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Jiao Y, Xu Y, Liu C, Miao R, Liu C, Wang Y, Liu J. The role of ADAR1 through and beyond its editing activity in cancer. Cell Commun Signal 2024; 22:42. [PMID: 38233935 PMCID: PMC10795376 DOI: 10.1186/s12964-023-01465-x] [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: 11/06/2023] [Accepted: 12/27/2023] [Indexed: 01/19/2024] Open
Abstract
Adenosine-to-inosine (A-to-I) editing of RNA, catalyzed by adenosine deaminase acting on RNA (ADAR) enzymes, is a prevalent RNA modification in mammals. It has been shown that A-to-I editing plays a critical role in multiple diseases, such as cardiovascular disease, neurological disorder, and particularly cancer. ADARs are the family of enzymes, including ADAR1, ADAR2, and ADAR3, that catalyze the occurrence of A-to-I editing. Notably, A-to-I editing is mainly catalyzed by ADAR1. Given the significance of A-to-I editing in disease development, it is important to unravel the complex roles of ADAR1 in cancer for the development of novel therapeutic interventions.In this review, we briefly describe the progress of research on A-to-I editing and ADARs in cancer, mainly focusing on the role of ADAR1 in cancer from both editing-dependent and independent perspectives. In addition, we also summarized the factors affecting the expression and editing activity of ADAR1 in cancer.
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Affiliation(s)
- Yue Jiao
- School of Basic Medicine Sciences, Weifang Medical University, Weifang, 261053, China
| | - Yuqin Xu
- School of Basic Medicine Sciences, Weifang Medical University, Weifang, 261053, China
| | - Chengbin Liu
- School of Basic Medicine Sciences, Weifang Medical University, Weifang, 261053, China
| | - Rui Miao
- School of Basic Medicine Sciences, Weifang Medical University, Weifang, 261053, China
| | - Chunyan Liu
- School of Basic Medicine Sciences, Weifang Medical University, Weifang, 261053, China
| | - Yilong Wang
- School of Basic Medicine Sciences, Weifang Medical University, Weifang, 261053, China
| | - Jiao Liu
- School of Basic Medicine Sciences, Weifang Medical University, Weifang, 261053, China.
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Weng S, Yang X, Yu N, Wang PC, Xiong S, Ruan H. Harnessing ADAR-Mediated Site-Specific RNA Editing in Immune-Related Disease: Prediction and Therapeutic Implications. Int J Mol Sci 2023; 25:351. [PMID: 38203521 PMCID: PMC10779106 DOI: 10.3390/ijms25010351] [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] [Revised: 12/15/2023] [Accepted: 12/23/2023] [Indexed: 01/12/2024] Open
Abstract
ADAR (Adenosine Deaminases Acting on RNA) proteins are a group of enzymes that play a vital role in RNA editing by converting adenosine to inosine in RNAs. This process is a frequent post-transcriptional event observed in metazoan transcripts. Recent studies indicate widespread dysregulation of ADAR-mediated RNA editing across many immune-related diseases, such as human cancer. We comprehensively review ADARs' function as pattern recognizers and their capability to contribute to mediating immune-related pathways. We also highlight the potential role of site-specific RNA editing in maintaining homeostasis and its relationship to various diseases, such as human cancers. More importantly, we summarize the latest cutting-edge computational approaches and data resources for predicting and analyzing RNA editing sites. Lastly, we cover the recent advancement in site-directed ADAR editing tool development. This review presents an up-to-date overview of ADAR-mediated RNA editing, how site-specific RNA editing could potentially impact disease pathology, and how they could be harnessed for therapeutic applications.
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Affiliation(s)
- Shenghui Weng
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou 215123, China; (S.W.); (P.-C.W.)
| | - Xinyi Yang
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou 215123, China; (S.W.); (P.-C.W.)
| | - Nannan Yu
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou 215123, China; (S.W.); (P.-C.W.)
| | - Peng-Cheng Wang
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou 215123, China; (S.W.); (P.-C.W.)
| | - Sidong Xiong
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou 215123, China; (S.W.); (P.-C.W.)
| | - Hang Ruan
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou 215123, China; (S.W.); (P.-C.W.)
- MOE Key Laboratory of Geriatric Diseases and Immunology, Suzhou Medical College of Soochow University, Suzhou 215123, China
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Janin M, Davalos V, Esteller M. Cancer metastasis under the magnifying glass of epigenetics and epitranscriptomics. Cancer Metastasis Rev 2023; 42:1071-1112. [PMID: 37369946 PMCID: PMC10713773 DOI: 10.1007/s10555-023-10120-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 06/15/2023] [Indexed: 06/29/2023]
Abstract
Most of the cancer-associated mortality and morbidity can be attributed to metastasis. The role of epigenetic and epitranscriptomic alterations in cancer origin and progression has been extensively demonstrated during the last years. Both regulations share similar mechanisms driven by DNA or RNA modifiers, namely writers, readers, and erasers; enzymes responsible of respectively introducing, recognizing, or removing the epigenetic or epitranscriptomic modifications. Epigenetic regulation is achieved by DNA methylation, histone modifications, non-coding RNAs, chromatin accessibility, and enhancer reprogramming. In parallel, regulation at RNA level, named epitranscriptomic, is driven by a wide diversity of chemical modifications in mostly all RNA molecules. These two-layer regulatory mechanisms are finely controlled in normal tissue, and dysregulations are associated with every hallmark of human cancer. In this review, we provide an overview of the current state of knowledge regarding epigenetic and epitranscriptomic alterations governing tumor metastasis, and compare pathways regulated at DNA or RNA levels to shed light on a possible epi-crosstalk in cancer metastasis. A deeper understanding on these mechanisms could have important clinical implications for the prevention of advanced malignancies and the management of the disseminated diseases. Additionally, as these epi-alterations can potentially be reversed by small molecules or inhibitors against epi-modifiers, novel therapeutic alternatives could be envisioned.
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Affiliation(s)
- Maxime Janin
- Cancer Epigenetics Group, Josep Carreras Leukaemia Research Institute (IJC), IJC Building, Germans Trias I Pujol, Ctra de Can Ruti, Cami de Les Escoles S/N, 08916 Badalona, Barcelona, Spain
- Centro de Investigacion Biomedica en Red Cancer (CIBERONC), Madrid, Spain
| | - Veronica Davalos
- Cancer Epigenetics Group, Josep Carreras Leukaemia Research Institute (IJC), IJC Building, Germans Trias I Pujol, Ctra de Can Ruti, Cami de Les Escoles S/N, 08916 Badalona, Barcelona, Spain
| | - Manel Esteller
- Cancer Epigenetics Group, Josep Carreras Leukaemia Research Institute (IJC), IJC Building, Germans Trias I Pujol, Ctra de Can Ruti, Cami de Les Escoles S/N, 08916 Badalona, Barcelona, Spain.
