1
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Nemeth K, Bayraktar R, Ferracin M, Calin GA. Non-coding RNAs in disease: from mechanisms to therapeutics. Nat Rev Genet 2024; 25:211-232. [PMID: 37968332 DOI: 10.1038/s41576-023-00662-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/19/2023] [Indexed: 11/17/2023]
Abstract
Non-coding RNAs (ncRNAs) are a heterogeneous group of transcripts that, by definition, are not translated into proteins. Since their discovery, ncRNAs have emerged as important regulators of multiple biological functions across a range of cell types and tissues, and their dysregulation has been implicated in disease. Notably, much research has focused on the link between microRNAs (miRNAs) and human cancers, although other ncRNAs, such as long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs), are also emerging as relevant contributors to human disease. In this Review, we summarize our current understanding of the roles of miRNAs, lncRNAs and circRNAs in cancer and other major human diseases, notably cardiovascular, neurological and infectious diseases. Further, we discuss the potential use of ncRNAs as biomarkers of disease and as therapeutic targets.
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Affiliation(s)
- Kinga Nemeth
- Translational Molecular Pathology Department, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Recep Bayraktar
- Translational Molecular Pathology Department, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Manuela Ferracin
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy.
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy.
| | - George A Calin
- Translational Molecular Pathology Department, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- The RNA Interference and Non-coding RNA Center, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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2
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Lee KH, Kim S, Song J, Han SR, Kim JH, Lee SW. Efficient circular RNA engineering by end-to-end self-targeting and splicing reaction using Tetrahymena group I intron ribozyme. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 33:587-598. [PMID: 37637208 PMCID: PMC10457212 DOI: 10.1016/j.omtn.2023.07.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 07/28/2023] [Indexed: 08/29/2023]
Abstract
Circular RNA (circRNA) has various advantages over linear mRNA that is gaining success as a new vaccine and therapeutic agent. Thus, circRNA and its engineering methods have attracted attention recently. In this study, we developed a new in vitro circRNA engineering method by end-to-end self-targeting and splicing (STS) reaction using Tetrahymena group I intron ribozyme. We found that only the P1 helix structure of the group I intron was enough to generate circRNA by STS reaction. The efficacy of circRNA generation by STS reaction was comparable to the method using a permuted intron-exon (PIE) reaction. However, an end-to-end STS reaction does not introduce any extraneous fragments, such as an intronic scar that can be generated by PIE reaction and might trigger unwanted innate immune responses in cells, into circRNA sequences. Moreover, generated circRNA was efficiently purified by ion pair-reversed phase high-pressure liquid chromatography and used for cell-based analysis. Of note, efficient protein expression and stability with least innate immune induction by the circRNA with coxsackievirus B3 IRES were observed in cells. In conclusion, our new in vitro circRNA strategy can effectively generate highly useful circRNAs in vitro as an alternative circRNA engineering method.
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Affiliation(s)
- Kyung Hyun Lee
- R&D Center, Rznomics Inc, Seongnam 13486, Republic of Korea
| | - Seongcheol Kim
- R&D Center, Rznomics Inc, Seongnam 13486, Republic of Korea
| | - Jaehwi Song
- R&D Center, Rznomics Inc, Seongnam 13486, Republic of Korea
| | - Seung Ryul Han
- R&D Center, Rznomics Inc, Seongnam 13486, Republic of Korea
| | - Ji Hyun Kim
- R&D Center, Rznomics Inc, Seongnam 13486, Republic of Korea
| | - Seong-Wook Lee
- R&D Center, Rznomics Inc, Seongnam 13486, Republic of Korea
- Department of Bioconvergence Engineering, Research Institute of Advanced Omics, Dankook University, Yongin 16890, Republic of Korea
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3
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Wang S, Ying Y, Ma X, Wang W, Wang X, Xie L. Diverse Roles and Therapeutic Potentials of Circular RNAs in Urological Cancers. Front Mol Biosci 2021; 8:761698. [PMID: 34869591 PMCID: PMC8640215 DOI: 10.3389/fmolb.2021.761698] [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: 08/20/2021] [Accepted: 10/20/2021] [Indexed: 12/14/2022] Open
Abstract
Circular RNAs (circRNAs) are a novel class of noncoding RNAs, which are mainly formed as a loop structure at the exons caused by noncanonical splicing; they are much more stable than linear transcripts; recent reports have suggested that the dysregulation of circRNAs is associated with the occurrence and development of diseases, especially various human malignancies. Emerging evidence demonstrated that a large number of circRNAs play a vital role in a series of biological processes such as tumor cell proliferation, migration, drug resistance, and immune escape. Additionally, circRNAs were also reported to be potential prognostic and diagnostic biomarkers in cancers. In this work, we systematically summarize the biogenesis and characteristics of circRNAs, paying special attention to potential mechanisms and clinical applications of circRNAs in urological cancers, which may help develop potential therapy targets for urological cancers in the future.
