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Chen S, Zhao Q, Zhang R, Liu J, Peng W, Xu H, Li X, Wang X, Wu S, Li G, Nan A. A transcribed ultraconserved noncoding RNA, uc.285+, promotes colorectal cancer proliferation through dual targeting of CDC42 by directly binding mRNA and protein. Transl Res 2024; 270:52-65. [PMID: 38552953 DOI: 10.1016/j.trsl.2024.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 03/15/2024] [Accepted: 03/24/2024] [Indexed: 04/12/2024]
Abstract
The transcribed ultraconserved region (T-UCR) belongs to a new type of lncRNAs that are conserved in homologous regions of the rat, mouse and human genomes. A lot of research has reported that differential expression of T-UCRs can influence the development of various cancers, revealing the ability of T-UCRs as new therapeutic targets or potential cancer biomarkers. Most studies on the molecular mechanisms of T-UCRs in cancer have focused on ceRNA regulatory networks and interactions with target proteins, but the present study reveals an innovative dual-targeted regulatory approach in which T-UCRs bind directly to mRNAs and directly to proteins. We screened T-UCRs that may be related to colorectal cancer (CRC) by performing a whole-genome T-UCR gene microarray and further studied the functional mechanism of T-UCR uc.285+ in the development of CRC. Modulation of uc.285+ affected the proliferation of CRC cell lines and influenced the expression of the CDC42 gene. We also found that uc.285+ promoted the proliferation of CRC cells by directly binding to CDC42 mRNA and enhancing its stability while directly binding to CDC42 protein and affecting its stability. In short, our research on the characteristics of cell proliferation found that uc.285+ has a biological function in promoting CRC proliferation. uc.285+ may have considerable potential as a new diagnostic biomarker for CRC.
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Affiliation(s)
- Sixian Chen
- School of Public Health, Guangxi Medical University, Nanning 530021, PR China; Guangxi Key Laboratory of Environment and Health Research, Guangxi Medical University, Nanning 530021, PR China
| | - Qingyun Zhao
- School of Public Health, Guangxi Medical University, Nanning 530021, PR China; Guangxi Key Laboratory of Environment and Health Research, Guangxi Medical University, Nanning 530021, PR China
| | - Ruirui Zhang
- School of Public Health, Guangxi Medical University, Nanning 530021, PR China; Guangxi Key Laboratory of Environment and Health Research, Guangxi Medical University, Nanning 530021, PR China; School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, PR China
| | - Jungang Liu
- Division of Colorectal & Anal Surgery, Department of Gastrointestinal Surgery, Guangxi Medical University Cancer Hospital, Nanning 530021, PR China
| | - Wenyi Peng
- School of Public Health, Guangxi Medical University, Nanning 530021, PR China; Guangxi Key Laboratory of Environment and Health Research, Guangxi Medical University, Nanning 530021, PR China
| | - Haotian Xu
- School of Public Health, Guangxi Medical University, Nanning 530021, PR China; Guangxi Key Laboratory of Environment and Health Research, Guangxi Medical University, Nanning 530021, PR China
| | - Xiaofei Li
- School of Public Health, Guangxi Medical University, Nanning 530021, PR China; Guangxi Key Laboratory of Environment and Health Research, Guangxi Medical University, Nanning 530021, PR China
| | - Xin Wang
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, PR China
| | - Shuilian Wu
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, PR China
| | - Gang Li
- School of Public Health, Guangxi Medical University, Nanning 530021, PR China; Guangxi Key Laboratory of Environment and Health Research, Guangxi Medical University, Nanning 530021, PR China.
| | - Aruo Nan
- School of Public Health, Guangxi Medical University, Nanning 530021, PR China; Guangxi Key Laboratory of Environment and Health Research, Guangxi Medical University, Nanning 530021, PR China; School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, PR China.
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Dai X, Yu Y, Zou C, Pan B, Wang H, Wang S, Wang X, Wang C, Liu D, Liu Y. Traditional Banxia Xiexin decoction inhibits invasion, metastasis, and epithelial mesenchymal transition in gastric cancer by reducing lncRNA TUC338 expression. Heliyon 2023; 9:e21064. [PMID: 37964840 PMCID: PMC10641127 DOI: 10.1016/j.heliyon.2023.e21064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 10/08/2023] [Accepted: 10/13/2023] [Indexed: 11/16/2023] Open
Abstract
Background Banxia Xiexin decoction (BXD) is a classic traditional Chinese medicine (TCM) formula clinically used to treat chronic gastritis, gastric ulcers, gastric cancer, and many other gastrointestinal diseases. Long noncoding RNAs (lncRNAs) have been shown to play an important role in maintaining the malignant phenotype of tumors. However, no relevant studies have shown whether Banxia Xiexin decoction regulates and controls lncRNA TUC338, and the effect of TUC338 on the regulation of gastric cancer invasion and metastasis remains unclear. Purpose To investigate the ability of the traditional Chinese medicine (TCM) Banxia Xiexin decoction (BXD) to inhibit the migration and invasion of human gastric cancer AGS cells by regulating the long noncoding RNA (lncRNA) TUC338. Methods UHPLC‒MS/MS was used to analyze the chemical components of BXD. MTT was performed to determine the effects of BXD on the proliferation of AGS cells. qRT‒PCR was used to determine the expression of lncRNA TUC338 in gastric cancer tissues, paracarcinoma tissues, AGS human gastric cancer cells and GES-1 normal gastric mucosa cells and to evaluate the effects of BXD on the expression of lncRNA TUC338 in AGS cells. Lentiviral transfection was used to establish human gastric cancer AGS cells with knocked down lncRNA TUC338 expression. The effects of lncRNA TUC338 knockdown on the migration and invasion of AGS cells were observed by a scratch assay and Transwell migration assay, respectively. Western blotting was performed to analyze the effects of lncRNA TUC338 knockdown on epithelial-to-mesenchymal transition (EMT) in AGS cells. We performed quality control on three batches of BXD. We used UHPLC‒MS/MS to control the quality of three random batches of BXD used throughout the study. Results Ninety-five chemical components were identified from the water extract of BXD, some of which have anticancer effects. The expression of TUC.338 in gastric cancer tissues was higher than that in para-carcinoma tissues. BXD inhibited the invasion and migration of gastric cancer cells by inhibiting the expression of lncRNA TUC338, which reduced EMT. After knockdown of lncRNA TUC338, the migration and invasion of AGS cells were reduced; the expression of the EMT-related protein E-cadherin was increased, and the expression of N-cadherin and vimentin was reduced. Conclusions The present results suggest that BXD has potential as an effective treatment for gastric cancer through the inhibition of lncRNA TUC338 expression.