- Centro de Investigacion Biomedica en Red Cancer (CIBERONC), Madrid, Spain.
- Institucio Catalana de Recerca I Estudis Avançats (ICREA), Barcelona, Catalonia, Spain.
- Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), Barcelona, Catalonia, Spain.
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Frezza V, Chellini L, Del Verme A, Paronetto MP. RNA Editing in Cancer Progression. Cancers (Basel) 2023; 15:5277. [PMID: 37958449 PMCID: PMC10648226 DOI: 10.3390/cancers15215277] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 10/31/2023] [Accepted: 10/31/2023] [Indexed: 11/15/2023] Open
Abstract
Coding and noncoding RNA molecules play their roles in ensuring cell function and tissue homeostasis in an ordered and systematic fashion. RNA chemical modifications can occur both at bases and ribose sugar, and, similarly to DNA and histone modifications, can be written, erased, and recognized by the corresponding enzymes, thus modulating RNA activities and fine-tuning gene expression programs. RNA editing is one of the most prevalent and abundant forms of post-transcriptional RNA modification in normal physiological processes. By altering the sequences of mRNAs, it makes them different from the corresponding genomic template. Hence, edited mRNAs can produce protein isoforms that are functionally different from the corresponding genome-encoded variants. Abnormalities in regulatory enzymes and changes in RNA-modification patterns are closely associated with the occurrence and development of various human diseases, including cancer. To date, the roles played by RNA modifications in cancer are gathering increasing interest. In this review, we focus on the role of RNA editing in cancer transformation and provide a new perspective on its impact on tumorigenesis, by regulating cell proliferation, differentiation, invasion, migration, stemness, metabolism, and drug resistance.
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Affiliation(s)
- Valentina Frezza
- Laboratory of Molecular and Cellular Neurobiology, Fondazione Santa Lucia, CERC, Via del Fosso di Fiorano, 64, 00143 Rome, Italy; (V.F.); (L.C.); (A.D.V.)
| | - Lidia Chellini
- Laboratory of Molecular and Cellular Neurobiology, Fondazione Santa Lucia, CERC, Via del Fosso di Fiorano, 64, 00143 Rome, Italy; (V.F.); (L.C.); (A.D.V.)
| | - Arianna Del Verme
- Laboratory of Molecular and Cellular Neurobiology, Fondazione Santa Lucia, CERC, Via del Fosso di Fiorano, 64, 00143 Rome, Italy; (V.F.); (L.C.); (A.D.V.)
| | - Maria Paola Paronetto
- Laboratory of Molecular and Cellular Neurobiology, Fondazione Santa Lucia, CERC, Via del Fosso di Fiorano, 64, 00143 Rome, Italy; (V.F.); (L.C.); (A.D.V.)
- Department of Movement, Human and Health Sciences, University of Rome “Foro Italico”, Piazza Lauro de Bosis, 15, 00135 Rome, Italy
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Hosseini-Abgir A, Naghizadeh MM, Igder S, Miladpour B. Insilco prediction of the role of the FriZZled5 gene in colorectal cancer. Cancer Treat Res Commun 2023; 36:100751. [PMID: 37595345 DOI: 10.1016/j.ctarc.2023.100751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 07/27/2023] [Accepted: 08/14/2023] [Indexed: 08/20/2023]
Abstract
INTRODUCTION In this study, we aimed to elucidate the crosstalk between the Wnt/β-catenin signaling pathway and colorectal cancer (CRC) associated with inflammatory bowel disease (IBD) using a bioinformatics analysis of putative common biomarkers and a systems biology approach. MATERIALS AND METHODS The following criteria were used to search the GEO and ArrayExpress databases for terms related to CRC and IBD: 1. The dataset containing the transcriptomic data, and 2. Untreated samples by medications or drugs. A total of 42 datasets were selected for additional analysis. The GEO2R identified the differentially expressed genes. The genes involved in the Wnt signaling pathway were extracted from the KEGG database. Enrichment analysis and miRNA target prediction were conducted through the ToppGene online tool. RESULTS In CRC datasets, there were 1168 up- and 998 down-regulated probes, whereas, in IBD datasets, there were 256 up- and 200 down-regulated probes. There were 65 upregulated and 57 downregulated genes shared by CRC and IBD. According to KEGG, there were 166 genes in the Wnt pathway. FriZZled5 (FZD5) was a down-regulated gene in both CRC and IBD, as determined by the intersection of CRC- and IBD-related DEGs with the Wnt pathway. It was also demonstrated that miR-191, miR-885-5p, miR-378a-3p, and miR-396-3p affect the FriZZled5 gene expression. CONCLUSION It is possible that increased expression of miR-191 and miR-885-5p, or decreased expression of miR-378a -3p and miR396-3, in IBD and CRC results in decreased expression of the FZD5 gene. Based on the function of this gene, FZD5 may be a potential therapeutic target in IBD that progresses to CRC.
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Affiliation(s)
| | | | - Somayeh Igder
- Department of Clinical Biochemistry, Faculty of Medicine, Ahvaz Jundishapur University of Medical Science, Ahvaz, Iran
| | - Behnoosh Miladpour
- Department of Clinical Biochemistry, Fasa University of Medical Sciences, Fasa, Iran.
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Tang Q, Li L, Wang Y, Wu P, Hou X, Ouyang J, Fan C, Li Z, Wang F, Guo C, Zhou M, Liao Q, Wang H, Xiang B, Jiang W, Li G, Zeng Z, Xiong W. RNA modifications in cancer. Br J Cancer 2023; 129:204-221. [PMID: 37095185 PMCID: PMC10338518 DOI: 10.1038/s41416-023-02275-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 03/30/2023] [Accepted: 04/06/2023] [Indexed: 04/26/2023] Open
Abstract
Currently, more than 170 modifications have been identified on RNA. Among these RNA modifications, various methylations account for two-thirds of total cases and exist on almost all RNAs. Roles of RNA modifications in cancer are garnering increasing interest. The research on m6A RNA methylation in cancer is in full swing at present. However, there are still many other popular RNA modifications involved in the regulation of gene expression post-transcriptionally besides m6A RNA methylation. In this review, we focus on several important RNA modifications including m1A, m5C, m7G, 2'-O-Me, Ψ and A-to-I editing in cancer, which will provide a new perspective on tumourigenesis by peeking into the complex regulatory network of epigenetic RNA modifications, transcript processing, and protein translation.