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Affiliation(s)
- Song Wang
- Department of Urology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yufan Ying
- Department of Urology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Xueyou Ma
- Department of Urology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Weiyu Wang
- Department of Urology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Xiao Wang
- Department of Urology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Liping Xie
- Department of Urology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
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4
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Li X, Li Z, Liu P, Ai S, Sun F, Hu Q, Dong Y, Xia X, Guan W, Liu S. Novel CircRNAs in Hub ceRNA Axis Regulate Gastric Cancer Prognosis and Microenvironment. Front Med (Lausanne) 2021; 8:771206. [PMID: 34820403 PMCID: PMC8606568 DOI: 10.3389/fmed.2021.771206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 10/08/2021] [Indexed: 12/24/2022] Open
Abstract
Gastric cancer (GC) is one of the most prevalent malignancies with an unfavorable survival rate. Immunotherapy may contribute to a better prognosis. However, several phase III trials failed. Circular RNA (circRNA) is a novel type of non-coding RNA, plays a vital role in the progression of tumors. The expression and function of circRNA in the GC immune microenvironment remain obscure. In this study, we utilized a bioinformatic analysis to construct a circRNA/microRNA (miRNA)/messenger RNA (mRNA) network involved in the progression and prognosis of GC. CircRNA DYRK1A_017, circRNA FLNA_118, miR-6512-3p, miR-6270-5p, and VCAN were identified as the key molecules in the hub regulatory axis. Dysregulation of this axis contributed to the cancer-associated signaling pathways (epithelial-mesenchymal transition [EMT], Nuclear factor kappa β-Tumor necrosis factor-α (NFκβ-TNFα) signaling, and angiogenesis) and aberrant immune microenvironment (infiltration by tumor associated macrophage, regulatory T cell, and mast cell). More importantly, the immunosuppressive tumor microenvironment may reveal the mechanism of novel circRNAs in tumors and serve as the target of immunotherapy.
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Affiliation(s)
- Xianghui Li
- Department of Gastrointestinal Surgery, Affiliated Drum Tower Hospital, Medical School of Nanjing University, Nanjing, China
| | - Zhiyan Li
- Department of Gastrointestinal Surgery, Affiliated Drum Tower Hospital, Medical School of Nanjing University, Nanjing, China
| | - Ping Liu
- Wuxi People's Hospital Affiliated to Nanjing Medical University, Wuxi, China
| | - Shichao Ai
- Department of Gastrointestinal Surgery, Affiliated Drum Tower Hospital, Medical School of Nanjing University, Nanjing, China
| | - Feng Sun
- Department of Gastrointestinal Surgery, Affiliated Drum Tower Hospital, Medical School of Nanjing University, Nanjing, China
| | - Qiongyuan Hu
- Department of Gastrointestinal Surgery, Affiliated Drum Tower Hospital, Medical School of Nanjing University, Nanjing, China
| | - Yuxiang Dong
- First Clinical Medical College of Nanjing Medical University, Nanjing, China
| | - Xuefeng Xia
- Department of Gastrointestinal Surgery, Affiliated Drum Tower Hospital, Medical School of Nanjing University, Nanjing, China
| | - Wenxian Guan
- Department of Gastrointestinal Surgery, Affiliated Drum Tower Hospital, Medical School of Nanjing University, Nanjing, China
| | - Song Liu
- Department of Gastrointestinal Surgery, Affiliated Drum Tower Hospital, Medical School of Nanjing University, Nanjing, China
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5
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Wei Y, Yang X, Gao L, Yang J, Zheng L, Gao L, Zhou X, Xiang X, Zhang J, Yi C. Identification of potential immune-related circRNA-miRNA-mRNA regulatory network in cutaneous squamous cell carcinoma. Am J Cancer Res 2021; 11:4826-4843. [PMID: 34765295 PMCID: PMC8569358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 09/21/2021] [Indexed: 06/13/2023] Open
Abstract
Circulating RNAs (circRNAs) are involved in tumor development and progression by participating in immune regulation. Nevertheless, the circRNAs expression profiles and their roles on the immunomodulatory effects in cutaneous squamous cell carcinoma (cSCC) have rarely been studied. In our study, we identified the differentially expressed circRNAs (DEcircRNAs), miRNAs (DEmiRNAs), mRNAs (DEmRNAs) in cSCC and established the circRNA competing endogenous RNAs (ceRNAs) network. Subsequently, the hub differentially expressed immune-related genes were identified and validated by immunochemistry as well as the GO and KEGG pathway analysis were performed. 54 differentially expressed circRNAs were identified and hub differentially expressed immune-related genes were identified and they were mostly associated with immune response in the progression of cSCC. Our results indicated that the potential immune-related circRNA-miRNA-mRNA network may assist in understanding the molecular mechanisms underlying the carcinogenesis and progression in cSCC. Moreover, the immune-related genes may provide an insight into the pathogenesis, molecular biomarkers, and potential therapeutic targets for cSCC patients.