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Affiliation(s)
- Xiaojun Dai
- Clinical College of Traditional Chinese Medicine, Yangzhou University, 577 Wenchang Middle Road, Yangzhou, 225002, China
- Traditional Chinese Medicine Hospital of Yangzhou, 577 Wenchang Middle Road, Yangzhou, 225002, China
- Medical School, Yangzhou University, 136 Jiangyang Middle Road, Yangzhou, 225001, China
| | - Yanwei Yu
- Medical School, Yangzhou University, 136 Jiangyang Middle Road, Yangzhou, 225001, China
| | - Chen Zou
- Medical School, Yangzhou University, 136 Jiangyang Middle Road, Yangzhou, 225001, China
| | - Bo Pan
- Medical School, Yangzhou University, 136 Jiangyang Middle Road, Yangzhou, 225001, China
| | - Haibo Wang
- Medical School, Yangzhou University, 136 Jiangyang Middle Road, Yangzhou, 225001, China
| | - Shanshan Wang
- Clinical College of Traditional Chinese Medicine, Yangzhou University, 577 Wenchang Middle Road, Yangzhou, 225002, China
| | - Xiaojuan Wang
- Medical School, Yangzhou University, 136 Jiangyang Middle Road, Yangzhou, 225001, China
| | - Chenghai Wang
- Department of Pathology, The Affiliated Hospital of Yangzhou University, Yangzhou University, 368 Hanjiang Middle Road, Yangzhou, 225009, China
| | - Dongmei Liu
- College of Chemistry and Chemical Engineering, Yangzhou University, 180 Siwangting Road, Yangzhou, 225002, China
- Jianghai Polytechnic College, 5 Yangzijiang South Road, Yangzhou, 225002, China
| | - Yanqing Liu
- Clinical College of Traditional Chinese Medicine, Yangzhou University, 577 Wenchang Middle Road, Yangzhou, 225002, China
- Medical School, Yangzhou University, 136 Jiangyang Middle Road, Yangzhou, 225001, China
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3
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Biyu H, GuangWen T, Ming Z, Lixin G, Mengshan L. A lncRNA-disease association prediction model based on the two-step PU learning and fully connected neural networks. Heliyon 2023; 9:e17726. [PMID: 37539215 PMCID: PMC10395133 DOI: 10.1016/j.heliyon.2023.e17726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 06/13/2023] [Accepted: 06/26/2023] [Indexed: 08/05/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) have been shown to play a regulatory role in various processes of human diseases. However, lncRNA experiments are inefficient, time-consuming and highly subjective, so that the number of experimentally verified associations between lncRNA and diseases is limited. In the era of big data, numerous machine learning methods have been proposed to predict the potential association between lncRNA and diseases, but the characteristics of the associated data were seldom explored. In these methods, negative samples are randomly selected for model training and the model is prone to learn the potential positive association error, thus affecting the prediction accuracy. In this paper, we proposed a cyclic optimization model of predicting lncRNA-disease associations (COPTLDA in short). In COPTLDA, the two-step training strategy is adopted to search for the samples with the greater probability of being negative examples from unlabeled samples and the determined samples are treated as negative samples, which are combined together with known positive samples to train the model. The searching and training steps are repeated until the best model is obtained as the final prediction model. In order to evaluate the performance of the model, 30% of the known positive samples are used to calculate the model accuracy and 10% of positive samples are used to calculate the recall rate of the model. The sampling strategy used in this paper can improve the accuracy and the AUC value reaches 0.9348. The results of case studies showed that the model could predict the potential associations between lncRNA and malignant tumors such as colorectal cancer, gastric cancer, and breast cancer. The predicted top 20 associated lncRNAs included 10 colorectal cancer lncRNAs, 2 gastric cancer lncRNAs, and 8 breast cancer lncRNAs.
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Affiliation(s)
| | | | | | | | - Li Mengshan
- Corresponding author. Gannan Normal University, China.
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4
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Gao SS, Zhang ZK, Wang XB, Ma Y, Yin GQ, Guo XB. Role of transcribed ultraconserved regions in gastric cancer and therapeutic perspectives. World J Gastroenterol 2022; 28:2900-2909. [PMID: 35978878 PMCID: PMC9280734 DOI: 10.3748/wjg.v28.i25.2900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 04/08/2022] [Accepted: 05/28/2022] [Indexed: 02/06/2023] Open
Abstract
Gastric cancer (GC) is the fourth leading cause of cancer-related death. The occurrence and development of GC is a complex process involving multiple biological mechanisms. Although traditional regulation modulates molecular functions related to the occurrence and development of GC, the comprehensive mechanisms remain unclear. Ultraconserved region (UCR) refers to a genome sequence that is completely conserved in the homologous regions of the human, rat and mouse genomes, with 100% identity, without any insertions or deletions, and often located in fragile sites and tumour-related genes. The transcribed UCR (T-UCR) is transcribed from the UCR and is a new type of long noncoding RNA. Recent studies have found that the expression level of T-UCRs changes during the occurrence and development of GC, revealing a new mechanism underlying GC. Therefore, this article aims to review the relevant research on T-UCRs in GC, as well as the function of T-UCRs and their regulatory role in the occurrence and development of GC, to provide new strategies for GC diagnosis and treatment.
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Affiliation(s)
- Shen-Shuo Gao
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan 250021, Shandong Province, China
| | - Zhi-Kai Zhang
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan 250021, Shandong Province, China
| | - Xu-Bin Wang
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan 250021, Shandong Province, China
| | - Yan Ma
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan 250021, Shandong Province, China
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan 250021, Shandong Province, China
| | - Guo-Qing Yin
- Department of Anus and Intestine Surgery, Qingzhou Hospital Affiliated to Shandong First Medical University, Qingzhou 262500, Shandong Province, China
| | - Xiao-Bo Guo
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan 250021, Shandong Province, China
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan 250021, Shandong Province, China
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Gibert MK, Sarkar A, Chagari B, Roig-Laboy C, Saha S, Bednarek S, Kefas B, Hanif F, Hudson K, Dube C, Zhang Y, Abounader R. Transcribed Ultraconserved Regions in Cancer. Cells 2022; 11:1684. [PMID: 35626721 PMCID: PMC9139194 DOI: 10.3390/cells11101684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/11/2022] [Accepted: 05/17/2022] [Indexed: 11/25/2022] Open
Abstract
Transcribed ultraconserved regions are putative lncRNA molecules that are transcribed from DNA that is 100% conserved in human, mouse, and rat genomes. This is notable, as lncRNAs are typically poorly conserved. TUCRs remain very understudied in many diseases, including cancer. In this review, we summarize the current literature on TUCRs in cancer with respect to expression deregulation, functional roles, mechanisms of action, and clinical perspectives.
