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Wang S, Qi X, Liu D, Xie D, Jiang B, Wang J, Wang X, Wu G. The implications for urological malignancies of non-coding RNAs in the the tumor microenvironment. Comput Struct Biotechnol J 2024; 23:491-505. [PMID: 38249783 PMCID: PMC10796827 DOI: 10.1016/j.csbj.2023.12.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 12/08/2023] [Accepted: 12/16/2023] [Indexed: 01/23/2024] Open
Abstract
Urological malignancies are a major global health issue because of their complexity and the wide range of ways they affect patients. There's a growing need for in-depth research into these cancers, especially at the molecular level. Recent studies have highlighted the importance of non-coding RNAs (ncRNAs) – these don't code for proteins but are crucial in controlling genes – and the tumor microenvironment (TME), which is no longer seen as just a background factor but as an active player in cancer progression. Understanding how ncRNAs and the TME interact is key for finding new ways to diagnose and predict outcomes in urological cancers, and for developing new treatments. This article reviews the basic features of ncRNAs and goes into detail about their various roles in the TME, focusing specifically on how different ncRNAs function and act in urological malignancies.
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Affiliation(s)
- Shijin Wang
- Department of Urology, The First Affiliated Hospital of Dalian Medical University, Dalian 116011, Liaoning, China
| | - Xiaochen Qi
- Department of Urology, The First Affiliated Hospital of Dalian Medical University, Dalian 116011, Liaoning, China
| | - Dequan Liu
- Department of Urology, The First Affiliated Hospital of Dalian Medical University, Dalian 116011, Liaoning, China
| | - Deqian Xie
- Department of Urology, The First Affiliated Hospital of Dalian Medical University, Dalian 116011, Liaoning, China
| | - Bowen Jiang
- Department of Urology, The First Affiliated Hospital of Dalian Medical University, Dalian 116011, Liaoning, China
| | - Jin Wang
- Department of Urology, The First Affiliated Hospital of Dalian Medical University, Dalian 116011, Liaoning, China
| | - Xiaoxi Wang
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian 116011, Liaoning, China
| | - Guangzhen Wu
- Department of Urology, The First Affiliated Hospital of Dalian Medical University, Dalian 116011, Liaoning, China
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Adjeroh DA, Zhou X, Paschoal AR, Dimitrova N, Derevyanchuk EG, Shkurat TP, Loeb JA, Martinez I, Lipovich L. Challenges in LncRNA Biology: Views and Opinions. Noncoding RNA 2024; 10:43. [PMID: 39195572 DOI: 10.3390/ncrna10040043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Revised: 06/26/2024] [Accepted: 07/04/2024] [Indexed: 08/29/2024] Open
Abstract
This is a mini-review capturing the views and opinions of selected participants at the 2021 IEEE BIBM 3rd Annual LncRNA Workshop, held in Dubai, UAE. The views and opinions are expressed on five broad themes related to problems in lncRNA, namely, challenges in the computational analysis of lncRNAs, lncRNAs and cancer, lncRNAs in sports, lncRNAs and COVID-19, and lncRNAs in human brain activity.
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Affiliation(s)
- Donald A Adjeroh
- Lane Department of Computer Science and Electrical Engineering, West Virginia University (WVU), Morgantown, WV 26506, USA
| | - Xiaobo Zhou
- Department of Bioinformatics and Systems Medicine, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Alexandre Rossi Paschoal
- Department of Computer Science, Bioinformatics and Pattern Recognition Group, Federal University of Technology-Paraná-UTFPR, Curitiba 86300-000, Brazil
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Nadya Dimitrova
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA
| | | | - Tatiana P Shkurat
- Department of Genetics, Southern Federal University, Rostov-on-Don 344090, Russia
| | - Jeffrey A Loeb
- Department of Neurology and Rehabilitation, The Center for Clinical and Translational Science, The University of Illinois NeuroRepository, University of Illinois, Chicago, IL 60607, USA
| | - Ivan Martinez
- Department of Microbiology, Immunology & Cell Biology, WVU Cancer Institute, West Virginia University (WVU) School of Medicine, Morgantown, WV 26505, USA
| | - Leonard Lipovich
- Shenzhen Huayuan Biological Science Research Institute, Shenzhen Huayuan Biotechnology Co., Ltd., Shenzhen 518000, China
- Center for Molecular Medicine and Genetics, School of Medicine, Wayne State University, Detroit, MI 48201, USA
- College of Science, Mathematics and Technology, Wenzhou-Kean University, Wenzhou 325060, China
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3
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Mohammad T, Zolotovskaia MA, Suntsova MV, Buzdin AA. Cancer fusion transcripts with human non-coding RNAs. Front Oncol 2024; 14:1415801. [PMID: 38919532 PMCID: PMC11196610 DOI: 10.3389/fonc.2024.1415801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Accepted: 05/27/2024] [Indexed: 06/27/2024] Open
Abstract
Cancer chimeric, or fusion, transcripts are thought to most frequently appear due to chromosomal aberrations that combine moieties of unrelated normal genes. When being expressed, this results in chimeric RNAs having upstream and downstream parts relatively to the breakpoint position for the 5'- and 3'-fusion components, respectively. As many other types of cancer mutations, fusion genes can be of either driver or passenger type. The driver fusions may have pivotal roles in malignisation by regulating survival, growth, and proliferation of tumor cells, whereas the passenger fusions most likely have no specific function in cancer. The majority of research on fusion gene formation events is concentrated on identifying fusion proteins through chimeric transcripts. However, contemporary studies evidence that fusion events involving non-coding RNA (ncRNA) genes may also have strong oncogenic potential. In this review we highlight most frequent classes of ncRNAs fusions and summarize current understanding of their functional roles. In many cases, cancer ncRNA fusion can result in altered concentration of the non-coding RNA itself, or it can promote protein expression from the protein-coding fusion moiety. Differential splicing, in turn, can enrich the repertoire of cancer chimeric transcripts, e.g. as observed for the fusions of circular RNAs and long non-coding RNAs. These and other ncRNA fusions are being increasingly recognized as cancer biomarkers and even potential therapeutic targets. Finally, we discuss the use of ncRNA fusion genes in the context of cancer detection and therapy.
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Affiliation(s)
- Tharaa Mohammad
- Laboratory for Translational and Genomic Bioinformatics, Moscow Center for Advanced Studies, Moscow, Russia
- Department of Molecular Genetic Technologies, Laboratory of Bioinformatics, Endocrinology Research Center, Moscow, Russia
| | - Marianna A. Zolotovskaia
- Laboratory for Translational and Genomic Bioinformatics, Moscow Center for Advanced Studies, Moscow, Russia
- Department of Molecular Genetic Technologies, Laboratory of Bioinformatics, Endocrinology Research Center, Moscow, Russia
- I.M. Sechenov First Moscow State Medical University, Moscow, Russia
| | | | - Anton A. Buzdin
- Laboratory for Translational and Genomic Bioinformatics, Moscow Center for Advanced Studies, Moscow, Russia
- Department of Molecular Genetic Technologies, Laboratory of Bioinformatics, Endocrinology Research Center, Moscow, Russia
- I.M. Sechenov First Moscow State Medical University, Moscow, Russia
- PathoBiology Group, European Organization for Research and Treatment of Cancer (EORTC), Brussels, Belgium
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
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Westemeier-Rice ES, Winters MT, Rawson TW, Martinez I. More than the SRY: The Non-Coding Landscape of the Y Chromosome and Its Importance in Human Disease. Noncoding RNA 2024; 10:21. [PMID: 38668379 PMCID: PMC11054740 DOI: 10.3390/ncrna10020021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 03/31/2024] [Accepted: 04/08/2024] [Indexed: 04/29/2024] Open
Abstract
Historically, the Y chromosome has presented challenges to classical methodology and philosophy of understanding the differences between males and females. A genetic unsolved puzzle, the Y chromosome was the last chromosome to be fully sequenced. With the advent of the Human Genome Project came a realization that the human genome is more than just genes encoding proteins, and an entire universe of RNA was discovered. This dark matter of biology and the black box surrounding the Y chromosome have collided over the last few years, as increasing numbers of non-coding RNAs have been identified across the length of the Y chromosome, many of which have played significant roles in disease. In this review, we will uncover what is known about the connections between the Y chromosome and the non-coding RNA universe that originates from it, particularly as it relates to long non-coding RNAs, microRNAs and circular RNAs.
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Affiliation(s)
- Emily S. Westemeier-Rice
- West Virginia University Cancer Institute, West Virginia University School of Medicine, Morgantown, WV 26506, USA;
| | - Michael T. Winters
- Department of Microbiology, Immunology and Cell Biology, West Virginia University School of Medicine, Morgantown, WV 26506, USA; (M.T.W.); (T.W.R.)
| | - Travis W. Rawson
- Department of Microbiology, Immunology and Cell Biology, West Virginia University School of Medicine, Morgantown, WV 26506, USA; (M.T.W.); (T.W.R.)
| | - Ivan Martinez
- West Virginia University Cancer Institute, West Virginia University School of Medicine, Morgantown, WV 26506, USA;
- Department of Microbiology, Immunology and Cell Biology, West Virginia University School of Medicine, Morgantown, WV 26506, USA; (M.T.W.); (T.W.R.)
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Wang J, Ren H, Xu C, Yu B, Cai Y, Wang J, Ni X. Identification of m6A/m5C-related lncRNA signature for prediction of prognosis and immunotherapy efficacy in esophageal squamous cell carcinoma. Sci Rep 2024; 14:8238. [PMID: 38589454 PMCID: PMC11001862 DOI: 10.1038/s41598-024-58743-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 04/02/2024] [Indexed: 04/10/2024] Open
Abstract
N6-methyladenosine (m6A) and 5-methylcytosine (m5C) RNA modifications have garnered significant attention in the field of epigenetic research due to their close association with human cancers. This study we focus on elucidating the expression patterns of m6A/m5C-related long non-coding RNAs (lncRNAs) in esophageal squamous cell carcinoma (ESCC) and assessing their prognostic significance and therapeutic potential. Transcriptomic profiles of ESCC were derived from public resources. m6A/m5C-related lncRNAs were obtained from TCGA using Spearman's correlations analysis. The m6A/m5C-lncRNAs prognostic signature was selected to construct a RiskScore model for survival prediction, and their correlation with the immune microenvironment and immunotherapy response was analyzed. A total of 606 m6A/m5C-lncRNAs were screened, and ESCC cases in the TCGA cohort were stratified into three clusters, which showed significantly distinct in various clinical features and immune landscapes. A RiskScore model comprising ten m6A/m5C-lncRNAs prognostic signature were constructed and displayed good independent prediction ability in validation datasets. Patients in the low-RiskScore group had a better prognosis, a higher abundance of immune cells (CD4 + T cell, CD4 + naive T cell, class-switched memory B cell, and Treg), and enhanced expression of most immune checkpoint genes. Importantly, patients with low-RiskScore were more cline benefit from immune checkpoint inhibitor treatment (P < 0.05). Our findings underscore the potential of RiskScore system comprising ten m6A/m5C-related lncRNAs as effective biomarkers for predicting survival outcomes, characterizing the immune landscape, and assessing response to immunotherapy in ESCC.
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Affiliation(s)
- Jianlin Wang
- Department of Radiotherapy, The Affiliated Changzhou Second People's Hospital of Nanjing Medical University, Changzhou, 213003, Jiangsu, China
- Center for Medical Physics, Nanjing Medical University, Changzhou, 213003, Jiangsu, China
| | - Huiwen Ren
- Department of Radiotherapy, The Affiliated Changzhou Second People's Hospital of Nanjing Medical University, Changzhou, 213003, Jiangsu, China
| | - Chao Xu
- Department of Radiotherapy, Jiangyin People's Hospital, Jiangyin, 214400, Jiangsu, China
| | - Bo Yu
- Department of Radiotherapy, Jiangyin People's Hospital, Jiangyin, 214400, Jiangsu, China
| | - Yiling Cai
- Department of Radiotherapy, Jiangyin People's Hospital, Jiangyin, 214400, Jiangsu, China
| | - Jian Wang
- Department of Radiotherapy, Jiangyin People's Hospital, Jiangyin, 214400, Jiangsu, China.
| | - Xinye Ni
- Department of Radiotherapy, The Affiliated Changzhou Second People's Hospital of Nanjing Medical University, Changzhou, 213003, Jiangsu, China.
- Center for Medical Physics, Nanjing Medical University, Changzhou, 213003, Jiangsu, China.
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6
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Yarahmadi G, Tavakoli Ataabadi S, Dashti Z, Dehghanian M. A review on expression and regulatory mechanisms of miR-337-3p in cancer. J Biomol Struct Dyn 2024:1-10. [PMID: 38500239 DOI: 10.1080/07391102.2024.2329294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 03/06/2024] [Indexed: 03/20/2024]
Abstract
A group of diseases generally referred to as cancer represents a serious threat to people's health all over the world and has a significant negative influence on every aspect of the lives of patients. The development of cancer is influenced by several environmental, genetic, and epigenetic factors. MicroRNAs (miRNAs), a class of non-coding RNAs, can alter the expression of genes involved in cell proliferation, migration, metastasis, and apoptosis, lead to the pathogenesis of cancer. Additionally, several effectors modify miRNAs directly, including methylation, circular RNAs, and long non-coding RNAs (lncRNAs). In this review, we have explained the role of mir-337-3p in the pathways related to the pathogenesis of different cancers. Studying the functional role of miR-337-3p is necessary for detecting novel molecules as tumor markers and discovering novel targets for cancer treatment.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ghafour Yarahmadi
- Department of Medical Genetics, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Sadegh Tavakoli Ataabadi
- Department of Medical Genetics School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Zahra Dashti
- Department of Medical Genetics, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
- Department of Genetics, Faculty of Medicine, Shahid Sadoughi University of Medical Sciences Campus, Yazd, Iran
| | - Mehran Dehghanian
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
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7
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Peng L, Huang L, Su Q, Tian G, Chen M, Han G. LDA-VGHB: identifying potential lncRNA-disease associations with singular value decomposition, variational graph auto-encoder and heterogeneous Newton boosting machine. Brief Bioinform 2023; 25:bbad466. [PMID: 38127089 PMCID: PMC10734633 DOI: 10.1093/bib/bbad466] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 10/05/2023] [Accepted: 11/25/2023] [Indexed: 12/23/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) participate in various biological processes and have close linkages with diseases. In vivo and in vitro experiments have validated many associations between lncRNAs and diseases. However, biological experiments are time-consuming and expensive. Here, we introduce LDA-VGHB, an lncRNA-disease association (LDA) identification framework, by incorporating feature extraction based on singular value decomposition and variational graph autoencoder and LDA classification based on heterogeneous Newton boosting machine. LDA-VGHB was compared with four classical LDA prediction methods (i.e. SDLDA, LDNFSGB, IPCARF and LDASR) and four popular boosting models (XGBoost, AdaBoost, CatBoost and LightGBM) under 5-fold cross-validations on lncRNAs, diseases, lncRNA-disease pairs and independent lncRNAs and independent diseases, respectively. It greatly outperformed the other methods with its prominent performance under four different cross-validations on the lncRNADisease and MNDR databases. We further investigated potential lncRNAs for lung cancer, breast cancer, colorectal cancer and kidney neoplasms and inferred the top 20 lncRNAs associated with them among all their unobserved lncRNAs. The results showed that most of the predicted top 20 lncRNAs have been verified by biomedical experiments provided by the Lnc2Cancer 3.0, lncRNADisease v2.0 and RNADisease databases as well as publications. We found that HAR1A, KCNQ1DN, ZFAT-AS1 and HAR1B could associate with lung cancer, breast cancer, colorectal cancer and kidney neoplasms, respectively. The results need further biological experimental validation. We foresee that LDA-VGHB was capable of identifying possible lncRNAs for complex diseases. LDA-VGHB is publicly available at https://github.com/plhhnu/LDA-VGHB.