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Affiliation(s)
- Yuanfeng Wei
- Department of Medical Oncology, Cancer Center, West China Hospital, Sichuan UniversityChengdu 610041, Sichuan, China
| | - Xi Yang
- Department of Medical Oncology, Cancer Center, West China Hospital, Sichuan UniversityChengdu 610041, Sichuan, China
| | - Limin Gao
- Department of Pathology, West China Hospital, Sichuan UniversityChengdu 610041, Sichuan, China
| | - Ju Yang
- Department of Pathophysiology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan UniversityChengdu 610041, Sichuan, China
| | - Lingnan Zheng
- Department of Medical Oncology, Cancer Center, West China Hospital, Sichuan UniversityChengdu 610041, Sichuan, China
| | - Ling Gao
- Department of Medical Oncology, Cancer Center, West China Hospital, Sichuan UniversityChengdu 610041, Sichuan, China
| | - Xiaohan Zhou
- Department of Medical Oncology, Cancer Center, West China Hospital, Sichuan UniversityChengdu 610041, Sichuan, China
| | - Xiaoyu Xiang
- Department of Pathology, West China Hospital, Sichuan UniversityChengdu 610041, Sichuan, China
| | - Jie Zhang
- Lab of Experimental Oncology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation CenterChengdu 610041, Sichuan, China
| | - Cheng Yi
- Department of Medical Oncology, Cancer Center, West China Hospital, Sichuan UniversityChengdu 610041, Sichuan, China
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6
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Yang Q, Li F, He AT, Yang BB. Circular RNAs: Expression, localization, and therapeutic potentials. Mol Ther 2021; 29:1683-1702. [PMID: 33484969 PMCID: PMC8116570 DOI: 10.1016/j.ymthe.2021.01.018] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 12/15/2020] [Accepted: 01/13/2021] [Indexed: 12/14/2022] Open
Abstract
Circular RNAs (circRNAs) are RNAs with a unique circular structure that is generated from back-splicing processes. These circular molecules were discovered more than 40 years ago but failed to raise scientific interest until lately. Increasing studies have found that these circular RNAs might not just be byproducts of the splicing process but possess important regulatory functions through different cellular events. Most circular RNAs are currently being studied in the field of cancer, and many of them have been confirmed to be involved in the process of tumorigenesis. However, many circular RNAs are implicated in the developmental stages of diseases other than cancer. In this review, we focus on discussing the role of circular RNAs in non-cancer diseases, especially in cardiovascular diseases. Following the summary of the life cycle of circRNAs, we provide input on studying circRNA-protein interactions based on our experience, which modulate protein translocation. Furthermore, we outline the potential of circRNAs to be potent biomarkers, effective therapeutic targets, and potential treatments in cardiovascular diseases as well as other non-cancer fields.
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Affiliation(s)
- Qiwei Yang
- Sunnybrook Research Institute, Toronto, ON, Canada; Medical Research Center, Second Hospital of Jilin University, Changchun, China; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M4N 3M5, Canada
| | - Feiya Li
- Sunnybrook Research Institute, Toronto, ON, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M4N 3M5, Canada
| | - Alina T He
- Sunnybrook Research Institute, Toronto, ON, Canada
| | - Burton B Yang
- Sunnybrook Research Institute, Toronto, ON, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M4N 3M5, Canada.