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Affiliation(s)
- Myron K. Gibert
- Department of Microbiology, Immunology, and Cancer Biology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA; (M.K.G.J.); (A.S.); (B.C.); (C.R.-L.); (S.S.); (S.B.); (B.K.); (F.H.); (K.H.); (C.D.); (Y.Z.)
| | - Aditya Sarkar
- Department of Microbiology, Immunology, and Cancer Biology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA; (M.K.G.J.); (A.S.); (B.C.); (C.R.-L.); (S.S.); (S.B.); (B.K.); (F.H.); (K.H.); (C.D.); (Y.Z.)
| | - Bilhan Chagari
- Department of Microbiology, Immunology, and Cancer Biology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA; (M.K.G.J.); (A.S.); (B.C.); (C.R.-L.); (S.S.); (S.B.); (B.K.); (F.H.); (K.H.); (C.D.); (Y.Z.)
| | - Christian Roig-Laboy
- Department of Microbiology, Immunology, and Cancer Biology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA; (M.K.G.J.); (A.S.); (B.C.); (C.R.-L.); (S.S.); (S.B.); (B.K.); (F.H.); (K.H.); (C.D.); (Y.Z.)
| | - Shekhar Saha
- Department of Microbiology, Immunology, and Cancer Biology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA; (M.K.G.J.); (A.S.); (B.C.); (C.R.-L.); (S.S.); (S.B.); (B.K.); (F.H.); (K.H.); (C.D.); (Y.Z.)
| | - Sylwia Bednarek
- Department of Microbiology, Immunology, and Cancer Biology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA; (M.K.G.J.); (A.S.); (B.C.); (C.R.-L.); (S.S.); (S.B.); (B.K.); (F.H.); (K.H.); (C.D.); (Y.Z.)
| | - Benjamin Kefas
- Department of Microbiology, Immunology, and Cancer Biology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA; (M.K.G.J.); (A.S.); (B.C.); (C.R.-L.); (S.S.); (S.B.); (B.K.); (F.H.); (K.H.); (C.D.); (Y.Z.)
| | - Farina Hanif
- Department of Microbiology, Immunology, and Cancer Biology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA; (M.K.G.J.); (A.S.); (B.C.); (C.R.-L.); (S.S.); (S.B.); (B.K.); (F.H.); (K.H.); (C.D.); (Y.Z.)
| | - Kadie Hudson
- Department of Microbiology, Immunology, and Cancer Biology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA; (M.K.G.J.); (A.S.); (B.C.); (C.R.-L.); (S.S.); (S.B.); (B.K.); (F.H.); (K.H.); (C.D.); (Y.Z.)
| | - Collin Dube
- Department of Microbiology, Immunology, and Cancer Biology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA; (M.K.G.J.); (A.S.); (B.C.); (C.R.-L.); (S.S.); (S.B.); (B.K.); (F.H.); (K.H.); (C.D.); (Y.Z.)
| | - Ying Zhang
- Department of Microbiology, Immunology, and Cancer Biology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA; (M.K.G.J.); (A.S.); (B.C.); (C.R.-L.); (S.S.); (S.B.); (B.K.); (F.H.); (K.H.); (C.D.); (Y.Z.)
| | - Roger Abounader
- Department of Microbiology, Immunology, and Cancer Biology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA; (M.K.G.J.); (A.S.); (B.C.); (C.R.-L.); (S.S.); (S.B.); (B.K.); (F.H.); (K.H.); (C.D.); (Y.Z.)
- Department of Neurology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
- NCI Designated Comprehensive Cancer Center, University of Virginia, Charlottesville, VA 22908, USA
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6
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Bozgeyik I. The dark matter of the human genome and its role in human cancers. Gene 2022; 811:146084. [PMID: 34843880 DOI: 10.1016/j.gene.2021.146084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 11/06/2021] [Accepted: 11/23/2021] [Indexed: 12/26/2022]
Abstract
The transcribed ultra-conserved regions (T-UCRs) are a novel family of non-coding RNAs which are absolutely conserved (100%) across orthologous regions of the human, mouse, and rat genomes. T-UCRs represent a small portion of the human genome that is likely to be functional but does not code for proteins and is referred to as the "dark matter" of the human genome. Although T-UCRs are ubiquitously expressed, tissue- and disease-specific expression of T-UCRs have also been observed. Accumulating evidence suggests that T-UCRs are differentially expressed and involved in the malignant transformation of human tumors through various genetic and epigenetic regulatory mechanisms. Therefore, T-UCRs are novel candidate predisposing biomarkers for cancer development. T-UCRs have shown to drive malignant transformation of human cancers through regulating non-coding RNAs and/or protein coding genes. However, the functions and fate of most T-UCRs remain mysterious. Here, we review and highlight the current knowledge on these ultra-conserved elements in the formation and progression of human cancers.
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Affiliation(s)
- Ibrahim Bozgeyik
- Department of Medical Biology, Faculty of Medicine, Adiyaman University, Adiyaman, Turkey.
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7
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Soler M, Davalos V, Sánchez-Castillo A, Mora-Martinez C, Setién F, Siqueira E, Castro de Moura M, Esteller M, Guil S. The transcribed ultraconserved region uc.160+ enhances processing and A-to-I editing of the miR-376 cluster: hypermethylation improves glioma prognosis. Mol Oncol 2021; 16:648-664. [PMID: 34665919 PMCID: PMC8807354 DOI: 10.1002/1878-0261.13121] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 10/01/2021] [Accepted: 10/15/2021] [Indexed: 11/11/2022] Open
Abstract
Transcribed ultraconserved regions (T‐UCRs) are noncoding RNAs derived from DNA sequences that are entirely conserved across species. Their expression is altered in many tumor types, and, although a role for T‐UCRs as regulators of gene expression has been proposed, their functions remain largely unknown. Herein, we describe the epigenetic silencing of the uc.160+ T‐UCR in gliomas and mechanistically define a novel RNA–RNA regulatory network in which uc.160+ modulates the biogenesis of several members of the miR‐376 cluster. This includes the positive regulation of primary microRNA (pri‐miRNA) cleavage and an enhanced A‐to‐I editing on its mature sequence. As a consequence, the expression of uc.160+ affects the downstream, miR‐376‐regulated genes, including the transcriptional coregulators RING1 and YY1‐binding protein (RYBP) and forkhead box P2 (FOXP2). Finally, we elucidate the clinical impact of our findings, showing that hypermethylation of the uc.160+ CpG island is an independent prognostic factor associated with better overall survival in lower‐grade gliomas, highlighting the importance of T‐UCRs in cancer pathophysiology.