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Affiliation(s)
- Lihong Peng
- School of Computer Science, Hunan University of Technology, 412007, Hunan, China
- College of Life Sciences and Chemistry, Hunan University of Technology, 412007, Hunan, China
| | - Liangliang Huang
- School of Computer Science, Hunan University of Technology, 412007, Hunan, China
| | - Qiongli Su
- Department of Pharmacy, the Affiliated Zhuzhou Hospital Xiangya Medical College CSU, 412007, Hunan, China
| | - Geng Tian
- Geneis (Beijing) Co. Ltd, China, 100102, Beijing, China
| | - Min Chen
- School of Computer Science, Hunan Institute of Technology, 421002, No. 18 Henghua Road, Zhuhui District, Hengyang, Hunan, China
| | - Guosheng Han
- School of Mathematics and Computational Science, Xiangtan University, 411105, Yuhu District, Xiangtan, Hunan, China
- Hunan Key Laboratory for Computation and Simulation in Science and Engineering, Xiangtan University, 411105, Yuhu District, Xiangtan, Hunan, China
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Yang F, Li J, Ge Q, Zhang Y, Zhang M, Zhou J, Wang H, Du J, Gao S, Liang C, Meng J. Non-coding RNAs: emerging roles in the characterization of immune microenvironment and immunotherapy of prostate cancer. Biochem Pharmacol 2023:115669. [PMID: 37364622 DOI: 10.1016/j.bcp.2023.115669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 06/17/2023] [Accepted: 06/20/2023] [Indexed: 06/28/2023]
Abstract
Prostate cancer is the most common tumor among men. Although the prognosis for early-stage prostate cancer is good, patients with advanced disease often progress to metastatic castration-resistant prostate cancer (mCRPC), which usually leads to death owing to resistance to existing treatments and lack of long-term effective therapy. In recent years, immunotherapy, especially immune checkpoint inhibitors (ICIs), has made great progress in the treatment of various solid tumors, including prostate cancer. However, the ICIs have only shown modest outcomes in mCRPC compared with other tumors. Previous studies have suggested that the suppressive tumor immune microenvironment (TIME) of prostate cancer leads to poor anti-tumor immune response and tumor resistance to immunotherapy. It has been reported that non-coding RNAs (ncRNAs) are capable of regulating upstream signaling at the transcriptional level, leading to a "cascade of changes" in downstream molecules. As a result, ncRNAs have been identified as an ideal class of molecules for cancer treatment. The discovery of ncRNAs provides a new perspective on TIME regulation in prostate cancer. ncRNAs have been associated with establishing an immunosuppressive microenvironment in prostate cancer through multiple pathways to modulate the immune escape of tumor cells which can promote resistance of prostate cancer to immunotherapy. Targeting these related ncRNAs presents an opportunity to improve the effectiveness of immunotherapy in this patient population.
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Affiliation(s)
- Feixiang Yang
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei 230022, China.
| | - Jiawei Li
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei 230022, China
| | - Qintao Ge
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei 230022, China
| | - Yuchen Zhang
- First School of Clinical Medicine, Anhui Medical University, Hefei 230022, China.
| | - Meng Zhang
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei 230022, China
| | - Jun Zhou
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei 230022, China
| | - Haitao Wang
- Center for Cancer Research, Clinical Research/NCI/NIH, Bethesda, MD 20892, USA
| | - Juan Du
- The Second Affiliated Hospital, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, Guangdong, China.
| | - Shenglin Gao
- Department of Urology, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou 213003, Jiangsu, China; Gonghe County Hospital of Traditional Chinese Medicine, Hainan 813099, Qinghai, China
| | - Chaozhao Liang
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei 230022, China
| | - Jialin Meng
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei 230022, China.
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Recent strategies for electrochemical sensing detection of miRNAs in lung cancer. Anal Biochem 2023; 661:114986. [PMID: 36384188 DOI: 10.1016/j.ab.2022.114986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Revised: 11/10/2022] [Accepted: 11/11/2022] [Indexed: 11/15/2022]
Abstract
MicroRNAs (miRNAs) associated with lung cancer are diversifying. MiR-21, Let-7, and miR-141 are common diagnostic targets. Some new lung cancer miRNAs, such as miR-25, miR-145, and miR-126, have received increasing attention. Although various techniques are available for the analysis of lung cancer miRNAs, electrochemistry has been recognized for its high sensitivity, low cost, and rapid response. However, how to realize the signal amplification is one of the most important contents in the design of electrochemical biosensors. Herein, we mainly introduce the amplification strategy based on enzyme-free amplification and signal conversion, including non-linear HCR, catalytic hairpin assembly (CHA), electrochemiluminescence (ECL), and Faraday cage. Furthermore, new progress has emerged in the fields of nanomaterials, low oxidation potential, and simultaneous detection of multiple targets. Finally, we summarize some new challenges that electrochemical techniques may encounter in the future, such as improving single-base discrimination ability, shortening electrochemical detection time, and providing real body fluid samples assay.
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Tan J, Li X, Zhang L, Du Z. Recent advances in machine learning methods for predicting LncRNA and disease associations. Front Cell Infect Microbiol 2022; 12:1071972. [PMID: 36530425 PMCID: PMC9748103 DOI: 10.3389/fcimb.2022.1071972] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 11/11/2022] [Indexed: 12/03/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are involved in almost the entire cell life cycle through different mechanisms and play an important role in many key biological processes. Mutations and dysregulation of lncRNAs have been implicated in many complex human diseases. Therefore, identifying the relationship between lncRNAs and diseases not only contributes to biologists' understanding of disease mechanisms, but also provides new ideas and solutions for disease diagnosis, treatment, prognosis and prevention. Since the existing experimental methods for predicting lncRNA-disease associations (LDAs) are expensive and time consuming, machine learning methods for predicting lncRNA-disease associations have become increasingly popular among researchers. In this review, we summarize some of the human diseases studied by LDAs prediction models, association and similarity features of LDAs prediction, performance evaluation methods of models and some advanced machine learning prediction models of LDAs. Finally, we discuss the potential limitations of machine learning-based methods for LDAs prediction and provide some ideas for designing new prediction models.
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11
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Hu M, Ren M, Zhao Z, Cui X, Shi M, Yang Y, Guo H. Long non‑coding RNA SNHG3 promotes prostate cancer progression by sponging microRNA‑1827. Oncol Lett 2022; 24:281. [PMID: 35814830 PMCID: PMC9260729 DOI: 10.3892/ol.2022.13401] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 05/13/2021] [Indexed: 12/24/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are important biological factors that contribute to the initiation and progression of different types of cancer, including gastric, bladder and colorectal cancer. Small nucleolar RNA host gene 3 (SNHG3) has been implicated in prostate cancer (PCa) progression. However, the expression pattern and function of SNHG3 in PCa remain unclear, impeding the development of novel treatment strategies for this cancer. The present study aimed to investigate a combination of molecular and biochemical approaches to determine the role of SNHG3 in patients at different stages of disease, and elucidate the pathway by which SNHG3 affects PCa progression. A Cell Counting Kit-8 assay was used to assess cell proliferation. Transwell assays were used to analyze cell migration and invasion. Reverse transcription-quantitative PCR and western blotting were used to evaluate the expression levels of RNAs and proteins, respectively. The results demonstrated that SNHG3 expression was upregulated in PCa tissues downloaded from The Cancer Genome Atlas database, which was associated with poor prognosis. Furthermore, cell proliferation, migration and invasion were significantly inhibited following SNHG3 knockdown in vitro, the effects of which were reversed following overexpression of SNHG3 in PCa cells. Bioinformatic analysis revealed that microRNA (miRNA/miR)-1827 was a downstream target of SNHG3. The direct interaction between SNHG3 and miR-1827 was validated via the dual-luciferase reporter and RNA immunoprecipitation assays. Pearson's correlation analysis demonstrated that SNHG3 expression was negatively correlated with miR-1827 expression at different stages of PCa. Furthermore, rescue assays indicated that cotransfection with small interfering-SNHG3 and miR-1827 inhibitor reversed the effects of SNHG3 knockdown on cell proliferation, migration and invasion. In addition, SNHG3 knockdown in vivo suppressed tumor growth. Notably, lncRNA SNHG3 promoted PCa progression through miR-1827 via the Wnt/AKT/mTOR pathway. Taken together, the results of the present study suggest that SNHG3 promotes PCa progression by sponging miR-1827, indicating that SNHG3 may be a promising diagnostic and therapeutic target of PCa.
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Affiliation(s)
- Ming Hu
- Department of Urology, The Sixth Affiliated Hospital, South China University of Technology (People's Hospital of Nanhai District), Foshan, Guangdong 528200, P.R. China
| | - Mingliang Ren
- The Affiliated Nanhai Hospital, Southern Medical University (People's Hospital of Nanhai District), Foshan, Guangdong 528200, P.R. China
| | - Zhenhua Zhao
- Department of Urology, The Sixth Affiliated Hospital, South China University of Technology (People's Hospital of Nanhai District), Foshan, Guangdong 528200, P.R. China
| | - Xuejiang Cui
- Department of Urology, The Sixth Affiliated Hospital, South China University of Technology (People's Hospital of Nanhai District), Foshan, Guangdong 528200, P.R. China
| | - Ming Shi
- Department of Urology, The Sixth Affiliated Hospital, South China University of Technology (People's Hospital of Nanhai District), Foshan, Guangdong 528200, P.R. China
| | - Yunjie Yang
- Department of Urology, The Sixth Affiliated Hospital, South China University of Technology (People's Hospital of Nanhai District), Foshan, Guangdong 528200, P.R. China
| | - Haiyan Guo
- The Affiliated Nanhai Hospital, Southern Medical University (People's Hospital of Nanhai District), Foshan, Guangdong 528200, P.R. China
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12
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Jiang J, Zeng T, Zhang L, Fan X, Jin Q, Ni H, Ye Y, Cheng L, Li L, Wang L, Xu S, Yang Y, Gu J, Guo B, Wang L, Li X, Qin Y, Li J, Wang J, Chen X, Wu M, Ying QL, Qin X, Wang Y, Wang Y. Optimization of Cas9 RNA sequence to reduce its unexpected effects as a microRNA sponge. Mol Cancer 2022; 21:136. [PMID: 35751058 PMCID: PMC9229757 DOI: 10.1186/s12943-022-01604-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 06/06/2022] [Indexed: 11/28/2022] Open
Abstract
Cas9 RNA functions as a miRNA sponge. Let-7 is the dominant regulated miRNA by Cas9 RNA. RNA sequence optimization of Cas9 by synonymous mutation improves its safety.
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Affiliation(s)
- Junfeng Jiang
- Histology and Embryology Department, Naval Medical University, Shanghai, 200433, China.,Research Center of Developmental Biology, Shanghai Key Laboratory of Cell Engineering, Naval Medical University, 800 Xiangyin Road, Shanghai, 200433, China
| | - Tao Zeng
- Histology and Embryology Department, Naval Medical University, Shanghai, 200433, China.,Research Center of Developmental Biology, Shanghai Key Laboratory of Cell Engineering, Naval Medical University, 800 Xiangyin Road, Shanghai, 200433, China.,The 901th Hospital of PLA Jiont Logistic Support Force, HeFei, 230031, China
| | - Li Zhang
- Department of Pathology, Faculty of Medical Imaging, Naval Medical University, Shanghai, 200433, China
| | - Xingfei Fan
- Histology and Embryology Department, Naval Medical University, Shanghai, 200433, China.,Research Center of Developmental Biology, Shanghai Key Laboratory of Cell Engineering, Naval Medical University, 800 Xiangyin Road, Shanghai, 200433, China
| | - Qishu Jin
- Department of Histology and Embryology, Harbin Medical University, Harbin, 150086, China
| | - Haitao Ni
- Histology and Embryology Department, Naval Medical University, Shanghai, 200433, China
| | - Yusheng Ye
- Histology and Embryology Department, Naval Medical University, Shanghai, 200433, China
| | - Lipeng Cheng
- Histology and Embryology Department, Naval Medical University, Shanghai, 200433, China
| | - Li Li
- Histology and Embryology Department, Naval Medical University, Shanghai, 200433, China
| | - Liujun Wang
- Histology and Embryology Department, Naval Medical University, Shanghai, 200433, China
| | - Sha Xu
- Histology and Embryology Department, Naval Medical University, Shanghai, 200433, China
| | - Yu Yang
- Histology and Embryology Department, Naval Medical University, Shanghai, 200433, China
| | - Juan Gu
- Histology and Embryology Department, Naval Medical University, Shanghai, 200433, China
| | - Bing Guo
- Department of Oral & Maxillofacial - Head & Neck Oncology, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China.,National Clinical Research Center for Oral Diseases, Shanghai, 200011, China.,Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Key Laboratory of Stomatology, 639 Zhi Zao Ju Road, Shanghai, 200011, China
| | - Lei Wang
- Department of Oral & Maxillofacial - Head & Neck Oncology, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China.,National Clinical Research Center for Oral Diseases, Shanghai, 200011, China.,Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Key Laboratory of Stomatology, 639 Zhi Zao Ju Road, Shanghai, 200011, China
| | - Xin Li
- Department of Oral & Maxillofacial - Head & Neck Oncology, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China.,National Clinical Research Center for Oral Diseases, Shanghai, 200011, China.,Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Key Laboratory of Stomatology, 639 Zhi Zao Ju Road, Shanghai, 200011, China
| | - Yingyi Qin
- Department of health statistics, Naval Medical University, Shanghai, 200433, China
| | - Jiaxi Li
- Department of Oncology, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200336, China
| | - Jinjiang Wang
- Department of Oncology, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200336, China
| | - Xi Chen
- Department of Cell and Neurobiology, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research at USC, Keck School of Medicine, University of Southern California, Los Angeles, California, 90033, USA
| | - Minjuan Wu
- Histology and Embryology Department, Naval Medical University, Shanghai, 200433, China
| | - Qi-Long Ying
- Department of Cell and Neurobiology, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research at USC, Keck School of Medicine, University of Southern California, Los Angeles, California, 90033, USA.
| | - Xingjun Qin
- Department of Oral & Maxillofacial - Head & Neck Oncology, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China. .,National Clinical Research Center for Oral Diseases, Shanghai, 200011, China. .,Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Key Laboratory of Stomatology, 639 Zhi Zao Ju Road, Shanghai, 200011, China.
| | - Yefei Wang
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China. .,Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200011, China.
| | - Yue Wang
- Histology and Embryology Department, Naval Medical University, Shanghai, 200433, China. .,Research Center of Developmental Biology, Shanghai Key Laboratory of Cell Engineering, Naval Medical University, 800 Xiangyin Road, Shanghai, 200433, China.
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13
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Wang H, Yang H, Chang M, Sun F, Qi H, Li X. Long non-coding RNA TTTY15 sponges miR-520a-3p to exacerbate neural apoptosis induced by cerebral ischemia/reperfusion via targeting IRF9 in vivo and in vitro. Biomed J 2022; 46:100530. [PMID: 35439640 DOI: 10.1016/j.bj.2022.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 03/17/2022] [Accepted: 04/07/2022] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Studies have proven that as competing endogenous RNAs (ceRNAs), long non-coding RNAs (lncRNAs) play vital roles in regulating RNA transcripts in ischemic stroke. It has been reported that TTTY15, a lncRNA, is dysregulated in cardiomyocytes after ischemic injury. We intended to explore the potential regulating mechanism of TTTY15 in ischemic stroke. METHODS TTTY15 and miR-520a-3p levels in vivo were measured in the cerebral ischemia/reperfusion (I/R) model. Cell apoptosis was measured by flow cytometry. To manifest TTTY15 functions in I/R injury, Neuro 2a (N2a) cells were exposed to oxygen-glucose deprivation/reoxygenation (OGD/R) and treated with si-NC, pcDNA3.1-NC, si-TTTY15 or pcDNA3.1-TTTY15. RESULTS TTTY15 expression was elevated and miR-520a-3p expression was declined in mouse brains exposed to I/R and in N2a cells exposed to OGD/R. Bioinformatics analyses predicted the binding sites of miR-520a-3p in the 3'-UTRs of interferon regulatory factor 9 (IRF9) and TTTY15. Luciferase reporter assay exhibited that TTTY15 bound to miR-520a-3p directly and IRF9 was targeted by miR-520a-3p. MiR-520a-3p overexpression diminished N2a cell apoptosis caused by OGD/R. TTTY15 overexpression antagonized the inhibitory impacts of miR-520a-3p on IRF9 expression and apoptosis after OGD/R, while TTTY15 knockdown enhanced the inhibitory impacts of miR-520a-3p. Additionally, TTTY15 knockdown alleviated brain damages and neurological deficits induced by I/R in vivo. Our results revealed that TTTY15 modulated IRF9 via acting as a ceRNA for miR-520a-3p. CONCLUSION The study revealed the roles of TTTY15/miR-520a-3p/IRF9 signaling pathway in regulating cerebral ischemia/reperfusion injury.
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Affiliation(s)
- Huan Wang
- Department of Neurology, The Fourth Affiliated Hospital, Harbin Medical University, Harbin City, Heilongjiang Province, PR China
| | - Hui Yang
- Department of Neurology, The Fourth Affiliated Hospital, Harbin Medical University, Harbin City, Heilongjiang Province, PR China
| | - Mingxiu Chang
- Department of Neurology, The Fourth Affiliated Hospital, Harbin Medical University, Harbin City, Heilongjiang Province, PR China
| | - Feifei Sun
- Department of Neurology, The Fourth Affiliated Hospital, Harbin Medical University, Harbin City, Heilongjiang Province, PR China
| | - Huiping Qi
- Department of Neurology, The Fourth Affiliated Hospital, Harbin Medical University, Harbin City, Heilongjiang Province, PR China
| | - Xuling Li
- Department of Neurology, The Fourth Affiliated Hospital, Harbin Medical University, Harbin City, Heilongjiang Province, PR China.
