 100005, China.
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203
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Identification of potential prognostic ceRNA module biomarkers in patients with pancreatic adenocarcinoma. Oncotarget 2017; 8:94493-94504. [PMID: 29212244 PMCID: PMC5706890 DOI: 10.18632/oncotarget.21783] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 09/08/2017] [Indexed: 12/13/2022] Open
Abstract
Accumulating evidence suggested that long non-coding RNAs (lncRNAs) can function as competing endogenous RNAs (ceRNAs) to interact with other RNA transcripts and ceRNAs perturbation play important roles in cancer initiation and progression including pancreatic adenocarcinoma (PAAD). In this study, we constructed a PAAD-specific hallmark gene-related ceRNA network (HceNet) using paired genome-wide expression profiles of mRNA, lncRNA and miRNA and regulatory relationships between them. Based on “ceRNA hypothesis”, we analyzed the characteristics of HceNet and identified a ceRNA module comprising of 29 genes (12 lncRNAs, two miRNAs and 15 mRNAs) as potential prognostic biomarkers related to overall survival of patients with PAAD. The prognostic value of ceRNA module biomarkers was further validated in the train (Hazard Ratio (HR) =1.661, 95% CI: 1.275–2.165, p<1.00e-4), test (HR=1.546, 95% CI: 1.238-1.930, p<1.00e-4), and entire (HR=1.559, 95% CI: 1.321-1.839, p<1.00e-4) datasets. Our study provides candidate prognostic biomarkers for PAAD and increases our understanding of ceRNA-related regulatory mechanism in PAAD pathogenesis.
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204
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Chen D, Liu L, Wang K, Yu H, Wang Y, Liu J, Guo Y, Zhang H. The role of MALAT-1 in the invasion and metastasis of gastric cancer. Scand J Gastroenterol 2017; 52:790-796. [PMID: 28276823 DOI: 10.1080/00365521.2017.1280531] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
OBJECTIVES The long non-coding RNA metastasis-associated lung adenocarcinoma transcript 1 (MALAT-1) has been reported to be over-expressed in several cancer types. However, its role in gastric cancer (GC) remains unclear. In the present study, we examined the expression of MALAT-1 in GC cells and tissues and explored its role in GC cell migration and invasion. MATERIALS AND METHODS Real-time quantitative polymerase chain reaction (qRT-PCR) was used to analyze the expression level of MALAT-1 in six GC cell lines and 20 gastric tissues (20 GC and 20 adjacent normal mucosa). Functional characterization for the role of MALAT-1 in GC was performed by small interfering RNA (siRNA) knockdown, followed by series of in vitro and in vivo experiments. RESULTS MALAT-1 was upregulated in GC cell lines and tissues compared with the immortalized gastric epithelial cell line GES and adjacent normal tissues, respectively. Moreover, MALAT-1 expression was higher in the high-metastatic-potential GC cell line SGC7901M than in the low-metastatic-potential GC cell line SGC7901NM. In vitro and in vivo assays showed that siRNA-mediated silencing of MALAT-1 inhibited GC cell migration and invasion. In addition, suppressing MALAT-1 expression resulted in a decrease in the expression of the Epithelial-mesenchymal transition (EMT)-associated marker vimentin and an increase in the expression of E-cadherin at both the mRNA and protein levels. CONCLUSIONS MALAT-1 may promote the migration and invasion of GC cells in part by regulating EMT.
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Affiliation(s)
- Di Chen
- a State Key Laboratory of Cancer Biology and Xijing Hospital of Digestive Diseases , the Fourth Military Medical University , Xi'an , China
| | - Lili Liu
- b Department of Oncology , Tangdu Hospital, the Fourth Military Medical University , Xi'an , China
| | - Kai Wang
- c Department of Gastroenterology , the 16th Hospital of the People's Liberation Army of China , A Letai , China
| | - Haiyan Yu
- d Air Force General Hospital of the People's Liberation Army of China , Beijing , China
| | - Yafang Wang
- b Department of Oncology , Tangdu Hospital, the Fourth Military Medical University , Xi'an , China
| | - Jiaming Liu
- e Department of Gastroenterology , Xi'an Central Hospital , Xi'an , China
| | - Yang Guo
- a State Key Laboratory of Cancer Biology and Xijing Hospital of Digestive Diseases , the Fourth Military Medical University , Xi'an , China
| | - Hongbo Zhang
- a State Key Laboratory of Cancer Biology and Xijing Hospital of Digestive Diseases , the Fourth Military Medical University , Xi'an , China
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205
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Shen P, Pichler M, Chen M, Calin GA, Ling H. To Wnt or Lose: The Missing Non-Coding Linc in Colorectal Cancer. Int J Mol Sci 2017; 18:ijms18092003. [PMID: 28930145 PMCID: PMC5618652 DOI: 10.3390/ijms18092003] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 09/09/2017] [Accepted: 09/13/2017] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancer (CRC) is the third most frequent cancer and one of the leading causes for cancer-related mortality. Aberrant activation of the Wnt signaling is an essential initiating factor in colon carcinogenesis, and a driving force of CRC progression. Recently, long non-coding RNAs (lncRNAs) have emerged as significant players in CRC pathogenesis through diversified mechanisms. Although both Wnt signaling and lncRNAs represent interesting research areas for CRC, an effort of directly connecting these two areas is lacking. To fill in the knowledge gap, we focus on the reported findings of lncRNAs that regulate Wnt signaling or essential Wnt signaling targets. These include several newly discovered lncRNAs originated from the amplified cancer-associated chromosome 8q24 region that surrounds the essential Wnt target MYC gene, lncRNAs reported to be involved in CRC stem cells, and several individual lncRNAs connected to Wnt signaling through other mechanisms. This review will provide essential information that assists in understanding the missing link of lncRNAs to the classical Wnt signaling in CRC.
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Affiliation(s)
- Peng Shen
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
- Nanfang Hospital, Southern Medical University/The First School of Clinical Medicine, Southern Medical University, Guangzhou 510515, Guangdong, China.
| | - Martin Pichler
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
- Research Unit of Non-Coding RNA and Genome Editing in Cancer, Division of Oncology, Medical University of Graz, Graz 8010, Austria.
| | - Meng Chen
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - George A Calin
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
- The Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Hui Ling
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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206
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Yang Y, Junjie P, Sanjun C, Ma Y. Long non-coding RNAs in Colorectal Cancer: Progression and Future Directions. J Cancer 2017; 8:3212-3225. [PMID: 29158793 PMCID: PMC5665037 DOI: 10.7150/jca.19794] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 08/29/2017] [Indexed: 12/25/2022] Open
Abstract
Identification of the colorectal adenoma-carcinoma sequence with its corresponding genetic and epigenetic alterations has significantly increased our knowledge of the etiopathogenesis of colorectal cancer (CRC). However, the molecular mechanisms of colorectal carcinogenesis and metastasis haven't been clearly elucidated. Long non-coding ribonucleic acids (lncRNAs) are key participants of gene regulations rather than “noises”. Accumulative studies have implicated that the aberrant expressions of lncRNAs are tightly corelated to CRC screening, diagnosis, prognosis and therapeutic outcomes. Our review focuses on recent findings on the involvement of lncRNAs in CRC oncogenesis and the lncRNA-based clinical implications in patients with CRC.
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Affiliation(s)
- Yongzhi Yang
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Peng Junjie
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Cai Sanjun
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Yanlei Ma
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
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207
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Terracciano D, Terreri S, de Nigris F, Costa V, Calin GA, Cimmino A. The role of a new class of long noncoding RNAs transcribed from ultraconserved regions in cancer. Biochim Biophys Acta Rev Cancer 2017; 1868:449-455. [PMID: 28916343 DOI: 10.1016/j.bbcan.2017.09.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 09/07/2017] [Accepted: 09/09/2017] [Indexed: 02/06/2023]
Abstract
Ultraconserved regions (UCRs) represent a relatively new class of non-coding genomic sequences highly conserved between human, rat and mouse genomes. These regions can reside within exons of protein-coding genes, despite the vast majority of them localizes within introns or intergenic regions. Several studies have undoubtedly demonstrated that most of these regions are actively transcribed in normal cells/tissues, where they contribute to regulate many cellular processes. Interestingly, these non-coding RNAs exhibit aberrant expression levels in human cancer cells and their expression profiles have been used as prognostic factors in human malignancies, as well as to unambiguously distinguish among distinct cancer types. In this review, we first describe their identification, then we provide some updated information about their genomic localization and classification. More importantly, we discuss about the available literature describing an overview of the mechanisms through which some transcribed UCRs (T-UCR) contribute to cancer progression or to the metastatic spread. To date, the interplay between T-UCRs and microRNAs is the most convincing evidence linking T-UCRs and tumorigenesis. The limitations of these studies and the future challenges to be addressed in order to understand the biological role of T-UCRs are also discussed herein. We envision that future efforts are needed to convincingly include this class of ncRNAs in the growing area of cancer therapeutics.
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Affiliation(s)
- Daniela Terracciano
- Dept. of Translational Medical Sciences, University of Naples "Federico II", Naples, Italy
| | - Sara Terreri
- Institute of Genetics and Biophysics "A. Buzzati Traverso", National Research Council (CNR), Naples, Italy
| | - Filomena de Nigris
- Department of Biochemistry, Biophysics and General Pathology, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Valerio Costa
- Institute of Genetics and Biophysics "A. Buzzati Traverso", National Research Council (CNR), Naples, Italy
| | - George A Calin
- Departments of Experimental Therapeutics and Leukemia, and the Center for small interfering RNA and non-coding RNAs, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Amelia Cimmino
- Institute of Genetics and Biophysics "A. Buzzati Traverso", National Research Council (CNR), Naples, Italy.
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208
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Guo Y, Wang C, Miao X, Chen S, Qian Y, Li G, Jiang Y. Upregulation of uc.189 in patients with esophageal squamous cell carcinoma and its clinicopathologic value. Pathol Res Pract 2017; 213:1400-1403. [PMID: 28941722 DOI: 10.1016/j.prp.2017.09.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 08/14/2017] [Accepted: 09/05/2017] [Indexed: 11/18/2022]
Abstract
Ultraconserved elements (UCEs) encoding noncoding RNAs serve as important regulators in cancer biology. Until now, the role of the UCE uc.189 in human cancers remains undefined and the clinical significance of uc.189 in esophageal cancers remains unknown. This study was to identify the prognostic value of uc.189 expression in esophageal squamous cell carcinomas (ESCC). Quantitative real-time polymerase chain reaction (qRT-PCR) was used to detect the expression level of uc.189 in matched cancerous tissues and adjacent noncancerous tissues from 152 patients with ESCC. The correlation of uc.189 with clinicopathological features and prognosis were also analyzed. The expression of uc.189 was significantly higher in human ESCC compared with the adjacent noncancerous tissues (122/152, 80.3%, p<0.01), and the high level of uc.189 expression was significantly correlated with invasion of the tumor (p=0.009), advanced clinical stage (p=0.000), lymph node metastasis (p=0.000), and poor prognosis. High expression of uc.189 might reflect poor prognosis of ESCC and indicate a potential diagnostic target in ESCC patients. Uc.189 might be considered as a novel molecule involved in ESCC progression, which provides a potential prognostic biomarker and therapeutic target.
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MESH Headings
- Aged
- Aged, 80 and over
- Biomarkers, Tumor/analysis
- Biomarkers, Tumor/genetics
- Carcinoma, Squamous Cell/diagnosis
- Carcinoma, Squamous Cell/genetics
- Carcinoma, Squamous Cell/metabolism
- Carcinoma, Squamous Cell/pathology
- Cell Line, Tumor
- Esophageal Neoplasms/diagnosis
- Esophageal Neoplasms/genetics
- Esophageal Neoplasms/metabolism
- Esophageal Neoplasms/pathology
- Esophageal Squamous Cell Carcinoma
- Female
- Gene Expression Regulation, Neoplastic
- Humans
- Lymphatic Metastasis/diagnosis
- Lymphatic Metastasis/genetics
- Lymphatic Metastasis/pathology
- Male
- Middle Aged
- Prognosis
- RNA, Long Noncoding/metabolism
- Up-Regulation
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Affiliation(s)
- Yan Guo
- Department of Geriatrics, Jingjiang People's Hospital, The Affiliated Training Hospital of Yangzhou University, 28 Zhongzhou Road, Jingjiang, Jiangsu,214500, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China
| | - Chenghai Wang
- Department of Pathology, The Affiliated Hospital of Yangzhou University, Yangzhou University,368 Hanjiang Middle Road, Yangzhou, China, 225009; Department of Pathology, Medical School, Yangzhou University, 11 Huaihai Road, Yangzhou, 225001, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China
| | - Xin Miao
- Department of Pathology, Medical School, Yangzhou University, 11 Huaihai Road, Yangzhou, 225001, China
| | - Siyu Chen
- Department of Pathology, Medical School, Yangzhou University, 11 Huaihai Road, Yangzhou, 225001, China
| | - Yu Qian
- Department of Pathology, Medical School, Yangzhou University, 11 Huaihai Road, Yangzhou, 225001, China
| | - Guoli Li
- Department of Pathology, Medical School, Yangzhou University, 11 Huaihai Road, Yangzhou, 225001, China; Institute of Translational Medicine, Medical School, Yangzhou University, Yangzhou, Jiangsu 225001, China; Jiangsu Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention and Treatment of Senile Diseases, Yangzhou, 225001, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China
| | - Ying Jiang
- Department of Pathology, Medical School, Yangzhou University, 11 Huaihai Road, Yangzhou, 225001, China; Institute of Translational Medicine, Medical School, Yangzhou University, Yangzhou, Jiangsu 225001, China; Jiangsu Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention and Treatment of Senile Diseases, Yangzhou, 225001, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China.