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Affiliation(s)
- Qiling Tang
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 410078, Changsha, Hunan, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, 410078, Changsha, Hunan, China
| | - Lvyuan Li
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 410078, Changsha, Hunan, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, 410078, Changsha, Hunan, China
| | - Yumin Wang
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, 410078, Changsha, Hunan, China
- Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, 410078, Changsha, Hunan, China
| | - Pan Wu
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 410078, Changsha, Hunan, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, 410078, Changsha, Hunan, China
| | - Xiangchan Hou
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 410078, Changsha, Hunan, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, 410078, Changsha, Hunan, China
| | - Jiawei Ouyang
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 410078, Changsha, Hunan, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, 410078, Changsha, Hunan, China
| | - Chunmei Fan
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 410078, Changsha, Hunan, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, 410078, Changsha, Hunan, China
| | - Zheng Li
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, 410078, Changsha, Hunan, China
| | - Fuyan Wang
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, 410078, Changsha, Hunan, China
| | - Can Guo
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, 410078, Changsha, Hunan, China
| | - Ming Zhou
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, 410078, Changsha, Hunan, China
| | - Qianjin Liao
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 410078, Changsha, Hunan, China
| | - Hui Wang
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 410078, Changsha, Hunan, China
| | - Bo Xiang
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 410078, Changsha, Hunan, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, 410078, Changsha, Hunan, China
| | - Weihong Jiang
- Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, 410078, Changsha, Hunan, China
| | - Guiyuan Li
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 410078, Changsha, Hunan, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, 410078, Changsha, Hunan, China
| | - Zhaoyang Zeng
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 410078, Changsha, Hunan, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, 410078, Changsha, Hunan, China
| | - Wei Xiong
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 410078, Changsha, Hunan, China.
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, 410078, Changsha, Hunan, China.
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Yuan J, Xu L, Bao HJ, Wang JL, Zhao Y, Chen S. Biological roles of A-to-I editing: implications in innate immunity, cell death, and cancer immunotherapy. J Exp Clin Cancer Res 2023; 42:149. [PMID: 37328893 DOI: 10.1186/s13046-023-02727-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 06/02/2023] [Indexed: 06/18/2023] Open
Abstract
Adenosine-to-inosine (A-to-I) editing, a key RNA modification widely found in eukaryotes, is catalyzed by adenosine deaminases acting on RNA (ADARs). Such RNA editing destabilizes endogenous dsRNAs, which are subsequently recognized by the sensors of innate immune and other proteins as autologous dsRNAs. This prevents the activation of innate immunity and type I interferon-mediated responses, thereby reducing the downstream cell death induced by the activation of the innate immune sensing system. ADARs-mediated editing can also occur in mRNAs and non-coding RNAs (ncRNAs) in different species. In mRNAs, A-to-I editing may lead to missense mutations and the selective splicing of coding regions. Meanwhile, in ncRNAs, A-to-I editing may affect targeting and disrupt ncRNAs maturation, leading to anomalous cell proliferation, invasion, and responses to immunotherapy. This review highlights the biological functions of A-to-I editing, its role in regulating innate immunity and cell death, and its potential molecular significance in tumorigenesis and cancer targeted therapy and immunotherapy.
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Affiliation(s)
- Jing Yuan
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Guangzhou Key Laboratory of Targeted Therapy for Gynecologic Oncology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, No.63 Duobao Road, Liwan District, Guangzhou City, Guangdong Province, 510150, P. R. China
| | - Li Xu
- Department of Laboratory Medicine, The First Hospital of China Medical University, Shenyang, 110001, China
| | - Hai-Juan Bao
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Guangzhou Key Laboratory of Targeted Therapy for Gynecologic Oncology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, No.63 Duobao Road, Liwan District, Guangzhou City, Guangdong Province, 510150, P. R. China
| | - Jie-Lin Wang
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Guangzhou Key Laboratory of Targeted Therapy for Gynecologic Oncology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, No.63 Duobao Road, Liwan District, Guangzhou City, Guangdong Province, 510150, P. R. China
| | - Yang Zhao
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Guangzhou Key Laboratory of Targeted Therapy for Gynecologic Oncology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, No.63 Duobao Road, Liwan District, Guangzhou City, Guangdong Province, 510150, P. R. China.
| | - Shuo Chen
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Guangzhou Key Laboratory of Targeted Therapy for Gynecologic Oncology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, No.63 Duobao Road, Liwan District, Guangzhou City, Guangdong Province, 510150, P. R. China.
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8
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Shutta KH, Balzer LB, Scholtens DM, Balasubramanian R. SpiderLearner: An ensemble approach to Gaussian graphical model estimation. Stat Med 2023; 42:2116-2133. [PMID: 37004994 DOI: 10.1002/sim.9714] [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: 01/20/2022] [Revised: 12/10/2022] [Accepted: 03/07/2023] [Indexed: 04/04/2023]
Abstract
Gaussian graphical models (GGMs) are a popular form of network model in which nodes represent features in multivariate normal data and edges reflect conditional dependencies between these features. GGM estimation is an active area of research. Currently available tools for GGM estimation require investigators to make several choices regarding algorithms, scoring criteria, and tuning parameters. An estimated GGM may be highly sensitive to these choices, and the accuracy of each method can vary based on structural characteristics of the network such as topology, degree distribution, and density. Because these characteristics are a priori unknown, it is not straightforward to establish universal guidelines for choosing a GGM estimation method. We address this problem by introducing SpiderLearner, an ensemble method that constructs a consensus network from multiple estimated GGMs. Given a set of candidate methods, SpiderLearner estimates the optimal convex combination of results from each method using a likelihood-based loss function.K $$ K $$ -fold cross-validation is applied in this process, reducing the risk of overfitting. In simulations, SpiderLearner performs better than or comparably to the best candidate methods according to a variety of metrics, including relative Frobenius norm and out-of-sample likelihood. We apply SpiderLearner to publicly available ovarian cancer gene expression data including 2013 participants from 13 diverse studies, demonstrating our tool's potential to identify biomarkers of complex disease. SpiderLearner is implemented as flexible, extensible, open-source code in the R package ensembleGGM at https://github.com/katehoffshutta/ensembleGGM.