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14
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Zheng X, Peng B, Wu X, Ye J, Zhao H, Li Y, Chen R, Gong X, Zhang H, Guo X. Male-specific long non-coding RNA testis-specific transcript, Y-linked 15 promotes gastric cancer cell growth by regulating Wnt family member 1/β-catenin signaling by sponging microRNA let-7a-5p. Bioengineered 2022; 13:8605-8616. [PMID: 35287556 PMCID: PMC9161946 DOI: 10.1080/21655979.2022.2053814] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The present study is aimed to investigate the regulatory effects and related mechanism of long non-coding RNA testis-specific transcript, Y-linked 15 (TTTY15) in gastric carcinoma (GC) cell proliferation, migration, invasion, apoptosis and epithelial–mesenchymal transition (EMT). TTTY15 expression in GC tissue samples and cells was detected by quantitative real-time PCR (qRT-PCR), and the correlation between TTTY15 expression and GC clinicopathological indicators was analyzed. Cell counting kit-8 (CCK-8), BrdU, flow cytometry and Transwell assays were performed for detecting GC cell proliferation, migration, invasion and apoptosis. Western blot was performed for detecting the expressions of EMT-associated proteins (N-cadherin and E-cadherin), Wnt family member 1 (Wnt1) protein and β-catenin protein. Bioinformatics analysis was conducted to predict, and RNA immunoprecipitation (RIP) assay and dual-luciferase reporter gene assay were performed to verify the targeted relationships of microRNA let-7a-5p (let-7a-5p) with TTTY15 and Wnt1 mRNA 3'UTR. It was found that TTTY15 expression was significantly up-regulated in GC tissues and cells, and was associated with advanced TNM stage and poor tumor differentiation. TTTY15 overexpression promoted GC cell proliferation, migration and invasion, the expressions of N-cadherin, Wnt1 and β-catenin protein, and inhibited the apoptosis and E-cadherin expression, while knocking down TTTY15 had the opposite effects. TTTY15 directly targeted let-7a-5p and negatively regulated its expression. Wnt1 was the target gene of let-7a-5p, and TTTY15 could indirectly and positively regulate Wnt1 expression. In conclusion, TTTY15 promotes GC progression, by regulating the let-7a-5p/Wnt1 axis to activate the Wnt/β-catenin pathway.
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Affiliation(s)
- XiaoYing Zheng
- Department of Pathology, Affiliated Hospital of Qinghai University, Xining 810001, Qinghai, China
| | - BingJun Peng
- Department of Medical Imaging Center, Affiliated Hospital of Qinghai University, Xining 810001, Qinghai, China
| | - XinChun Wu
- Fourth Department of Internal Medicine, Qianxi County People's Hospital, Tangshan 063000, Hebei, China
| | - JunLing Ye
- Department of Pathology, Affiliated Hospital of Qinghai University, Xining 810001, Qinghai, China
| | - HaiYun Zhao
- Department of Pathology, Menyuan Hui Autonomous County traditional Chinese Medicine Hospital, Qinghai, China
| | - YanJun Li
- Department of Pathology, Affiliated Hospital of Qinghai University, Xining 810001, Qinghai, China
| | - RuiHui Chen
- Department of Pathology, Affiliated Hospital of Qinghai University, Xining 810001, Qinghai, China
| | - Xue Gong
- Department of Pathology, Affiliated Hospital of Qinghai University, Xining 810001, Qinghai, China
| | - HaiYan Zhang
- Department of Pathology, Affiliated Hospital of Qinghai University, Xining 810001, Qinghai, China
| | - XinJian Guo
- Department of Pathology, Affiliated Hospital of Qinghai University, Xining 810001, Qinghai, China
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15
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Wen X, Han W, Liu C. Long non-coding RNA TTTY15 silencing inhibits gastric cancer progression by sponging microRNA-98-5p to down-regulate cyclin D2 expression. Bioengineered 2022; 13:7380-7391. [PMID: 35266852 PMCID: PMC9208520 DOI: 10.1080/21655979.2022.2047398] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
Gastric cancer is the most common malignant tumor in the digestive system. However, the detection rate of early gastric cancer is low, resulting in delayed prognosis and poor outcomes. The identification of effective therapeutic targets for gastric cancer is, therefore, of profound significance. Recently, various lncRNAs have been shown to be biomarkers for different cancers. This study investigated the role of long non-coding RNA (lncRNA) TTTY15 in gastric cancer. The expression level of TTTY15, miR-98-5p, and cyclin D2 (CCND2) were evaluated by quantitative reverse transcription polymerase chain reaction (qRT-PCR) and Western blot assay using tumor and non-tumor tissues collected from 30 patients with gastric cancer, gastric cancer cell lines (AGS, SNU-5, and NCI-N87), and the normal gastric epithelial cell line GES-1. The interaction between TTTY15 and miR-98-5p and between miR-98-5p and CCND2 were predicted by bioinformatics and then further verified by dual-luciferase and RNA pull-down analyses. Cell proliferation was evaluated by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-2 H-tetrazolium bromide (MTT) assay, and apoptosis was measured using flow cytometry and caspase-3 assay. The results indicate that TTTY15 and CCND2 expression increased and miR-98-5p expression decreased in gastric cancer tumor tissues and cell lines. TTTY15 knockdown inhibited gastric cancer cell proliferation but promoted apoptosis by sponging miR-98-5p, which acted as a tumor suppressor gene by reducing the expression of its target gene CCND2 in gastric cancer. In conclusion, lncRNA TTTY15 is a potential oncogene involved in gastric cancer and may be a novel therapeutic target for gastric cancer treatment.
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Affiliation(s)
- Xigang Wen
- Department of Gastrointestinal Surgery, The Third People's Hospital of Hubei Province, Wuhan, China
| | - Wenling Han
- Department of Hospital Infection Office, The Third People's Hospital of Hubei Province, Wuhan, China
| | - Chao Liu
- Department of Gastrointestinal Surgery, The Third People's Hospital of Hubei Province, Wuhan, China
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16
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Crosstalk between Long Non Coding RNAs, microRNAs and DNA Damage Repair in Prostate Cancer: New Therapeutic Opportunities? Cancers (Basel) 2022; 14:cancers14030755. [PMID: 35159022 PMCID: PMC8834032 DOI: 10.3390/cancers14030755] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/20/2022] [Accepted: 01/21/2022] [Indexed: 02/04/2023] Open
Abstract
Simple Summary Non-coding RNAs are a type of genetic material that doesn’t make protein, but performs diverse regulatory functions. In prostate cancer, most treatments target proteins, and resistance to such therapies is common, leading to disease progression. Targeting non-coding RNAs may provide alterative treatment options and potentially overcome drug resistance. Major types of non-coding RNAs include tiny ‘microRNAs’ and much longer ‘long non-coding RNAs’. Scientific studies have shown that these form a major part of the human genome, and play key roles in altering gene activity and determining the fate of cells. Importantly, in cancer, their activity is altered. Recent evidence suggests that microRNAs and long non-coding RNAs play important roles in controlling response to DNA damage. In this review, we explore how different types of non-coding RNA interact to control cell DNA damage responses, and how this knowledge may be used to design better prostate cancer treatments and tests. Abstract It is increasingly appreciated that transcripts derived from non-coding parts of the human genome, such as long non-coding RNAs (lncRNAs) and microRNAs (miRNAs), are key regulators of biological processes both in normal physiology and disease. Their dysregulation during tumourigenesis has attracted significant interest in their exploitation as novel cancer therapeutics. Prostate cancer (PCa), as one of the most diagnosed malignancies and a leading cause of cancer-related death in men, continues to pose a major public health problem. In particular, survival of men with metastatic disease is very poor. Defects in DNA damage response (DDR) pathways culminate in genomic instability in PCa, which is associated with aggressive disease and poor patient outcome. Treatment options for metastatic PCa remain limited. Thus, researchers are increasingly targeting ncRNAs and DDR pathways to develop new biomarkers and therapeutics for PCa. Increasing evidence points to a widespread and biologically-relevant regulatory network of interactions between lncRNAs and miRNAs, with implications for major biological and pathological processes. This review summarises the current state of knowledge surrounding the roles of the lncRNA:miRNA interactions in PCa DDR, and their emerging potential as predictive and diagnostic biomarkers. We also discuss their therapeutic promise for the clinical management of PCa.
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17
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Yao L, Man CF, He R, He L, Huang JB, Xiang SY, Dai Z, Wang XY, Fan Y. The Interaction Between N 6-Methyladenosine Modification and Non-Coding RNAs in Gastrointestinal Tract Cancers. Front Oncol 2022; 11:784127. [PMID: 35070987 PMCID: PMC8776638 DOI: 10.3389/fonc.2021.784127] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 12/15/2021] [Indexed: 12/13/2022] Open
Abstract
N6-methyladenosine (m6A) is the most common epigenetic modification of eukaryotic RNA, which can participate in the growth and development of the body and a variety of physiological and disease processes by affecting the splicing, processing, localization, transport, translation, and degradation of RNA. Increasing evidence shows that non-coding RNAs, particularly microRNA, long non-coding RNA, and circular RNA, can also regulate the RNA m6A modification process by affecting the expression of m6A-related enzymes. The interaction between m6A modification and non-coding RNAs provides a new perspective for the exploration of the potential mechanism of tumor genesis and development. In this review, we summarize the potential mechanisms and effects of m6A and non-coding RNAs in gastrointestinal tract cancers.
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Affiliation(s)
- Lin Yao
- Cancer Institute, The Affiliated People's Hospital of Jiangsu University, Zhenjiang, China
| | - Chang-Feng Man
- Cancer Institute, The Affiliated People's Hospital of Jiangsu University, Zhenjiang, China
| | - Rong He
- Cancer Institute, The Affiliated People's Hospital of Jiangsu University, Zhenjiang, China
| | - Lian He
- Cancer Institute, The Affiliated People's Hospital of Jiangsu University, Zhenjiang, China
| | - Jia-Bin Huang
- Cancer Institute, The Affiliated People's Hospital of Jiangsu University, Zhenjiang, China
| | - Shou-Yan Xiang
- Cancer Institute, The Affiliated People's Hospital of Jiangsu University, Zhenjiang, China
| | - Zhe Dai
- Cancer Institute, The Affiliated People's Hospital of Jiangsu University, Zhenjiang, China
| | - Xiao-Yan Wang
- Digestive Department, The Affiliated Suqian first People's Hospital of Nanjing Medical University, Suqian, China
| | - Yu Fan
- Cancer Institute, The Affiliated People's Hospital of Jiangsu University, Zhenjiang, China
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18
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Heydari R, Jangravi Z, Maleknia S, Seresht-Ahmadi M, Bahari Z, Salekdeh GH, Meyfour A. Y chromosome is moving out of sex determination shadow. Cell Biosci 2022; 12:4. [PMID: 34983649 PMCID: PMC8724748 DOI: 10.1186/s13578-021-00741-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 12/21/2021] [Indexed: 01/05/2023] Open
Abstract
Although sex hormones play a key role in sex differences in susceptibility, severity, outcomes, and response to therapy of different diseases, sex chromosomes are also increasingly recognized as an important factor. Studies demonstrated that the Y chromosome is not a 'genetic wasteland' and can be a useful genetic marker for interpreting various male-specific physiological and pathophysiological characteristics. Y chromosome harbors male‑specific genes, which either solely or in cooperation with their X-counterpart, and independent or in conjunction with sex hormones have a considerable impact on basic physiology and disease mechanisms in most or all tissues development. Furthermore, loss of Y chromosome and/or aberrant expression of Y chromosome genes cause sex differences in disease mechanisms. With the launch of the human proteome project (HPP), the association of Y chromosome proteins with pathological conditions has been increasingly explored. In this review, the involvement of Y chromosome genes in male-specific diseases such as prostate cancer and the cases that are more prevalent in men, such as cardiovascular disease, neurological disease, and cancers, has been highlighted. Understanding the molecular mechanisms underlying Y chromosome-related diseases can have a significant impact on the prevention, diagnosis, and treatment of diseases.
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Affiliation(s)
- Raheleh Heydari
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Zohreh Jangravi
- Department of Biochemistry, Faculty of Medicine, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Samaneh Maleknia
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mehrshad Seresht-Ahmadi
- Department of Basic Science and Advanced Technologies in Biology, University of Science and Culture, Tehran, Iran
| | - Zahra Bahari
- Department of Physiology and Medical Physics, Faculty of Medicine, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | | | - Anna Meyfour
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran.
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19
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Liang X, Li X, Wang P, Chen Z, Yan Z, Ao X, Liu Y, Zhu J, Xi T, Zhou S, Li Z, Li C, Zhu M, Zhou PK, Gu Y. OUP accepted manuscript. Toxicol Res (Camb) 2022; 11:348-360. [PMID: 35510230 PMCID: PMC9052326 DOI: 10.1093/toxres/tfac008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 02/17/2022] [Accepted: 02/23/2022] [Indexed: 11/14/2022] Open
Abstract
Radioresistance is one of the key obstacles that may lead to the failure of cancer treatment. The underlying mechanisms of radioresistance remain largely unknown; however, increasing evidence has shown that long noncoding RNAs (lncRNAs) are involved in radiotherapy resistance of several cancers. In the present study, we demonstrated that radiation-elevated transcript (RET), a newly identified lnRNA, was highly expressed in cancer cells. Knockdown of RET significantly inhibited the proliferation and colony formation of cancer cells and markedly inhibited apoptosis. Furthermore, downregulation of RET in cancer cells significantly inhibited cell growth, decreased colony survival fractions, and promoted apoptosis in response to radiation treatment, indicating a role in radiation resistance. Moreover, RET knockdown significantly increased the expression of γ-H2AX, an indicator of DNA double strand damage, and reversed radiation-induced EMT, both of which contributed to its radiation resistance. In addition, a negative correlation was found between the expression of RET and PTEN. Rescue assays confirmed RET knockdown enhanced radiosensitivity of cancer cells by upregulating the expression of PTEN. Mechanistically, RET positively regulated Slug, a repressor of PTEN transcription, by acting as a molecular sponge of miR-3179. Our present study showed that RET conferred radioresistance by regulating miR-3179/Slug/PTEN axis, indicating that RET may be a potential target for the clinical application in cancer patients with radioresistance.
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Affiliation(s)
| | | | | | - Zhongmin Chen
- PLA Rocket Force Characteristic Medical Center, Beijing 100088, China
| | - Ziyan Yan
- Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, AMMS, Beijing 100850, China
| | - Xingkun Ao
- Hengyang Medical College, University of South China, Hengyang, Hunan 421001, China
- Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, AMMS, Beijing 100850, China
| | - Yuhao Liu
- Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, AMMS, Beijing 100850, China
| | - Jiaojiao Zhu
- Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, AMMS, Beijing 100850, China
| | - Tingting Xi
- Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, AMMS, Beijing 100850, China
| | - Shenghui Zhou
- Hengyang Medical College, University of South China, Hengyang, Hunan 421001, China
- Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, AMMS, Beijing 100850, China
| | - Zhongqiu Li
- Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, AMMS, Beijing 100850, China
- Medical School, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Chao Li
- Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, AMMS, Beijing 100850, China
- School of Life Science, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Maoxiang Zhu
- Corresponding authors: Yongqing Gu. , ; Ping-Kun Zhou. ; Maoxiang Zhu.
| | - Ping-Kun Zhou
- Corresponding authors: Yongqing Gu. , ; Ping-Kun Zhou. ; Maoxiang Zhu.
| | - Yongqing Gu
- Corresponding authors: Yongqing Gu. , ; Ping-Kun Zhou. ; Maoxiang Zhu.
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21
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Hu CY, Wu KY, Lin TY, Chen CC. The Crosstalk of Long Non-Coding RNA and MicroRNA in Castration-Resistant and Neuroendocrine Prostate Cancer: Their Interaction and Clinical Importance. Int J Mol Sci 2021; 23:ijms23010392. [PMID: 35008817 PMCID: PMC8745162 DOI: 10.3390/ijms23010392] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 12/02/2021] [Accepted: 12/28/2021] [Indexed: 12/18/2022] Open
Abstract
Prostate cancer is featured by its heterogeneous nature, which indicates a different prognosis. Castration-resistant prostate cancer (CRPC) is a hallmark of the treatment-refractory stage, and the median survival of patients is only within two years. Neuroendocrine prostate cancer (NEPC) is an aggressive variant that arises from de novo presentation of small cell carcinoma or treatment-related transformation with a median survival of 1–2 years from the time of diagnosis. The epigenetic regulators, such as long non-coding RNAs (lncRNAs) and microRNAs (miRNAs), have been proven involved in multiple pathologic mechanisms of CRPC and NEPC. LncRNAs can act as competing endogenous RNAs to sponge miRNAs that would inhibit the expression of their targets. After that, miRNAs interact with the 3’ untranslated region (UTR) of target mRNAs to repress the step of translation. These interactions may modulate gene expression and influence cancer development and progression. Otherwise, epigenetic regulators and genetic mutation also promote neuroendocrine differentiation and cancer stem-like cell formation. This step may induce neuroendocrine prostate cancer development. This review aims to provide an integrated, synthesized overview under current evidence to elucidate the crosstalk of lncRNAs with miRNAs and their influence on castration resistance or neuroendocrine differentiation of prostate cancer. Notably, we also discuss the mechanisms of lncRNA–miRNA interaction in androgen receptor-independent prostate cancer, such as growth factors, oncogenic signaling pathways, cell cycle dysregulation, and cytokines or other transmembrane proteins. Conclusively, we underscore the potential of these communications as potential therapeutic targets in the future.