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Affiliation(s)
- Marta Soler
- Josep Carreras Leukaemia Research Institute (IJC), Barcelona, Spain
| | - Veronica Davalos
- Josep Carreras Leukaemia Research Institute (IJC), Barcelona, Spain
| | - Anaís Sánchez-Castillo
- Department of Radiation Oncology (MAASTRO), GROW School for Oncology and Developmental Biology, Maastricht University Medical Center, The Netherlands
| | - Carlos Mora-Martinez
- Centre of Excellence in Experimental and Computational Developmental Biology, Institute of Biotechnology, University of Helsinki, Finland
| | - Fernando Setién
- Josep Carreras Leukaemia Research Institute (IJC), Barcelona, Spain
| | - Edilene Siqueira
- Josep Carreras Leukaemia Research Institute (IJC), Barcelona, Spain.,Conselho Nacional de Desenvolvimento Cientifico e Tecnológico (CNPq), Brasilia, Brazil
| | | | - Manel Esteller
- Josep Carreras Leukaemia Research Institute (IJC), Barcelona, Spain.,Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.,Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), Spain
| | - Sonia Guil
- Josep Carreras Leukaemia Research Institute (IJC), Barcelona, Spain.,Germans Trias i Pujol Health Science Research Institute, Barcelona, Spain
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8
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Ding Z, Yan Y, Guo YL, Wang C. Esophageal carcinoma cell-excreted exosomal uc.189 promotes lymphatic metastasis. Aging (Albany NY) 2021; 13:13846-13858. [PMID: 34024769 PMCID: PMC8202844 DOI: 10.18632/aging.202979] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 02/16/2021] [Indexed: 04/12/2023]
Abstract
Most cancers are old age-related diseases. Patients with lymphatic metastasis have an extremely poor prognosis in esophageal cancers (ECs). Previous studies showed ultraconserved RNAs are involved in tumorigenesis and ultraconserved RNA 189 (uc.189) served as an oncogene in cervical cancer, but the effect of exosomal uc.189 in esophageal squamous cell carcinoma (ESCC) remains undefined. This study revealed that uc.189 is closely correlated with lymph node (LN) metastasis and the number of lymphatic vessels in ESCC. ESCC-secreted exosomal uc.189 is transferred into human lymphatic endothelial cells (HLECs) to promote its proliferation, migration and tube formation to facilitate lymph node metastasis. Mechanistically, uc.189 regulated EPHA2 expression by directly binding to its 3'UTR region through dual-luciferase reporter assay. Over-expression and knockdown of EPHA2 could respectively rescue and simulate the effects induced by exosomal uc.189. Especially, the uc.189-EPHA2 axis activates the P38MAPK/VEGF-C pathway in HLECs. Finally, ESCC-secreted exosomal of uc.189 promotes HLECs sprouting in vitro, migration, and lymphangiogenesis. Thus, these findings suggested that exosomal uc.189 targets the EPHA2 of HLECs to promote lymphangiogenesis, and may represent a novel marker of diagnosis and treatment for ESCC patients in early stages.
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Affiliation(s)
- Zhiyan Ding
- Department of Pathology, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou 225009, PR China
| | - Yun Yan
- Department of Pathology, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou 225009, PR China
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou 225001, PR China
| | - Yu Lian Guo
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou 225001, PR China
| | - Chenghai Wang
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou 225001, PR China
- Jiangsu Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention and Treatment of Senile Diseases, Yangzhou University, Yangzhou 225001, PR China
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Zheng Z, Hong D, Zhang X, Chang Y, Sun N, Lin Z, Li H, Huang S, Zhang R, Xie Q, Huang H, Jin H. uc.77- Downregulation Promotes Colorectal Cancer Cell Proliferation by Inhibiting FBXW8-Mediated CDK4 Protein Degradation. Front Oncol 2021; 11:673223. [PMID: 34094975 PMCID: PMC8172171 DOI: 10.3389/fonc.2021.673223] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 04/06/2021] [Indexed: 01/15/2023] Open
Abstract
Transcribed ultraconserved regions (T-UCRs) are a new type of long non-coding RNA, and the UCR has 481 segments longer than 200 base pairs that are 100% conserved between humans, rats, and mice. T-UCRs involved in colorectal cancer (CRC) have not been studied in detail. We performed T-UCR microarray analysis and found that uc.77- was significantly downregulated in CRC tissues and cell lines. Ectopic expression of uc.77- significantly inhibited the proliferation of CRC cells in vitro and the growth of xenograft tumors in nude mice in vivo. Mechanistic studies showed that uc.77- competed with FBXW8 mRNA for binding to microRNA (miR)-4676-5p through a competing endogenous RNA mechanism and inhibited the proliferation of CRC cells by negatively regulating CDK4. The present findings highlight the role of the uc.77-/miR-4676-5p/FBXW8 axis in CRC and identify uc.77- as a potential novel target for the treatment of CRC.
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Affiliation(s)
- Zhijian Zheng
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Dan Hong
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Xiaodong Zhang
- Department of Colorectal Anal Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yixin Chang
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Ning Sun
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Zhenni Lin
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Hongyan Li
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Shirui Huang
- Department of Clinical Laboratory, The Second Affiliated Hospital & Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China
| | - Ruirui Zhang
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Qipeng Xie
- Department of Clinical Laboratory, The Second Affiliated Hospital & Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China
| | - Haishan Huang
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Honglei Jin
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
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10
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Qi T, Cao H, Sun H, Feng H, Li N, Wang C, Wang L. piR-19166 inhibits migration and metastasis through CTTN/MMPs pathway in prostate carcinoma. Aging (Albany NY) 2020; 12:18209-18220. [PMID: 32881713 PMCID: PMC7585067 DOI: 10.18632/aging.103677] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 05/27/2020] [Indexed: 01/24/2023]
Abstract
Tumor metastasis is one of death causes for patients of prostate carcinoma. PIWI-interacting RNAs (piRNAs) are a subtype of noncoding protein RNAs that are involved in tumorigenesis, but the effect of piRNAs in prostate carcinoma (PCa) remains unclear. This article showed the identification of piRNAs was performed using a piRNA microarray screen in PCa tissues and several piRNAs were identified as dysregulated. The two up-regulated piRNAs (piR-19004 and piR-2878) and one down-regulated piR-19166 have been validated in the tissues and cell lines of PCa using quantitative reverse transcription polymerase chain reaction (qRT-PCR). Further studies showed that piR-19166 is transfected into PCa cells to suppress its migration and metastasis. Mechanistically, cortactin (CTTN) 3' untranslated region (UTR) was complementary combined with piR-19166 by bioinformatic prediction and identified as a direct target of piR-19166 through dual-luciferase reporter assay. Over-expression and knockdown of CTTN could respectively rescue and simulate the effects induced by piR-19166. Finally, piR-19166 suppresses migration and metastasis by the CTTN/matrix metalloproteinases (MMPs) pathway in PCa cells. Thus, these findings suggested that piR-19166 targets the CTTN of prostate cancer cells to inhibit migration and distant metastasis, and may represent a new marker of diagnosis and treatment for PCa patients in early stages.