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209
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Gu Y, Yang F, Xu RM, Zhang YY, Li Y, Liu SX, Zhang GX, Wang GK, Ma LP. Differential expression profile of long non-coding RNA in cardiomyocytes autophagy induced by angiotensin II. Cell Biol Int 2017; 41:1076-1082. [PMID: 28653781 DOI: 10.1002/cbin.10809] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 06/24/2017] [Indexed: 01/01/2023]
Affiliation(s)
- Ying Gu
- Department of Cardiology; Changhai Hospital; The Second Military Medical University; Shanghai 200433 China
| | - Fan Yang
- Department of Cardiovascular Surgery; Institution of Cardiac Surgery; Changhai Hospital; The Second Military Medical University; Shanghai 200433 China
| | - Ru-ming Xu
- Department of Cardiology; Changhai Hospital; The Second Military Medical University; Shanghai 200433 China
| | - Yun-yan Zhang
- Department of Cardiology; Changhai Hospital; The Second Military Medical University; Shanghai 200433 China
| | - Yang Li
- Department of Cardiovascular Surgery; Institution of Cardiac Surgery; Changhai Hospital; The Second Military Medical University; Shanghai 200433 China
| | - Su-xuan Liu
- Department of Cardiology; Changhai Hospital; The Second Military Medical University; Shanghai 200433 China
| | - Guan-xin Zhang
- Department of Cardiovascular Surgery; Institution of Cardiac Surgery; Changhai Hospital; The Second Military Medical University; Shanghai 200433 China
| | - Guo-kun Wang
- Department of Cardiovascular Surgery; Institution of Cardiac Surgery; Changhai Hospital; The Second Military Medical University; Shanghai 200433 China
| | - Li-ping Ma
- Department of Cardiology; Changhai Hospital; The Second Military Medical University; Shanghai 200433 China
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210
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Sutaria DS, Jiang J, Azevedo-Pouly ACP, Lee EJ, Lerner MR, Brackett DJ, Vandesompele J, Mestdagh P, Schmittgen TD. Expression Profiling Identifies the Noncoding Processed Transcript of HNRNPU with Proliferative Properties in Pancreatic Ductal Adenocarcinoma. Noncoding RNA 2017; 3:ncrna3030024. [PMID: 29657295 PMCID: PMC5831917 DOI: 10.3390/ncrna3030024] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 08/10/2017] [Accepted: 08/21/2017] [Indexed: 02/06/2023] Open
Abstract
A gene array was used to profile the expression of 22,875 long non-coding RNAs (lncRNAs) and a large number of protein coding genes in 47 specimens of pancreatic ductal adenocarcinoma (PDAC), adjacent benign pancreas and the pancreas from patients without pancreatic disease. Of the lncRNAs profiled, the expression of 126 were significantly increased and 260 were decreased in the tumors (p < 0.05, 2-fold). The expression of one lncRNA in particular, heterogeneous nuclear ribonucleoprotein U (HNRNPU) processed transcript (also known as ncRNA00201) was among the most significantly deregulated (increased four-fold) in the tumors compared to normal/adjacent benign tissues. Increased expression of HNRNPU processed transcript was associated with poor prognosis for patients with PDAC. The expression of HNRNPU processed transcript was increased in PDAC cell lines compared to noncancerous pancreatic cell lines. LNATM gapmer mediated inhibition of HNRNPU processed transcript reduced cell proliferation in Patu-T and PL45 pancreatic cancer cell lines. Reduced invasion and migration was reported upon HNRNPU processed transcript knockdown in Patu-T cells. Small interfering RNA (siRNA) knockdown of the HNRNPU protein coding gene correlated with a 55% reduction in the HNRNPU processed transcript expression and a corresponding reduction in proliferation of Patu-T and PL45 cells. However, gapmer inhibition of HNRNPU processed transcript did not affect HNRNPU mRNA levels. The lncRNA HNRNPU processed transcript expression is increased in both PDAC tissues and cell lines; knockdown of this lncRNA further reduces proliferation and invasion/migration of pancreatic carcinoma cells.
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Affiliation(s)
- Dhruvitkumar S Sutaria
- Department of Pharmaceutics, College of Pharmacy, University of Florida Gainesville, 32608 Florida, USA.
- Department of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, Ohio State University Columbus, 43210 Ohio, USA.
| | - Jinmai Jiang
- Department of Pharmaceutics, College of Pharmacy, University of Florida Gainesville, 32608 Florida, USA.
| | - Ana Clara P Azevedo-Pouly
- Department of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, Ohio State University Columbus, 43210 Ohio, USA.
| | - Eun Joo Lee
- College of Pharmacy and Wonkwang Oriental Medicines Research Institute, Wonkwang University, 54538 Iksan, Korea.
| | - Megan R Lerner
- Department of Surgery, University of Oklahoma Heath Science Center, 73104 Oklahoma, USA.
| | - Daniel J Brackett
- Department of Surgery, University of Oklahoma Heath Science Center, 73104 Oklahoma, USA.
| | - Jo Vandesompele
- Center for Medical Genetics, Ghent University Hospital, 9000 Ghent, Belgium.
| | - Pieter Mestdagh
- Center for Medical Genetics, Ghent University Hospital, 9000 Ghent, Belgium.
| | - Thomas D Schmittgen
- Department of Pharmaceutics, College of Pharmacy, University of Florida Gainesville, 32608 Florida, USA.
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211
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Kolenda T, Guglas K, Ryś M, Bogaczyńska M, Teresiak A, Bliźniak R, Łasińska I, Mackiewicz J, Lamperska KM. Biological role of long non-coding RNA in head and neck cancers. Rep Pract Oncol Radiother 2017; 22:378-388. [PMID: 28794691 DOI: 10.1016/j.rpor.2017.07.001] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 04/26/2017] [Accepted: 07/11/2017] [Indexed: 12/12/2022] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) are one of the worst prognosis cancers with high mortality of patients. The treatment strategy is primarily based on surgery and radiotherapy but chemotherapy is also used. Every year the knowledge concerning HNSCC biology is updated with new elements such as the recent discovered molecules - long non-coding RNAs. Long non-coding RNAs are involved in regulatory processes in the cells. It has been revealed that the expression levels of lncRNAs are disturbed in tumor cells what results in the acquisition of their specific phenotype. lncRNAs influence cell growth, cell cycle, cell phenotype, migration and invasion ability as well as apoptosis. Development of the lncRNA panel characteristic for HNSCC and validation of specific lncRNA functions are yet to be elucidated. In this work, we collected available data concerning lncRNAs in HNSCC and characterized their biological role. We believe that the tumor examination, in the context of lncRNA expression, may lead to understanding complex biology of the cancer and improve therapeutic methods in the future.
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Affiliation(s)
- Tomasz Kolenda
- Laboratory of Cancer Genetic, Greater Poland Cancer Centre, 15th Garbary Street, Room 5025, 61-866 Poznan, Poland.,Postgraduate School of Molecular Medicine, Medical University of Warsaw, 61th Zwirki i Wigury Street, 02-091 Warszawa, Poland.,Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8th Rokietnicka Street, 60-806 Poznan, Poland
| | - Kacper Guglas
- Laboratory of Cancer Genetic, Greater Poland Cancer Centre, 15th Garbary Street, Room 5025, 61-866 Poznan, Poland.,Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8th Rokietnicka Street, 60-806 Poznan, Poland
| | - Marcel Ryś
- Laboratory of Cancer Genetic, Greater Poland Cancer Centre, 15th Garbary Street, Room 5025, 61-866 Poznan, Poland.,Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8th Rokietnicka Street, 60-806 Poznan, Poland
| | - Marta Bogaczyńska
- Laboratory of Cancer Genetic, Greater Poland Cancer Centre, 15th Garbary Street, Room 5025, 61-866 Poznan, Poland.,HAN University of Applied Sciences, Laan van Scheut 2, 6525 EM Nijmegen, The Netherlands
| | - Anna Teresiak
- Laboratory of Cancer Genetic, Greater Poland Cancer Centre, 15th Garbary Street, Room 5025, 61-866 Poznan, Poland
| | - Renata Bliźniak
- Laboratory of Cancer Genetic, Greater Poland Cancer Centre, 15th Garbary Street, Room 5025, 61-866 Poznan, Poland
| | - Izabela Łasińska
- Department of Medical and Experimental Oncology, Heliodor Swiecicki Clinical Hospital, Poznan University of Medical Sciences, 16/18th Grunwaldzka Street, 60-786 Poznan, Poland
| | - Jacek Mackiewicz
- Department of Medical and Experimental Oncology, Heliodor Swiecicki Clinical Hospital, Poznan University of Medical Sciences, 16/18th Grunwaldzka Street, 60-786 Poznan, Poland.,Department of Biology and Environmental Sciences, Poznan University of Medical Sciences, 8th Rokietnicka Street, 60-806 Poznan, Poland.,Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Centre, 15th Garbary Street, 61-866 Poznan, Poland
| | - Katarzyna M Lamperska
- Laboratory of Cancer Genetic, Greater Poland Cancer Centre, 15th Garbary Street, Room 5025, 61-866 Poznan, Poland
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212
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Li X, Lu H, Fan G, He M, Sun Y, Xu K, Shi F. A novel interplay between HOTAIR and DNA methylation in osteosarcoma cells indicates a new therapeutic strategy. J Cancer Res Clin Oncol 2017; 143:2189-2200. [DOI: 10.1007/s00432-017-2478-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 07/15/2017] [Indexed: 12/27/2022]
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213
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Chen Z, Liu H, Yang H, Gao Y, Zhang G, Hu J. The long noncoding RNA, TINCR, functions as a competing endogenous RNA to regulate PDK1 expression by sponging miR-375 in gastric cancer. Onco Targets Ther 2017; 10:3353-3362. [PMID: 28744139 PMCID: PMC5513873 DOI: 10.2147/ott.s137726] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Accumulating evidence indicates that the long noncoding RNA, TINCR, plays a critical role in cancer progression and metastasis. However, the overall biological role and mechanisms of TINCR that were involved in human gastric cancer (GC) progression remain largely unknown. METHODS TINCR expression was measured in 56 paired tumor and adjacent nontumor tissue samples by real-time polymerase chain reaction (PCR). Insights of the mechanism of competitive endogenous RNAs (ceRNAs) were gained from bioinformatic analysis, luciferase assays. The effects of TINCR and miR-375 on GC cell apoptosis and proliferation were studied by RNA interference approaches in vitro and in vivo. The correlation of TINCR and PDK1 was identified by real-time PCR and Western blot analysis. RESULTS Our results showed that miR-375 level decreased and TINCR level increased in tumor tissues. In addition, TINCR was a target of miR-375 and inhibited its expression in GC cells. Furthermore, the low expression of TINCR increased cell apoptosis and inhibited the proliferation of GC cells, while the downregulation of miR-375 reversed the function. In particular, TINCR could negatively regulate the miR-375 expression and increased the PDK1 expression in GC cells. Finally, tumor growth suppression was retarded with miR-375 downregulated in TINCR knockdown of GC cell xenografts. CONCLUSION The long noncoding RNA TINCR functions as a competing endogenous RNA to regulate PDK1 expression by sponging miR-375 in GC. The ceRNA regulatory network of TINCR/miR-375/PDK1 allows us to better understand the pathogenesis of GC and facilitate the development of long noncoding RNA (lncRNA)-directed diagnostics in GC.
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Affiliation(s)
- Zhaoliang Chen
- Department of Oncology, Binzhou Central Hospital, Binzhou, Shandong
| | - Hong Liu
- Department of Oncology, Binzhou Central Hospital, Binzhou, Shandong
| | - Huili Yang
- Department of Oncology, Binzhou Central Hospital, Binzhou, Shandong
| | - Yukai Gao
- Department of Oncology, Binzhou Central Hospital, Binzhou, Shandong
| | - Gongwen Zhang
- Department of Oncology, Binzhou Central Hospital, Binzhou, Shandong
| | - Jiaojiao Hu
- Department of Hematology, Zhongda Hospital, Southeast University, Nanjing, China
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214
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Schmitt AM, Chang HY. Long Noncoding RNAs: At the Intersection of Cancer and Chromatin Biology. Cold Spring Harb Perspect Med 2017; 7:cshperspect.a026492. [PMID: 28193769 DOI: 10.1101/cshperspect.a026492] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Although only 2% of the genome encodes protein, RNA is transcribed from the majority of the genetic sequence, suggesting a massive degree of cellular functionality is programmed in the noncoding genome. The mammalian genome contains tens of thousands of long noncoding RNAs (lncRNAs), many of which occur at disease-associated loci or are specifically expressed in cancer. Although the vast majority of lncRNAs have no known function, recurring molecular mechanisms for lncRNAs are now being observed in chromatin regulation and cancer pathways and emerging technologies are now providing tools to interrogate lncRNA molecular interactions and determine function of these abundant cellular macromolecules.