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Affiliation(s)
- Katherine H Shutta
- Department of Biostatistics and Epidemiology, University of Massachusetts-Amherst, Amherst, Massachusetts, USA
- Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, USA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Laura B Balzer
- Division of Biostatistics, University of California-Berkeley, Berkeley, California, USA
| | - Denise M Scholtens
- Division of Biostatistics, Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Raji Balasubramanian
- Department of Biostatistics and Epidemiology, University of Massachusetts-Amherst, Amherst, Massachusetts, USA
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Lu D, Lu J, Liu Q, Zhang Q. Emerging role of the RNA-editing enzyme ADAR1 in stem cell fate and function. Biomark Res 2023; 11:61. [PMID: 37280687 DOI: 10.1186/s40364-023-00503-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 05/13/2023] [Indexed: 06/08/2023] Open
Abstract
Stem cells are critical for organism development and the maintenance of tissue homeostasis. Recent studies focusing on RNA editing have indicated how this mark controls stem cell fate and function in both normal and malignant states. RNA editing is mainly mediated by adenosine deaminase acting on RNA 1 (ADAR1). The RNA editing enzyme ADAR1 converts adenosine in a double-stranded RNA (dsRNA) substrate into inosine. ADAR1 is a multifunctional protein that regulate physiological processes including embryonic development, cell differentiation, and immune regulation, and even apply to the development of gene editing technologies. In this review, we summarize the structure and function of ADAR1 with a focus on how it can mediate distinct functions in stem cell self-renewal and differentiation. Targeting ADAR1 has emerged as a potential novel therapeutic strategy in both normal and dysregulated stem cell contexts.
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Affiliation(s)
- Di Lu
- The Biotherapy Center, the Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510630, China
| | - Jianxi Lu
- The Biotherapy Center, the Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510630, China
| | - Qiuli Liu
- The Biotherapy Center, the Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510630, China.
| | - Qi Zhang
- The Biotherapy Center, the Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510630, China.
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10
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Xie W, Yang J, Zhou N, Ding H, Zhou G, Wu S, Guo S, Li W, Zhang L, Yang H, Mao C, Zheng Y. Identification of microRNA editing sites in three subtypes of leukemia. Front Mol Biosci 2022; 9:1014288. [PMID: 36452459 PMCID: PMC9702332 DOI: 10.3389/fmolb.2022.1014288] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 10/28/2022] [Indexed: 09/15/2023] Open
Abstract
Leukemia is an aberrant hyper-proliferation of immature blood cells that do not form solid tumors. The transcriptomes of microRNAs (miRNAs) of leukemia have been intensively explored. However, miRNA editing of leukemia has not been extensively studied. To identify miRNA editing patterns and explore their functional relevance in leukemia, we analyzed 200 small RNA sequencing profiles of three subtypes of leukemia and identified hundreds of miRNA editing sites in three subtypes of leukemia. Then, we compared the editing levels of identified miRNA editing sites in leukemia and normal controls. Many miRNAs were differential edited in different subtypes of leukemia. We also found the editing levels of 3'-A editing sites of hsa-mir-21-5p and hsa-mir-155-5p decreased in chronic lymphocytic leukemia patients with radiation treatments. By integrating PAR-CLIP sequencing profiles, we predicted the targets of original and edited miRNAs. One of the edited miRNA, hsa-let-7b_5c, with an additional cytosine at 5' end of hsa-let-7b-5p, potentially targeted VBP1 and CTDSP1. CTDSP1 was significantly downregulated in T-ALL compared to normal controls, which might be originated from the hyperediting of hsa-let-7b-5p in T-ALL. Our study provides a comprehensive view of miRNA editing in three different subtypes of leukemia.
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Affiliation(s)
- Wenping Xie
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Jun Yang
- Yunnan Police College, Kunming, Yunnan, China
| | - Nan Zhou
- Faculty of Information Engineering and Automation, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Hao Ding
- Faculty of Information Engineering and Automation, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Guangchen Zhou
- Faculty of Information Engineering and Automation, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Shuai Wu
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Shiyong Guo
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Wanran Li
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Lei Zhang
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Huaide Yang
- Faculty of Information Engineering and Automation, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Chunyi Mao
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Yun Zheng
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan, China
- Faculty of Information Engineering and Automation, Kunming University of Science and Technology, Kunming, Yunnan, China
- College of Horticulture and Landscape, Yunnan Agricultural University, Kunming, Yunnan, China
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11
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Qu M, Yu K, Rehman Aziz AU, Zhang H, Zhang Z, Li N, Liu B. The role of Actopaxin in tumor metastasis. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2022; 175:90-102. [PMID: 36150525 DOI: 10.1016/j.pbiomolbio.2022.09.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 08/06/2022] [Accepted: 09/13/2022] [Indexed: 06/16/2023]
Abstract
Actopaxin is a newly discovered focal adhesions (FAs) protein, actin-binding protein and pseudopodia-enriched molecule. It can not only bind to a variety of FAs proteins (such as Paxillin, ILK and PINCH) and non-FAs proteins (such as TESK1, CdGAP, β2-adaptin, G3BP2, ADAR1 and CD29), but also participates in multiple signaling pathways. Thus, it plays a crucial role in regulating important processes of tumor metastasis, including matrix degradation, migration, and invasion, etc. This review covers the latest progress in the structure and function of Actopaxin, its interaction with other proteins as well as its involvement in regulating tumor development and metastasis. Additionally, the current limitations for Actopaxin related studies and the possible research directions on it in the future are also discussed. It is hoped that this review can assist relevant researchers to obtain a deep understanding of the role that Actopaxin plays in tumor progression, and also enlighten further research and development of therapeutic approaches for the treatment of tumor metastasis.
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Affiliation(s)
- Manrong Qu
- School of Biomedical Engineering, Dalian University of Technology, Key Laboratory for Integrated Circuit and Biomedical Electronic System of Liaoning Province, Dalian, 116024, China
| | - Kehui Yu
- School of Biomedical Engineering, Dalian University of Technology, Key Laboratory for Integrated Circuit and Biomedical Electronic System of Liaoning Province, Dalian, 116024, China
| | - Aziz Ur Rehman Aziz
- School of Biomedical Engineering, Dalian University of Technology, Key Laboratory for Integrated Circuit and Biomedical Electronic System of Liaoning Province, Dalian, 116024, China
| | - Hangyu Zhang
- School of Biomedical Engineering, Dalian University of Technology, Key Laboratory for Integrated Circuit and Biomedical Electronic System of Liaoning Province, Dalian, 116024, China
| | - Zhengyao Zhang
- School of Life and Pharmaceutical Sciences, Dalian University of Technology, Panjin, 124221, China
| | - Na Li
- School of Biomedical Engineering, Dalian University of Technology, Key Laboratory for Integrated Circuit and Biomedical Electronic System of Liaoning Province, Dalian, 116024, China.
| | - Bo Liu
- School of Biomedical Engineering, Dalian University of Technology, Key Laboratory for Integrated Circuit and Biomedical Electronic System of Liaoning Province, Dalian, 116024, China.