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Affiliation(s)
- Che-Yuan Hu
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan 704, Taiwan;
- Department of Urology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 704, Taiwan;
| | - Kuan-Yu Wu
- Department of Urology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 704, Taiwan;
| | - Tsung-Yen Lin
- Department of Urology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 704, Taiwan;
- Division of Urology, Department of Surgery, Dou-Liou Branch, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Yunlin 640, Taiwan
- Correspondence: (T.-Y.L.); (C.-C.C.); Tel.: +886-6235-3535 (ext. 5251) (T.-Y.L.); +886-5276-5041 (ext. 7521) (C.-C.C.)
| | - Chien-Chin Chen
- Department of Pathology, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chiayi 600, Taiwan
- Department of Cosmetic Science, Chia Nan University of Pharmacy and Science, Tainan 717, Taiwan
- Correspondence: (T.-Y.L.); (C.-C.C.); Tel.: +886-6235-3535 (ext. 5251) (T.-Y.L.); +886-5276-5041 (ext. 7521) (C.-C.C.)
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22
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Slabáková E, Kahounová Z, Procházková J, Souček K. Regulation of Neuroendocrine-like Differentiation in Prostate Cancer by Non-Coding RNAs. Noncoding RNA 2021; 7:ncrna7040075. [PMID: 34940756 PMCID: PMC8704250 DOI: 10.3390/ncrna7040075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 11/18/2021] [Accepted: 11/29/2021] [Indexed: 12/21/2022] Open
Abstract
Neuroendocrine prostate cancer (NEPC) represents a variant of prostate cancer that occurs in response to treatment resistance or, to a much lesser extent, de novo. Unravelling the molecular mechanisms behind transdifferentiation of cancer cells to neuroendocrine-like cancer cells is essential for development of new treatment opportunities. This review focuses on summarizing the role of small molecules, predominantly microRNAs, in this phenomenon. A published literature search was performed to identify microRNAs, which are reported and experimentally validated to modulate neuroendocrine markers and/or regulators and to affect the complex neuroendocrine phenotype. Next, available patients’ expression datasets were surveyed to identify deregulated microRNAs, and their effect on NEPC and prostate cancer progression is summarized. Finally, possibilities of miRNA detection and quantification in body fluids of prostate cancer patients and their possible use as liquid biopsy in prostate cancer monitoring are discussed. All the addressed clinical and experimental contexts point to an association of NEPC with upregulation of miR-375 and downregulation of miR-34a and miR-19b-3p. Together, this review provides an overview of different roles of non-coding RNAs in the emergence of neuroendocrine prostate cancer.
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23
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Maier MC, McInerney MRA, Graves JAM, Charchar FJ. Noncoding Genes on Sex Chromosomes and Their Function in Sex Determination, Dosage Compensation, Male Traits, and Diseases. Sex Dev 2021; 15:432-440. [PMID: 34794153 DOI: 10.1159/000519622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 09/13/2021] [Indexed: 11/19/2022] Open
Abstract
The mammalian Y chromosome has evolved in many species into a specialized chromosome that contributes to sex development among other male phenotypes. This function is well studied in terms of protein-coding genes. Less is known about the noncoding genome on the Y chromosome and its contribution to both sex development and other traits. Once considered junk genetic material, noncoding RNAs are now known to contribute to the regulation of gene expression and to play an important role in refining cellular functions. The prime examples are noncoding genes on the X chromosome, which mitigate the differential dosage of genes on sex chromosomes. Here, we discuss the evolution of noncoding RNAs on the Y chromosome and the emerging evidence of how micro, long, and circular noncoding RNAs transcribed from the Y chromosome contribute to sex differentiation. We briefly touch on emerging evidence that these noncoding RNAs also contribute to some other important clinical phenotypes in humans.
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Affiliation(s)
- Michelle C Maier
- Health Innovation & Transformation Centre, Federation University, Mt Helen, Victoria, Australia.,School of Science, Psychology and Sport, Federation University Australia, Ballarat, Victoria, Australia
| | - Molly-Rose A McInerney
- Health Innovation & Transformation Centre, Federation University, Mt Helen, Victoria, Australia.,School of Science, Psychology and Sport, Federation University Australia, Ballarat, Victoria, Australia
| | | | - Fadi J Charchar
- Health Innovation & Transformation Centre, Federation University, Mt Helen, Victoria, Australia.,Department of Cardiovascular Sciences, University of Leicester, Leicester, United Kingdom.,Department of Anatomy and Physiology, University of Melbourne, Melbourne, Victoria, Australia
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24
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Long noncoding RNA TTTY15 promotes growth and metastasis of esophageal squamous cell carcinoma by sponging microRNA-337-3p to upregulate the expression of JAK2. Anticancer Drugs 2021; 31:1038-1045. [PMID: 32868648 DOI: 10.1097/cad.0000000000000960] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Long noncoding RNA (lncRNA) testis-specific transcript, Y-linked 15 (TTTY15) plays an important regulatory role in prostate cancer, but its role in esophageal squamous cell carcinoma (ESCC) remains unclear. This study aimed to explore the expression pattern, biological function and underlying mechanism of TTTY15 in ESCC. Quantitative real-time PCR (qRT-PCR) was used to detect the expression of TTTY15 and microRNA (miR)-337-3p in ESCC tissues and cell lines. Cell counting kit-8 method was used to detect the proliferation of ESCC cells. Transwell method was used to determine the migration and invasion of ESCC cells. Luciferase reporter assay was used to verify the interaction between TTTY15 and miR-337-3p. Western blot was used to analyze the effects of TTTY15 and miR-337-3p on Janus kinase 2 (JAK2) expression. In the present study, we demonstrated that the expression level of TTTY15 was significantly upregulated in ESCC tissues, while the expression of miR-337-3p was downregulated. In ESCC samples, the expression levels of TTTY15 and miR-337-3p were negatively correlated. TTTY15 knockdown could significantly reduce the proliferation, migration and invasion of ESCC cells, and miR-337-3p mimics had similar effects. In addition, overexpression of TTTY15 inhibited miR-337-3p by binding with it. TTTY15 could indirectly modulate JAK2, and overexpression of TTTY15 could reverse the inhibitory effects of miR-337-3p on malignant phenotypes of ESCC cells. In conclusion, TTTY15 plays an oncogenic role in ESCC by targeting miR-337-3p/JAK2 axis.
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25
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Singh N. Role of mammalian long non-coding RNAs in normal and neuro oncological disorders. Genomics 2021; 113:3250-3273. [PMID: 34302945 DOI: 10.1016/j.ygeno.2021.07.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 07/10/2021] [Accepted: 07/14/2021] [Indexed: 12/09/2022]
Abstract
Long non-coding RNAs (lncRNAs) are expressed at lower levels than protein-coding genes but have a crucial role in gene regulation. LncRNA is distinct, they are being transcribed using RNA polymerase II, and their functionality depends on subcellular localization. Depending on their niche, they specifically interact with DNA, RNA, and proteins and modify chromatin function, regulate transcription at various stages, forms nuclear condensation bodies and nucleolar organization. lncRNAs may also change the stability and translation of cytoplasmic mRNAs and hamper signaling pathways. Thus, lncRNAs affect the physio-pathological states and lead to the development of various disorders, immune responses, and cancer. To date, ~40% of lncRNAs have been reported in the nervous system (NS) and are involved in the early development/differentiation of the NS to synaptogenesis. LncRNA expression patterns in the most common adult and pediatric tumor suggest them as potential biomarkers and provide a rationale for targeting them pharmaceutically. Here, we discuss the mechanisms of lncRNA synthesis, localization, and functions in transcriptional, post-transcriptional, and other forms of gene regulation, methods of lncRNA identification, and their potential therapeutic applications in neuro oncological disorders as explained by molecular mechanisms in other malignant disorders.
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Affiliation(s)
- Neetu Singh
- Molecular Biology Unit, Department of Centre for Advance Research, King George's Medical University, Lucknow, Uttar Pradesh 226 003, India.
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26
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Lei F, Lei T, Huang Y, Yang M, Liao M, Huang W. Radio-Susceptibility of Nasopharyngeal Carcinoma: Focus on Epstein- Barr Virus, MicroRNAs, Long Non-Coding RNAs and Circular RNAs. Curr Mol Pharmacol 2021; 13:192-205. [PMID: 31880267 DOI: 10.2174/1874467213666191227104646] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 11/22/2019] [Accepted: 12/29/2019] [Indexed: 02/07/2023]
Abstract
Nasopharyngeal carcinoma (NPC) is a type of head and neck cancer. As a neoplastic disorder, NPC is a highly malignant squamous cell carcinoma that is derived from the nasopharyngeal epithelium. NPC is radiosensitive; radiotherapy or radiotherapy combining with chemotherapy are the main treatment strategies. However, both modalities are usually accompanied by complications and acquired resistance to radiotherapy is a significant impediment to effective NPC therapy. Therefore, there is an urgent need to discover effective radio-sensitization and radio-resistance biomarkers for NPC. Recent studies have shown that Epstein-Barr virus (EBV)-encoded products, microRNAs (miRNAs), long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs), which share several common signaling pathways, can function in radio-related NPC cells or tissues. Understanding these interconnected regulatory networks will reveal the details of NPC radiation sensitivity and resistance. In this review, we discuss and summarize the specific molecular mechanisms of NPC radio-sensitization and radio-resistance, focusing on EBV-encoded products, miRNAs, lncRNAs and circRNAs. This will provide a foundation for the discovery of more accurate, effective and specific markers related to NPC radiotherapy. EBVencoded products, miRNAs, lncRNAs and circRNAs have emerged as crucial molecules mediating the radio-susceptibility of NPC. This understanding will improve the clinical application of markers and inform the development of novel therapeutics for NPC.
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Affiliation(s)
- Fanghong Lei
- Cancer Research Institute, Hengyang Medical College of University of South China; Hunan Province Key Laboratory of Tumor Cellular & Molecular Pathology (2016TP1015), Hengyang 421001, Hunan Province, China
| | - Tongda Lei
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Yun Huang
- Cancer Research Institute, Hengyang Medical College of University of South China; Hunan Province Key Laboratory of Tumor Cellular & Molecular Pathology (2016TP1015), Hengyang 421001, Hunan Province, China
| | - Mingxiu Yang
- Cancer Research Institute, Hengyang Medical College of University of South China; Hunan Province Key Laboratory of Tumor Cellular & Molecular Pathology (2016TP1015), Hengyang 421001, Hunan Province, China
| | - Mingchu Liao
- Department of Oncology, The First Affiliated Hospital of University of South China, Hengyang 421001, Hunan Province, China
| | - Weiguo Huang
- Cancer Research Institute, Hengyang Medical College of University of South China; Hunan Province Key Laboratory of Tumor Cellular & Molecular Pathology (2016TP1015), Hengyang 421001, Hunan Province, China
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27
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Zhao S, Guan B, Mi Y, Shi D, Wei P, Gu Y, Cai S, Xu Y, Li X, Yan D, Huang M, Li D. LncRNA MIR17HG promotes colorectal cancer liver metastasis by mediating a glycolysis-associated positive feedback circuit. Oncogene 2021; 40:4709-4724. [PMID: 34145399 PMCID: PMC8282501 DOI: 10.1038/s41388-021-01859-6] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 05/12/2021] [Accepted: 05/24/2021] [Indexed: 02/07/2023]
Abstract
Glycolysis plays a crucial role in reprogramming the metastatic tumor microenvironment. A series of lncRNAs have been identified to function as oncogenic molecules by regulating glycolysis. However, the roles of glycolysis-related lncRNAs in regulating colorectal cancer liver metastasis (CRLM) remain poorly understood. In the present study, the expression of the glycolysis-related lncRNA MIR17HG gradually increased from adjacent normal to CRC to the paired liver metastatic tissues, and high MIR17HG expression predicted poor survival, especially in patients with liver metastasis. Functionally, MIR17HG promoted glycolysis in CRC cells and enhanced their invasion and liver metastasis in vitro and in vivo. Mechanistically, MIR17HG functioned as a ceRNA to regulate HK1 expression by sponging miR-138-5p, resulting in glycolysis in CRC cells and leading to their invasion and liver metastasis. More interestingly, lactate accumulated via glycolysis activated the p38/Elk-1 signaling pathway to promote the transcriptional expression of MIR17HG in CRC cells, forming a positive feedback loop, which eventually resulted in persistent glycolysis and the invasion and liver metastasis of CRC cells. In conclusion, the present study indicates that the lactate-responsive lncRNA MIR17HG, acting as a ceRNA, promotes CRLM through a glycolysis-mediated positive feedback circuit and might be a novel biomarker and therapeutic target for CRLM.
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Affiliation(s)
- Senlin Zhao
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Bingjie Guan
- Department of General Surgery, Shanghai General Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Yushuai Mi
- Department of Gastrointestinal Surgery, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Debing Shi
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ping Wei
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Cancer Institute, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Yanzi Gu
- Department of Biobank, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Sanjun Cai
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ye Xu
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xinxiang Li
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Dongwang Yan
- Department of General Surgery, Shanghai General Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China.
| | - Mingzhu Huang
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, China.
| | - Dawei Li
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
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28
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Sun Z, Wei N, Yao S, Wang G, Sun Y, Wang Z, Yuan D. LINC01158 works as an oncogene in glioma via sponging miR-6734-3p to boost CENPK expression. Cancer Cell Int 2021; 21:280. [PMID: 34044826 PMCID: PMC8161569 DOI: 10.1186/s12935-021-01931-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 04/13/2021] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) have been certified to play vital biological functions in glioma and have received considerable attention in the recent literature. Nonetheless, the role of LINC01158 in glioma remains to be elucidated. METHODS qRT-PCR, western blot and GEPIA database were applied for reporting the expression of CENPK and LINC01158 in glioma and the correlation between LINC01158 and CENPK expression. EdU, colony formation, CCK-8, caspase-3 activity and TUNEL assays probed the impacts of LINC01158 on glioma cell growth. Subcellular fractionation and FISH assays revealed the cellular distribution of LINC01158. Luciferase reporter and RIP assays examined ceRNA network of LINC01158, CENPK and miR-6734-3p. RESULTS LINC01158 and CENPK were both overexpressed in glioma and a positive regulation of LINC01158 on CENPK was corroborated. LINC01158 served a pro-proliferative and anti-apoptotic part in glioma by sponging miR-6734-3p to augment CENPK. CONCLUSION LINC01158 enhances CENPK by serving as sponge for miR-6734-3p to facilitate glioma development, proposing LINC01158 as a new player in glioma.