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7
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Fang N, Ding GW, Ding H, Li J, Liu C, Lv L, Shi YJ. Research Progress of Circular RNA in Gastrointestinal Tumors. Front Oncol 2021; 11:665246. [PMID: 33937077 PMCID: PMC8082141 DOI: 10.3389/fonc.2021.665246] [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: 02/07/2021] [Accepted: 03/15/2021] [Indexed: 01/17/2023] Open
Abstract
circular RNA (circRNA) is a closed ring structure formed by cyclic covalent bonds connecting the 5’-end and 3’-end of pre-mRNA. circRNA is widely distributed in eukaryotic cells. Recent studies have shown that circRNA is involved in the pathogenesis and development of multiple types of diseases, including tumors. circRNA is specifically expressed in tissues. And the stability of circRNA is higher than that of linear RNA, which can play biological roles through sponge adsorption of miRNA, interaction with RNA binding protein, regulation of gene transcription, the mRNA and protein translation brake, and translation of protein and peptides. These characteristics render circRNAs as biomarkers and therapeutic targets of tumors. Gastrointestinal tumors are common malignancies worldwide, which seriously threaten human health. In this review, we summarize the generation and biological characteristics of circRNA, molecular regulation mechanism and related effects of circRNA in gastrointestinal tumors.
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Affiliation(s)
- Na Fang
- Department of Oncology, The Affiliated People's Hospital, Jiangsu University, Zhenjiang, China
| | - Guo-Wen Ding
- Department of Thoracic and Cardiovascular Surgery, The Affiliated People's Hospital, Jiangsu University, Zhenjiang, China
| | - Hao Ding
- Department of Respiratory, The Affiliated People's Hospital, Jiangsu University, Zhenjiang, China
| | - Juan Li
- Department of Oncology, The Affiliated People's Hospital, Jiangsu University, Zhenjiang, China
| | - Chao Liu
- Department of Thoracic and Cardiovascular Surgery, The Affiliated People's Hospital, Jiangsu University, Zhenjiang, China
| | - Lu Lv
- Department of Thoracic and Cardiovascular Surgery, The Affiliated People's Hospital, Jiangsu University, Zhenjiang, China
| | - Yi-Jun Shi
- Department of Thoracic and Cardiovascular Surgery, The Affiliated People's Hospital, Jiangsu University, Zhenjiang, China
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8
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Qiu W, Zhang Q, Zhang R, Lu Y, Wang X, Tian H, Yang Y, Gu Z, Gao Y, Yang X, Cui G, Sun B, Peng Y, Deng H, Peng H, Yang A, Yang YG, Yang P. N 6-methyladenosine RNA modification suppresses antiviral innate sensing pathways via reshaping double-stranded RNA. Nat Commun 2021; 12:1582. [PMID: 33707441 PMCID: PMC7952553 DOI: 10.1038/s41467-021-21904-y] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Accepted: 02/19/2021] [Indexed: 12/11/2022] Open
Abstract
Double-stranded RNA (dsRNA) is a virus-encoded signature capable of triggering intracellular Rig-like receptors (RLR) to activate antiviral signaling, but whether intercellular dsRNA structural reshaping mediated by the N6-methyladenosine (m6A) modification modulates this process remains largely unknown. Here, we show that, in response to infection by the RNA virus Vesicular Stomatitis Virus (VSV), the m6A methyltransferase METTL3 translocates into the cytoplasm to increase m6A modification on virus-derived transcripts and decrease viral dsRNA formation, thereby reducing virus-sensing efficacy by RLRs such as RIG-I and MDA5 and dampening antiviral immune signaling. Meanwhile, the genetic ablation of METTL3 in monocyte or hepatocyte causes enhanced type I IFN expression and accelerates VSV clearance. Our findings thus implicate METTL3-mediated m6A RNA modification on viral RNAs as a negative regulator for innate sensing pathways of dsRNA, and also hint METTL3 as a potential therapeutic target for the modulation of anti-viral immunity.