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12
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Li M, Yan C, Jiao Y, Xu Y, Bai C, Miao R, Jiang J, Liu J. Site-directed RNA editing by harnessing ADARs: advances and challenges. Funct Integr Genomics 2022; 22:1089-1103. [DOI: 10.1007/s10142-022-00910-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 10/12/2022] [Accepted: 10/17/2022] [Indexed: 11/04/2022]
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13
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Playfoot CJ, Sheppard S, Planet E, Trono D. Transposable elements contribute to the spatiotemporal microRNA landscape in human brain development. RNA (NEW YORK, N.Y.) 2022; 28:1157-1171. [PMID: 35732404 PMCID: PMC9380744 DOI: 10.1261/rna.079100.122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 06/15/2022] [Indexed: 06/15/2023]
Abstract
Transposable elements (TEs) contribute to the evolution of gene regulatory networks and are dynamically expressed throughout human brain development and disease. One gene regulatory mechanism influenced by TEs is the miRNA system of post-transcriptional control. miRNA sequences frequently overlap TE loci and this miRNA expression landscape is crucial for control of gene expression in adult brain and different cellular contexts. Despite this, a thorough investigation of the spatiotemporal expression of TE-embedded miRNAs in human brain development is lacking. Here, we identify a spatiotemporally dynamic TE-embedded miRNA expression landscape between childhood and adolescent stages of human brain development. These miRNAs sometimes arise from two apposed TEs of the same subfamily, such as for L2 or MIR elements, but in the majority of cases stem from solo TEs. They give rise to in silico predicted high-confidence pre-miRNA hairpin structures, likely represent functional miRNAs, and have predicted genic targets associated with neurogenesis. TE-embedded miRNA expression is distinct in the cerebellum when compared to other brain regions, as has previously been described for gene and TE expression. Furthermore, we detect expression of previously nonannotated TE-embedded miRNAs throughout human brain development, suggestive of a previously undetected miRNA control network. Together, as with non-TE-embedded miRNAs, TE-embedded sequences give rise to spatiotemporally dynamic miRNA expression networks, the implications of which for human brain development constitute extensive avenues of future experimental research. To facilitate interactive exploration of these spatiotemporal miRNA expression dynamics, we provide the "Brain miRTExplorer" web application freely accessible for the community.
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Affiliation(s)
- Christopher J Playfoot
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Shaoline Sheppard
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Evarist Planet
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Didier Trono
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
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14
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Ain U, Firdaus H. Parvin: A hub of intracellular signalling pathways regulating cellular behaviour and disease progression. Acta Histochem 2022; 124:151935. [PMID: 35932544 DOI: 10.1016/j.acthis.2022.151935] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 07/27/2022] [Accepted: 07/27/2022] [Indexed: 11/15/2022]
Abstract
α-actinin superfamily houses the family of parvins, comprising α, β and γ isoforms in the vertebrates and a single orthologue in the invertebrates. Parvin as an adaptor protein is a member of the ternary IPP-complex including Integrin Linked Kinase (ILK) and particularly-interesting-Cys-His-rich protein (PINCH). Each of the complex proteins showed a conserved lineage and was principally used by the evolutionarily primitive integrin-adhesome machinery to regulate cellular behaviour and signalling pathways. Parvin facilitated integrin mediated integration of the extracellular matrix with cytoskeletal framework culminating in regulation of cellular adhesion and spreading, cytoskeleton reorganisation and cell survival. Studies have established role of parvin in pregnancy, lactation, matrix degradation, blood vessel formation and in several diseases such as cancer, NAFLD and cardiac diseases etc. This review narrates the history of parvin discovery, its elaborate gene structure and conservation across phyla including cellular expression, localisation and interacting partners in vertebrates as well as invertebrates. The review further discusses how parvin acts as an epicentre of signalling pathways, its associated mutants and diseased conditions.
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Affiliation(s)
- Ushashi Ain
- Department of Life Sciences, Central University of Jharkhand, CTI Campus, Ratu-Lohardaga Road, Ranchi 835205, India
| | - Hena Firdaus
- Department of Life Sciences, Central University of Jharkhand, CTI Campus, Ratu-Lohardaga Road, Ranchi 835205, India.
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15
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del Valle-Morales D, Le P, Saviana M, Romano G, Nigita G, Nana-Sinkam P, Acunzo M. The Epitranscriptome in miRNAs: Crosstalk, Detection, and Function in Cancer. Genes (Basel) 2022; 13:genes13071289. [PMID: 35886072 PMCID: PMC9316458 DOI: 10.3390/genes13071289] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 07/09/2022] [Accepted: 07/19/2022] [Indexed: 02/06/2023] Open
Abstract
The epitranscriptome encompasses all post-transcriptional modifications that occur on RNAs. These modifications can alter the function and regulation of their RNA targets, which, if dysregulated, result in various diseases and cancers. As with other RNAs, miRNAs are highly modified by epitranscriptomic modifications such as m6A methylation, 2′-O-methylation, m5C methylation, m7G methylation, polyuridine, and A-to-I editing. miRNAs are a class of small non-coding RNAs that regulates gene expression at the post-transcriptional level. miRNAs have gathered high clinical interest due to their role in disease, development, and cancer progression. Epitranscriptomic modifications alter the targeting, regulation, and biogenesis of miRNAs, increasing the complexity of miRNA regulation. In addition, emerging studies have revealed crosstalk between these modifications. In this review, we will summarize the epitranscriptomic modifications—focusing on those relevant to miRNAs—examine the recent crosstalk between these modifications, and give a perspective on how this crosstalk expands the complexity of miRNA biology.