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Affiliation(s)
- Zhenxing Sun
- Department of Neurosurgery, School of Clinical Medicine, Beijing Tsinghua Changgung Hospital, Tsinghua University, Beijing, 102218 China
| | - Naili Wei
- Department of Neurosurgery, The First Affiliated Hospital of Shantou University Medical College, Shantou, 515041 Guangdong China
| | - Shenglian Yao
- School of Material Science and Engineering, University of Science and Technology Beijing, Beijing, China
| | - Guihuai Wang
- Department of Neurosurgery, School of Clinical Medicine, Beijing Tsinghua Changgung Hospital, Tsinghua University, Beijing, 102218 China
| | - Yaxing Sun
- Department of Psychiatry, Zaozhuang Mental Health Center, Zaozhuang, 277103 Shandong China
| | - Zhenze Wang
- Department of Neurosurgery, Haicheng Zhenggu Hospital, Anshan City, 114200 Liaoning China
| | - Dan Yuan
- Department of Nephrology, Beijing Luhe Hospital, Capital Medical University, No. 82, Xinhuanan Road, Tongzhou District, Beijing, 102218 China
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29
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Zheng XY, Cao MZ, Ba Y, Li YF, Ye JL. LncRNA testis-specific transcript, Y-linked 15 (TTTY15) promotes proliferation, migration and invasion of colorectal cancer cells via regulating miR-29a-3p/DVL3 axis. Cancer Biomark 2021; 31:1-11. [PMID: 33016900 DOI: 10.3233/cbm-201709] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND Long non-coding RNA testis-specific transcript, Y-linked 15 (TTTY15) is oncogenic in prostate cancer, however its expression and function in colorectal cancer remain largely unknown. METHODS Paired colorectal cancer samples/normal tissues were collected, and the expression levels of TTTY15, miR-29a-3p and disheveled segment polarity protein 3 (DVL3) were examined by quantitative real-time polymerase chain reaction (qRT-PCR); TTTY15 shRNA and overexpression plasmids were transfected into HT29 and HCT-116 cell lines using lipofectamine reagent, respectively; the proliferation and colony formation were detected by CCK-8 assay and plate colony formation assay; qRT-PCR and Western blot were used to analyze the changes of miR-29a-3p and DVL3; dual-luciferase reporter gene assay was used to determine the regulatory relationships between miR-29a-3p and TTTY15, miR-29a-3p and DVL3. RESULTS TTTY15 was significantly up-regulated in cancerous tissues of colorectal cancer samples, positively correlated with the expression of DVL3, while negatively correlated with the expression of miR-29a-3p. After TTTY15 shRNAs were transfected into colorectal cancer cells, the proliferation and metastasis of cancer cells were significantly inhibited, while TTTY15 overexpression had opposite biological effects. TTTY15 shRNA could reduce the expression of DVL3 on both mRNA and protein levels, and the luciferase activity of TTTY15 sequence was also inhibited by miR-29a-3p. DVL3 was also validated as a target gene of miR-29a-3p, and it could be repressed by miR-29a-3p mimics or TTTY15 shRNA. CONCLUSION TTTY15 is abnormally upregulated in colorectal cancer tissues, and it can modulate the proliferation and metastasis of colorectal cancer cells. It functions as the ceRNA to regulate the expression of DVL3 by sponging miR-29a-3p.
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Affiliation(s)
- Xiao-Ying Zheng
- Department of Pathology, Qinghai University Affiliated Hospital, Xining, Qinghai, China
| | - Ming-Zheng Cao
- Department of General Surgery, Linyi Central Hospital, Linyi, Shandong, China
| | - Ying Ba
- Department of Nursing, Linyi Central Hospital, Linyi, Shandong, China
| | - Yue-Feng Li
- Department of Oncology, Linyi Central Hospital, Linyi, Shandong, China
| | - Jun-Ling Ye
- Department of Pathology, Qinghai University Affiliated Hospital, Xining, Qinghai, China
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30
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Sun Z, Dang Q, Liu Z, Shao B, Chen C, Guo Y, Chen Z, Zhou Q, Hu S, Liu J, Yuan W. LINC01272/miR-876/ITGB2 axis facilitates the metastasis of colorectal cancer via epithelial-mesenchymal transition. J Cancer 2021; 12:3909-3919. [PMID: 34093798 PMCID: PMC8176243 DOI: 10.7150/jca.55666] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 04/26/2021] [Indexed: 12/29/2022] Open
Abstract
Background: At the time of diagnosis, colorectal cancer (CRC) patients are usually in an advanced stage of disease, which is accompanied by metastasis. Long noncoding RNAs (lncRNAs) play critical regulatory roles in cancer biology. However, the contributions of lncRNA LINC01272 to CRC remain elusive. Methods: Bioinformatics and the survminer R package were used to predict intermolecular correlations and prognostic indicators. Quantitative real-time PCR was used to examine molecular expression. In vitro experiments, including migration assays, invasion assays, and wound healing assays, were used to investigate the effects of LINC01272, ITGB2 and miR-876 on CRC cell migration and invasion abilities. Furthermore, a dual-luciferase reporter gene assay was performed to explore the potential mechanism by which LINC01272 contributes to CRC. Results: We found that LINC01272 was highly expressed in multiple cancers and closely related to core epithelial-mesenchymal transition (EMT) factors and that high levels of LINC01272 are associated with a poor prognosis in CRC patients. qRT-PCR revealed that LINC01272 was highly expressed and negatively associated with miR-876 in CRC. Additionally, LINC01272 or ITGB2 silencing reduced, while miR-876 overexpression promoted, the invasiveness and metastatic capacity of CRC cells in vitro. Moreover, LINC01272 potentially targeted miR-876, and miR-876 potentially targeted ITGB2. Conclusion: LINC01272 was highly expressed in CRC and predicted a poor prognosis. LINC01272 promoted EMT and metastasis by regulating miR-876/ITGB2 to act as an oncogene in CRC. LINC01272 may be a promising prognostic biomarker and therapeutic target for the treatment of CRC patients in the future.
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Affiliation(s)
- Zhenqiang Sun
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, China
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou 450052, Henan, China
| | - Qin Dang
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, China
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou 450052, Henan, China
| | - Zaoqu Liu
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou, University, Zhengzhou, 450052, Henan, China
| | - Bo Shao
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, China
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou 450052, Henan, China
| | - Chen Chen
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou 450052, Henan, China
| | - Yuying Guo
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, China
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou 450052, Henan, China
| | - Zhuang Chen
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, China
| | - Quanbo Zhou
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, China
| | - Shengyun Hu
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, China
| | - Jinbo Liu
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, China
| | - Weitang Yuan
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, China
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31
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Jiang L, Xie X, Ding F, Mei J, Bi R. Silencing LINC00511 inhibits cell proliferation, migration, and epithelial-mesenchymal transition via the PTEN-AKT-FOXO1 signaling pathway in lung cancer. Biochem Cell Biol 2021; 99:1-8. [PMID: 31415720 DOI: 10.1139/bcb-2018-0364] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Affiliation(s)
- Lianyong Jiang
- Department of Cardiothoracic Surgery, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200092, P.R. China
| | - Xiao Xie
- Department of Cardiothoracic Surgery, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200092, P.R. China
| | - Fangbao Ding
- Department of Cardiothoracic Surgery, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200092, P.R. China.,Department of Cardiothoracic Surgery, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200092, P.R. China
| | - Ju Mei
- Department of Cardiothoracic Surgery, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200092, P.R. China.,Department of Cardiothoracic Surgery, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200092, P.R. China
| | - Rui Bi
- Department of Cardiothoracic Surgery, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200092, P.R. China.,Department of Cardiothoracic Surgery, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200092, P.R. China
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32
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Li Z, Li Y, Wang X, Liang Y, Luo D, Han D, Li C, Chen T, Zhang H, Liu Y, Wang Z, Chen B, Wang L, Zhao W, Yang Q. LINC01977 Promotes Breast Cancer Progression and Chemoresistance to Doxorubicin by Targeting miR-212-3p/GOLM1 Axis. Front Oncol 2021; 11:657094. [PMID: 33869063 PMCID: PMC8046671 DOI: 10.3389/fonc.2021.657094] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 03/15/2021] [Indexed: 12/12/2022] Open
Abstract
Long non-coding RNAs(lncRNAs) play an important role in cancer initiation and progression. However, hub lncRNAs involved in breast cancer still remain underexplored. In this study, integrated bioinformatics analysis was used to define LINC01977 as a key oncogenic driver in breast cancer. Subsequently, in vitro assays showed that LINC01977 could significantly promote breast cancer progression and chemoresistance to doxorubicin. To further investigate its biological mechanism, we performed dual-luciferase reporter assay, real-time PCR, RNA immunoprecipitation (RIP), and rescue assay. Our results indicated that LINC01977 may function as ceRNA to prevent GOLM1 gene from miRNA-mediated repression by sponging miR-212-3p. Overall, LINC01977 can serve as a novel prognostic indicator, and help develop more effective therapeutic approaches for breast cancer patients.
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Affiliation(s)
- Zheng Li
- Department of Breast Surgery, General Surgery, Qilu Hospital of Shandong University, Jinan, China
| | - Yaming Li
- Department of Breast Surgery, General Surgery, Qilu Hospital of Shandong University, Jinan, China
| | - Xiaolong Wang
- Department of Breast Surgery, General Surgery, Qilu Hospital of Shandong University, Jinan, China
| | - Yiran Liang
- Department of Breast Surgery, General Surgery, Qilu Hospital of Shandong University, Jinan, China
| | - Dan Luo
- Department of Breast Surgery, General Surgery, Qilu Hospital of Shandong University, Jinan, China
| | - Dianwen Han
- Department of Breast Surgery, General Surgery, Qilu Hospital of Shandong University, Jinan, China
| | - Chen Li
- Department of Breast Surgery, General Surgery, Qilu Hospital of Shandong University, Jinan, China
| | - Tong Chen
- Department of Breast Surgery, General Surgery, Qilu Hospital of Shandong University, Jinan, China
| | - Hanwen Zhang
- Department of Breast Surgery, General Surgery, Qilu Hospital of Shandong University, Jinan, China
| | - Ying Liu
- Department of Breast Surgery, General Surgery, Qilu Hospital of Shandong University, Jinan, China
| | - Zekun Wang
- Department of Breast Surgery, General Surgery, Qilu Hospital of Shandong University, Jinan, China
| | - Bing Chen
- Pathology Tissue Bank, Qilu Hospital of Shandong University, Jinan, China
| | - Lijuan Wang
- Pathology Tissue Bank, Qilu Hospital of Shandong University, Jinan, China
| | - Wenjing Zhao
- Pathology Tissue Bank, Qilu Hospital of Shandong University, Jinan, China
| | - Qifeng Yang
- Department of Breast Surgery, General Surgery, Qilu Hospital of Shandong University, Jinan, China.,Pathology Tissue Bank, Qilu Hospital of Shandong University, Jinan, China.,Research Institute of Breast Cancer, Shandong University, Jinan, China
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Liu Z, Wang Y, Yuan S, Wen F, Liu J, Zou L, Zhang J. Regulatory role of long non-coding RNA UCA1 in signaling pathways and its clinical applications. Oncol Lett 2021; 21:404. [PMID: 33777227 PMCID: PMC7988699 DOI: 10.3892/ol.2021.12665] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Accepted: 02/11/2021] [Indexed: 12/15/2022] Open
Abstract
Long non-coding RNA metastasis-associated urothelial carcinoma associated 1 (UCA1) plays a pivotal role in various human diseases. Its gene expression is regulated by several factors, including transcription factors, chromatin remodeling and epigenetic modification. UCA1 is involved in the regulation of the PI3K/AKT, Wnt/β-catenin, MAPK, NF-κB and JAK/STAT signaling pathways, affecting a series of cellular biological functions, such as cell proliferation, apoptosis, migration, invasion and tumor drug resistance. Furthermore, UCA1 is used as a novel potential biomarker for disease diagnosis and prognosis, as well as a target for clinical gene therapy. The present review systematically summarizes and elucidates the mechanisms of upstream transcriptional regulation of UCA1, the regulatory role of UCA1 in multiple signaling pathways in the occurrence and development of several diseases, and its potential applications in clinical treatment.
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Affiliation(s)
- Zhaoping Liu
- Department of Rheumatology, The First Affiliated Hospital, University of South China, Hengyang, Hunan 421001, P.R. China
| | - Yanyan Wang
- Department of Rheumatology, The First Affiliated Hospital, University of South China, Hengyang, Hunan 421001, P.R. China
| | - Shunling Yuan
- Department of Rheumatology, The First Affiliated Hospital, University of South China, Hengyang, Hunan 421001, P.R. China
| | - Feng Wen
- Department of Hematology, The First Affiliated Hospital, University of South China, Hengyang, Hunan 421001, P.R. China
| | - Jing Liu
- Molecular Biology Research Center and Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410078, P.R. China
| | - Liheng Zou
- Department of Rheumatology, The First Affiliated Hospital, University of South China, Hengyang, Hunan 421001, P.R. China
| | - Ji Zhang
- Department of Rheumatology, The First Affiliated Hospital, University of South China, Hengyang, Hunan 421001, P.R. China.,Department of Clinical Laboratory, Shenzhen Traditional Chinese Medicine Hospital, Shenzhen, Guangdong 518033, P.R. China
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Liu B, Qian D, Zhou W, Jiang H, Xiang Z, Wu D. A Novel Androgen-Induced lncRNA FAM83H-AS1 Promotes Prostate Cancer Progression via the miR-15a/CCNE2 Axis. Front Oncol 2021; 10:620306. [PMID: 33614501 PMCID: PMC7890020 DOI: 10.3389/fonc.2020.620306] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 11/23/2020] [Indexed: 01/07/2023] Open
Abstract
Prostate cancer (PCa) is one of the most common types of tumors among males worldwide. However, the roles of long noncoding RNAs (lncRNAs) in PCa remain unclear. This study shows that lncRNA FAM83H-AS1 is upregulated in prostate adenocarcinoma, bladder urothelial carcinoma, and kidney renal papillary cell carcinoma samples. Androgen receptor (AR) signaling plays the most important role in PCa tumorigenesis and development. In this study, the results validate that AR signaling is involved in upregulating FAM83H-AS1 expression in PCa cells. Loss-of-function assays demonstrate that FAM83H-AS1 acts as an oncogene in PCa by modulating cell proliferation, cell cycle, and migration. Bioinformatics analysis demonstrates that FAM83H-AS1 is remarkably related to the regulation of the cell cycle and DNA replication through affecting multiple regulators related to these pathways, such as CCNE2. Mechanically, we found that FAM83H-AS1 plays its roles through sponging miR-15a to promote CCNE2 expression. These findings indicate that FAM83H-AS1 is a novel diagnostic and therapeutic marker for PCa.
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Affiliation(s)
- Bo Liu
- Department of Urology, Tongji Hospital, Tongji University of Medicine, Shanghai, China
| | - Duocheng Qian
- Department of Urology, Shanghai Fourth People's Hospital affiliated to Tongji University School of Medicine, Shanghai, China
| | - Weidong Zhou
- Department of Urology, Tongji Hospital, Tongji University of Medicine, Shanghai, China
| | - Huiyang Jiang
- Department of Urology, Tongji Hospital, Tongji University of Medicine, Shanghai, China
| | - Zhendong Xiang
- Department of Urology, Tongji Hospital, Tongji University of Medicine, Shanghai, China
| | - Denglong Wu
- Department of Urology, Tongji Hospital, Tongji University of Medicine, Shanghai, China
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Chen Y, Li Z, Chen X, Zhang S. Long non-coding RNAs: From disease code to drug role. Acta Pharm Sin B 2021; 11:340-354. [PMID: 33643816 PMCID: PMC7893121 DOI: 10.1016/j.apsb.2020.10.001] [Citation(s) in RCA: 260] [Impact Index Per Article: 86.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 08/06/2020] [Accepted: 08/21/2020] [Indexed: 12/30/2022] Open
Abstract
Enormous studies have corroborated that long non-coding RNAs (lncRNAs) extensively participate in crucial physiological processes such as metabolism and immunity, and are closely related to the occurrence and development of tumors, cardiovascular diseases, nervous system disorders, nephropathy, and other diseases. The application of lncRNAs as biomarkers or intervention targets can provide new insights into the diagnosis and treatment of diseases. This paper has focused on the emerging research into lncRNAs as pharmacological targets and has reviewed the transition of lncRNAs from the role of disease coding to acting as drug candidates, including the current status and progress in preclinical research. Cutting-edge strategies for lncRNA modulation have been summarized, including the sources of lncRNA-related drugs, such as genetic technology and small-molecule compounds, and related delivery methods. The current progress of clinical trials of lncRNA-targeting drugs is also discussed. This information will form a latest updated reference for research and development of lncRNA-based drugs.