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Affiliation(s)
- Adam M Schmitt
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York 10065
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California 94305
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215
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Abraham JM, Meltzer SJ. Long Noncoding RNAs in the Pathogenesis of Barrett's Esophagus and Esophageal Carcinoma. Gastroenterology 2017; 153:27-34. [PMID: 28528706 PMCID: PMC5515484 DOI: 10.1053/j.gastro.2017.04.046] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 04/26/2017] [Accepted: 04/28/2017] [Indexed: 12/13/2022]
Abstract
For many years, only a small fraction of the human genome was believed to regulate cell function and development. This protein-coding portion composed only 1% to 2% of 3 billion human DNA base pairs-the remaining sequence was classified as junk DNA. Subsequent research has revealed that most of the genome is transcribed into a broad array of noncoding RNAs, ranging in size from microRNA (20-23 nucleotides) to long noncoding RNA (lncRNA, more than 200 nucleotides). These noncoding RNA classes have been shown to use diverse molecular mechanisms to control gene expression and organ system development. As anticipated, alterations in this large control system can contribute to disease pathogenesis and carcinogenesis. We review the involvement of noncoding RNAs, lncRNAs in particular, in development of Barrett's esophagus and esophageal carcinoma.
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216
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Fernández-Barrena MG, Perugorria MJ, Banales JM. Novel lncRNA T-UCR as a potential downstream driver of the Wnt/β-catenin pathway in hepatobiliary carcinogenesis. Gut 2017; 66:1177-1178. [PMID: 27986786 DOI: 10.1136/gutjnl-2016-312899] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 11/12/2016] [Accepted: 11/26/2016] [Indexed: 01/30/2023]
Affiliation(s)
- Maite G Fernández-Barrena
- Hepatology Program, CIMA of the University of Navarra, Pamplona, Spain.,National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Instituto de Salud Carlos III), Spain
| | - Maria J Perugorria
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Instituto de Salud Carlos III), Spain.,Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute-Donostia University Hospital, University of the Basque Country (UPV/EHU), San Sebastian, Spain.,IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | - Jesus M Banales
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Instituto de Salud Carlos III), Spain.,Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute-Donostia University Hospital, University of the Basque Country (UPV/EHU), San Sebastian, Spain.,IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
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217
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Carotenuto P, Fassan M, Pandolfo R, Lampis A, Vicentini C, Cascione L, Paulus-Hock V, Boulter L, Guest R, Quagliata L, Hahne JC, Ridgway R, Jamieson T, Athineos D, Veronese A, Visone R, Murgia C, Ferrari G, Guzzardo V, Evans TRJ, MacLeod M, Feng GJ, Dale T, Negrini M, Forbes SJ, Terracciano L, Scarpa A, Patel T, Valeri N, Workman P, Sansom O, Braconi C. Wnt signalling modulates transcribed-ultraconserved regions in hepatobiliary cancers. Gut 2017; 66:1268-1277. [PMID: 27618837 PMCID: PMC5530482 DOI: 10.1136/gutjnl-2016-312278] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 08/05/2016] [Accepted: 08/17/2016] [Indexed: 12/13/2022]
Abstract
OBJECTIVE Transcribed-ultraconserved regions (T-UCR) are long non-coding RNAs which are conserved across species and are involved in carcinogenesis. We studied T-UCRs downstream of the Wnt/β-catenin pathway in liver cancer. DESIGN Hypomorphic Apc mice (Apcfl/fl) and thiocetamide (TAA)-treated rats developed Wnt/β-catenin dependent hepatocarcinoma (HCC) and cholangiocarcinoma (CCA), respectively. T-UCR expression was assessed by microarray, real-time PCR and in situ hybridisation. RESULTS Overexpression of the T-UCR uc.158- could differentiate Wnt/β-catenin dependent HCC from normal liver and from β-catenin negative diethylnitrosamine (DEN)-induced HCC. uc.158- was overexpressed in human HepG2 versus Huh7 cells in line with activation of the Wnt pathway. In vitro modulation of β-catenin altered uc.158- expression in human malignant hepatocytes. uc.158- expression was increased in CTNNB1-mutated human HCCs compared with non-mutated human HCCs, and in human HCC with nuclear localisation of β-catenin. uc.158- was increased in TAA rat CCA and reduced after treatment with Wnt/β-catenin inhibitors. uc.158- expression was negative in human normal liver and biliary epithelia, while it was increased in human CCA in two different cohorts. Locked nucleic acid-mediated inhibition of uc.158- reduced anchorage cell growth, 3D-spheroid formation and spheroid-based cell migration, and increased apoptosis in HepG2 and SW1 cells. miR-193b was predicted to have binding sites within the uc.158- sequence. Modulation of uc.158- changed miR-193b expression in human malignant hepatocytes. Co-transfection of uc.158- inhibitor and anti-miR-193b rescued the effect of uc.158- inhibition on cell viability. CONCLUSIONS We showed that uc.158- is activated by the Wnt pathway in liver cancers and drives their growth. Thus, it may represent a promising target for the development of novel therapeutics.
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Affiliation(s)
| | - Matteo Fassan
- Department of Medicine, University of Padua, Padua, Italy
- ARC-NET Research Centre, University of Verona, Verona, Italy
| | | | | | | | | | | | - Luke Boulter
- MRC Human Genetics Unit, University of Edinburgh, Edinburgh, UK
| | - Rachel Guest
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, UK
| | - Luca Quagliata
- Molecular Pathology Division, Institute of Pathology, University of Basel, Basel, Switzerland
| | | | - Rachel Ridgway
- Cancer Research UK Beatson Institute for Cancer Research, Glasgow, UK
| | - Tam Jamieson
- Cancer Research UK Beatson Institute for Cancer Research, Glasgow, UK
| | - Dimitris Athineos
- Cancer Research UK Beatson Institute for Cancer Research, Glasgow, UK
| | - Angelo Veronese
- Department of Medical, Oral and Biotechnological Sciences, G. d'Annunzio University, Chieti, Italy
| | - Rosa Visone
- Department of Medical, Oral and Biotechnological Sciences, G. d'Annunzio University, Chieti, Italy
| | - Claudio Murgia
- Cancer Research UK Beatson Institute for Cancer Research, Glasgow, UK
| | | | | | | | - Martin MacLeod
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Gui Ji Feng
- School of Biosciences, Cardiff University, Cardiff, UK
| | - Trevor Dale
- School of Biosciences, Cardiff University, Cardiff, UK
| | | | - Stuart J Forbes
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, UK
| | - Luigi Terracciano
- Molecular Pathology Division, Institute of Pathology, University of Basel, Basel, Switzerland
| | - Aldo Scarpa
- ARC-NET Research Centre, University of Verona, Verona, Italy
| | | | - Nicola Valeri
- The Institute of Cancer Research, London, UK
- The Royal Marsden NHS Foundation Trust, London and Surrey, UK
| | | | - Owen Sansom
- Cancer Research UK Beatson Institute for Cancer Research, Glasgow, UK
| | - Chiara Braconi
- The Institute of Cancer Research, London, UK
- The Royal Marsden NHS Foundation Trust, London and Surrey, UK
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218
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Lai Y, Xu P, Liu J, Li Q, Ren D, Zhang J, Wang J. Decreased expression of the long non-coding RNA MLLT4 antisense RNA 1 is a potential biomarker and an indicator of a poor prognosis for gastric cancer. Oncol Lett 2017; 14:2629-2634. [PMID: 28927028 PMCID: PMC5588117 DOI: 10.3892/ol.2017.6478] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 10/14/2016] [Indexed: 01/16/2023] Open
Abstract
In recent years, the identification of long non-coding RNAs (lncRNAs) led to the analysis of their characteristics in cancer biology. However, the expression of lncRNAs in cancer and their clinical significance remain unclear. In the present study, an investigation of lncRNAs that may be involved in the regulation of metastasis using microarray and polymerase chain reaction analyses resulted in the identification of MLLT4 antisense RNA 1 (MLLT4-AS1) as a significantly downregulated lncRNA in gastric cancer tissue compared with normal adjacent tissue (P=0.006). Furthermore, the downregulation of MLL4-AS1 was significantly associated with advanced Tumor-Node-Metastasis stage (P=0.007) and lymph node metastasis (P=0.008). Cox regression analysis showed that MLLT4-AS1 expression was an independent predictor for overall survival (hazard ratio, 13.136; 95% confidence interval, 5.065–34.068; P<0.001). These data suggest that the decreased expression of MLLT4-AS1 is a potential biomarker and a predictor of a poor prognosis for gastric cancer.
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Affiliation(s)
- Yuexing Lai
- Department of Gastroenterology, Shanghai Songjiang Hospital Affiliated to Nanjing Medical University, Shanghai 201600, P.R. China
| | - Ping Xu
- Department of Gastroenterology, Shanghai Songjiang Hospital Affiliated to Nanjing Medical University, Shanghai 201600, P.R. China
| | - Jie Liu
- Department of Digestive Diseases, Huashan Hospital, Fudan University, Shanghai 200040, P.R. China
| | - Qinghua Li
- Department of Gastroenterology, Shanghai Songjiang Hospital Affiliated to Nanjing Medical University, Shanghai 201600, P.R. China
| | - Dabin Ren
- Department of Gastroenterology, Shanghai Songjiang Hospital Affiliated to Nanjing Medical University, Shanghai 201600, P.R. China
| | - Jun Zhang
- Department of Digestive Diseases, Huashan Hospital, Fudan University, Shanghai 200040, P.R. China
| | - Jing Wang
- Department of Gastroenterology, Shanghai Songjiang Hospital Affiliated to Nanjing Medical University, Shanghai 201600, P.R. China
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219
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Genomic Insight into the Role of lncRNA in Cancer Susceptibility. Int J Mol Sci 2017; 18:ijms18061239. [PMID: 28598379 PMCID: PMC5486062 DOI: 10.3390/ijms18061239] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 06/06/2017] [Accepted: 06/07/2017] [Indexed: 12/13/2022] Open
Abstract
With the development of advanced genomic methods, a large amount of long non-coding RNAs (lncRNAs) has been found to be important for cancer initiation and progression. Given that most of the genome-wide association study (GWAS)-identified cancer risk SNPs are located in the noncoding region, the expression and function of lncRNAs are more likely to be affected by the SNPs. The SNPs may affect the expression of lncRNAs directly through disrupting the binding of transcription factors or indirectly by affecting the expression of regulatory factors. Moreover, SNPs may disrupt the interaction between lncRNAs and other RNAs or proteins. Unveiling the relationship of lncRNA, protein-coding genes, transcription factors and miRNAs from the angle of genomics will improve the accuracy of disease prediction and help find new therapeutic targets.
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220
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Détrée C, Núñez-Acuña G, Tapia F, Gallardo-Escárate C. Long non-coding RNAs are associated with spatiotemporal gene expression profiles in the marine gastropod Tegula atra. Mar Genomics 2017; 33:39-45. [DOI: 10.1016/j.margen.2017.01.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Revised: 12/27/2016] [Accepted: 01/07/2017] [Indexed: 01/05/2023]
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221
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Terracciano D, Ferro M, Terreri S, Lucarelli G, D'Elia C, Musi G, de Cobelli O, Mirone V, Cimmino A. Urinary long noncoding RNAs in nonmuscle-invasive bladder cancer: new architects in cancer prognostic biomarkers. Transl Res 2017; 184:108-117. [PMID: 28438520 DOI: 10.1016/j.trsl.2017.03.005] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 03/22/2017] [Accepted: 03/28/2017] [Indexed: 12/14/2022]
Abstract
Several reports over the last 10 years provided evidence that long noncoding RNAs (lncRNAs) are often altered in bladder cancers. lncRNAs are longer than 200 nucleotides and function as important regulators of gene expression, interacting with the major pathways of cell growth, proliferation, differentiation, and survival. A large number of lncRNAs has oncogenic function and is more expressed in tumor compared with normal tissues. Their overexpression may be associated with tumor formation, progression, and metastasis in a variety of tumors including bladder cancer. Although lncRNAs have been shown to have critical regulatory roles in cancer biology, the biological functions and prognostic values in nonmuscle-invasive bladder cancer remain largely unknown. Nevertheless, a growing body of evidence suggests that several lncRNAs expression profiles in bladder malignancies are associated with poor prognosis, and they can be detected in biological fluids, such as urines. Here, we review current progress in the biology and the implication of lncRNAs associated with bladder cancer, and we discuss their potential use as diagnosis and prognosis biomarkers in bladder malignancies with a focus on their role in high-risk nonmuscle-invasive tumors.