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Affiliation(s)
- Daniel del Valle-Morales
- Division of Pulmonary Diseases and Critical Care Medicine, Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA; (D.d.V.-M.); (P.L.); (M.S.); (G.R.); (P.N.-S.)
| | - Patricia Le
- Division of Pulmonary Diseases and Critical Care Medicine, Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA; (D.d.V.-M.); (P.L.); (M.S.); (G.R.); (P.N.-S.)
| | - Michela Saviana
- Division of Pulmonary Diseases and Critical Care Medicine, Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA; (D.d.V.-M.); (P.L.); (M.S.); (G.R.); (P.N.-S.)
| | - Giulia Romano
- Division of Pulmonary Diseases and Critical Care Medicine, Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA; (D.d.V.-M.); (P.L.); (M.S.); (G.R.); (P.N.-S.)
| | - Giovanni Nigita
- Comprehensive Cancer Center, Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH 43210, USA;
| | - Patrick Nana-Sinkam
- Division of Pulmonary Diseases and Critical Care Medicine, Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA; (D.d.V.-M.); (P.L.); (M.S.); (G.R.); (P.N.-S.)
| | - Mario Acunzo
- Division of Pulmonary Diseases and Critical Care Medicine, Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA; (D.d.V.-M.); (P.L.); (M.S.); (G.R.); (P.N.-S.)
- Correspondence:
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16
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Liu J, Wang F, Zhang Y, Liu J, Zhao B. ADAR1-Mediated RNA Editing and Its Role in Cancer. Front Cell Dev Biol 2022; 10:956649. [PMID: 35898396 PMCID: PMC9309331 DOI: 10.3389/fcell.2022.956649] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 06/23/2022] [Indexed: 11/13/2022] Open
Abstract
It is well known that the stability of RNA, the interaction between RNA and protein, and the correct translation of protein are significant forces that drive the transition from normal cell to malignant tumor. Adenosine deaminase acting on RNA 1 (ADAR1) is an RNA editing enzyme that catalyzes the deamination of adenosine to inosine (A-to-I), which is one dynamic modification that in a combinatorial manner can give rise to a very diverse transcriptome. ADAR1-mediated RNA editing is essential for survival in mammals and its dysregulation results in aberrant editing of its substrates that may affect the phenotypic changes in cancer. This overediting phenomenon occurs in many cancers, such as liver, lung, breast, and esophageal cancers, and promotes tumor progression in most cases. In addition to its editing role, ADAR1 can also play an editing-independent role, although current research on this mechanism is relatively shallowly explored in tumors. In this review, we summarize the nature of ADAR1, mechanisms of ADAR1 editing-dependent and editing-independent and implications for tumorigenesis and prognosis, and pay special attention to effects of ADAR1 on cancers by regulating non-coding RNA formation and function.
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Affiliation(s)
- Jizhe Liu
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, China
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, China
| | - Fei Wang
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, China
- Mengchao Med-X Center, Fuzhou University, Fuzhou, China
| | - Yindan Zhang
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, China
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, China
| | - Jingfeng Liu
- Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou, China
- *Correspondence: Jingfeng Liu, ; Bixing Zhao,
| | - Bixing Zhao
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, China
- Mengchao Med-X Center, Fuzhou University, Fuzhou, China
- *Correspondence: Jingfeng Liu, ; Bixing Zhao,
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17
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Baker AR, Slack FJ. ADAR1 and its implications in cancer development and treatment. Trends Genet 2022; 38:821-830. [PMID: 35459560 PMCID: PMC9283316 DOI: 10.1016/j.tig.2022.03.013] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/14/2022] [Accepted: 03/17/2022] [Indexed: 12/12/2022]
Abstract
The family of adenosine deaminases acting on RNA (ADARs) regulates global gene expression output by catalyzing adenosine-to-inosine (A-to-I) editing of double-stranded RNA (dsRNA) and through interacting with RNA and other proteins. ADARs play important roles in development and disease, including an increasing connection to cancer progression. ADAR1 has demonstrated a largely pro-oncogenic role in a growing list of cancer types, and its function in cancer has been attributed to diverse mechanisms. Here, we review existing literature on ADAR1 biology and function, its roles in human disease including cancer, and summarize known cancer-associated phenotypes and mechanisms. Lastly, we discuss implications and outstanding questions in the field, including strategies for targeting ADAR1 in cancer.
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Affiliation(s)
- Allison R Baker
- Harvard Medical School Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
| | - Frank J Slack
- Harvard Medical School Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA.
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18
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Cannistraci A, Hascoet P, Ali A, Mundra P, Clarke NW, Pavet V, Marais R. MiR-378a inhibits glucose metabolism by suppressing GLUT1 in prostate cancer. Oncogene 2022; 41:1445-1455. [PMID: 35039635 PMCID: PMC8897193 DOI: 10.1038/s41388-022-02178-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 12/07/2021] [Accepted: 01/05/2022] [Indexed: 12/24/2022]
Abstract
Prostate cancer (PCa) is the fifth leading cause of cancer related deaths worldwide, in part due to a lack of molecular stratification tools that can distinguish primary tumours that will remain indolent from those that will metastasise. Amongst potential molecular biomarkers, microRNAs (miRs) have attracted particular interest because of their high stability in body fluids and fixed tissues. These small non-coding RNAs modulate several physiological and pathological processes, including cancer progression. Herein we explore the prognostic potential and the functional role of miRs in localised PCa and their relation to nodal metastasis. We define a 7-miR signature that is associated with poor survival independently of age, Gleason score, pathological T state, N stage and surgical margin status and that is also prognostic for disease-free survival in patients with intermediate-risk localised disease. Within our 7-miR signature, we show that miR-378a-3p (hereafter miR-378a) levels are low in primary tumours compared to benign prostate tissue, and also lower in Gleason score 8-9 compared to Gleason 6-7 PCa. We demonstrate that miR-378a impairs glucose metabolism and reduces proliferation in PCa cells through independent mechanisms, and we identify glucose transporter 1 (GLUT1) messenger RNA as a direct target of miR-378a. We show that GLUT1 inhibition hampers glycolysis, leading to cell death. Our data provides a rational for a new PCa stratification strategy based on miR expression, and it reveals that miR-378a and GLUT1 are potential therapeutic targets in highly aggressive glycolytic PCa.