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Affiliation(s)
- Weinan Qiu
- Key Laboratory of Infection and Immunity of CAS, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Qingyang Zhang
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, China National Center for Bioinformation, Beijing Institute of Genomics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China.,Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
| | - Rui Zhang
- The State Key Laboratory of Cancer Biology, Department of Immunology, Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Yangxu Lu
- Key Laboratory of Infection and Immunity of CAS, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Xin Wang
- Key Laboratory of Infection and Immunity of CAS, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Huabin Tian
- Key Laboratory of Infection and Immunity of CAS, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Ying Yang
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, China National Center for Bioinformation, Beijing Institute of Genomics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China.,Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
| | - Zijuan Gu
- Key Laboratory of Infection and Immunity of CAS, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Yanan Gao
- Key Laboratory of Infection and Immunity of CAS, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Xin Yang
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, China National Center for Bioinformation, Beijing Institute of Genomics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China.,Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
| | - Guanshen Cui
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, China National Center for Bioinformation, Beijing Institute of Genomics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China.,Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
| | - Baofa Sun
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, China National Center for Bioinformation, Beijing Institute of Genomics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China.,Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
| | - Yanan Peng
- Key Laboratory of Infection and Immunity of CAS, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Hongyu Deng
- Key Laboratory of Infection and Immunity of CAS, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Hua Peng
- Key Laboratory of Infection and Immunity of CAS, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Angang Yang
- The State Key Laboratory of Cancer Biology, Department of Immunology, Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Yun-Gui Yang
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, China National Center for Bioinformation, Beijing Institute of Genomics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China. .,Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China.
| | - Pengyuan Yang
- Key Laboratory of Infection and Immunity of CAS, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China. .,Chongqing International Institute for Immunology, Chongqing, China.
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9
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He X, Xu T, Hu W, Tan Y, Wang D, Wang Y, Zhao C, Yi Y, Xiong M, Lv W, Wu M, Li X, Wu Y, Zhang Q. Circular RNAs: Their Role in the Pathogenesis and Orchestration of Breast Cancer. Front Cell Dev Biol 2021; 9:647736. [PMID: 33777954 PMCID: PMC7991790 DOI: 10.3389/fcell.2021.647736] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 02/11/2021] [Indexed: 12/12/2022] Open
Abstract
As one of the most frequently occurring malignancies in women, breast cancer (BC) is still an enormous threat to women all over the world. The high mortality rates in BC patients are associated with BC recurrence, metastatic progression to distant organs, and therapeutic resistance. Circular RNAs (circRNAs), belonging to the non-coding RNAs (ncRNAs), are connected end to end to form covalently closed single-chain circular molecules. CircRNAs are widely found in different species and a variety of human cells, with the features of diversity, evolutionary conservation, stability, and specificity. CircRNAs are emerging important participators in multiple diseases, including cardiovascular disease, inflammation, and cancer. Recent studies have shown that circRNAs are involved in BC progress by regulating gene expression at the transcriptional or post-transcriptional level via binding to miRNAs then inhibiting their function, suggesting that circRNAs may be potential targets for early diagnosis, treatment, and prognosis of BC. Herein, in this article, we have reviewed and summarized the current studies about the biogenesis, features, and functions of circRNAs. More importantly, we emphatically elucidate the pivotal functions and mechanisms of circRNAs in BC growth, metastasis, diagnosis, and drug resistance. Deciphering the complex networks, especially the circRNA-miRNA target gene axis, will endow huge potentials in developing therapeutic strategies for combating BC.
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Affiliation(s)
- Xiao He
- Department of Plastic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Tao Xu
- Department of Thyroid and Breast Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Weijie Hu
- Department of Plastic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yufang Tan
- Department of Plastic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Dawei Wang
- Department of Plastic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yichen Wang
- Department of Plastic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Chongru Zhao
- Department of Plastic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yi Yi
- Department of Plastic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Mingchen Xiong
- Department of Plastic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wenchang Lv
- Department of Plastic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Min Wu
- Department of Plastic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xingrui Li
- Department of Thyroid and Breast Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yiping Wu
- Department of Plastic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qi Zhang
- Department of Plastic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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10
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Vidal AF. Read-through circular RNAs reveal the plasticity of RNA processing mechanisms in human cells. RNA Biol 2020; 17:1823-1826. [PMID: 32783578 PMCID: PMC7714478 DOI: 10.1080/15476286.2020.1805233] [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: 06/23/2020] [Revised: 07/29/2020] [Accepted: 07/30/2020] [Indexed: 01/22/2023] Open
Abstract
In the human genome, there are several genes whose primary transcripts are both canonically and non-canonically spliced to generate mRNAs and RNA circles, respectively. These RNA circles are a novel class of long non-coding RNAs that became known as circular RNAs (circRNAs). Recently, a new type of circRNA was discovered and called read-through circRNAs (rt-circRNAs). They are hybrid circles that include coding exons from two adjacent and similarly oriented genes. The function of rt-circRNAs, as well as the impact of read-through transcription in our transcriptome, remains to be elucidated. Although we have just begun to scratch it, here I discussed some insights that these fascinating circRNAs are already giving us about the plasticity of RNA processing in our cells.