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Affiliation(s)
- Daniela Terracciano
- Department of Translational Medical Sciences, University "Federico II", Naples, Italy.
| | - Matteo Ferro
- Division of Urology, European Institute of Oncology, Milan, Italy.
| | - Sara Terreri
- Institute of Genetics and Biophysics "A. Buzzati Traverso", National Research Council (CNR), Naples, Italy
| | - Giuseppe Lucarelli
- Department of Emergency and Organ Transplantation-Urology, Andrology and Kidney Transplantation Unit, University of Bari, Bari, Italy
| | - Carolina D'Elia
- Urology Department, Central Hospital of Bolzano, Bolzano, Italy
| | - Gennaro Musi
- Division of Urology, European Institute of Oncology, Milan, Italy
| | | | - Vincenzo Mirone
- Urology Department, University of Naples Federico II, Naples, Italy
| | - Amelia Cimmino
- Institute of Genetics and Biophysics "A. Buzzati Traverso", National Research Council (CNR), Naples, Italy.
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222
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Marini A, Lena AM, Panatta E, Ivan C, Han L, Liang H, Annicchiarico-Petruzzelli M, Di Daniele N, Calin GA, Candi E, Melino G. Ultraconserved long non-coding RNA uc.63 in breast cancer. Oncotarget 2017; 8:35669-35680. [PMID: 27447964 PMCID: PMC5482607 DOI: 10.18632/oncotarget.10572] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 05/13/2016] [Indexed: 12/13/2022] Open
Abstract
Transcribed-ultraconserved regions (T-UCRs) are long non-coding RNAs (lncRNA) encoded by a subset of long ultraconserved stretches in the human genome. Recent studies revealed that the expression of several T-UCRs is altered in cancer and growing evidences underline the importance of T-UCRs in oncogenesis, offering also potential new strategies for diagnosis and prognosis. We found that overexpression of one specific T-UCRs named uc.63 is associated with bad outcome in luminal A subtype of breast cancer patients. uc.63 is localized in the third intron of exportin-1 gene (XPO1) and is transcribed in the same orientation of its host gene. Interestingly, silencing of uc.63 induces apoptosis in vitro. However, silencing of host gene XPO1 does not cause the same effect suggesting that the transcription of uc.63 is independent of XPO1. Our results reveal an important role of uc.63 in promoting breast cancer cells survival and offer the prospect to identify a signature associated with poor prognosis.
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Affiliation(s)
- Alberto Marini
- Medical Research Council, Toxicology Unit, Hodgkin Building, University of Leicester, Leicester, UK
| | - Anna Maria Lena
- Department of Experimental Medicine and Surgery, University of Rome “Tor Vergata”, Rome, Italy
| | - Emanuele Panatta
- Department of Experimental Medicine and Surgery, University of Rome “Tor Vergata”, Rome, Italy
| | - Cristina Ivan
- Department of Experimental Therapeutics and The Center for RNA interference and non-coding RNA, The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Leng Han
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX, USA
| | - Han Liang
- Department of Bioinformatics and Computational Biology, The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | | | - Nicola Di Daniele
- Department of Experimental Medicine and Surgery, University of Rome “Tor Vergata”, Rome, Italy
| | - George A. Calin
- Department of Experimental Therapeutics and The Center for RNA interference and non-coding RNA, The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Eleonora Candi
- Department of Experimental Medicine and Surgery, University of Rome “Tor Vergata”, Rome, Italy
- IDI-IRCCS, Biochemistry Laboratory, Rome, Italy
| | - Gerry Melino
- Medical Research Council, Toxicology Unit, Hodgkin Building, University of Leicester, Leicester, UK
- Department of Experimental Medicine and Surgery, University of Rome “Tor Vergata”, Rome, Italy
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223
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Abstract
Long noncoding RNAs (lncRNAs) are a relatively well-characterized class of noncoding RNA (ncRNA) molecules, involved in the regulation of various cell processes, including transcription, intracellular trafficking, and chromosome remodeling. Their deregulation has been associated with the development and progression of various cancer types, the fact which makes them suitable as biomarkers for cancer diagnosis and prognosis. In recent years, detection of cancer-associated lncRNAs in body fluids of cancer patients has proven itself as an especially valuable method to effectively diagnose cancer. Cancer diagnosis and prognosis employing circulating lncRNAs are preferential when compared to classical biopsies of tumor tissues, especially due to their noninvasiveness, and have great potential for routine usage in clinical practice. Thus, this review focuses on summarizing the perspectives of lncRNAs as biomarkers in cancer, based on evaluating their expression profiles determined in body fluids of cancer patients.
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224
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Rigoutsos I, Lee SK, Nam SY, Anfossi S, Pasculli B, Pichler M, Jing Y, Rodriguez-Aguayo C, Telonis AG, Rossi S, Ivan C, Catela Ivkovic T, Fabris L, Clark PM, Ling H, Shimizu M, Redis RS, Shah MY, Zhang X, Okugawa Y, Jung EJ, Tsirigos A, Huang L, Ferdin J, Gafà R, Spizzo R, Nicoloso MS, Paranjape AN, Shariati M, Tiron A, Yeh JJ, Teruel-Montoya R, Xiao L, Melo SA, Menter D, Jiang ZQ, Flores ER, Negrini M, Goel A, Bar-Eli M, Mani SA, Liu CG, Lopez-Berestein G, Berindan-Neagoe I, Esteller M, Kopetz S, Lanza G, Calin GA. N-BLR, a primate-specific non-coding transcript leads to colorectal cancer invasion and migration. Genome Biol 2017; 18:98. [PMID: 28535802 PMCID: PMC5442648 DOI: 10.1186/s13059-017-1224-0] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 04/26/2017] [Indexed: 12/13/2022] Open
Abstract
Background Non-coding RNAs have been drawing increasing attention in recent years as functional data suggest that they play important roles in key cellular processes. N-BLR is a primate-specific long non-coding RNA that modulates the epithelial-to-mesenchymal transition, facilitates cell migration, and increases colorectal cancer invasion. Results We performed multivariate analyses of data from two independent cohorts of colorectal cancer patients and show that the abundance of N-BLR is associated with tumor stage, invasion potential, and overall patient survival. Through in vitro and in vivo experiments we found that N-BLR facilitates migration primarily via crosstalk with E-cadherin and ZEB1. We showed that this crosstalk is mediated by a pyknon, a short ~20 nucleotide-long DNA motif contained in the N-BLR transcript and is targeted by members of the miR-200 family. In light of these findings, we used a microarray to investigate the expression patterns of other pyknon-containing genomic loci. We found multiple such loci that are differentially transcribed between healthy and diseased tissues in colorectal cancer and chronic lymphocytic leukemia. Moreover, we identified several new loci whose expression correlates with the colorectal cancer patients’ overall survival. Conclusions The primate-specific N-BLR is a novel molecular contributor to the complex mechanisms that underlie metastasis in colorectal cancer and a potential novel biomarker for this disease. The presence of a functional pyknon within N-BLR and the related finding that many more pyknon-containing genomic loci in the human genome exhibit tissue-specific and disease-specific expression suggests the possibility of an alternative class of biomarkers and therapeutic targets that are primate-specific. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1224-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Isidore Rigoutsos
- Computational Medicine Center, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA, USA.
| | - Sang Kil Lee
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Present address: Institute of Gastroenterology, Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Su Youn Nam
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Gastroenterology, Department of Internal Medicine, Kyungpook National University Medical School, Daegu, Korea
| | - Simone Anfossi
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Barbara Pasculli
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Present address: Laboratory of Oncology, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, FG, Italy
| | - Martin Pichler
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Present address: Division of Oncology, Medical University of Graz, Graz, Austria
| | - Yi Jing
- Computational Medicine Center, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA, USA
| | - Cristian Rodriguez-Aguayo
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Center for RNA interference and non-coding RNA, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Aristeidis G Telonis
- Computational Medicine Center, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA, USA
| | - Simona Rossi
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Present address: Institute of Oncology Research (IOR), Research Division of the Oncology Institute of Southern Switzerland (IOSI), Bellinzona, Switzerland
| | - Cristina Ivan
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Center for RNA interference and non-coding RNA, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Tina Catela Ivkovic
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Department of Molecular Medicine, Ruder Boskovic Institute, Zagreb, Croatia
| | - Linda Fabris
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Peter M Clark
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Hui Ling
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Masayoshi Shimizu
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Roxana S Redis
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Present address: ProQR Therapeutics, Leiden, Netherlands
| | - Maitri Y Shah
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xinna Zhang
- Center for RNA interference and non-coding RNA, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yoshinaga Okugawa
- Center for Gastrointestinal Research, and Center for Translational Genomics and Oncology, Baylor Scott & White Research Institute and Charles A. Sammons Cancer Center, Baylor University Medical Center, Dallas, TX, USA
| | - Eun Jung Jung
- Department of Surgery, School of Medicine, Gyeongsang National University, Jin-ju, South Korea
| | | | - Li Huang
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jana Ferdin
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Present address: Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Roberta Gafà
- Department of Morphology, Surgery and Experimental Medicine, University of Ferrara, Ferrara, Italy
| | - Riccardo Spizzo
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Present address: CRO, National Cancer Institute, 33081, Aviano, Italy
| | - Milena S Nicoloso
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Present address: CRO, National Cancer Institute, 33081, Aviano, Italy
| | - Anurag N Paranjape
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Present address: National Cancer Institute, Bethesda, MD, USA
| | - Maryam Shariati
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Aida Tiron
- Department of Medicine, Nassau University Medical Center, 2201 Hempstead Tpke, East Meadow, NY, 11554, USA
| | - Jen Jen Yeh
- Departments of Surgery and Pharmacology, UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Raul Teruel-Montoya
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Present address: Centro Regional de Hemodonación, Universidad de Murcia, IMIB-Arrixaca, CIBEER (CB15/00055), Murcia, Spain
| | - Lianchun Xiao
- Division of Quantitative Science, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sonia A Melo
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, and Ipatimup - Institute of Pathology and Molecular Immunology of the University of Porto, 4200, Porto, Portugal.,Department of Pathology, Faculty of Medicine of Porto University, 4200-319, Porto, Portugal
| | - David Menter
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Zhi-Qin Jiang
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Elsa R Flores
- Department of Molecular Oncology, Moffitt Cancer Center, Tampa, FL, USA
| | - Massimo Negrini
- Department of Morphology, Surgery and Experimental Medicine, University of Ferrara, Ferrara, Italy
| | - Ajay Goel
- Center for Gastrointestinal Research, and Center for Translational Genomics and Oncology, Baylor Scott & White Research Institute and Charles A. Sammons Cancer Center, Baylor University Medical Center, Dallas, TX, USA
| | - Menashe Bar-Eli
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sendurai A Mani
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Chang Gong Liu
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Gabriel Lopez-Berestein
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Center for RNA interference and non-coding RNA, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ioana Berindan-Neagoe
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Medfuture, Cluj-Napoca, Romania.,Research Center for Advanced Medicine - University of Medicine and Pharmacy "Iuliu Haţieganu", Cluj-Napoca, Romania.,Department of Functional Genomics, Proteomics and Experimental Pathology- The Oncology Institute " Prof Dr. Ion Chiricuta, Cluj-Napoca, Romania
| | - Manel Esteller
- Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, Barcelona, Catalonia, Spain.,Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), Barcelona, Catalonia, Spain.,Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain
| | - Scott Kopetz
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Giovanni Lanza
- Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - George A Calin
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA. .,Center for RNA interference and non-coding RNA, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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225
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Sakamoto N, Honma R, Sekino Y, Goto K, Sentani K, Ishikawa A, Oue N, Yasui W. Non-coding RNAs are promising targets for stem cell-based cancer therapy. Noncoding RNA Res 2017; 2:83-87. [PMID: 30159424 PMCID: PMC6096406 DOI: 10.1016/j.ncrna.2017.05.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 05/19/2017] [Accepted: 05/19/2017] [Indexed: 12/19/2022] Open
Abstract
The term “non-coding RNA” (ncRNA) is generally used to indicate RNA that does not encode a protein and includes several classes of RNAs, such as microRNA and long non-coding RNA. Several lines of evidence suggest that ncRNAs appear to be involved in a hidden layer of biological procedures that control various levels of gene expression in physiology and development including stem cell biology. Stem cells have recently constituted a revolution in regenerative medicine by providing the possibility of generating suitable cell types for therapeutic use. Here, we review the recent progress that has been made in elaborating the interaction between ncRNAs and tissue/cancer stem cells, discuss related technical and biological challenges, and highlight plausible solutions to surmount these difficulties. This review particularly emphasises the involvement of ncRNAs in stem cell biology and in vivo modulation to treat and cure specific pathological disorders especially in cancer. We believe that a better understanding of the molecular machinery of ncRNAs as related to pluripotency, cellular reprogramming, and lineage-specific differentiation is essential for progress of cancer therapy.