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Affiliation(s)
- A Cannistraci
- Molecular Oncology Group, Cancer Research UK Manchester Institute, The University of Manchester, Alderley Park, Macclesfield, Cheshire, SK10 4TG, UK
| | - P Hascoet
- Molecular Oncology Group, Cancer Research UK Manchester Institute, The University of Manchester, Alderley Park, Macclesfield, Cheshire, SK10 4TG, UK
| | - A Ali
- Genito-Urinary Cancer Research Group and the FASTMAN Prostate Cancer Centre for Excellence, Division of Cancer Sciences, Manchester Cancer Research Centre, The University of Manchester, 555 Wilmslow Road, Manchester, M20 4GJ, UK
| | - P Mundra
- Molecular Oncology Group, Cancer Research UK Manchester Institute, The University of Manchester, Alderley Park, Macclesfield, Cheshire, SK10 4TG, UK
| | - N W Clarke
- Genito-Urinary Cancer Research Group and the FASTMAN Prostate Cancer Centre for Excellence, Division of Cancer Sciences, Manchester Cancer Research Centre, The University of Manchester, 555 Wilmslow Road, Manchester, M20 4GJ, UK.,The Christie NHS Foundation Trust, Wilmslow Road, Manchester, M20 4BX, UK
| | - V Pavet
- Molecular Oncology Group, Cancer Research UK Manchester Institute, The University of Manchester, Alderley Park, Macclesfield, Cheshire, SK10 4TG, UK.
| | - R Marais
- Molecular Oncology Group, Cancer Research UK Manchester Institute, The University of Manchester, Alderley Park, Macclesfield, Cheshire, SK10 4TG, UK.
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19
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Amweg A, Tusup M, Cheng P, Picardi E, Dummer R, Levesque MP, French LE, Guenova E, Läuchli S, Kundig T, Mellett M, Pascolo S. The A to I editing landscape in melanoma and its relation to clinical outcome. RNA Biol 2022; 19:996-1006. [PMID: 35993275 PMCID: PMC9415457 DOI: 10.1080/15476286.2022.2110390] [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: 12/03/2022] Open
Abstract
RNA editing refers to non-transient RNA modifications that occur after transcription and prior to translation by the ribosomes. RNA editing is more widespread in cancer cells than in non-transformed cells and is associated with tumorigenesis of various cancer tissues. However, RNA editing can also generate neo-antigens that expose tumour cells to host immunosurveillance. Global RNA editing in melanoma and its relevance to clinical outcome currently remain poorly characterized. The present study compared RNA editing as well as gene expression in tumour cell lines from melanoma patients of short or long metastasis-free survival, patients relapsing or not after immuno- and targeted therapy and tumours harbouring BRAF or NRAS mutations. Overall, our results showed that NTRK gene expression can be a marker of resistance to BRAF and MEK inhibition and gives some insights of candidate genes as potential biomarkers. In addition, this study revealed an increase in Adenosine-to-Inosine editing in Alu regions and in non-repetitive regions, including the hyperediting of the MOK and DZIP3 genes in relapsed tumour samples during targeted therapy and of the ZBTB11 gene in NRAS mutated melanoma cells. Therefore, RNA editing could be a promising tool for identifying predictive markers, tumour neoantigens and targetable pathways that could help in preventing relapses during immuno- or targeted therapies.
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Affiliation(s)
- Austeja Amweg
- Department of Dermatology, University Hospital Zürich (USZ), Zürich, Switzerland.,Faculty of Medicine, University of Zürich (UZH), Zürich, Switzerland
| | - Marina Tusup
- Department of Dermatology, University Hospital Zürich (USZ), Zürich, Switzerland.,Faculty of Medicine, University of Zürich (UZH), Zürich, Switzerland
| | - Phil Cheng
- Department of Dermatology, University Hospital Zürich (USZ), Zürich, Switzerland.,Faculty of Medicine, University of Zürich (UZH), Zürich, Switzerland
| | - Ernesto Picardi
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari "A. Moro", Bari, Italy.,Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), National Research Council, Bari, Italy
| | - Reinhard Dummer
- Department of Dermatology, University Hospital Zürich (USZ), Zürich, Switzerland.,Faculty of Medicine, University of Zürich (UZH), Zürich, Switzerland
| | - Mitchell P Levesque
- Department of Dermatology, University Hospital Zürich (USZ), Zürich, Switzerland.,Faculty of Medicine, University of Zürich (UZH), Zürich, Switzerland
| | - Lars E French
- Department of Dermatology and Allergy, University Hospital, LMU Munich, Munich, Germany.,Dr. Philip Frost, Department of Dermatology and Cutaneous Surgery, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Emmanuella Guenova
- Department of Dermatology, University Hospital Zürich (USZ), Zürich, Switzerland.,Faculty of Medicine, University of Zürich (UZH), Zürich, Switzerland.,Department of Dermatology, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland
| | - Severin Läuchli
- Department of Dermatology, University Hospital Zürich (USZ), Zürich, Switzerland.,Faculty of Medicine, University of Zürich (UZH), Zürich, Switzerland
| | - Thomas Kundig
- Department of Dermatology, University Hospital Zürich (USZ), Zürich, Switzerland.,Faculty of Medicine, University of Zürich (UZH), Zürich, Switzerland
| | - Mark Mellett
- Department of Dermatology, University Hospital Zürich (USZ), Zürich, Switzerland.,Faculty of Medicine, University of Zürich (UZH), Zürich, Switzerland
| | - Steve Pascolo
- Department of Dermatology, University Hospital Zürich (USZ), Zürich, Switzerland.,Faculty of Medicine, University of Zürich (UZH), Zürich, Switzerland
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20
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Song B, Shiromoto Y, Minakuchi M, Nishikura K. The role of RNA editing enzyme ADAR1 in human disease. WILEY INTERDISCIPLINARY REVIEWS. RNA 2022; 13:e1665. [PMID: 34105255 PMCID: PMC8651834 DOI: 10.1002/wrna.1665] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 03/02/2021] [Accepted: 04/22/2021] [Indexed: 12/19/2022]
Abstract
Adenosine deaminase acting on RNA (ADAR) catalyzes the posttranscriptional conversion of adenosine to inosine in double-stranded RNA (dsRNA), which can lead to the creation of missense mutations in coding sequences. Recent studies show that editing-dependent functions of ADAR1 protect dsRNA from dsRNA-sensing molecules and inhibit innate immunity and the interferon-mediated response. Deficiency in these ADAR1 functions underlie the pathogenesis of autoinflammatory diseases such as the type I interferonopathies Aicardi-Goutieres syndrome and dyschromatosis symmetrica hereditaria. ADAR1-mediated editing of endogenous coding and noncoding RNA as well as ADAR1 editing-independent interactions with DICER can also have oncogenic or tumor suppressive effects that affect tumor proliferation, invasion, and response to immunotherapy. The combination of proviral and antiviral roles played by ADAR1 in repressing the interferon response and editing viral RNAs alters viral morphogenesis and cell susceptibility to infection. This review analyzes the structure and function of ADAR1 with a focus on its position in human disease pathways and the mechanisms of its disease-associated effects. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA Processing > RNA Editing and Modification RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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Affiliation(s)