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Affiliation(s)
- Amanda F. Vidal
- Laboratory of Human and Medical Genetics, Federal University of Pará, Belém, Brazil
- Graduate Program of Genetics and Molecular Biology, Institute of Biological Sciences, Federal University of Pará, Belém, Brazil
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11
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Zhang C, Xiong Y, Zeng L, Peng Z, Liu Z, Zhan H, Yang Z. The Role of Non-coding RNAs in Viral Myocarditis. Front Cell Infect Microbiol 2020; 10:312. [PMID: 32754448 PMCID: PMC7343704 DOI: 10.3389/fcimb.2020.00312] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Accepted: 05/22/2020] [Indexed: 12/13/2022] Open
Abstract
Viral myocarditis (VMC) is a disease characterized as myocardial parenchyma or interstitium inflammation caused by virus infection, especially Coxsackievirus B3 (CVB3) infection, which has no accurate non-invasive examination for diagnosis and specific drugs for treatment. The mechanism of CVB3-induced VMC may be related to direct myocardial damage of virus infection and extensive damage of abnormal immune response after infection. Non-coding RNA (ncRNA) refers to RNA that is not translated into protein and plays a vital role in many biological processes. There is expanding evidence to reveal that ncRNAs regulate the occurrence and development of VMC, which may provide new treatment or diagnosis targets. In this review, we mainly demonstrate an overview of the potential role of ncRNAs in the pathogenesis, diagnosis and treatment of CVB3-induced VMC.
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Affiliation(s)
- Cong Zhang
- Division of Emergency Medicine, Department of Emergency Intensive Care Unit, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Department of Cardiology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,NHC Key Laboratory on Assisted Circulation (Sun Yat-sen University), Guangzhou, China
| | - Yan Xiong
- Division of Emergency Medicine, Department of Emergency Intensive Care Unit, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Lijin Zeng
- Division of Emergency Medicine, Department of Emergency Intensive Care Unit, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Department of Cardiology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,NHC Key Laboratory on Assisted Circulation (Sun Yat-sen University), Guangzhou, China
| | - Zhihua Peng
- Division of Emergency Medicine, Department of Emergency Intensive Care Unit, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Department of Cardiology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,NHC Key Laboratory on Assisted Circulation (Sun Yat-sen University), Guangzhou, China
| | - Zhihao Liu
- Division of Emergency Medicine, Department of Emergency Intensive Care Unit, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Hong Zhan
- Division of Emergency Medicine, Department of Emergency Intensive Care Unit, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Zhen Yang
- Division of Emergency Medicine, Department of Emergency Intensive Care Unit, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Department of Cardiology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,NHC Key Laboratory on Assisted Circulation (Sun Yat-sen University), Guangzhou, China
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12
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Santarpia M, Aguilar A, Chaib I, Cardona AF, Fancelli S, Laguia F, Bracht JWP, Cao P, Molina-Vila MA, Karachaliou N, Rosell R. Non-Small-Cell Lung Cancer Signaling Pathways, Metabolism, and PD-1/PD-L1 Antibodies. Cancers (Basel) 2020; 12:E1475. [PMID: 32516941 PMCID: PMC7352732 DOI: 10.3390/cancers12061475] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 05/25/2020] [Accepted: 06/01/2020] [Indexed: 12/16/2022] Open
Abstract
Treatment of advanced (metastatic) non-small-cell lung cancer (NSCLC) is currently mainly based on immunotherapy with antibodies against PD-1 or PD-L1, alone, or in combination with chemotherapy. In locally advanced NSCLC and in early resected stages, immunotherapy is also employed. Tumor PD-L1 expression by immunohistochemistry is considered the standard practice. Response rate is low, with median progression free survival very short in the vast majority of studies reported. Herein, numerous biological facets of NSCLC are described involving driver genetic lesions, mutations ad fusions, PD-L1 glycosylation, ferroptosis and metabolic rewiring in NSCLC and lung adenocarcinoma (LUAD). Novel concepts, such as immune-transmitters and the effect of neurotransmitters in immune evasion and tumor growth, the nascent relevance of necroptosis and pyroptosis, possible new biomarkers, such as gasdermin D and gasdermin E, the conundrum of K-Ras mutations in LUADs, with the growing recognition of liver kinase B1 (LKB1) and metabolic pathways, including others, are also commented. The review serves to charter diverse treatment solutions, depending on the main altered signaling pathways, in order to have effectual immunotherapy. Tumor PDCD1 gene (encoding PD-1) has been recently described, in equilibrium with tumor PD-L1 (encoded by PDCD1LG1). Such description explains tumor hyper-progression, which has been reported in several studies, and poises the fundamental criterion that IHC PD-L1 expression as a biomarker should be revisited.