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Affiliation(s)
- Tingyue Qi
- Department of Ultrasound, Medical Imaging Center, Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou 225009, China
| | - Haiyan Cao
- Department of Ultrasound, Medical Imaging Center, Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou 225009, China
| | - Hongguang Sun
- Department of Ultrasound, Medical Imaging Center, Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou 225009, China
| | - Hao Feng
- Department of Ultrasound, Medical Imaging Center, Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou 225009, China
| | - Nianfeng Li
- Department of Ultrasound, Medical Imaging Center, Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou 225009, China
| | - Chenghai Wang
- Department of Pathology, Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou 225009, China
| | - Lei Wang
- Department of Pathology, Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou 225009, China
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11
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Wang Y, Zhou D, Feng Y, Chen G, Li N. T-UCRs with digestive and respiratory diseases. Bioorg Med Chem Lett 2020; 30:127306. [PMID: 32631526 DOI: 10.1016/j.bmcl.2020.127306] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 05/31/2020] [Accepted: 06/01/2020] [Indexed: 12/23/2022]
Abstract
From the perspective of histoembryology, the lung, gaster, and intestines that derived from the endoderm of the gastrula are structurally homologous. The interplay of intestines and lung in many pathologic changes is called the gut-lung axis. RNAs transcribed from ultraconserved regions (T-UCRs) are highly evolutionarily conserved in many mammalian genomes and have been found to be important in the pathogenesis and diagnosis of many diseases. More and more studies in recent years have shown that T-UCRs play important roles both in digestive and respiratory diseases. Taking the gut-lung axis as the entry point, this review summarizes the T-UCRs related to digestive and respiratory diseases in recent years. Meanwhile, these T-UCRs and their targets can lay a foundation for future drug research.
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Affiliation(s)
- Yajun Wang
- School of Traditional Chinese Materia Medica, Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Di Zhou
- School of Traditional Chinese Materia Medica, Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Yuan Feng
- School of Traditional Chinese Materia Medica, Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Gang Chen
- School of Traditional Chinese Materia Medica, Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug, Shenyang Pharmaceutical University, Shenyang 110016, China.
| | - Ning Li
- School of Traditional Chinese Materia Medica, Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug, Shenyang Pharmaceutical University, Shenyang 110016, China.
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12
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Navarro E, Mallén A, Cruzado JM, Torras J, Hueso M. Unveiling ncRNA regulatory axes in atherosclerosis progression. Clin Transl Med 2020; 9:5. [PMID: 32009226 PMCID: PMC6995802 DOI: 10.1186/s40169-020-0256-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 01/05/2020] [Indexed: 02/06/2023] Open
Abstract
Completion of the human genome sequencing project highlighted the richness of the cellular RNA world, and opened the door to the discovery of a plethora of short and long non-coding RNAs (the dark transcriptome) with regulatory or structural potential, which shifted the balance of pathological gene alterations from coding to non-coding RNAs. Thus, disease risk assessment currently has to also evaluate the expression of new RNAs such as small micro RNAs (miRNAs), long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), competing endogenous RNAs (ceRNAs), retrogressed elements, 3'UTRs of mRNAs, etc. We are interested in the pathogenic mechanisms of atherosclerosis (ATH) progression in patients suffering Chronic Kidney Disease, and in this review, we will focus in the role of the dark transcriptome (non-coding RNAs) in ATH progression. We will focus in miRNAs and in the formation of regulatory axes or networks with their mRNA targets and with the lncRNAs that function as miRNA sponges or competitive inhibitors of miRNA activity. In this sense, we will pay special attention to retrogressed genomic elements, such as processed pseudogenes and Alu repeated elements, that have been recently seen to also function as miRNA sponges, as well as to the use or miRNA derivatives in gene silencing, anti-ATH therapies. Along the review, we will discuss technical developments associated to research in lncRNAs, from sequencing technologies to databases, repositories and algorithms to predict miRNA targets, as well as new approaches to miRNA function, such as integrative or enrichment analysis and their potential to unveil RNA regulatory networks.
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Affiliation(s)
- Estanislao Navarro
- Independent Researcher, Barcelona, Spain. .,Department of Nephrology, Hospital Universitari Bellvitge and Bellvitge Research Institute (IDIBELL), C/Feixa Llarga, s/n; L'Hospitalet de Llobregat, 08907, Barcelona, Spain.
| | - Adrian Mallén
- Department of Nephrology, Hospital Universitari Bellvitge and Bellvitge Research Institute (IDIBELL), C/Feixa Llarga, s/n; L'Hospitalet de Llobregat, 08907, Barcelona, Spain
| | - Josep M Cruzado
- Department of Nephrology, Hospital Universitari Bellvitge and Bellvitge Research Institute (IDIBELL), C/Feixa Llarga, s/n; L'Hospitalet de Llobregat, 08907, Barcelona, Spain
| | - Joan Torras
- Department of Nephrology, Hospital Universitari Bellvitge and Bellvitge Research Institute (IDIBELL), C/Feixa Llarga, s/n; L'Hospitalet de Llobregat, 08907, Barcelona, Spain
| | - Miguel Hueso
- Department of Nephrology, Hospital Universitari Bellvitge and Bellvitge Research Institute (IDIBELL), C/Feixa Llarga, s/n; L'Hospitalet de Llobregat, 08907, Barcelona, Spain.