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Key Words
- CD, cytosine deaminase
- CSC, cancer stem cell
- EMT, epithelial to mesenchymal transition
- ESCs, embryonic stem cells
- MET, mesenchymal to epithelial transition
- MSCs, mesenchymal stem cells
- Non-coding RNA
- Stem cell-based therapy
- T-UCR, transcribed ultraconserved region
- Transcribed ultraconserved region
- iPSCs, induced pluripotent stem cells
- lincRNA, long inverting non-coding RNA
- lncRNA, long ncRNA
- miRNAs, microRNAs
- ncRNAs, non-coding RNAs
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Affiliation(s)
- Naoya Sakamoto
- Department of Molecular Pathology, Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Ririno Honma
- Department of Molecular Pathology, Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Yohei Sekino
- Department of Molecular Pathology, Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Keisuke Goto
- Department of Molecular Pathology, Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan.,Cancer Biology Program, University of Hawaii Cancer Center, United States
| | - Kazuhiro Sentani
- Department of Molecular Pathology, Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Akira Ishikawa
- Department of Molecular Pathology, Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Naohide Oue
- Department of Molecular Pathology, Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Wataru Yasui
- Department of Molecular Pathology, Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
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226
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Gao X, Gao X, Li C, Zhang Y, Gao L. Knockdown of Long Noncoding RNA uc.338 by siRNA Inhibits Cellular Migration and Invasion in Human Lung Cancer Cells. Oncol Res 2017; 24:337-343. [PMID: 27712590 PMCID: PMC7838692 DOI: 10.3727/096504016x14666990347671] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Lung cancer remains a critical health concern worldwide. Long noncoding RNAs with ultraconserved elements have recently been implicated in human tumorigenesis. The present study investigated the role of ultraconserved element 338 (uc.338) in the regulation of cell proliferation and metastasis in human lung cancer. Our data showed that the expression of uc.338 in lung cancer was remarkably increased in vivo and in vitro. Depletion of uc.338 with specific siRNA interference retarded the cell proliferative rate in lung cancer cell lines NCI-H929 and H1688. Furthermore, knockdown of uc.338 caused cell cycle arrest in the G0/G1 phase in both cell lines. Transwell assays showed that inhibition of uc.338 notably decreased migration and invasion in NCI-H929 and H1688 cells. Moreover, uc.338 depletion decreased the expression of cyclin B1, Cdc25C, Snail, vimentin, and N-cadherin while increasing the protein level of E-cadherin, shown with Western blot analysis. These results suggested the pro-oncogenic potential of uc.338 in lung cancer, which might provide novel clues for the diagnosis and treatment of lung cancer in the clinic.
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Affiliation(s)
- Xuexin Gao
- Department of Thoracic Surgery, Central Hospital of Tai'an, Tai'an, Shandong, China
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227
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Li Q, Shen F, Wang C. TUC338 promotes cell migration and invasion by targeting TIMP1 in cervical cancer. Oncol Lett 2017; 13:4526-4532. [PMID: 28599453 DOI: 10.3892/ol.2017.5971] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2015] [Accepted: 01/26/2017] [Indexed: 02/04/2023] Open
Abstract
Ultraconserved regions (UCRs) are non-protein-coding gene sequences that are strictly conserved across numerous distinct species. It has been demonstrated previously that UCRs encoding non-coding RNAs serve as regulators of gene expression. In recent decades, there has been increasing evidence for the involvement of UCRs in carcinogenesis. In previous studies, the non-coding RNA transcribed ultraconserved element 338 (TUC338) was identified to serve an oncogenic role in hepatocellular cancer; however, thus far, the role of TUC338 in cervical cancer (CC) remains undefined. The results of the present study revealed that TUC338 is significantly upregulated in CC tissues and cell lines, and that the upregulation of TUC338 is associated with lymph node metastasis. Transfection with small interfering RNA (siRNA) against TUC338 could markedly inhibit cell migration and invasion in HeLa and C33A CC cell lines. Using a dual-luciferase reporter assay, tissue inhibitor of metalloproteinase 1 (TIMP1) was demonstrated to be negatively regulated by TUC338 at the post-transcriptional level, via a specific target site within the 3' untranslated region. The expression of TIMP1 was also observed to be inversely associated with TUC338 expression in CC tissues. Overexpression of TIMP1 with MigRI-TIMP1-green fluorescent protein inhibited CC cell migration and invasion and downregulated matrix metalloproteinase 9, resembling the effects of TUC338 siRNA. Therefore, the results of the present study suggest that TUC338 acts as a novel oncogene by targeting the TIMP1 gene, and inhibiting CC cell migration and invasion.
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Affiliation(s)
- Qin Li
- Department of Clinic, School of Medicine, Yangzhou Polytechnic College, Yangzhou, Jiangsu 225009, P.R. China
| | - Feiyang Shen
- School of Medicine, Yangzhou University, Yangzhou, Jiangsu 225000, P.R. China
| | - Chenghai Wang
- Department of Pathology, The Affiliated Hospital of Yangzhou University, Yangzhou, Jiangsu 225000, P.R. China.,Jiangsu Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention and Treatment of Senile Disease, Yangzhou University, Yangzhou, Jiangsu 225001, P.R. China.,Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou University, Yangzhou, Jiangsu 225001, P.R. China
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228
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Hu Y, Xie H, Liu Y, Liu W, Liu M, Tang H. miR-484 suppresses proliferation and epithelial-mesenchymal transition by targeting ZEB1 and SMAD2 in cervical cancer cells. Cancer Cell Int 2017; 17:36. [PMID: 28286418 PMCID: PMC5339969 DOI: 10.1186/s12935-017-0407-9] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 03/01/2017] [Indexed: 12/31/2022] Open
Abstract
Background MicroRNAs (miRNAs) play important roles in cancer initiation and development. Epithelial–mesenchymal transition (EMT) is a form of cellular plasticity that is critical for embryonic development and metastasis. The purpose of the study was to determine the function and mechanism of miR-484 in initiation and development of cervical cancer (CC). Methods We determined the expression levels of miR-484 in cervical cancer tissues and cell lines with RT-qPCR. Prediction algorithms and EGFP reporter assay were performed to evaluate the targets for miR-484. MTT assay, colony formation assay, flow cytometric analysis, transwell cell migration and invasion assays, and detection of EMT markers were employed to investigate the roles of miR-484 and the targets in regulation of cell proliferation and EMT process. We also used rescue experiments to confirm the effect of miR-484 on CC cells through directly regulating the expression of its targets. Results Firstly we found miR-484 was down-regulated in cervical cancer tissues and cell lines compared with their matched non-cancerous tissues or normal cervical keratinocytes cells. Further studies revealed that overexpression of miR-484 suppressed the cell proliferation, while exacerbates apoptosis. Besides, miR-484 suppressed cellular migration, invasion and EMT process of CC cells. EGFP reporter assay showed that miR-484 binds to ZEB1 and SMAD2 3′UTR region and reduced their expression. The expression of miR-484 had reverse correlation with SMAD2/ZEB1, and SMAD2/ZEB1 had positive correlation with each other in cervical cancer tissues and cell lines. Furthermore, the ectopic expression of ZEB1 or SMAD2 could rescue the malignancies suppressed by miR-484, suggesting that miR-484 down-regulates ZEB1 and SMAD2 to repress tumorigenic activities. Conclusion We found miR-484 inhibits cell proliferation and the EMT process by targeting both ZEB1 and SMAD2 genes and functions as a tumor suppressor, which may served as potential biomarkers for cervical cancer.
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Affiliation(s)
- Yang Hu
- Tianjin Life Science Research Center and Department of Pathogen Biology, School of Basic Medical Sciences, Tianjin Medical University, 22 Qi-Xiang-Tai Road, Tianjin, 300070 China
| | - Hong Xie
- Tianjin Life Science Research Center and Department of Pathogen Biology, School of Basic Medical Sciences, Tianjin Medical University, 22 Qi-Xiang-Tai Road, Tianjin, 300070 China
| | - Yankun Liu
- Tianjin Life Science Research Center and Department of Pathogen Biology, School of Basic Medical Sciences, Tianjin Medical University, 22 Qi-Xiang-Tai Road, Tianjin, 300070 China
| | - Weiying Liu
- Tianjin Life Science Research Center and Department of Pathogen Biology, School of Basic Medical Sciences, Tianjin Medical University, 22 Qi-Xiang-Tai Road, Tianjin, 300070 China
| | - Min Liu
- Tianjin Life Science Research Center and Department of Pathogen Biology, School of Basic Medical Sciences, Tianjin Medical University, 22 Qi-Xiang-Tai Road, Tianjin, 300070 China
| | - Hua Tang
- Tianjin Life Science Research Center and Department of Pathogen Biology, School of Basic Medical Sciences, Tianjin Medical University, 22 Qi-Xiang-Tai Road, Tianjin, 300070 China
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229
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Affiliation(s)
- Chao-Po Lin
- Division of Cellular and Developmental Biology, Department of Molecular and Cell Biology, University of California, Berkeley, California 94705
| | - Lin He
- Division of Cellular and Developmental Biology, Department of Molecular and Cell Biology, University of California, Berkeley, California 94705
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230
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Nie ZL, Wang YS, Mei YP, Lin X, Zhang GX, Sun HL, Wang YL, Xia YX, Wang SK. Prognostic significance of long noncoding RNA Z38 as a candidate biomarker in breast cancer. J Clin Lab Anal 2017; 32. [PMID: 28247935 DOI: 10.1002/jcla.22193] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 02/05/2017] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Long noncoding RNA (lncRNA) Z38 has been shown to promote cell proliferation and tumorigenesis in breast cancer. However, expression pattern and prognostic value of lncRNA Z38 in breast cancer patients remain elusive. METHODS The expression levels of SPRY4-IT1 in 110 self-paired specimens of breast cancer and adjacent normal breast tissues were measured by quantitative real-time PCR (qRT-PCR), and its correlation with overall survival of patients with breast cancer was further statistically analyzed. RESULTS Compared with normal breast tissues, Z38 was upregulated in breast cancer tissues. Furthermore, of 110 breast cancer patients, high Z38 expression was significantly associated with tumor-node-metastasis stage and lymph node metastasis. Further analysis using the Cox regression model revealed that Z38 expression was an independent prognostic factor of overall survival in patients with breast cancer (hazard ratio=4.74, 95% confidence interval 2.41-9.32). The nomogram presents a good prediction of the probability of overall survival of breast cancer patients (c-index: 0.792), and its predictive efficiency was further confirmed by the calibration curve. CONCLUSION Our data highlighted the potential of lncRNA Z38 as novel candidate biomarker to identify patients with breast cancer at high risk of tumor death.
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Affiliation(s)
- Zhen-Lin Nie
- Department of Laboratory Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Yi-Shan Wang
- Department of Laboratory Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Yan-Ping Mei
- Department of Laboratory Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Xin Lin
- Department of Laboratory Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Guo-Xing Zhang
- Department of Laboratory Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Hui-Ling Sun
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Yi-Lian Wang
- Department of Cardiology, The Second People's Hospital of Lianyungang, Lianyungang, China
| | - Yong-Xiang Xia
- Department of Laboratory Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Shu-Kui Wang
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
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231
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Oliveto S, Mancino M, Manfrini N, Biffo S. Role of microRNAs in translation regulation and cancer. World J Biol Chem 2017; 8:45-56. [PMID: 28289518 PMCID: PMC5329714 DOI: 10.4331/wjbc.v8.i1.45] [Citation(s) in RCA: 282] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 10/20/2016] [Accepted: 01/18/2017] [Indexed: 02/05/2023] Open
Abstract
MicroRNAs (miRNAs) are pervasively expressed and regulate most biological functions. They function by modulating transcriptional and translational programs and therefore they orchestrate both physiological and pathological processes, such as development, cell differentiation, proliferation, apoptosis and tumor growth. miRNAs work as small guide molecules in RNA silencing, by negatively regulating the expression of several genes both at mRNA and protein level, by degrading their mRNA target and/or by silencing translation. One of the most recent advances in the field is the comprehension of their role in oncogenesis. The number of miRNA genes is increasing and an alteration in the level of miRNAs is involved in the initiation, progression and metastases formation of several tumors. Some tumor types show a distinct miRNA signature that distinguishes them from normal tissues and from other cancer types. Genetic and biochemical evidence supports the essential role of miRNAs in tumor development. Although the abnormal expression of miRNAs in cancer cells is a widely accepted phenomenon, the cause of this dysregulation is still unknown. Here, we discuss the biogenesis of miRNAs, focusing on the mechanisms by which they regulate protein synthesis. In addition we debate on their role in cancer, highlighting their potential to become therapeutic targets.