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Affiliation(s)
- Mariacarmela Santarpia
- Department of Human Pathology “G. Barresi”, Medical Oncology Unit, University of Messina, 98122 Messina, Italy;
| | - Andrés Aguilar
- Instituto Oncológico Dr Rosell, Hospital Universitario Quirón-Dexeus, 08028 Barcelona, Spain;
| | - Imane Chaib
- Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), 08916 Badalona, Spain; (I.C.); (S.F.); (F.L.)
| | - Andrés Felipe Cardona
- Foundation for Clinical and Applied Cancer Research-FICMAC Translational Oncology, Bogotá 100110, Colombia;
| | - Sara Fancelli
- Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), 08916 Badalona, Spain; (I.C.); (S.F.); (F.L.)
| | - Fernando Laguia
- Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), 08916 Badalona, Spain; (I.C.); (S.F.); (F.L.)
| | | | - Peng Cao
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, China;
| | - Miguel Angel Molina-Vila
- Pangaea Oncology, Hospital Universitario Quirón-Dexeus, 08028 Barcelona, Spain; (J.W.P.B.); (M.A.M.-V.)
| | | | - Rafael Rosell
- Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), 08916 Badalona, Spain; (I.C.); (S.F.); (F.L.)
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13
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Xuan J, Xiong Y, Shi L, Aramini B, Wang H. Do lncRNAs and circRNAs expression profiles influence discoid lupus erythematosus progression?-a comprehensive analysis. ANNALS OF TRANSLATIONAL MEDICINE 2019; 7:728. [PMID: 32042744 DOI: 10.21037/atm.2019.12.10] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Background Long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs)are involved in the progression of discoid lupus erythematosus (DLE), but an understanding of their underlying mechanisms remains elusive. To explore the expression profiles of lncRNAs and circRNAs in DLE, we surveyed the lncRNA/circRNA and mRNA expression profiles in the epithelia of oral DLE and adjacent normal tissues. Methods The lesional and non-lesional lower lips of three DLE patients were analysed by RNA-sequencing (RNA-seq). The principal functions of the significantly deregulated genes were identified using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. And the correlated expression networks (coding-noncoding co-expression and lncRNAs-transcription factor-mRNA) were evaluated as well. Results Hundreds of significantly changed lncRNAs and mRNAs and dozens of significantly changed circRNAs were identified. lncRNA lnc-MIPOL1-6 and IncRNA IncDDX47-3 expressions were correlated with immune response-related genes, including IL19, CXCL1, CXCL11, and TNFSF15. Up-regulated IncRNA-TF network consists of 8 TFs and 74 related lncRNAs. The lncRNA-TF-gene trans-regulation consisting of 204 lncRNAs,39 TFs, and correlated 3 genes. Conclusions These results demonstrate that lncRNAs and circRNAs can influence the progression of DLE. Certain mRNAs/lncRNAs/circRNAs may have substantial value in DLE diagnosis and therapy.
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Affiliation(s)
- Jing Xuan
- Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 200071, China
| | - Yaoyang Xiong
- Department of Prosthodontics, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China.,Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, National Clinical Research Center of Stomatology, Shanghai 200011, China
| | - Linjun Shi
- Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, National Clinical Research Center of Stomatology, Shanghai 200011, China.,Department of Oral Mucosa Diseases, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
| | - Beatrice Aramini
- Division of Thoracic Surgery, Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Haiyan Wang
- Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, National Clinical Research Center of Stomatology, Shanghai 200011, China.,Department of Oral Mucosa Diseases, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
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