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13
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Pereira Zambalde E, Mathias C, Rodrigues AC, Souza Fonseca Ribeiro EM, Fiori Gradia D, Calin GA, Carvalho de Oliveira J. Highlighting transcribed ultraconserved regions in human diseases. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 11:e1567. [DOI: 10.1002/wrna.1567] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 08/02/2019] [Accepted: 08/13/2019] [Indexed: 12/18/2022]
Affiliation(s)
| | - Carolina Mathias
- Department of Genetics Universidade Federal do Paraná Curitiba Brazil
| | | | | | | | - George A. Calin
- Department of Experimental Therapeutics, MD Anderson Cancer Center University of Texas Houston Texas
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14
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The Transcribed-Ultra Conserved Regions: Novel Non-Coding RNA Players in Neuroblastoma Progression. Noncoding RNA 2019; 5:ncrna5020039. [PMID: 31167408 PMCID: PMC6631508 DOI: 10.3390/ncrna5020039] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 05/30/2019] [Accepted: 06/03/2019] [Indexed: 12/15/2022] Open
Abstract
The Transcribed-Ultra Conserved Regions (T-UCRs) are a class of novel non-coding RNAs that arise from the dark matter of the genome. T-UCRs are highly conserved between mouse, rat, and human genomes, which might indicate a definitive role for these elements in health and disease. The growing body of evidence suggests that T-UCRs contribute to oncogenic pathways. Neuroblastoma is a type of childhood cancer that is challenging to treat. The role of non-coding RNAs in the pathogenesis of neuroblastoma, in particular for cancer development, progression, and therapy resistance, has been documented. Exosmic non-coding RNAs are also involved in shaping the biology of the tumor microenvironment in neuroblastoma. In recent years, the involvement of T-UCRs in a wide variety of pathways in neuroblastoma has been discovered. Here, we present an overview of the involvement of T-UCRs in various cellular pathways, such as DNA damage response, proliferation, chemotherapy response, MYCN (v-myc myelocytomatosis viral related oncogene, neuroblastoma derived (avian)) amplification, gene copy number, and immune response, as well as correlate it to patient survival in neuroblastoma.
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15
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LncRNAs with miRNAs in regulation of gastric, liver, and colorectal cancers: updates in recent years. Appl Microbiol Biotechnol 2019; 103:4649-4677. [PMID: 31062053 DOI: 10.1007/s00253-019-09837-5] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 04/07/2019] [Accepted: 04/08/2019] [Indexed: 12/15/2022]
Abstract
Long noncoding RNA (lncRNA) is a kind of RNAi molecule composed of hundreds to thousands of nucleotides. There are several major types of functional lncRNAs which participate in some important cellular pathways. LncRNA-RNA interaction controls mRNA translation and degradation or serves as a microRNA (miRNA) sponge for silencing. LncRNA-protein interaction regulates protein activity in transcriptional activation and silencing. LncRNA guide, decoy, and scaffold regulate transcription regulators of enhancer or repressor region of the coding genes for alteration of expression. LncRNA plays a role in cellular responses including the following activities: regulation of chromatin structural modification and gene expression for epigenetic and cell function control, promotion of hematopoiesis and maturation of immunity, cell programming in stem cell and somatic cell development, modulation of pathogen infection, switching glycolysis and lipid metabolism, and initiation of autoimmune diseases. LncRNA, together with miRNA, are considered the critical elements in cancer development. It has been demonstrated that tumorigenesis could be driven by homeostatic imbalance of lncRNA/miRNA/cancer regulatory factors resulting in biochemical and physiological alterations inside the cells. Cancer-driven lncRNAs with other cellular RNAs, epigenetic modulators, or protein effectors may change gene expression level and affect the viability, immortality, and motility of the cells that facilitate cancer cell cycle rearrangement, angiogenesis, proliferation, and metastasis. Molecular medicine will be the future trend for development. LncRNA/miRNA could be one of the potential candidates in this category. Continuous studies in lncRNA functional discrepancy between cancer cells and normal cells and regional and rational genetic differences of lncRNA profiles are critical for clinical research which is beneficial for clinical practice.
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16
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Sekino Y, Sakamoto N, Goto K, Honma R, Shigematsu Y, Quoc TP, Sentani K, Oue N, Teishima J, Kawakami F, Karam JA, Sircar K, Matsubara A, Yasui W. Uc.416 + A promotes epithelial-to-mesenchymal transition through miR-153 in renal cell carcinoma. BMC Cancer 2018; 18:952. [PMID: 30286729 PMCID: PMC6172711 DOI: 10.1186/s12885-018-4863-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 09/26/2018] [Indexed: 12/17/2022] Open
Abstract
Background The transcribed ultraconserved regions (T-UCRs) are a novel class of non-coding RNAs that are absolutely conserved across species and are involved in carcinogenesis in some cancers. However, the expression and biological role of T-UCRs in renal cell carcinoma (RCC) remain poorly understood. This study aimed to examine the expression and functional role of Uc.416 + A and analyze the association between Uc.416 + A and epithelial-to-mesenchymal transition in RCC. Methods Expression of Uc.416 + A in 35 RCC tissues, corresponding normal kidney tissues and 13 types of normal tissue samples was determined by quantitative reverse transcription-polymerase chain reaction (qRT-PCR). We performed a cell growth and migration assay in RCC cell line 786-O transfected with negative control and siRNA for Uc.416 + A. We evaluated the relation between Uc.416 + A and miR-153, which has a complimentary site of Uc.416 + A. Results qRT-PCR analysis revealed that the expression of Uc.416 + A was higher in RCC tissues than that in corresponding normal kidney tissues. Inhibition of Uc.416 + A reduced cell growth and cell migration activity. There was an inverse correlation between Uc.416 + A and miR-153. Western blot analysis showed Uc.416 + A modulated E-cadherin, vimentin and snail. The expression of Uc.416 + A was positively associated with the expression of SNAI1, VIM and inversely associated with the expression of CDH1. Conclusions The expression of Uc.416 + A was upregulated in RCC and especially in RCC tissues with sarcomatoid change. Uc.416 + A promoted epithelial-to-mesenchymal transition through miR-153. These results suggest that Uc.416 + A may be a promising therapeutic target. Electronic supplementary material The online version of this article (10.1186/s12885-018-4863-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yohei Sekino
- Department of Molecular Pathology, Hiroshima University Institute of Biomedical and Health Sciences, 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8551, Japan.,Department of Urology, Hiroshima University Institute of Biomedical and Health Sciences, Hiroshima, Japan
| | - Naoya Sakamoto
- Department of Molecular Pathology, Hiroshima University Institute of Biomedical and Health Sciences, 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8551, Japan
| | - Keisuke Goto
- Cancer Biology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Ririno Honma
- Department of Molecular Pathology, Hiroshima University Institute of Biomedical and Health Sciences, 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8551, Japan
| | - Yoshinori Shigematsu
- Department of Molecular Pathology, Hiroshima University Institute of Biomedical and Health Sciences, 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8551, Japan.,Department of Urology, Hiroshima University Institute of Biomedical and Health Sciences, Hiroshima, Japan
| | - Thang Pham Quoc
- Department of Molecular Pathology, Hiroshima University Institute of Biomedical and Health Sciences, 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8551, Japan
| | - Kazuhiro Sentani
- Department of Molecular Pathology, Hiroshima University Institute of Biomedical and Health Sciences, 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8551, Japan
| | - Naohide Oue
- Department of Molecular Pathology, Hiroshima University Institute of Biomedical and Health Sciences, 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8551, Japan
| | - Jun Teishima
- Department of Urology, Hiroshima University Institute of Biomedical and Health Sciences, Hiroshima, Japan
| | - Fumi Kawakami
- Departments of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jose A Karam
- Departments of Urology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kanishka Sircar
- Departments of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Departments of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Akio Matsubara
- Department of Urology, Hiroshima University Institute of Biomedical and Health Sciences, Hiroshima, Japan
| | - Wataru Yasui
- Department of Molecular Pathology, Hiroshima University Institute of Biomedical and Health Sciences, 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8551, Japan.