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232
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Lu L, Yu X, Zhang L, Ding X, Pan H, Wen X, Xu S, Xing Y, Fan J, Ge S, Zhang H, Jia R, Fan X. The Long Non-Coding RNA RHPN1-AS1 Promotes Uveal Melanoma Progression. Int J Mol Sci 2017; 18:ijms18010226. [PMID: 28124977 PMCID: PMC5297855 DOI: 10.3390/ijms18010226] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 01/14/2017] [Accepted: 01/16/2017] [Indexed: 12/21/2022] Open
Abstract
Increasing evidence suggests that aberrant long non-coding RNAs (lncRNAs) are significantly correlated with the pathogenesis, development and metastasis of cancers. RHPN1 antisense RNA 1 (RHPN1-AS1) is a 2030-bp transcript originating from human chromosome 8q24. However, the role of RHPN1-AS1 in uveal melanoma (UM) remains to be clarified. In this study, we aimed to elucidate the molecular function of RHPN1-AS1 in UM. The RNA levels of RHPN1-AS1 in UM cell lines were examined using the quantitative real-time polymerase chain reaction (qRT-PCR). Short interfering RNAs (siRNAs) were designed to quench RHPN1-AS1 expression, and UM cells stably expressing short hairpin (sh) RHPN1-AS1 were established. Next, the cell proliferation and migration abilities were determined using a colony formation assay and a transwell migration/invasion assay. A tumor xenograft model in nude mice was established to confirm the function of RHPN1-AS1 in vivo. RHPN1-AS1 was significantly upregulated in a number of UM cell lines compared with the normal human retinal pigment epithelium (RPE) cell line. RHPN1-AS1 knockdown significantly inhibited UM cell proliferation and migration in vitro and in vivo. Our data suggest that RHPN1-AS1 could be an oncoRNA in UM, which may serve as a candidate prognostic biomarker and target for new therapies in malignant UM.
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Affiliation(s)
- Linna Lu
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
| | - Xiaoyu Yu
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
| | - Leilei Zhang
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
| | - Xia Ding
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
| | - Hui Pan
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
| | - Xuyang Wen
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
| | - Shiqiong Xu
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
| | - Yue Xing
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
| | - Jiayan Fan
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
| | - Shengfang Ge
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
| | - He Zhang
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
| | - Renbing Jia
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
| | - Xianqun Fan
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
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Ramalho-Carvalho J, Fromm B, Henrique R, Jerónimo C. Deciphering the function of non-coding RNAs in prostate cancer. Cancer Metastasis Rev 2017; 35:235-62. [PMID: 27221068 DOI: 10.1007/s10555-016-9628-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The advent of next-generation sequencing methods is fuelling the discovery of multiple non-coding RNA transcripts with direct implication in cell biology and homeostasis. This new layer of biological regulation seems to be of particular importance in human pathogenesis, including cancer. The aberrant expression of ncRNAs is a feature of prostate cancer, as they promote tumor-suppressive or oncogenic activities, controlling multicellular events leading to carcinogenesis and tumor progression. From the small RNAs involved in the RNAi pathway to the long non-coding RNAs controlling chromatin remodeling, alternative splicing, and DNA repair, the non-coding transcriptome represents the significant majority of transcriptional output. As such, ncRNAs appear as exciting new diagnostic, prognostic, and therapeutic tools. However, additional work is required to characterize the RNA species, their functions, and their applicability to clinical practice in oncology. In this review, we summarize the most important features of ncRNA biology, emphasizing its relevance in prostate carcinogenesis and its potential for clinical applications.
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Affiliation(s)
- João Ramalho-Carvalho
- Cancer Biology & Epigenetics Group - Research Center, Portuguese Oncology Institute of Porto (CI-IPOP), Porto, Portugal.,Biomedical Sciences Graduate Program, Institute of Biomedical Sciences Abel Salazar-University of Porto (ICBAS-UP), Porto, Portugal
| | - Bastian Fromm
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Nydalen, N-0424, Oslo, Norway
| | - Rui Henrique
- Cancer Biology & Epigenetics Group - Research Center, Portuguese Oncology Institute of Porto (CI-IPOP), Porto, Portugal.,Departments of Pathology, Portuguese Oncology Institute of Porto, Porto, Portugal.,Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar, University of Porto (ICBAS-UP), Porto, Portugal
| | - Carmen Jerónimo
- Cancer Biology & Epigenetics Group - Research Center, Portuguese Oncology Institute of Porto (CI-IPOP), Porto, Portugal. .,Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar, University of Porto (ICBAS-UP), Porto, Portugal. .,Portuguese Oncology Institute of Porto, Research Center-LAB 3, F Bdg, 1st floor, Rua Dr António Bernardino de Almeida, 4200-072, Porto, Portugal.
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234
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Wang P, Guo Q, Gao Y, Zhi H, Zhang Y, Liu Y, Zhang J, Yue M, Guo M, Ning S, Zhang G, Li X. Improved method for prioritization of disease associated lncRNAs based on ceRNA theory and functional genomics data. Oncotarget 2017; 8:4642-4655. [PMID: 27992375 PMCID: PMC5354861 DOI: 10.18632/oncotarget.13964] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2016] [Accepted: 12/07/2016] [Indexed: 02/01/2023] Open
Abstract
Although several computational models that predict disease-associated lncRNAs (long non-coding RNAs) exist, only a limited number of disease-associated lncRNAs are known. In this study, we mapped lncRNAs to their functional genomics context using competing endogenous RNAs (ceRNAs) theory. Based on the criteria that similar lncRNAs are likely involved in similar diseases, we proposed a disease lncRNA prioritization method, DisLncPri, to identify novel disease-lncRNA associations. Using a leave-one-out cross validation (LOOCV) strategy, DisLncPri achieved reliable area under curve (AUC) values of 0.89 and 0.87 for the LncRNADisease and Lnc2Cancer datasets that further improved to 0.90 and 0.89 by integrating a multiple rank fusion strategy. We found that DisLncPri had the highest rank enrichment score and AUC value in comparison to several other methods for case studies of alzheimer's disease, ovarian cancer, pancreatic cancer and gastric cancer. Several novel lncRNAs in the top ranks of these diseases were found to be newly verified by relevant databases or reported in recent studies. Prioritization of lncRNAs from a microarray (GSE53622) of oesophageal cancer patients highlighted ENSG00000226029 (top 2), a previously unidentified lncRNA as a potential prognostic biomarker. Our analysis thus indicates that DisLncPri is an excellent tool for identifying lncRNAs that could be novel biomarkers and therapeutic targets in a variety of human diseases.
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Affiliation(s)
- Peng Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Qiuyan Guo
- The First Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Yue Gao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Hui Zhi
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yan Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yue Liu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Jizhou Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Ming Yue
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Maoni Guo
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Shangwei Ning
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
- Key Laboratory of Cardiovascular Medicine Research, Harbin Medical University, Ministry of Education, China
| | - Guangmei Zhang
- The First Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Xia Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
- Key Laboratory of Cardiovascular Medicine Research, Harbin Medical University, Ministry of Education, China
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Abstract
Protein-coding RNAs represent only a small fraction of the transcriptional output in higher eukaryotes. The remaining RNA species encompass a broad range of molecular functions and regulatory roles, a consequence of the structural polyvalence of RNA polymers. Albeit several classes of small noncoding RNAs are relatively well characterized, the accessibility of affordable high-throughput sequencing is generating a wealth of novel, unannotated transcripts, especially long noncoding RNAs (lncRNAs) that are derived from genomic regions that are antisense, intronic, intergenic, and overlapping protein-coding loci. Parsing and characterizing the functions of noncoding RNAs-lncRNAs in particular-is one of the great challenges of modern genome biology. Here we discuss concepts and computational methods for the identification of structural domains in lncRNAs from genomic and transcriptomic data. In the first part, we briefly review how to identify RNA structural motifs in individual lncRNAs. In the second part, we describe how to leverage the evolutionary dynamics of structured RNAs in a computationally efficient screen to detect putative functional lncRNA motifs using comparative genomics.
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Affiliation(s)
- Martin A Smith
- RNA Biology and Plasticity Laboratory, Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, NSW, 2010, Australia. .,St-Vincent's Clinical School, Faculty of Medicine, UNSW Australia, Sydney, NSW, 2052, Australia.
| | - John S Mattick
- RNA Biology and Plasticity Laboratory, Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, NSW, 2010, Australia.,St-Vincent's Clinical School, Faculty of Medicine, UNSW Australia, Sydney, NSW, 2052, Australia
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236
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Understanding the Genomic Ultraconservations: T-UCRs and Cancer. MIRNAS IN DIFFERENTIATION AND DEVELOPMENT 2017; 333:159-172. [DOI: 10.1016/bs.ircmb.2017.04.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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237
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Wang C, Wang Z, Zhou J, Liu S, Wu C, Huang C, Ding Y. TUC.338 promotes invasion and metastasis in colorectal cancer. Int J Cancer 2016; 140:1457-1464. [PMID: 27914101 DOI: 10.1002/ijc.30542] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 11/16/2016] [Indexed: 12/21/2022]
Abstract
Ultraconserved regions (UCRs) are non-protein coding gene sequences that are strictly conserved across among different species. Emerging evidence demonstrates that transcribed ultraconserved regions (TUCRs) encoding noncoding RNAs serve as regulators of gene expression. In recent decades, increasing evidence implicates the involvement of UCRs in carcinogenesis. The role of TUC.338 in cervical cancers was an oncogene in previous studies. Until now, the role of TUC.338 in colorectal cancers remains undefined. This study revealed that TUC.338 is significantly up-regulated in colorectal cancers (CRC) tissue and CRC cell lines, and the up-regulated TUC.338 is associated with lymph node metastasis. Transfection with small interfering RNA (siRNA) markedly inhibited cell migration and invasion in SW480 and HCT116 colorectal cancer cell lines. TIMP-1 was demonstrated to be negatively regulated by TUC.338 at the posttranscriptional level, via a specific target site within the 3' untranslated region by dual-luciferase reporter assay. The expression of TIMP-1 was also observed to inversely correlate with TUC.338 expression in CRC tissues. Over-expression of TIMP-1 with migRI-TIMP-1-GFP inhibited CRC cell migration and invasion and down-regulates MMP9, resembling that of TUC.338-siRNA. Thus, these findings suggested that TUC.338 acts as a novel oncogene by targeting the TIMP-1 gene thus promoting colorectal cancer cell migration and invasion.
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Affiliation(s)
- Chenghai Wang
- Department of Pathology, The Second Clinical Medical College, Yangzhou University, 368 Hanjiang Middle Road, Yangzhou, China.,Department of Pathology, The First People's Hospital of Yangzhou, 368 Hanjiang Middle Road, Yangzhou, China.,Jiangsu Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention and Treatment of Senile Disease, Yangzhou University, 11 Huaihai Road, Yangzhou, China
| | - Zheng Wang
- Department of Pathology, The First People's Hospital of Yangzhou, 368 Hanjiang Middle Road, Yangzhou, China
| | - Jie Zhou
- Department of Pathology, The First People's Hospital of Yangzhou, 368 Hanjiang Middle Road, Yangzhou, China
| | - Shuang Liu
- Department of Pathology, The First People's Hospital of Yangzhou, 368 Hanjiang Middle Road, Yangzhou, China
| | - Cong Wu
- Department of Pathology, The First People's Hospital of Yangzhou, 368 Hanjiang Middle Road, Yangzhou, China
| | - Caihong Huang
- Department of Pathology, The First People's Hospital of Yangzhou, 368 Hanjiang Middle Road, Yangzhou, China
| | - Yongling Ding
- Department of Pathology, The Second Clinical Medical College, Yangzhou University, 368 Hanjiang Middle Road, Yangzhou, China.,Department of Pathology, The First People's Hospital of Yangzhou, 368 Hanjiang Middle Road, Yangzhou, China
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238
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Terreri S, Durso M, Colonna V, Romanelli A, Terracciano D, Ferro M, Perdonà S, Castaldo L, Febbraio F, de Nigris F, Cimmino A. New Cross-Talk Layer between Ultraconserved Non-Coding RNAs, MicroRNAs and Polycomb Protein YY1 in Bladder Cancer. Genes (Basel) 2016; 7:genes7120127. [PMID: 27983635 PMCID: PMC5192503 DOI: 10.3390/genes7120127] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 11/23/2016] [Accepted: 12/01/2016] [Indexed: 12/20/2022] Open
Abstract
MicroRNAs (miRNAs) are highly conserved elements in mammals, and exert key regulatory functions. Growing evidence shows that miRNAs can interact with another class of non-coding RNAs, so-called transcribed ultraconserved regions (T-UCRs), which take part in transcriptional, post-transcriptional and epigenetic regulation processes. We report here the interaction of miRNAs and T-UCRs as a network modulating the availability of these non-coding RNAs in bladder cancer cells. In our cell system, antagomiR-596 increased the expression of T-UCR 201+. Moreover, T-UCR 8+ silencing increased miR-596 expression, which in turn reduced total T-UCR 283+, showing that the perturbation of one element in this network changes the expression of other interactors. In addition, we identify the polycomb protein Yin Yang 1 (YY1) as mediator of binding between miR-596 and T-UCR 8+. These new findings describe for the first time a network between T-UCRs, miRNAs and YY1 protein, highlighting the existence of an additional layer of gene expression regulation.