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Key Words
- AD, Alzheimer's disease
- ANRIL, antisense noncoding RNA gene at the INK4 locus
- ASO, antisense oligonucleotide
- ASncmtRNA
- ASncmtRNA, antisense noncoding mitochondrial RNA
- BCAR4, breast cancer anti-estrogen resistance 4
- BDNF-AS, brain-derived neurotrophic factor antisense
- CASC9, cancer susceptibility candidate 9
- CDK, cyclin dependent kinase 1
- CHRF, cardiac hypertrophy related factor
- CRISPR, clustered regularly interspaced short palindromic repeats
- Clinical trials
- DACH1, dachshund homolog 1
- DANCR, differentiation antagonizing non-protein coding RNA
- DKD, diabetic kidney disease
- DPF, diphenyl furan
- Delivery
- EBF3-AS, early B cell factor 3-antisense
- ENE, element for nuclear expression
- Erbb4-IR, Erb-B2 receptor tyrosine kinase 4-immunoreactivity
- FDA, U.S. Food and Drug Administration
- GAPDH, glyceraldehyde-3-phosphate dehydrogenase
- GAS5, growth arrest specific 5
- Gene therapy
- HISLA, HIF-1α-stabilizing long noncoding RNA
- HOTAIR, HOX transcript antisense intergenic RNA
- HULC, highly upregulated in liver cancer
- LIPCAR, long intergenic noncoding RNA predicting cardiac remodeling
- LNAs, locked nucleic acids
- LncRNAs
- MALAT1, metastasis associated lung adenocarcinoma transcript 1
- MEG3, maternally expressed gene 3
- MHRT, myosin heavy chain associated RNA transcripts
- MM, multiple myeloma
- NEAT1, nuclear enriched abundant transcript 1
- NKILA, NF-kappaB interacting lncRNA
- NPs, nanoparticles
- Norad, non-coding RNA activated by DNA damage
- OIP5-AS1, opa-interacting protein 5 antisense transcript 1
- PD, Parkinson's disease
- PEG, polyethylene glycol
- PNAs, peptide nucleic acids
- PTO, phosphorothioate
- PVT1, plasmacytoma variant translocation 1
- RGD, arginine-glycine-aspartic acid peptide
- RISC, RNA-induced silencing complex
- SALRNA1, senescence associated long non-coding RNA 1
- SNHG1, small nucleolar RNA host gene 1
- Small molecules
- SncmtRNA, sense noncoding mitochondrial RNA
- THRIL, TNF and HNRNPL related immunoregulatory
- TTTY15, testis-specific transcript, Y-linked 15
- TUG1, taurine-upregulated gene 1
- TWIST1, twist family BHLH transcription factor 1
- Targeted drug
- TncRNA, trophoblast-derived noncoding RNA
- Translational medicine
- UCA1, urothelial carcinoma-associated 1
- UTF1, undifferentiated transcription factor 1
- XIST, X-inactive specific transcript
- lincRNA-p21, long intergenic noncoding RNA p21
- lncRNAs, long non-coding RNAs
- mtlncRNA, mitochondrial long noncoding RNA
- pHLIP, pH-low insertion peptide
- sgRNA, single guide RNA
- siRNAs, small interfering RNAs
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Zhao X, Zeng H, Lei L, Tong X, Yang L, Yang Y, Li S, Zhou Y, Luo L, Huang J, Xiao R, Chen J, Zeng Q. Tight junctions and their regulation by non-coding RNAs. Int J Biol Sci 2021; 17:712-727. [PMID: 33767583 PMCID: PMC7975691 DOI: 10.7150/ijbs.45885] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 10/06/2020] [Indexed: 02/06/2023] Open
Abstract
Tight junction (TJ) is a “zippering up” junction structure located at the uppermost portion of adjacent epithelial/endothelial cells in organs and tissues. TJs maintain the relative stability of intracellular substances and functions by closing or opening intercellular pathways, coordinating the entry and exit of molecules of different sizes and charges, and regulating the permeability of paracellular barrier. TJs also prevent microbial invasion, maintain epithelial/endothelial cell polarity, and regulate cell proliferation. TJs are widely present in the skin and mucosal epithelial barriers, intestinal epithelial barrier, glomerular filtration barrier, bladder epithelial barrier, blood-brain barrier, brain-blood tumor barrier, and blood-testis barrier. TJ dysfunction in different organs can lead to a variety of diseases. In addition to signal pathways, transcription factors, DNA methylation, histone modification, TJ proteins can also be regulated by a variety of non-coding RNAs, such as micro-RNAs, long-noncoding RNAs, and circular RNAs, directly or indirectly. This review summarizes the structure of TJs and introduces the functions and regulatory mechanisms of TJs in different organs and tissues. The roles and mechanisms of non-coding RNAs in the regulation of TJs are also highlighted in this review.
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Affiliation(s)
- Xiaojiao Zhao
- Department of Dermatology, Third Xiangya Hospital, Central South University, 138 Tongzipo Road, Changsha, Hunan 410013, P.R. China
| | - Hongliang Zeng
- Institute of Chinese Materia Medica, Hunan Academy of Chinese Medicine, Yuehua Road, Changsha, Hunan 410013, P.R. China
| | - Li Lei
- Department of Dermatology, Third Xiangya Hospital, Central South University, 138 Tongzipo Road, Changsha, Hunan 410013, P.R. China
| | - Xiaoliang Tong
- Department of Dermatology, Third Xiangya Hospital, Central South University, 138 Tongzipo Road, Changsha, Hunan 410013, P.R. China
| | - Lun Yang
- Department of Dermatology, Third Xiangya Hospital, Central South University, 138 Tongzipo Road, Changsha, Hunan 410013, P.R. China
| | - Yan Yang
- Department of Dermatology, Third Xiangya Hospital, Central South University, 138 Tongzipo Road, Changsha, Hunan 410013, P.R. China
| | - Si Li
- Department of Dermatology, Third Xiangya Hospital, Central South University, 138 Tongzipo Road, Changsha, Hunan 410013, P.R. China
| | - Ying Zhou
- Department of Dermatology, Third Xiangya Hospital, Central South University, 138 Tongzipo Road, Changsha, Hunan 410013, P.R. China
| | - Liping Luo
- Department of Dermatology, Third Xiangya Hospital, Central South University, 138 Tongzipo Road, Changsha, Hunan 410013, P.R. China
| | - Jinhua Huang
- Department of Dermatology, Third Xiangya Hospital, Central South University, 138 Tongzipo Road, Changsha, Hunan 410013, P.R. China
| | - Rong Xiao
- Department of Dermatology, Second Xiangya Hospital, Central South University, 139 Renminzhong Road, Changsha, Hunan 410013, P.R. China
| | - Jing Chen
- Department of Dermatology, Third Xiangya Hospital, Central South University, 138 Tongzipo Road, Changsha, Hunan 410013, P.R. China.,Institute of Chinese Materia Medica, Hunan Academy of Chinese Medicine, Yuehua Road, Changsha, Hunan 410013, P.R. China.,Department of Dermatology, Second Xiangya Hospital, Central South University, 139 Renminzhong Road, Changsha, Hunan 410013, P.R. China
| | - Qinghai Zeng
- Department of Dermatology, Third Xiangya Hospital, Central South University, 138 Tongzipo Road, Changsha, Hunan 410013, P.R. China.,Institute of Chinese Materia Medica, Hunan Academy of Chinese Medicine, Yuehua Road, Changsha, Hunan 410013, P.R. China.,Department of Dermatology, Second Xiangya Hospital, Central South University, 139 Renminzhong Road, Changsha, Hunan 410013, P.R. China
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Guo Y, Yang PT, Wang ZW, Xu K, Kou WH, Luo H. Identification of Three Autophagy-Related Long Non-Coding RNAs as a Novel Head and Neck Squamous Cell Carcinoma Prognostic Signature. Front Oncol 2021; 10:603864. [PMID: 33575215 PMCID: PMC7871905 DOI: 10.3389/fonc.2020.603864] [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: 09/08/2020] [Accepted: 11/09/2020] [Indexed: 01/08/2023] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) has a poor prognosis. Considerable evidence indicates that autophagy and non-coding RNA play essential roles in the biological processes involved in cancers, but associations between autophagy-related long non-coding RNAs (lncRNAs) and HNSCC remain unclear. In the present study, HNSCC RNA sequences and autophagy-related gene data were extracted from The Cancer Genome Atlas database and the Human Autophagy Database. A total of 1,153 autophagy-related lncRNAs were selected via calculating Pearson’s correlation coefficient. Three prognosis-related autophagy lncRNAs were identified via univariate Cox regression, least absolute shrinkage and selection operator analysis, and multivariate Cox regression analysis. We also constructed a prognostic model based on these autophagy-related lncRNAs and evaluated its ability to accurately and independently predict the prognosis of HNSCC patients. The area under the curve (AUC) was 0.864 (3-year) and 0.836 (5-year), and our model can independently predict the prognosis of HNSCC. The prognostic value of the three autophagy lncRNAs was confirmed via analysis of samples from five databases. To further identify the functions of the three lncRNAs, a co-expression network was constructed and pathway analysis was performed. In that analysis the lncRNAs were correlated with 189 related genes and 20 autophagy-related genes, and these lncRNAs mainly involved homologous recombination, the Fanconi anemia pathway, the autophagy-related pathway, and immune-related pathways. In addition, we validated the expression levels of three lncRNAs and autophagy markers (ATG12, BECN1, and MAP1LC3B) based on TIMER, Oncomine, and HPA database analysis. Our results indicated that TTTY15 was increased in HPV positive and HPV negative HNSCC patients, and three autophagy markers were up-regulated in all HNSCCC patients. Lastly, association between three lncRNAs and autophagy markers was performed, and our results showed that TTTY15 and MIF-AS1 were associated with autophagy markers. Collectively, these results suggested that three autophagy-related lncRNAs have prognostic value in HNSCC patients.
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Affiliation(s)
- Ya Guo
- Department of Radiation Oncology, Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Peng Tao Yang
- Department of Radiation Oncology, Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Zhong Wei Wang
- Department of Radiation Oncology, Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Kun Xu
- Department of Radiation Oncology, Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Wei Hua Kou
- Department of Radiation Oncology, Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Heng Luo
- Department of Radiation Oncology, Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
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38
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Wang L, Xiao B, Yu T, Gong L, Wang Y, Zhang X, Zou Q, Zuo Q. lncRNA PVT1 promotes the migration of gastric cancer by functioning as ceRNA of miR-30a and regulating Snail. J Cell Physiol 2021; 236:536-548. [PMID: 32557622 DOI: 10.1002/jcp.29881] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 05/26/2020] [Accepted: 06/03/2020] [Indexed: 01/17/2023]
Abstract
Although the incidence and mortality of gastric cancer (GC) are slowly decreasing, the overall prognosis of GC patients with distal metastasis remains dismal. Long non-coding RNA PVT1 has been verified to function as a tumor promoter in several types of cancer. However, the role of PVT1 in GC metastasis remains obscure. Herein, we found that PVT1 was highly expressed in GC tissues and high PVT1 level was associated with tumor stage, lymph node metastasis, and poor prognosis. Overexpression of PVT1 significantly elevated epithelial-to-mesenchymal transition (EMT) marker (N-cadherin, ZEB1, and ZEB2) levels and promoted GC cell EMT process and tumor metastasis in vitro and in vivo. Mechanistically, Snail was identified as a direct target of miR-30a. PVT1 could bind with miR-30a and increase the expression of Snail by acting as a competing endogenous RNA, whereas re-expression of miR-30a in GC cells rescued the EMT markers, decreased Snail level, and inhibited GC cell migration. Taken together, these findings provide a new light on PVT1 in the pathogenesis and development of GC and an important implication for future therapy of the GC.
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Affiliation(s)
- Lina Wang
- Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science, Army Medical University, Chongqing, China
| | - Bin Xiao
- College of Pharmacy, Chongqing Medical University, Chongqing, China
| | - Ting Yu
- Department of Clinical Laboratory, The 89th Hospital of The People's Liberation Army, Weifang, China
| | - Li Gong
- Department of Laboratory Medicine, The Third Affiliated Hospital of Chongqing Medical University (General Hospital), Chongqing, China
| | - Yu Wang
- Department of Basic Courses, NCO School, Army Medical University, Shijiazhuang, China
| | - Xiaokai Zhang
- Department of Microbiology and Biochemical Pharmacy, National Engineering Research Center of Immunological Products, College of Pharmacy, Army Medical University, Chongqing, China
| | - Quanming Zou
- Department of Microbiology and Biochemical Pharmacy, National Engineering Research Center of Immunological Products, College of Pharmacy, Army Medical University, Chongqing, China
| | - Qianfei Zuo
- Department of Microbiology and Biochemical Pharmacy, National Engineering Research Center of Immunological Products, College of Pharmacy, Army Medical University, Chongqing, China
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39
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Tezerjani MD, Kalantar SM. Unraveling the dark matter, long non-coding RNAs, in male reproductive diseases: A narrative review. Int J Reprod Biomed 2020; 18:921-934. [PMID: 33349800 PMCID: PMC7749978 DOI: 10.18502/ijrm.v13i11.7959] [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: 12/02/2019] [Revised: 05/10/2020] [Accepted: 06/28/2020] [Indexed: 12/09/2022] Open
Abstract
Recent advances in human transcriptome have revealed the fundamental and functional roles of long non-coding RNA in the susceptibility to diverse diseases and pathological conditions. They participate in wide range of biological processes such as the modulating of chromatin structure, transcription, translation, and post-translation modification. In addition, based on their unique expression profiles and their association with clinical abnormalities such as those of related to male reproductive diseases, they can be used to develop therapeutic methods and biomarkers for screening of the diseases. In this study, we will review the identified lncRNAs and their molecular functions in the pathogenesis of male reproductive diseases such as prostate cancer, benign prostatic hyperplasia, prostatitis, testicular cancer, varicocele, and sperm abnormalities.
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Affiliation(s)
- Masoud Dehghan Tezerjani
- Abortion Research Centre, Yazd Reproductive Sciences Institute, Shahid Sadoughi University of Medical Science, Yazd, Iran
| | - Seyed Mehdi Kalantar
- Abortion Research Centre, Yazd Reproductive Sciences Institute, Shahid Sadoughi University of Medical Science, Yazd, Iran.,Department of Genetics, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
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40
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Zhao A, Liu W, Cui X, Wang N, Wang Y, Sun L, Xue H, Wu L, Cui S, Yang Y, Bai R. lncRNA TUSC7 inhibits osteosarcoma progression through the miR‑181a/RASSF6 axis. Int J Mol Med 2020; 47:583-594. [PMID: 33416181 PMCID: PMC7797460 DOI: 10.3892/ijmm.2020.4825] [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: 08/04/2020] [Accepted: 11/16/2020] [Indexed: 01/04/2023] Open
Abstract
Osteosarcoma (OS) is one of the most aggressive malignancies, accompanied by an elevated incidence and a decreased rate of healing. Recently, several long non-coding RNAs (lncRNAs) have been reported to be involved in OS progression. Although tumor suppressor candidate 7 (TUSC7) was reported as a novel lncRNA, little is known about its biological functions in OS. The present study was designed to explore whether TUSC7 was involved in the pathological development of OS using various methods, including hematoxylin and eosin staining, Cell Counting Kit-8 assay, colony formation assay and Transwell assay. The present study revealed that TUSC7 expression was downregulated in OS tissues and cell lines compared with in normal tissues and cell lines. Functionally, the current results revealed that overexpression of TUSC7 inhibited OS cell proliferation, migration and invasion, while promoting apoptosis in vitro and in vivo. Next, the subcellular distribution of TUSC7 was examined by nuclear/cytoplasmic RNA fractionation and reverse transcription-quantitative PCR. Mechanistic studies revealed that TUSC7 exerted its role by sponging microRNA (miR)-181a in OS cell lines. Ras association domain family member 6 (RASSF6) was confirmed as a target gene of miR-181a, and the expression levels of RASSF6 were negatively regulated by miR-181a. Additionally, the results of rescue experiments suggested that overexpression of miR-181a neutralized the inhibitory effects of TUSC7 overexpression on OS cells. Overall, the present study demonstrated that the tumor suppressor role of TUSC7 in OS progression was mediated through the miR-181a/RASSF6 axis, which may represent a new therapeutic target for OS.
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Affiliation(s)
- Aiqing Zhao
- Department of Joint Surgery, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot, Inner Mongolia 10030, P.R. China
| | - Wanlin Liu
- Department of Joint Surgery, The Second Affiliated Hospital of Inner Mongolia Medical University, Hohhot, Inner Mongolia 10030, P.R. China
| | - Xiaolong Cui
- Department of Joint Surgery, The Second Affiliated Hospital of Inner Mongolia Medical University, Hohhot, Inner Mongolia 10030, P.R. China
| | - Na Wang
- Department of Joint Surgery, The Second Affiliated Hospital of Inner Mongolia Medical University, Hohhot, Inner Mongolia 10030, P.R. China
| | - Yuxin Wang
- Department of Joint Surgery, The Second Affiliated Hospital of Inner Mongolia Medical University, Hohhot, Inner Mongolia 10030, P.R. China
| | - Liang Sun
- Department of Joint Surgery, The Second Affiliated Hospital of Inner Mongolia Medical University, Hohhot, Inner Mongolia 10030, P.R. China
| | - Huiqin Xue
- Department of Joint Surgery, The Second Affiliated Hospital of Inner Mongolia Medical University, Hohhot, Inner Mongolia 10030, P.R. China
| | - Lishuan Wu
- Department of Joint Surgery, The Second Affiliated Hospital of Inner Mongolia Medical University, Hohhot, Inner Mongolia 10030, P.R. China
| | - Shuxia Cui
- Department of Joint Surgery, The Second Affiliated Hospital of Inner Mongolia Medical University, Hohhot, Inner Mongolia 10030, P.R. China
| | - Yun Yang
- Department of Joint Surgery, The Second Affiliated Hospital of Inner Mongolia Medical University, Hohhot, Inner Mongolia 10030, P.R. China
| | - Rui Bai
- Department of Joint Surgery, The Second Affiliated Hospital of Inner Mongolia Medical University, Hohhot, Inner Mongolia 10030, P.R. China
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Han Y, Li X, Zhang M, Yang Y, Ge G, Wang K, Gong Y, Liang Y, Niu H, Ci W. Enhanced Detection of Genitourinary Cancers Using Fragmentation and Copy Number Profiles Obtained from Urinary Cell-Free DNA. Clin Chem 2020; 67:394-403. [PMID: 33523215 DOI: 10.1093/clinchem/hvaa283] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 10/23/2020] [Indexed: 12/30/2022]
Abstract
BACKGROUND Recent studies have reported that examining the fragmentation profiles (FP) of plasma cell-free DNA (cfDNA) further improves the clinical sensitivity of tumor detection. We hypothesized that considering the differences of the FP of urinary cfDNA would increase the clinical sensitivity of genitourinary (GU) cancer detection. METHODS 177 patients with GU cancer and 94 individuals without tumors were enrolled in the discovery cohort. An independent validation dataset comprising 30 patients without tumors and 66 patients with GU cancer was also collected. We constructed an ensemble classifier, GUIDER, to detect and localize GU cancers using fragmentation and copy number profiles obtained from shallow whole-genome sequencing of urinary cfDNA. RESULTS Urinary cfDNA of patients with GU cancer had a higher proportion of long fragments (209-280 bp) and a lower proportion of short fragments (140-208 bp) compared to controls. The overall mean classification accuracy of the FP was 74.62%-85.39% for different algorithms, and integration of the FP and copy number alteration (CNA) features further enhanced the classification of samples from patients with GU cancer. The mean diagnostic accuracy was further improved by the ensemble classifier GUIDER, which integrated the FP and CNA profiles and resulted in a higher mean accuracy (87.52%) compared to the analysis performed without FP features (74.62%). GUIDER performed well in an independent validation dataset. CONCLUSIONS The lengthening and shortening of urinary cfDNA within specific size ranges were identified in patients with GU cancer. Integration of the FP should further enhance the ability to use urinary cfDNA as a molecular diagnostic tool.