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17
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Zhou J, Wang C, Gong W, Wu Y, Xue H, Jiang Z, Shi M. uc.454 Inhibited Growth by Targeting Heat Shock Protein Family A Member 12B in Non-Small-Cell Lung Cancer. MOLECULAR THERAPY-NUCLEIC ACIDS 2018; 12:174-183. [PMID: 30195756 PMCID: PMC6023848 DOI: 10.1016/j.omtn.2018.05.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 04/30/2018] [Accepted: 05/07/2018] [Indexed: 01/18/2023]
Abstract
Transcribed ultraconserved regions (T-UCRs) classified as long non-coding RNAs (Lnc-RNAs) are transcripts longer than 200-nt RNA with no protein-coding capacity. Previous studies showed that T-UCRs serve as novel oncogenes, or tumor suppressors are involved in tumorigenesis and cancer progressive. Nevertheless, the clinicopathologic significance and regulatory mechanism of T-UCRs in lung cancer (LC) remain largely unknown. We found that uc.454 was downregulated in both non-small-cell LC (NSCLC) tissues and LC cell lines, and the downregulated uc.454 is associated with tumor size and tumors with more advanced stages. Transfection with uc.454 markedly induced apoptosis and inhibited cell proliferation in SPC-A-1 and NCI-H2170 LC cell lines. Above results suggested that uc.454 played a suppressive role in LC. Heat shock protein family A member 12B (HSPA12B) protein was negatively regulated by uc.454 at the posttranscriptional level by dual-luciferase reporter assay and affected the expressions of Bcl-2 family members, which finally induced LC apoptosis. The uc.454/HSPA12B axis furthers our understanding of the molecular mechanisms involved in tumor apoptosis, which may potentially serve as a therapeutic target for lung carcinoma.
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Affiliation(s)
- Jun Zhou
- Department of Respiratory Medicine, The 2nd Affiliated Hospital of Soochow University, 1055 Sanxiang Road, Suzhou, Jiangsu 215004, China; Department of Respiratory Medicine, The Affiliated Hospital of Yangzhou University, Yangzhou University, 368 Hanjiang Middle Road, Yangzhou 225009, China
| | - Chenghai Wang
- Department of Pathology, The Affiliated Hospital of Yangzhou University, Yangzhou University, 368 Hanjiang Middle Road, Yangzhou 225009, China
| | - Weijuan Gong
- Department of Molecular Immunology, The Affiliated Hospital of Yangzhou University, Yangzhou University, 368 Hanjiang Middle Road, Yangzhou 225009, China
| | - Yandan Wu
- Department of Pathology, The Affiliated Hospital of Yangzhou University, Yangzhou University, 368 Hanjiang Middle Road, Yangzhou 225009, China
| | - Huimin Xue
- Department of Pathology, The Affiliated Hospital of Yangzhou University, Yangzhou University, 368 Hanjiang Middle Road, Yangzhou 225009, China
| | - Zewei Jiang
- Department of Pathology, The Affiliated Hospital of Yangzhou University, Yangzhou University, 368 Hanjiang Middle Road, Yangzhou 225009, China
| | - Minhua Shi
- Department of Respiratory Medicine, The 2nd Affiliated Hospital of Soochow University, 1055 Sanxiang Road, Suzhou, Jiangsu 215004, China.
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18
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Kottorou AE, Antonacopoulou AG, Dimitrakopoulos FID, Diamantopoulou G, Sirinian C, Kalofonou M, Theodorakopoulos T, Oikonomou C, Katsakoulis EC, Koutras A, Makatsoris T, Demopoulos N, Stephanou G, Stavropoulos M, Thomopoulos KC, Kalofonos HP. Deregulation of methylation of transcribed-ultra conserved regions in colorectal cancer and their value for detection of adenomas and adenocarcinomas. Oncotarget 2018; 9:21411-21428. [PMID: 29765549 PMCID: PMC5940382 DOI: 10.18632/oncotarget.25115] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 03/02/2018] [Indexed: 02/06/2023] Open
Abstract
Expression of Transcribed Ultraconserved Regions (T-UCRs) is often deregulated in cancer. The present study assesses the expression and methylation of three T-UCRs (Uc160, Uc283 and Uc346) in colorectal cancer (CRC) and explores the potential of T-UCR methylation in circulating DNA for the detection of adenomas and adenocarcinomas. Expression levels of Uc160, Uc283 and Uc346 were lower in neoplastic tissues from 64 CRC patients (statistically significant for Uc160, p<0.001), compared to non-malignant tissues, while methylation levels displayed the inverse pattern (p<0.001, p=0.001 and p=0.004 respectively). In colon cancer cell lines, overexpression of Uc160 and Uc346 led to increased proliferation and migration rates. Methylation levels of Uc160 in plasma of 50 CRC, 59 adenoma patients, 40 healthy subjects and 12 patients with colon inflammation or diverticulosis predicted the presence of CRC with 35% sensitivity and 89% specificity (p=0.016), while methylation levels of the combination of all three T-UCRs resulted in 45% sensitivity and 74.3% specificity (p=0.013). In conclusion, studied T-UCRs’ expression and methylation status are deregulated in CRC while Uc160 and Uc346 appear to have a complicated role in CRC progression. Moreover their methylation status appears a promising non-invasive screening test for CRC, provided that the sensitivity of the assay is improved.