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Affiliation(s)
- Sara Terreri
- Institute of Genetics and Biophysics-CNR. Via P. Castellino, 111, 80131 Naples, Italy.
| | - Montano Durso
- Bioker srl multimedica spa, via Brin, 49/65 80142 Naples, Italy.
| | - Vincenza Colonna
- Institute of Genetics and Biophysics-CNR. Via P. Castellino, 111, 80131 Naples, Italy.
| | - Alessandra Romanelli
- Dipartimento di Farmacia, Università di Napoli "Federico II", 80131 Naples, Italy.
| | - Daniela Terracciano
- Department of Translational Medical Sciences, University of Naples "Federico II", 80131 Naples, Italy.
| | - Matteo Ferro
- Division of Urology, European Institute of Oncology, 20141 Milan, Italy.
| | - Sisto Perdonà
- Division of Urology, IRCS National Tumor Institute, 80131 Naples, Italy.
| | - Luigi Castaldo
- Division of Urology, IRCS National Tumor Institute, 80131 Naples, Italy.
| | - Ferdinando Febbraio
- Institute of Protein Biochemistry-CNR. Via P. Castellino, 111, 80131 Naples, Italy.
| | - Filomena de Nigris
- Department of Biochemistry, Biophysic and General Pathology, University of Campania Luigi Vanvitelli, Via De Crecchio 7, 80138 Naples, Italy.
| | - Amelia Cimmino
- Institute of Genetics and Biophysics-CNR. Via P. Castellino, 111, 80131 Naples, Italy.
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239
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Hamed EA, El-Saied MM, Saad K, Yousef HAZ, Mohamed AO, Sabry D. Molecular mechanisms underlying fibrosis and elastin destruction in childhood interstitial lung diseases. PATHOPHYSIOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY FOR PATHOPHYSIOLOGY 2016; 23:275-283. [PMID: 27686729 DOI: 10.1016/j.pathophys.2016.09.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 08/22/2016] [Accepted: 09/18/2016] [Indexed: 02/05/2023]
Abstract
OBJECTIVE This study aimed to evaluate fibrosis and elastin destruction in childhood interstitial lung disease (chILD) patients. METHODS Sixty patients and twenty healthy children were recruited. On admission, evaluation of chILD severity was made using Fan chILD score. Participants provided urine and blood samples. Plasma levels of transforming growth factor (TGF)-β1, connective tissue growth factor (CCN2), soluble factor related apoptosis (sFas) and long non-coding RNAs and urinary levels of desmosine/urinary creatinine (UDes/UCr) were measured. RESULTS In patients, clinical findings were crackles (100.00%), tachypnea (65.00%), cardiomegaly (45.00%), digital clubbing (43.30%), cough (33.00%), cyanosis (26.70%), hepatomegaly (28.30%) and wheezes (23.30%). Categorizing of the patients with Fan chILD clinical score revealed that most patients 33.30% scored (3, symptomatic with abnormal saturation/cyanosis during exercise) then 28.30% scored (5, symptomatic with clinical and echocardiographic features of pulmonary hypertension), 18.30% scored (2, symptomatic with normal room air saturations), 15.00% scored (1, asymptomatic) and 5.00% scored (4, symptomatic with abnormal room air saturation/cyanosis at rest). TGF-β1, CCN2, sFas, lncrRNA-2700086A05Rik relative gene expression and UDes/UCr levels were higher in patients than controls (P=0.002, P=0.001, P=0.001, P=0.001, P=0.001, respectively). In patients, significant positive correlations were found between TGF-β1 and CCN2, sFas, UDes/UCr; between CCN2 and both sFas and UDes/UCr; between UDes/UCr and sFas. Morbidity and mortality rates were 46.70% and 10.00%, respectively. CONCLUSION Markers of fibrosis (TGF-β1, sFas, CCN2) and elastin destruction (UDes/UCr) were increased in chILD especially in patients with long disease duration. So blockage of their pathways signals may offer novel therapeutic targets.
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Affiliation(s)
- Enas A Hamed
- Department of Pediatrics, Faculty of Medicine, Assiut University, Assiut, Egypt.
| | - Mostafa M El-Saied
- Department of Pediatrics, Faculty of Medicine, Assiut University, Assiut, Egypt
| | - Khaled Saad
- Department of Pediatrics, Faculty of Medicine, Assiut University, Assiut, Egypt
| | | | - Amany O Mohamed
- Department of Medical Biochemistry, Faculty of Medicine, Assiut, University, Assiut, Egypt
| | - Dina Sabry
- Department of Medical Biochemistry, Faculty of Medicine, Cairo University, Cairo, Egypt
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240
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Noncoding Transcribed Ultraconserved Region (T-UCR) uc.261 Participates in Intestinal Mucosa Barrier Damage in Crohn's Disease. Inflamm Bowel Dis 2016; 22:2840-2852. [PMID: 27846191 DOI: 10.1097/mib.0000000000000945] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
BACKGROUND To date, 481 ultraconserved regions (UCRs) have been discovered in human genome. We aimed to investigate the transcribed UCR (T-UCR) characteristics in Crohn's disease (CD ) and determine whether T-UCR uc.261 participated in intestinal mucosa barrier damage. METHODS T-UCRs were screened in active CD mucosa using the Arraystar Human T-UCR Microarray and validated with quantitative real-time reverse transcription PCR, together with tight junction proteins (TJPs) including junctional adhesion molecule-A, occludin, claudin-1, and zonula occluden-1. T-UCR uc.261 in active CD mucosa was validated by RNA fluorescence in situ hybridization. Caco2 and T84 cells were employed to determine transepithelial electrical resistance. Cdc42, protein kinase C ζ, PAR3, and PAR6 were assessed with quantitative real-time reverse transcription PCR and Western blotting. The assembly of TJPs was detected using cell immunofluorescence assay. RESULTS Four T-UCRs were significantly upregulated (uc.290-, uc.144-, uc.261-, and uc.477+) and 4 T-UCRs were downregulated (uc.166-, uc.141-, uc.478+, and uc.479+). Uc.261 was inversely correlated with transepithelial electrical resistance during tight junction formation. The levels of TJPs were diminished in active CD mucosa. Most uc.261s were located in the cytoplasm of colonic epithelial cells. Overexpression of uc.261 reduced transepithelial electrical resistance, inhibited the expression and assembly of TJPs, activated Cdc42, and suppressed protein kinase C ζ. Silencing of uc.261 in TNF-α-treated cells reversed the tight junction damage. CONCLUSIONS Overexpression of uc.261 participates in intestinal mucosa barrier damage. Suppression of uc.261 reverses the damage to tight junction in inflammation. Attenuation of uc.261 overexpression might be a rational strategy to manage patients with CD.
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Kasagi Y, Oki E, Ando K, Ito S, Iguchi T, Sugiyama M, Nakashima Y, Ohgaki K, Saeki H, Mimori K, Maehara Y. The Expression of CCAT2, a Novel Long Noncoding RNA Transcript, and rs6983267 Single-Nucleotide Polymorphism Genotypes in Colorectal Cancers. Oncology 2016; 92:48-54. [PMID: 27875818 DOI: 10.1159/000452143] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 09/29/2016] [Indexed: 01/17/2023]
Abstract
Colon cancer-associated transcription 2 (CCAT2) was recently identified as a novel long noncoding RNA transcript encompassing the single-nucleotide polymorphism rs6983267. CCAT2 is overexpressed in colorectal cancer (CRC) where it promotes tumor growth, metastasis, and chromosomal instability, although the clinical relevance of this enhanced expression is unknown. In this retrospective study, CCAT2 expression was evaluated using real-time polymerase chain reaction in 149 CRC patients, and its associations with clinicopathological characteristics, outcome, rs6983267 genotypes, microsatellite status, DNA ploidy, and BubR1 expression were analyzed. CCAT2 expression in cancer tissue was significantly higher than in noncancer tissue (p < 0.001), particularly in cases of metastatic cancer (p < 0.001). However, relative CCAT2 expression levels and rs6983267 genotypes were not correlated with clinicopathological features or patient prognosis. CRC cases demonstrating high CCAT2 expression were all microsatellite stable (p < 0.005). Together, this indicates that CCAT2 expression was associated with microsatellite-stable CRC.
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Affiliation(s)
- Yuta Kasagi
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
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Althoff K, Schulte JH, Schramm A. Towards diagnostic application of non-coding RNAs in neuroblastoma. Expert Rev Mol Diagn 2016; 16:1307-1313. [PMID: 27813435 DOI: 10.1080/14737159.2016.1256207] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
INTRODUCTION Neuroblastoma is a solid cancer of childhood, which is devastating upon recurrence. Markers for minimal residual disease and early detection of relapse are eagerly awaited to improve the outcome of affected patients. Several miRNAs have been identified as key regulators of neuroblastoma pathogenesis. Areas covered: Here, we focus on miRNAs that have been linked to MYCN, a prominent oncogenic driver, and we review the hitherto known interactions between miRNAs and other important players in neuroblastoma. Expert commentary: Existing diagnostic miRNA signatures remain to be established in clinical settings. Moreover, inhibition of individual oncogenic miRNAs or enhancement of tumor suppressive miRNA function could represent a new therapeutic approach in cancer treatment, including NB.
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Affiliation(s)
- Kristina Althoff
- a Department of Pediatric Oncology and Hematology , University Children's Hospital Essen , Essen , Germany
| | - Johannes H Schulte
- b Department of Pediatric Oncology and Hematology , Charité University Medicine , Berlin , Germany.,c Berlin Institute of Health (BIH) , Germany.,d German Cancer Consortium (DKTK Berlin) , Germany
| | - Alexander Schramm
- a Department of Pediatric Oncology and Hematology , University Children's Hospital Essen , Essen , Germany
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243
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Nan A, Zhou X, Chen L, Liu M, Zhang N, Zhang L, Luo Y, Liu Z, Dai L, Jiang Y. A transcribed ultraconserved noncoding RNA, Uc.173, is a key molecule for the inhibition of lead-induced neuronal apoptosis. Oncotarget 2016; 7:112-24. [PMID: 26683706 PMCID: PMC4807986 DOI: 10.18632/oncotarget.6590] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 11/26/2015] [Indexed: 01/05/2023] Open
Abstract
As a common toxic metal, lead has significant neurotoxicity to brain development. Long non-coding RNAs (lncRNAs) function in multiple biological processes. However, whether lncRNAs are involved in lead-induced neurotoxicity remains unclear. Uc.173 is a lncRNA from a transcribed ultra-conservative region (T-UCR) of human, mouse and rat genomes. We established a lead-induced nerve injury mouse model. It showed the levels of Uc.173 decreased significantly in hippocampus tissue and serum of the model. We further tested the expression of Uc.173 in serum of lead-exposed children, which also showed a tendency to decrease. To explore the effects of Uc.173 on lead-induced nerve injury, we overexpressed Uc.173 in an N2a mouse nerve cell line and found Uc.173 had an inhibitory effect on lead-induced apoptosis of N2a. To investigate the molecular mechanisms of Uc.173 in apoptosis associated with lead-induced nerve injury, we predicted the target microRNAs of Uc.173 by using miRanda, TargetScan and RegRNA. After performing quantitative real-time PCR and bioinformatics analysis, we showed Uc.173 might inter-regulate with miR-291a-3p in lead-induced apoptosis and regulate apoptosis-associated genes. Our study suggests Uc.173 significantly inhibits the apoptosis of nerve cells, which may be mediated by inter-regulation with miRNAs in lead-induced nerve injury.
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Affiliation(s)
- Aruo Nan
- State Key Laboratory of Respiratory Disease, Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou, PR China
| | - Xinke Zhou
- Institute for Chemical Carcinogenesis, The Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, PR China
| | - Lijian Chen
- State Key Laboratory of Respiratory Disease, Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou, PR China
| | - Meiling Liu
- State Key Laboratory of Respiratory Disease, Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou, PR China
| | - Nan Zhang
- State Key Laboratory of Respiratory Disease, Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou, PR China
| | - Li Zhang
- School of Public Health, Guangdong Pharmaceutical University, Guangzhou, PR China
| | - Yuanwei Luo
- Institute for Chemical Carcinogenesis, The Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, PR China
| | - Zhenzhong Liu
- State Key Laboratory of Respiratory Disease, Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou, PR China
| | - Lijun Dai
- Laboratory Animal Center, Guangzhou Medical University, Guangzhou, PR China
| | - Yiguo Jiang
- State Key Laboratory of Respiratory Disease, Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou, PR China
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Ho TT, Huang J, Zhou N, Zhang Z, Koirala P, Zhou X, Wu F, Ding X, Mo YY. Regulation of PCGEM1 by p54/nrb in prostate cancer. Sci Rep 2016; 6:34529. [PMID: 27682980 PMCID: PMC5041109 DOI: 10.1038/srep34529] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 09/15/2016] [Indexed: 02/06/2023] Open
Abstract
PCGEM1 is a long non-coding RNA (lncRNA) that is often upregulated in prostate cancer. However, little is known how PCGEM1 is regulated. In the present study, we show transcriptional regulation of PCGEM1 in response to androgen deprivation by p54/nrb. While ectopic expression of p54/nrb increases, suppression of p54/nrb by RNAi or knockout (KO) reduces PCGEM1. Moreover, rescue experiments indicate that re-expression of p54/nrb in KO cells restores the ability to induce PCGEM1, leading to upregulation of the androgen receptor splice variant AR3 which has been shown to play a role in castration resistance. Finally, 3,3′-Diindolylmethane (DIM), a known chemoprevention agent, is capable of suppressing PCGEM1 expression by preventing the interaction of p54/nrb with the PCGEM1 promoter. In particular, DIM reduces tumor growth by suppression of PCGEM1 and promoting apoptosis in the castrated xenograft mouse model. Together, these results demonstrate a novel mechanism of p54/nrb-mediated expression of PCGEM1 and AR3, contributing to castration resistance in prostate cancer.