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Affiliation(s)
- Yang Han
- Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing China.,China National Center for Bioinformation, Beijing China.,University of the Chinese Academy of Sciences, Beijing China
| | - Xinxin Li
- Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing China.,China National Center for Bioinformation, Beijing China
| | - Mingxin Zhang
- Department of Urology, the Affiliated Hospital of Qingdao University, Qingdao China
| | - Yang Yang
- Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing China.,China National Center for Bioinformation, Beijing China.,University of the Chinese Academy of Sciences, Beijing China
| | - Guangzhe Ge
- Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing China.,China National Center for Bioinformation, Beijing China
| | - Kunxiang Wang
- Department of Urology, the Affiliated Hospital of Qingdao University, Qingdao China
| | - Yanqing Gong
- Department of Urology, Peking University First Hospital, Beijing China.,Institute of Urology, Peking University, Beijing China.,National Urological Cancer Center, Beijing China
| | - Yuan Liang
- Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing China.,China National Center for Bioinformation, Beijing China
| | - Haitao Niu
- Department of Urology, the Affiliated Hospital of Qingdao University, Qingdao China
| | - Weimin Ci
- Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing China.,China National Center for Bioinformation, Beijing China.,University of the Chinese Academy of Sciences, Beijing China.,Institute of Stem Cells and Regeneration, Chinese Academy of Sciences, Beijing China
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42
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Simchovitz-Gesher A, Soreq H. Pharmaceutical Implications of Sex-Related RNA Divergence in Psychiatric Disorders. Trends Pharmacol Sci 2020; 41:840-850. [DOI: 10.1016/j.tips.2020.09.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 08/29/2020] [Accepted: 09/10/2020] [Indexed: 02/08/2023]
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Rong J, Xu L, Hu Y, Liu F, Yu Y, Guo H, Ni X, Huang Y, Zhao L, Wang Z. Inhibition of let-7b-5p contributes to an anti-tumorigenic macrophage phenotype through the SOCS1/STAT pathway in prostate cancer. Cancer Cell Int 2020; 20:470. [PMID: 33005103 PMCID: PMC7526222 DOI: 10.1186/s12935-020-01563-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 09/17/2020] [Indexed: 12/22/2022] Open
Abstract
Background Dysfunction of microRNAs (miRNAs) is a major cause of aberrant expression of inflammatory cytokines and contributes to macrophage polarization. Proinflammatory M1 macrophages promote T helper (Th) 1 responses and show tumoricidal activity, whereas M2 macrophages display regulatory functions in tissue repair and remodeling and promote Th2 immune responses. Previous studies have shown that miRNA let-7 is associated with cellular differentiation and that the expression of let-7b-5p is significantly augmented in M2 macrophages. However, the mechanism by which let-7b-5p regulates macrophage differentiation in prostate cancer (PCa) remains largely unknown. Methods Human macrophages were induced by blood monocytes from healthy male donors, and M1 macrophages were polarized by stimulating them overnight with 100 ng/ml of lipopolysaccharides and 100 ng/ml of IFN-γ. Conditioned medium from PC-3 cells was used to induce prostatic macrophages (M-CMs) in vitro, and we then transfected let-7b-5p mimics or inhibitors into M1 and M-CMs for 72 h. The expression of cluster of differentiation 206 (CD206) in each group was detected with the High-Throughput Connotation of Imaging System. We used quantitative real-time polymerase chain reaction (qRT-PCR) to examine the expression of the inflammatory cytokines IL-10, IL-12, IL-13, TNF-alpha, and let-7b in macrophages. SOCS1 protein levels were evaluated by ELISA, and the phosphorylation difference in STAT family member proteins was analyzed using CST signal-pathway chip. Phagocytosis by macrophages and the effect of macrophages on the proliferation of prostate cancer PC-3 cells were evaluated with phagocytosis assay or the Cell Counting Kit-8 (CCK-8) and colony formation assay. The relationship between SOCS1 and let-7b-5p was confirmed with a dual-luciferase reporter. Results The expression of cluster of differentiation 206 (CD206, a M2-like macrophage surface molecule) was significantly increased in M1 macrophages treated with let-7b-5p mimics, while CD206 expression was decreased in M-CMs treated with let-7b-5p inhibitors. Overexpression or knockdown of let-7b-5p significantly affected the expression of inflammatory factors in macrophages-including interleukin 10 (IL-10), IL-12, IL-13, and tumor necrosis factor alpha. Let-7b-5p downregulated the expression of suppressor of cytokine signaling 1 (SOCS1) and increased the phosphorylation of signal transducer and activator of transcription 1 (STAT1), STAT3, and STAT5a proteins in M-CMs and M1 macrophages with let-7b-5p mimics relative to the other groups. In addition, with the elevated expression of let-7b-5p, the phagocytosis by macrophages showed a commensurate and significant decrease. As a result, M-CMs treated with let-7b-5p inhibitors reduced the proliferation of PC-3 PCa cells. Conclusions Collectively, these data indicated that let-7b-5p may regulate M2 polarization through the SOCS1/STAT pathway and that reversal of M2 differentiation by let-7b-5p inhibitors enhanced macrophage phagocytosis, ultimately inhibiting the proliferation of PCa cells.
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Affiliation(s)
- Jiping Rong
- Jiangxi Academy of Medical Sciences, and Jiangxi Provincial Key Laboratory of Immunotherapy, Nanchang, China
| | - Lu Xu
- Medical College of Nanchang University, Nanchang, China
| | - Yinying Hu
- Jiangxi Academy of Medical Sciences, and Jiangxi Provincial Key Laboratory of Immunotherapy, Nanchang, China
| | - Fan Liu
- Medical College of Nanchang University, Nanchang, China
| | - Yanrong Yu
- Jiangxi Academy of Medical Sciences, and Jiangxi Provincial Key Laboratory of Immunotherapy, Nanchang, China
| | - Hongyan Guo
- Jiangxi Academy of Medical Sciences, and Jiangxi Provincial Key Laboratory of Immunotherapy, Nanchang, China
| | - Xudong Ni
- Medical College of Nanchang University, Nanchang, China
| | - Yanqin Huang
- Jiangxi Academy of Medical Sciences, and Jiangxi Provincial Key Laboratory of Immunotherapy, Nanchang, China
| | - Lin Zhao
- Jiangxi Academy of Medical Sciences, and Jiangxi Provincial Key Laboratory of Immunotherapy, Nanchang, China
| | - Zhigang Wang
- Jiangxi Academy of Medical Sciences, and Jiangxi Provincial Key Laboratory of Immunotherapy, Nanchang, China
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Zhang H, Zou X, Liu F. Silencing TTTY15 mitigates hypoxia-induced mitochondrial energy metabolism dysfunction and cardiomyocytes apoptosis via TTTY15/let-7i-5p and TLR3/NF-κB pathways. Cell Signal 2020; 76:109779. [PMID: 32926961 DOI: 10.1016/j.cellsig.2020.109779] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 09/08/2020] [Accepted: 09/09/2020] [Indexed: 01/21/2023]
Abstract
Noncoding RNAs are interweaved in pathological processes in myocardial ischemia (MI), such as long noncoding RNA (lncRNA) and microRNAs (miRNAs). The aim of this study was to figure out the role of Testis-specific transcript Y-linked 15 (TTTY15) and let-7i-5p in cell model of MI in cardiomyocytes. Hypoxia-induced cell injury was assessed by Cell counting kit 8 assay, flow cytometry, commercial kits and western blotting. As a result, hypoxia stress induced inhibition on cell proliferation, glucose uptake, and ATP production, and promotion on apoptosis, lactate dehydrogenase (LDH) release, and lactic acid production in human cardiomyocyte AC16 cells. During hypoxia injury, expression of TTTY15 and let-7i-5p was measured by real-time quantitative polymerase chain reaction, and TTTY15 was upregulated, accompanied with let-7i-5p downregulation. Functionally, either silencing TTTY15 or overexpressing let-7i-5p could attenuate hypoxia-induced apoptosis and mitochondrial energy metabolism dysfunction in AC16 cells. Moreover, there was an interaction between TTTY15 and let-7i-5p via target binding, as evidenced by dual-luciferase reporter assay and RNA immunoprecipitation assay. Knockdown of let-7i-5p could counteract the protective role of TTTY15 deletion in hypoxic AC16 cells. Meanwhile, toll-like receptor 3 (TLR3)/nuclear factor-kappa B (NF-κB) signaling was validated by western blotting. Expression of TLR3, tumor necrosis factor receptor-associated factor 6 (TRAF6) and phosphorylated p65 was promoted in hypoxic AC16 cells, which was abrogated by TTTY15 silencing along with let-7i-5p upregulation. Collectively, TTTY15 knockdown protects cardiomyocytes against hypoxia-induced apoptosis and mitochondrial energy metabolism dysfunction in vitro through let-7i-5p/TLR3/NF-κB pathway to suppress.
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Affiliation(s)
- Han Zhang
- Department of Cardiology, Huaihe Hospital, Henan University, Kaifeng, Henan, China.
| | - Xiufang Zou
- Department of Cardiology, Huaihe Hospital, Henan University, Kaifeng, Henan, China
| | - Feng Liu
- Department of Critical Care Medicine, Huaihe Hospital, Henan University, Kaifeng, Henan, China
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45
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Ma R, Gao L, Liu Y, Du P, Chen X, Li G. LncRNA TTTY15 knockdown alleviates H 2O 2-stimulated myocardial cell injury by regulating the miR-98-5p/CRP pathway. Mol Cell Biochem 2020; 476:81-92. [PMID: 32888161 DOI: 10.1007/s11010-020-03887-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 08/14/2020] [Indexed: 12/21/2022]
Abstract
Acute myocardial infarction (AMI) can lead to myocardial injury, and long non-coding RNA (lncRNA) has been found to play an important regulatory role in the process of myocardial injury. However, the role and potential mechanisms of lncRNA testis-specific transcript Y-linked 15 (TTTY15) in AMI-induced myocardial injury has not been fully elucidated. Hydrogen peroxide (H2O2)-induced AMI cell model was built and AMI mice model were constructed. Relative expression levels of TTTY15, miR-98-5p and C-reactive protein (CRP) were determined by quantitative real-time PCR (qRT-PCR). Cell counting kit 8 (CCK8) assay, flow cytometry and enzyme-linked immunosorbent assay (ELISA) were employed to assess cell viability, apoptosis, inflammatory response and oxidative stress. Western blot (WB) analysis was used to assess the protein expression levels. The mechanism of TTTY15 was confirmed by dual-luciferase reporter assay and RNA immunoprecipitation (RIP) assay. Our results revealed that TTTY15 was upregulated and miR-98-5p was downregulated in AMI patients and H2O2-stimulated myocardial cells. Knockdown of TTTY15 could alleviate H2O2-stimulated myocardial cell injury in vitro and AMI progression in vivo. Bioinformatics analysis and the rescue experiments confirmed that TTTY15 positively regulated H2O2-induced myocardial cell injury via regulating CRP by sponging miR-98-5p. Our research proposed that lncRNA TTTY15 promoted myocardial cell injury by regulating the miR-98-5p/CRP axis, suggesting that TTTY15 might be a potential target for alleviating AMI-caused myocardial cell injury.
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Affiliation(s)
- Rufei Ma
- Department of Clinical Laboratory, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, No.7 Weiwu Road, Zhengzhou, 450003, Henan, China
| | - Lan Gao
- Department of Clinical Laboratory, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, No.7 Weiwu Road, Zhengzhou, 450003, Henan, China
| | - Yanhong Liu
- Department of Clinical Laboratory, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, No.7 Weiwu Road, Zhengzhou, 450003, Henan, China
| | - Pengqiang Du
- Department of Medicine, Fuwai Central China Cardiovascular Hospital, Zhengzhou, 450046, Henan, China
| | - Xiaozhen Chen
- Department of Cardiology, Fuwai Central China Cardiovascular Hospital, Zhengzhou, 450046, Henan, China
| | - Gang Li
- Department of Clinical Laboratory, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, No.7 Weiwu Road, Zhengzhou, 450003, Henan, China.
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Dai F, Wu Y, Lu Y, An C, Zheng X, Dai L, Guo Y, Zhang L, Li H, Xu W, Gao W. Crosstalk between RNA m 6A Modification and Non-coding RNA Contributes to Cancer Growth and Progression. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 22:62-71. [PMID: 32911345 PMCID: PMC7486578 DOI: 10.1016/j.omtn.2020.08.004] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 06/04/2020] [Accepted: 08/07/2020] [Indexed: 12/17/2022]
Abstract
N6-methyladenosine (m6A) is the most common RNA modification and has an important role in normal development and tumorigenesis. The abnormal expression of m6A regulators can lead to an imbalance in m6A levels in cancer cells, leading to the dysregulated expression of oncogenes and tumor suppressor genes that may contribute to cancer development, patient response to chemoradiotherapy, and clinical prognosis. Recent studies demonstrate that non-coding RNAs are involved in epigenetic modification of both DNA and RNA in tumor cells, and may also affect the development and progression of cancer by targeting m6A regulators. In this review, we describe the functional crosstalk between m6A and non-coding RNAs, particularly microRNA, long non-coding RNA, and circular RNA, and illustrate their roles in tumor regulation. Finally, we discuss the significance of non-coding RNA and m6A modification in the diagnosis, treatment, and prognosis of cancer patients, as well as potential future research directions.
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Affiliation(s)
- Fengsheng Dai
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan 030001, P. R. China; Department of Otolaryngology Head & Neck Surgery, First Hospital of Shanxi Medical University, Taiyuan 030001, P. R. China
| | - Yongyan Wu
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan 030001, P. R. China; Shanxi Province Clinical Medical Research Center for Precision Medicine of Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan 030001, P. R. China; Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan 030001, P. R. China.
| | - Yan Lu
- Department of Otolaryngology Head & Neck Surgery, The First Hospital of Jinzhou Medical University, Jinzhou 121001, P. R. China
| | - Changming An
- Department of Head and Neck Surgery, Cancer Hospital, National Cancer Center, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100021, P. R. China
| | - Xiwang Zheng
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan 030001, P. R. China; Shanxi Province Clinical Medical Research Center for Precision Medicine of Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan 030001, P. R. China
| | - Li Dai
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan 030001, P. R. China; Department of Otolaryngology Head & Neck Surgery, First Hospital of Shanxi Medical University, Taiyuan 030001, P. R. China
| | - Yujia Guo
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan 030001, P. R. China; Shanxi Province Clinical Medical Research Center for Precision Medicine of Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan 030001, P. R. China
| | - Linshi Zhang
- Department of Thyroid Surgery, Second Affiliated Hospital of Zhejiang University, Hangzhou 310009, P. R. China
| | - Huizheng Li
- Department of Otolaryngology Head & Neck Surgery, Dalian Municipal Friendship Hospital of Dalian Medical University, Dalian 116100, P. R. China
| | - Wei Xu
- Department of Head & Neck Surgery, Shandong Provincial ENT Hospital Affiliated to Shandong University, Jinan 250022, P. R. China; Shandong Provincial Institute of Otolaryngology, Jinan 250022, P. R. China; Key Laboratory of Otolaryngology, Ministry of Health, Shandong University, Jinan 250022, P. R. China.
| | - Wei Gao
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan 030001, P. R. China; Shanxi Province Clinical Medical Research Center for Precision Medicine of Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan 030001, P. R. China; Department of Otolaryngology Head & Neck Surgery, First Hospital of Shanxi Medical University, Taiyuan 030001, P. R. China; Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan 030001, P. R. China.