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Affiliation(s)
- Anastasia E Kottorou
- Clinical and Molecular Oncology Laboratory, Division of Oncology, Medical School, University of Patras, Patras, Greece
| | - Anna G Antonacopoulou
- Clinical and Molecular Oncology Laboratory, Division of Oncology, Medical School, University of Patras, Patras, Greece
| | - Foteinos-Ioannis D Dimitrakopoulos
- Clinical and Molecular Oncology Laboratory, Division of Oncology, Medical School, University of Patras, Patras, Greece.,Division of Oncology, University Hospital of Patras, Patras, Greece
| | | | - Chaido Sirinian
- Clinical and Molecular Oncology Laboratory, Division of Oncology, Medical School, University of Patras, Patras, Greece
| | - Melpomeni Kalofonou
- Clinical and Molecular Oncology Laboratory, Division of Oncology, Medical School, University of Patras, Patras, Greece.,Institute of Biomedical Engineering, Imperial College London, London, UK
| | | | - Chrysa Oikonomou
- Division of Oncology, University Hospital of Patras, Patras, Greece
| | | | - Angelos Koutras
- Clinical and Molecular Oncology Laboratory, Division of Oncology, Medical School, University of Patras, Patras, Greece.,Division of Oncology, University Hospital of Patras, Patras, Greece
| | - Thomas Makatsoris
- Clinical and Molecular Oncology Laboratory, Division of Oncology, Medical School, University of Patras, Patras, Greece.,Division of Oncology, University Hospital of Patras, Patras, Greece
| | - Nikos Demopoulos
- Division of Genetics, Cell and Developmental Biology, Department of Biology, University of Patras, Patras, Greece
| | - Georgia Stephanou
- Division of Genetics, Cell and Developmental Biology, Department of Biology, University of Patras, Patras, Greece
| | | | | | - Haralabos P Kalofonos
- Clinical and Molecular Oncology Laboratory, Division of Oncology, Medical School, University of Patras, Patras, Greece.,Division of Oncology, University Hospital of Patras, Patras, Greece
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19
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Wang L, Wang XC, Li X, Gu Y, Zhou J, Jiang S, Liu J, Wu C, Ding Z, Wan Y, Wang C. Expression of uc.189 and its clinicopathologic significance in gynecological cancers. Oncotarget 2017; 9:7453-7463. [PMID: 29484123 PMCID: PMC5800915 DOI: 10.18632/oncotarget.23761] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 12/23/2017] [Indexed: 01/01/2023] Open
Abstract
In recent decades, emerging evidence demonstrates that ultraconserved elements (UCEs) encoding noncoding RNAs serve as regulators of gene expression. Until now, the role of uc.189 in human cancers remains undefined and the clinical significance of uc.189 in gynecological cancers remains unknown. This study was to identify the prognostic value of uc.189 expression in gynecological cancers. Tissue microarrays were constructed with 243 samples including 116 cervical squamous cell carcinomas (CSCCs), 98 endometrial adenocarcinomas (EACs), 29 ovarian cystoadenocarcinomas(OCAs), and corresponding normal tissues. In CSCC, uc.189 expression was increased in 78.5% of cases (91/116), decreased in 4.3% (5/116), and unchanged in 17.2% (20/116). In EAC its expression was increased in 74.5% (73/98), decreased in 3.1% (3/98), and unchanged in 22.4% (22/98). Expression of uc.189 was increased in 23, and unchanged/decreased in 6, of 29 cases of ovarian cystoadenocarcinomas. Univariate and multivariate Cox regression analysis demonstrated that over-expression of uc.189 predicted poor prognosis in CSCC and EAC. Thus, these findings suggested uc.189 might be an evaluating prognosis marker of gynecological tumors.
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Affiliation(s)
- Lei Wang
- Department of Pathology, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, Jiangsu 225009, China.,Department of Pharmacy, Medical College, Yangzhou University, Yangzhou, Jiangsu 225001, China.,Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu 225009, China
| | - Xing Cheng Wang
- Department of Pharmacy, Medical College, Yangzhou University, Yangzhou, Jiangsu 225001, China.,Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu 225009, China
| | - Xinyu Li
- Department of Basic Medical, Medical College, Yangzhou University, Yangzhou, Jiangsu 225001, China.,Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu 225009, China
| | - Yan Gu
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, Jiangsu 225001, China
| | - Jun Zhou
- Department of Pathology, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Shuwan Jiang
- Department of Pathology, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Jiajia Liu
- Department of Pathology, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Chong Wu
- Department of Pathology, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Zhiyan Ding
- Department of Pathology, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Yafeng Wan
- Department of Pharmacy, Medical College, Yangzhou University, Yangzhou, Jiangsu 225001, China.,Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu 225009, China
| | - Chenghai Wang
- Department of Pathology, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, Jiangsu 225009, China.,Department of Pharmacy, Medical College, Yangzhou University, Yangzhou, Jiangsu 225001, China.,Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, Jiangsu 225001, China.,Jiangsu Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention and Treatment of Senile Diseases, Yangzhou, Jiangsu 225001, China.,Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu 225009, China
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20
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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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21
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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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22
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Bhan A, Soleimani M, Mandal SS. Long Noncoding RNA and Cancer: A New Paradigm. Cancer Res 2017; 77:3965-3981. [PMID: 28701486 DOI: 10.1158/0008-5472.can-16-2634] [Citation(s) in RCA: 1926] [Impact Index Per Article: 275.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 04/05/2017] [Accepted: 05/04/2017] [Indexed: 12/11/2022]
Abstract
In addition to mutations or aberrant expression in the protein-coding genes, mutations and misregulation of noncoding RNAs, in particular long noncoding RNAs (lncRNA), appear to play major roles in cancer. Genome-wide association studies of tumor samples have identified a large number of lncRNAs associated with various types of cancer. Alterations in lncRNA expression and their mutations promote tumorigenesis and metastasis. LncRNAs may exhibit tumor-suppressive and -promoting (oncogenic) functions. Because of their genome-wide expression patterns in a variety of tissues and their tissue-specific expression characteristics, lncRNAs hold strong promise as novel biomarkers and therapeutic targets for cancer. In this article, we have reviewed the emerging functions and association of lncRNAs in different types of cancer and discussed their potential implications in cancer diagnosis and therapy. Cancer Res; 77(15); 3965-81. ©2017 AACR.
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Affiliation(s)
- Arunoday Bhan
- Gene Regulation and Epigenetics Research Lab, Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, Texas
| | - Milad Soleimani
- Gene Regulation and Epigenetics Research Lab, Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, Texas
| | - Subhrangsu S Mandal
- Gene Regulation and Epigenetics Research Lab, Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, Texas.
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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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