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Affiliation(s)
- Tsui-Ting Ho
- Department of Pharmacology and Toxicology, Cancer Institute, University of Mississippi Medical Center, Jackson, MS, USA.,Department of Radiation Oncology, University of Mississippi Medical Center, Jackson, MS, USA
| | - Jianguo Huang
- Department of Biochemistry, Cancer Institute, University of Mississippi Medical Center, Jackson, MS, USA.,Department of Radiation Oncology, Duke University Medical Center, Durham, NC, USA
| | - Nanjiang Zhou
- Department of Biochemistry, Cancer Institute, University of Mississippi Medical Center, Jackson, MS, USA.,System Biosciences, Mountain View, CA, USA
| | - Ziqiang Zhang
- Department of Pulmonary Medicine, Tongji Hospital, Tongji University, Shanghai, China
| | - Pratirodh Koirala
- Department of Biochemistry, Cancer Institute, University of Mississippi Medical Center, Jackson, MS, USA
| | - Xinchun Zhou
- Department of Pathology, University of Mississippi Medical Center, Jackson, MS, USA
| | | | - Xianfeng Ding
- Department of Pharmacology and Toxicology, Cancer Institute, University of Mississippi Medical Center, Jackson, MS, USA.,College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, China
| | - Yin-Yuan Mo
- Department of Pharmacology and Toxicology, Cancer Institute, University of Mississippi Medical Center, Jackson, MS, USA
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Yan W, Xue W, Chen J, Hu G. Biological Networks for Cancer Candidate Biomarkers Discovery. Cancer Inform 2016; 15:1-7. [PMID: 27625573 PMCID: PMC5012434 DOI: 10.4137/cin.s39458] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 06/06/2016] [Accepted: 06/16/2016] [Indexed: 12/16/2022] Open
Abstract
Due to its extraordinary heterogeneity and complexity, cancer is often proposed as a model case of a systems biology disease or network disease. There is a critical need of effective biomarkers for cancer diagnosis and/or outcome prediction from system level analyses. Methods based on integrating omics data into networks have the potential to revolutionize the identification of cancer biomarkers. Deciphering the biological networks underlying cancer is undoubtedly important for understanding the molecular mechanisms of the disease and identifying effective biomarkers. In this review, the networks constructed for cancer biomarker discovery based on different omics level data are described and illustrated from recent advances in the field.
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Affiliation(s)
- Wenying Yan
- Center for Systems Biology, Soochow University, Suzhou, Jiangsu, China
| | - Wenjin Xue
- Department of Electrical Engineering, Technician College of Taizhou, Taizhou, Jiangsu, China
| | - Jiajia Chen
- School of Chemistry, Biology and Material Engineering, Suzhou University of Science and Technology, Suzhou, China
| | - Guang Hu
- Center for Systems Biology, Soochow University, Suzhou, Jiangsu, China
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246
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Berger H, Marques MS, Zietlow R, Meyer TF, Machado JC, Figueiredo C. Gastric cancer pathogenesis. Helicobacter 2016; 21 Suppl 1:34-8. [PMID: 27531537 DOI: 10.1111/hel.12338] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Gastric cancer (GC) results from a multistep process that is influenced by Helicobacter pylori infection, genetic susceptibility of the host, as well as of other environmental factors. GC results from the accumulation of numerous genetic and epigenetic alterations in oncogenes and tumor suppressor genes, leading to dysregulation of multiple signaling pathways, which disrupt the cell cycle and the balance between cell proliferation and cell death. For this special issue, we have selected to review last year's advances related to three main topics: the cell of origin that initiates malignant growth in GC, the mechanisms of direct genotoxicity induced by H. pylori infection, and the role of aberrantly expressed long noncoding RNAs in GC transformation. The understanding of the molecular basis of GC development is of utmost importance for the identification of novel targets for GC prevention and treatment.
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Affiliation(s)
- Hilmar Berger
- Department of Molecular Biology, Max Planck Institute for Infection Biology, Berlin, Germany
| | - Miguel S Marques
- i3S - Institute of Investigation and Innovation in Health/Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal.,Institute of Molecular Pathology and Immunology of the University of Porto (Ipatimup), Porto, Portugal.,Faculty of Medicine of the University of Porto, Porto, Portugal
| | - Rike Zietlow
- Department of Molecular Biology, Max Planck Institute for Infection Biology, Berlin, Germany
| | - Thomas F Meyer
- Department of Molecular Biology, Max Planck Institute for Infection Biology, Berlin, Germany
| | - Jose C Machado
- i3S - Institute of Investigation and Innovation in Health/Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal.,Institute of Molecular Pathology and Immunology of the University of Porto (Ipatimup), Porto, Portugal.,Faculty of Medicine of the University of Porto, Porto, Portugal
| | - Ceu Figueiredo
- i3S - Institute of Investigation and Innovation in Health/Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal.,Institute of Molecular Pathology and Immunology of the University of Porto (Ipatimup), Porto, Portugal.,Faculty of Medicine of the University of Porto, Porto, Portugal
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247
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Ouyang KX, Zou R, Liang J, Bai ZB, Li ZQ, Zhao JJ. TUC338 Overexpression Leads to Enhanced Proliferation and Reduced Apoptosis in Tongue Squamous Cell Carcinoma Cells In Vitro. J Oral Maxillofac Surg 2016; 75:423-428. [PMID: 27637778 DOI: 10.1016/j.joms.2016.08.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Revised: 07/28/2016] [Accepted: 08/08/2016] [Indexed: 01/07/2023]
Abstract
PURPOSE Long noncoding RNAs are closely related to the development of tumors. In this study, we explored the contribution of the long noncoding RNA TUC338 to cellular processes in tongue squamous cell carcinoma (TSCC). MATERIALS AND METHODS First, we detected TUC338 expression using quantitative reverse transcription-polymerase chain reaction in 25 patients. Then, we transfected a short hairpin RNA to silence TUC338 expression in the CAL-27 and SCC-9 cell lines. Tumor cell growth was determined by the 3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyl-2-H-tetrazolium bromide (MTT) assay, and apoptosis and cell-cycle analyses were performed via flow cytometry. RESULTS The results indicated that TUC338 was overexpressed in TSCCs (P < .05). In addition, silencing TUC338 in CAL-27 and SCC-9 cells inhibited cell growth and increased apoptosis significantly in vivo (P < .05). CONCLUSIONS Long noncoding RNA TUC338 overexpression leads to enhanced proliferation and reduced apoptosis in TSCC.
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Affiliation(s)
- Ke-Xiong Ouyang
- Professor, Department of Oral and Maxillofacial Surgery, Stomatological Hospital of Guangzhou Medical University, Guangzhou, China
| | - Rui Zou
- Resident Doctor, Department of Oral and Maxillofacial Surgery, Stomatological Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jun Liang
- Professor, Department of Oral and Maxillofacial Surgery, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
| | - Zhi-Bao Bai
- Professor, Department of Stomatology, Guangzhou First People's Hospital, Guangzhou, China
| | - Zhi-Qiang Li
- Professor, Department of Oral and Maxillofacial Surgery, The Affiliated Stomatological Hospital of Southern Medical University-Guangdong Provincial Stomatological Hospital, Guangzhou, China
| | - Jian-Jiang Zhao
- Professor, Department of Oral and Maxillofacial Surgery, The Affiliated Stomatological Hospital of Southern Medical University-Guangdong Provincial Stomatological Hospital, Guangzhou, China.
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248
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Flippot R, Malouf GG, Su X, Mouawad R, Spano JP, Khayat D. Cancer subtypes classification using long non-coding RNA. Oncotarget 2016; 7:54082-54093. [PMID: 27340923 PMCID: PMC5288243 DOI: 10.18632/oncotarget.10213] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2015] [Accepted: 05/30/2016] [Indexed: 12/16/2022] Open
Abstract
Inter-tumor heterogeneity might explain divergent clinical evolution of cancers bearing similar pathological features. In the last decade, genomic has highly improved tumor subtypes classification through the identification of oncogenic or tumor suppressor drivers. In addition, epigenetics and long non-coding RNAs (lncRNAs) are emerging as new fields for investigation, which might also account for tumor heterogeneity. There is growing evidence that modifications of lncRNA expression profiles are involved in cancer progression through epigenetic regulation, activation of pro-oncogenic pathways and crosstalks with other RNA subtypes. Consequently, the study of lncRNA expression profile will be a key factor in the future for charting cancer subtype classifications as well as defining prognostic and progression biomarkers. Herein we discuss the interest of lncRNA as potent prognostic and predictive biomarkers, and provide a glimpse on the impact of emerging cancer subtypes classification based on lncRNAs.
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Affiliation(s)
- Ronan Flippot
- Groupe Hospitalier Pitié-Salpêtrière, Department of Medical Oncology, University Pierre and Marie Curie (Paris VI), Institut Universitaire de Cancérologie, AP-HP, Paris, France
| | - Gabriel G. Malouf
- Groupe Hospitalier Pitié-Salpêtrière, Department of Medical Oncology, University Pierre and Marie Curie (Paris VI), Institut Universitaire de Cancérologie, AP-HP, Paris, France
| | - Xiaoping Su
- Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Roger Mouawad
- Groupe Hospitalier Pitié-Salpêtrière, Department of Medical Oncology, University Pierre and Marie Curie (Paris VI), Institut Universitaire de Cancérologie, AP-HP, Paris, France
| | - Jean-Philippe Spano
- Groupe Hospitalier Pitié-Salpêtrière, Department of Medical Oncology, University Pierre and Marie Curie (Paris VI), Institut Universitaire de Cancérologie, AP-HP, Paris, France
| | - David Khayat
- Groupe Hospitalier Pitié-Salpêtrière, Department of Medical Oncology, University Pierre and Marie Curie (Paris VI), Institut Universitaire de Cancérologie, AP-HP, Paris, France
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249
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Zhong Z, Lv M, Chen J. Screening differential circular RNA expression profiles reveals the regulatory role of circTCF25-miR-103a-3p/miR-107-CDK6 pathway in bladder carcinoma. Sci Rep 2016; 6:30919. [PMID: 27484176 PMCID: PMC4971518 DOI: 10.1038/srep30919] [Citation(s) in RCA: 329] [Impact Index Per Article: 41.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 07/11/2016] [Indexed: 12/19/2022] Open
Abstract
Circular RNAs (circRNAs), a kind of non-coding RNAs, have shown large capabilities in gene regulation. However, the mechanisms underlying circRNAs remain largely unknown so far. Recent studies demonstrated that circRNAs play miRNA sponge effects and regulate gene expression by microRNA response elements. Here, we screened circRNA expression profiles of bladder carcinoma using microarray assay. A total of 469 dysregulated circular transcripts are found in bladder cancer compared with normal tissues, among which 285 were up-regulated and 184 were down-regulated. Six circRNAs were identified to have significant differences by qRT-PCR. We speculated that circRNAs might involve in cancer-related pathways via interactions with miRNA by multiple bioinformatical approaches. Therefore, we further predicted that circTCF25 could sequester miR-103a-3p/miR-107, which potentially lead to the up-regulation of thirteen targets related to cell proliferation, migration and invasion. Subsequently, we demonstrated that over-expression of circTCF25 could down-regulate miR-103a-3p and miR-107, increase CDK6 expression, and promote proliferation and migration in vitro and vivo. This is the first study to exploit circRNA profiling and circRNA/miRNA interactions in bladder cancer. Our work laid the foundation to investigate the functions of circRNAs in cancers. The data also suggest that circTCF25 might be a new promising marker for bladder cancer.
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Affiliation(s)
- Zhenyu Zhong
- The First Clinical College, Chongqing Medical University, Chongqing 400016, China
| | - Mengxin Lv
- Department of Cell Biology and Genetics, Chongqing Medical University, Chongqing 400016, China
| | - Junxia Chen
- Department of Cell Biology and Genetics, Chongqing Medical University, Chongqing 400016, China
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250
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Evans JR, Feng FY, Chinnaiyan AM. The bright side of dark matter: lncRNAs in cancer. J Clin Invest 2016; 126:2775-82. [PMID: 27479746 DOI: 10.1172/jci84421] [Citation(s) in RCA: 338] [Impact Index Per Article: 42.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The traditional view of genome organization has been upended in the last decade with the discovery of vast amounts of non-protein-coding transcription. After initial concerns that this "dark matter" of the genome was transcriptional noise, it is apparent that a subset of these noncoding RNAs are functional. Long noncoding RNA (lncRNA) genes resemble protein-coding genes in several key aspects, and they have myriad molecular functions across many cellular pathways and processes, including oncogenic signaling. The number of lncRNA genes has recently been greatly expanded by our group to triple the number of protein-coding genes; therefore, lncRNAs are likely to play a role in many biological processes. Based on their large number and expression specificity in a variety of cancers, lncRNAs are likely to serve as the basis for many clinical applications in oncology.
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