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Long non-coding RNA CCDC144NL-AS1 sponges miR-143-3p and regulates MAP3K7 by acting as a competing endogenous RNA in gastric cancer. Cell Death Dis 2020; 11:521. [PMID: 32647147 PMCID: PMC7347562 DOI: 10.1038/s41419-020-02740-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 06/23/2020] [Accepted: 06/29/2020] [Indexed: 12/24/2022]
Abstract
Gastric cancer (GC) has been one of the most leading cause of cancer-death worldwide. Long non-coding RNAs (lncRNAs) have been found to be related with the carcinogenesis and the development of various cancers, including GC. However, there are still many GC-related lncRNAs functional roles and molecular mechanisms that have not yet been clearly studied. Herein, we report lncRNA CCDC144NL-AS1, which has not been explored in GC, and it is markedly upregulated in GC tissues, which may serve as an independent predictor of poor prognosis. We found that CCDC144NL-AS1 expression was significantly positively associated with a larger tumor size and more pronounced lymph node metastasis. Through a series of in vivo and in vitro functional experiments, we observed that CCDC144NL-AS1 could facilitate cell proliferation, invasion and migration and inhibit cell apoptosis in GC. Further mechanism investigation revealed that CCDC144NL-AS1 acted as a competing endogenous RNA (ceRNA) for sponging miR-143-3p and upregulated the expression of its direct endogenous target MAP3K7 in GC. Taken together, our results elucidate the oncogenic roles of CCDC144NL-AS1/miR-143-3p/MAP3K7 axis in GC progression, providing inspiration for further understanding of the mechanism of GC and making CCDC144NL-AS1 as a potential novel diagnostic and therapeutic target for GC.
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Brownmiller T, Juric JA, Ivey AD, Harvey BM, Westemeier ES, Winters MT, Stevens AM, Stanley AN, Hayes KE, Sprowls SA, Ammer ASG, Walker M, Bey EA, Wu X, Lim ZF, Zhu L, Wen S, Hu G, Ma PC, Martinez I. Y Chromosome LncRNA Are Involved in Radiation Response of Male Non-Small Cell Lung Cancer Cells. Cancer Res 2020; 80:4046-4057. [PMID: 32616503 DOI: 10.1158/0008-5472.can-19-4032] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 04/01/2020] [Accepted: 06/29/2020] [Indexed: 12/15/2022]
Abstract
Numerous studies have implicated changes in the Y chromosome in male cancers, yet few have investigated the biological importance of Y chromosome noncoding RNA. Here we identify a group of Y chromosome-expressed long noncoding RNA (lncRNA) that are involved in male non-small cell lung cancer (NSCLC) radiation sensitivity. Radiosensitive male NSCLC cell lines demonstrated a dose-dependent induction of linc-SPRY3-2/3/4 following irradiation, which was not observed in radioresistant male NSCLC cell lines. Cytogenetics revealed the loss of chromosome Y (LOY) in the radioresistant male NSCLC cell lines. Gain- and loss-of-function experiments indicated that linc-SPRY3-2/3/4 transcripts affect cell viability and apoptosis. Computational prediction of RNA binding proteins (RBP) motifs and UV-cross-linking and immunoprecipitation (CLIP) assays identified IGF2BP3, an RBP involved in mRNA stability, as a binding partner for linc-SPRY3-2/3/4 RNA. The presence of linc-SPRY3-2/3/4 reduced the half-life of known IGF2BP3 binding mRNA, such as the antiapoptotic HMGA2 mRNA, as well as the oncogenic c-MYC mRNA. Assessment of Y chromosome in NSCLC tissue microarrays and expression of linc-SPRY3-2/3/4 in NSCLC RNA-seq and microarray data revealed a negative correlation between the loss of the Y chromosome or linc-SPRY3-2/3/4 and overall survival. Thus, linc-SPRY3-2/3/4 expression and LOY could represent an important marker of radiotherapy in NSCLC. SIGNIFICANCE: This study describes previously unknown Y chromosome-expressed lncRNA regulators of radiation response in male NSCLC and show a correlation between loss of chromosome Y and radioresistance. GRAPHICAL ABSTRACT: http://cancerres.aacrjournals.org/content/canres/80/19/4046/F1.large.jpg.
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Affiliation(s)
- Tayvia Brownmiller
- Department of Microbiology, Immunology & Cell Biology, West Virginia University Cancer Institute, School of Medicine, West Virginia University, Morgantown, West Virginia
| | - Jamie A Juric
- Department of Microbiology, Immunology & Cell Biology, West Virginia University Cancer Institute, School of Medicine, West Virginia University, Morgantown, West Virginia
| | - Abby D Ivey
- Department of Microbiology, Immunology & Cell Biology, West Virginia University Cancer Institute, School of Medicine, West Virginia University, Morgantown, West Virginia
| | - Brandon M Harvey
- Department of Microbiology, Immunology & Cell Biology, West Virginia University Cancer Institute, School of Medicine, West Virginia University, Morgantown, West Virginia
| | - Emily S Westemeier
- Department of Microbiology, Immunology & Cell Biology, West Virginia University Cancer Institute, School of Medicine, West Virginia University, Morgantown, West Virginia
| | - Michael T Winters
- Department of Microbiology, Immunology & Cell Biology, West Virginia University Cancer Institute, School of Medicine, West Virginia University, Morgantown, West Virginia
| | - Alyson M Stevens
- Department of Microbiology, Immunology & Cell Biology, West Virginia University Cancer Institute, School of Medicine, West Virginia University, Morgantown, West Virginia
| | - Alana N Stanley
- Department of Microbiology, Immunology & Cell Biology, West Virginia University Cancer Institute, School of Medicine, West Virginia University, Morgantown, West Virginia
| | - Karen E Hayes
- Modulation Therapeutics, West Virginia University, Morgantown, West Virginia
| | - Samuel A Sprowls
- Department of Pharmaceutical Sciences, School of Pharmacy, West Virginia University, Morgantown, West Virginia
| | - Amanda S Gatesman Ammer
- Department of Microbiology, Immunology & Cell Biology, West Virginia University Cancer Institute, School of Medicine, West Virginia University, Morgantown, West Virginia
| | - Mackenzee Walker
- Department of Microbiology, Immunology & Cell Biology, West Virginia University Cancer Institute, School of Medicine, West Virginia University, Morgantown, West Virginia
| | - Erik A Bey
- Department of Biochemistry and Molecular Biology, School of Medicine, Indiana University, Indianapolis, Indiana
| | - Xiaoliang Wu
- Penn State Cancer Institute, Penn State Health Milton S. Hershey Medical Center, Pennsylvania State University, Hershey, Pennsylvania
| | - Zuan-Fu Lim
- Penn State Cancer Institute, Penn State Health Milton S. Hershey Medical Center, Pennsylvania State University, Hershey, Pennsylvania.,Cancer Cell Biology Program, West Virginia University School of Graduate Studies, West Virginia University, Morgantown, West Virginia
| | - Lin Zhu
- Penn State Cancer Institute, Penn State Health Milton S. Hershey Medical Center, Pennsylvania State University, Hershey, Pennsylvania
| | - Sijin Wen
- Department of Biostatistics, School of Public Health, West Virginia University, Morgantown, West Virginia
| | - Gangqing Hu
- Department of Microbiology, Immunology & Cell Biology, West Virginia University Cancer Institute, School of Medicine, West Virginia University, Morgantown, West Virginia.,Bioinformatics Core, West Virginia University, Morgantown, West Virginia
| | - Patrick C Ma
- Penn State Cancer Institute, Penn State Health Milton S. Hershey Medical Center, Pennsylvania State University, Hershey, Pennsylvania
| | - Ivan Martinez
- Department of Microbiology, Immunology & Cell Biology, West Virginia University Cancer Institute, School of Medicine, West Virginia University, Morgantown, West Virginia.
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Gao L, Nie X, Zhang W, Gou R, Hu Y, Qi Y, Li X, Liu Q, Liu J, Lin B. Identification of long noncoding RNA RP11-89K21.1 and RP11-357H14.17 as prognostic signature of endometrial carcinoma via integrated bioinformatics analysis. Cancer Cell Int 2020; 20:268. [PMID: 32587476 PMCID: PMC7313119 DOI: 10.1186/s12935-020-01359-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 06/16/2020] [Indexed: 12/15/2022] Open
Abstract
Background Endometrial carcinoma (EC) is one of the most common malignant tumors in gynecology. The potential functions and mechanisms of long noncoding RNAs (lncRNAs) in the occurrence and progression of EC remains unclear. It’s meaningful to explore lncRNAs signature for providing prognostic value of EC. Methods The differentially expressed lncRNAs and their prognostic values in EC were investigated based on The Cancer Genome Atlas (TCGA) database; the transcriptional factors (TFs), the competing endogenous RNA (ceRNA) mechanism, functional regulatory network and immune infiltration of RP11-89K21.1 and RP11-357H14.17 were further explored by various bioinformatics tools and databases. Results We firstly identified high expression of RP11-89K21.1 and RP11-357H14.17 were closely associated with shorten overall survival (OS) and poor prognosis in patients with EC. We also elucidated the networks of transcription factor and co-expression genes associated with RP11-89K21.1 and RP11-357H14.17. Furthermore, the ceRNA network mechanism was successfully constructed through 2 lncRNAs (RP11-89K21.1 and RP11-357H14.17), 11 miRNAs and 183 mRNAs. Functional enrichment analysis revealed that the targeting genes of RP11-89K21.1 and RP11-357H14.17 were strongly associated with microRNAs in cancer, vessel development, growth regulation, growth factor and cell differentiation, and involved in pathways including pathways in cancer, microRNAs in cancer and apoptotic signaling pathway. Conclusions We demonstrated for the first time that RP11-89K21.1 and RP11-357H14.17 may play crucial roles in the occurrence, development and malignant biological behavior of EC, and can be regarded as potential prognostic biomarkers for EC.
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Affiliation(s)
- Lingling Gao
- Department of Obstetrics and Gynaecology, Shengjing Hospital of China Medical University, No.36 Sanhao Street, Heping District, Shenyang, 110004 Liaoning China.,Key Laboratory of Maternal-Fetal Medicine of Liaoning Province, Key Laboratory of Obstetrics and Gynecology of Higher Education of Liaoning Province, Liaoning, China
| | - Xin Nie
- Department of Obstetrics and Gynaecology, Shengjing Hospital of China Medical University, No.36 Sanhao Street, Heping District, Shenyang, 110004 Liaoning China.,Key Laboratory of Maternal-Fetal Medicine of Liaoning Province, Key Laboratory of Obstetrics and Gynecology of Higher Education of Liaoning Province, Liaoning, China
| | - Wenchao Zhang
- Department of Obstetrics and Gynaecology, Shengjing Hospital of China Medical University, No.36 Sanhao Street, Heping District, Shenyang, 110004 Liaoning China.,Key Laboratory of Maternal-Fetal Medicine of Liaoning Province, Key Laboratory of Obstetrics and Gynecology of Higher Education of Liaoning Province, Liaoning, China
| | - Rui Gou
- Department of Obstetrics and Gynaecology, Shengjing Hospital of China Medical University, No.36 Sanhao Street, Heping District, Shenyang, 110004 Liaoning China.,Key Laboratory of Maternal-Fetal Medicine of Liaoning Province, Key Laboratory of Obstetrics and Gynecology of Higher Education of Liaoning Province, Liaoning, China
| | - Yuexin Hu
- Department of Obstetrics and Gynaecology, Shengjing Hospital of China Medical University, No.36 Sanhao Street, Heping District, Shenyang, 110004 Liaoning China.,Key Laboratory of Maternal-Fetal Medicine of Liaoning Province, Key Laboratory of Obstetrics and Gynecology of Higher Education of Liaoning Province, Liaoning, China
| | - Yue Qi
- Department of Obstetrics and Gynaecology, Shengjing Hospital of China Medical University, No.36 Sanhao Street, Heping District, Shenyang, 110004 Liaoning China.,Key Laboratory of Maternal-Fetal Medicine of Liaoning Province, Key Laboratory of Obstetrics and Gynecology of Higher Education of Liaoning Province, Liaoning, China
| | - Xiao Li
- Department of Obstetrics and Gynaecology, Shengjing Hospital of China Medical University, No.36 Sanhao Street, Heping District, Shenyang, 110004 Liaoning China.,Key Laboratory of Maternal-Fetal Medicine of Liaoning Province, Key Laboratory of Obstetrics and Gynecology of Higher Education of Liaoning Province, Liaoning, China
| | - Qing Liu
- Department of Obstetrics and Gynaecology, Shengjing Hospital of China Medical University, No.36 Sanhao Street, Heping District, Shenyang, 110004 Liaoning China.,Key Laboratory of Maternal-Fetal Medicine of Liaoning Province, Key Laboratory of Obstetrics and Gynecology of Higher Education of Liaoning Province, Liaoning, China
| | - Juanjuan Liu
- Department of Obstetrics and Gynaecology, Shengjing Hospital of China Medical University, No.36 Sanhao Street, Heping District, Shenyang, 110004 Liaoning China.,Key Laboratory of Maternal-Fetal Medicine of Liaoning Province, Key Laboratory of Obstetrics and Gynecology of Higher Education of Liaoning Province, Liaoning, China
| | - Bei Lin
- Department of Obstetrics and Gynaecology, Shengjing Hospital of China Medical University, No.36 Sanhao Street, Heping District, Shenyang, 110004 Liaoning China.,Key Laboratory of Maternal-Fetal Medicine of Liaoning Province, Key Laboratory of Obstetrics and Gynecology of Higher Education of Liaoning Province, Liaoning, China
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50
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Zhang W, Shi X, Chen R, Zhu Y, Peng S, Chang Y, Nian X, Xiao G, Fang Z, Li Y, Cao Z, Zhao L, Liu G, Sun Y, Ren S. Novel Long Non-coding RNA lncAMPC Promotes Metastasis and Immunosuppression in Prostate Cancer by Stimulating LIF/LIFR Expression. Mol Ther 2020; 28:2473-2487. [PMID: 32592689 DOI: 10.1016/j.ymthe.2020.06.013] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 05/17/2020] [Accepted: 06/10/2020] [Indexed: 11/29/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) participate in the development and progression of prostate cancer (PCa). We aimd to identify a novel lncRNA, named lncRNA activated in metastatic PCa (lncAMPC), and investigate its mechanisms and clinical significance in PCa. First, the biological capacity of lncAMPC in PCa was demonstrated both in vitro and in vivo. The lncAMPC was overexpressed in tumor tissue and urine of metastatic PCa patients and promoted PCa tumorigenesis and metastasis. Then, a mechanism study was conducted to determine how the lncAMPC-activated pathway contributed to PCa metastasis and immunosuppression. In the cytoplasm, lncAMPC upregulated LIF expression by sponging miR-637 and inhibiting its activity. In the nucleus, lncAMPC enhanced LIFR transcription by decoying histone H1.2 away from the upstream sequence of the LIFR gene. The lncAMPC-activated LIF/LIFR expressions stimulated the Jak1-STAT3 pathway to simultaneously maintain programmed death-ligand 1 (PD-L1) protein stability and promote metastasis-associated gene expression. Finally, the prognostic value of the expression of lncAMPC and its downstream genes in PCa patients was evaluated. High LIF/LIFR levels indicated shorter biochemical recurrence-free survival among patients who underwent radical prostatectomy. Therefore, the lncAMPC/LIF/LIFR axis plays a critical role in PCa metastasis and immunosuppression and may serve as a prognostic biomarker and potential therapeutic target.
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Affiliation(s)
- Wei Zhang
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai 200433, China
| | - Xiaolei Shi
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai 200433, China
| | - Rui Chen
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai 200433, China
| | - Yasheng Zhu
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai 200433, China
| | - Shihong Peng
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Yifan Chang
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai 200433, China
| | - Xinwen Nian
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai 200433, China
| | - Guang'an Xiao
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai 200433, China
| | - Ziyu Fang
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai 200433, China
| | - Yaoming Li
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai 200433, China; Department of Urology, Daping Hospital, Third Military Medical University, Chongqing, China
| | - Zhexu Cao
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai 200433, China
| | - Lin Zhao
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai 200433, China
| | - Guang Liu
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai 200433, China; Department of Urology, Jiangsu Armed Police General Hospital, Yangzhou, Jiangsu, China
| | - Yinghao Sun
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai 200433, China.
| | - Shancheng Ren
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai 200433, China.
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