- Brian Song
- Department of Gene Expression and Regulation, The Wistar Institute, Philadelphia, Pennsylvania, USA
| | - Yusuke Shiromoto
- Department of Gene Expression and Regulation, The Wistar Institute, Philadelphia, Pennsylvania, USA
| | - Moeko Minakuchi
- Department of Gene Expression and Regulation, The Wistar Institute, Philadelphia, Pennsylvania, USA
| | - Kazuko Nishikura
- Department of Gene Expression and Regulation, The Wistar Institute, Philadelphia, Pennsylvania, USA
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21
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Xu L, Zhang C, Yin H, Gong S, Wu N, Ren Z, Zhang Y. RNA modifications act as regulators of cell death. RNA Biol 2021; 18:2183-2193. [PMID: 34313542 PMCID: PMC8632120 DOI: 10.1080/15476286.2021.1925460] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 04/26/2021] [Accepted: 04/29/2021] [Indexed: 12/14/2022] Open
Abstract
Currently, more than one hundred types of RNA modifications have been found, and many of these modifications are reversible and dynamically regulated. RNA modifications can regulate RNA stability and translation and are thus involved in multiple biological activities. Recently, RNA modifications have been shown to have important roles in the regulation of cell death. Cell death is a critical process that maintains tissue homoeostasis and is regulated by multiple pathways in response to specific stimuli. In this review, we summarize the current understanding of the roles of RNA modifications in cell death mediation and discuss the prospects of such research.Abbreviations: m6A, N6-Methyladenosine; m6Am, N6,2'-O-Dimethyladenosine; m1A, N1-Methyladenosine; m5C, 5-Methylcytosine; hm5C, 5-Hydroxymethylcytosine; Ψ, pseudouridine; A-to-I, adenosine-to- inosine; hnRNPs, heterogeneous nuclear ribonucleoproteins; MOMP, mitochondrial outer membrane permeabilization; DD, death domain; DISC, death-inducing signalling complex; DED, death effector domain; FADD, FAS-associated protein with the death domain; TRADD, TNF receptor-associated protein with death domain; CMA, chaperone- mediated autophagy; PE, phosphatidylethanolamine; AD, alzheimer's disease; AML, acute myeloid leukaemia; miR, microRNA; 6-OHDA, 6-hydroxydopamine hydrochloride; R-2HG, R-2-hydroxyglutarate; IRES, internal ribosome entry site; BMSCs, bone-derived mesenchymal stem cells; NPCs, nucleus pulposus cells; HsCG, human chorionic gonadotropin; snoRNAs, small nucleolar RNAs; ER, endoplasmic reticulum; lncRNAs, long noncoding RNAs; TNM, tumour-node-metastasis.
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Affiliation(s)
- Lei Xu
- Department of General Surgery, Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | - Chong Zhang
- Department of General Surgery, Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | - Hang Yin
- Department of General Surgery, Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | - Shuai Gong
- Department of General Surgery, Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | - Nai Wu
- Department of General Surgery, Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | - Zeqiang Ren
- Department of General Surgery, Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | - Yi Zhang
- Department of General Surgery, Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
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22
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Voss G, Edsjö A, Bjartell A, Ceder Y. Quantification of microRNA editing using two-tailed RT-qPCR for improved biomarker discovery. RNA (NEW YORK, N.Y.) 2021; 27:1412-1424. [PMID: 34433636 PMCID: PMC8522694 DOI: 10.1261/rna.078867.121] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 08/18/2021] [Indexed: 06/13/2023]
Abstract
Even though microRNAs have been viewed as promising biomarkers for years, their clinical implementation is still lagging far behind. This is in part due to the lack of RT-qPCR technologies that can differentiate between microRNA isoforms. For example, A-to-I editing of microRNAs through adenosine deaminase acting on RNA (ADAR) enzymes can affect their expression levels and functional roles, but editing isoform-specific assays are not commercially available. Here, we describe RT-qPCR assays that are specific for editing isoforms, using microRNA-379 (miR-379) as a model. The assays are based on two-tailed RT-qPCR, and we show them to be compatible both with SYBR Green and hydrolysis-based chemistries, as well as with both qPCR and digital PCR. The assays could readily detect different miR-379 editing isoforms in various human tissues as well as changes of editing levels in ADAR-overexpressing cell lines. We found that the miR-379 editing frequency was higher in prostate cancer samples compared to benign prostatic hyperplasia samples. Furthermore, decreased expression of unedited miR-379, but not edited miR-379, was associated with treatment resistance, metastasis, and shorter overall survival. Taken together, this study presents the first RT-qPCR assays that were demonstrated to distinguish A-to-I-edited microRNAs, and shows that they can be useful in the identification of biomarkers that previously have been masked by other isoforms.
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Affiliation(s)
- Gjendine Voss
- Department of Laboratory Medicine, Division of Translational Cancer Research, Lund University, 22381 Lund, Sweden
| | - Anders Edsjö
- Department of Clinical Genetics and Pathology, Laboratory Medicine, Medical Services, Region Skåne, 22185 Lund, Sweden
| | - Anders Bjartell
- Department of Urology, Skåne University Hospital, 20502 Malmö, Sweden
| | - Yvonne Ceder
- Department of Laboratory Medicine, Division of Translational Cancer Research, Lund University, 22381 Lund, Sweden
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23
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The Mechanism of miR-141 Regulating the Proliferation and Metastasis of Liver Cancer Cells by Targeting STAT4. JOURNAL OF ONCOLOGY 2021; 2021:5425491. [PMID: 34675977 PMCID: PMC8526259 DOI: 10.1155/2021/5425491] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/16/2021] [Accepted: 09/18/2021] [Indexed: 02/07/2023]
Abstract
Background In recent years, it has been reported that miRNA can be used as one of the markers of tumor diagnosis, treatment, and prognosis (including liver cancer), and it plays an important role in tumorigenesis. However, there are still very few studies on the mechanism and role of miR-141 in liver cancer. Methods qRT-PCR was used to test the expressions of miR-141 and STAT4 in collected liver cancer tissues and adjacent tissues, cultured liver cancer cell lines MHCC97H, Hep3B, and Huh7, and normal human liver cells HL7702. After processing the results of the qRT-PCR experiment, liver cancer cell MHCC97H which has the lowest expression level was decided to be taken as the research object. miR-NC, miR-141 mimics, si-NC, si-STAT4, miR-141 mimics and pcDNA-NC, and miR-141 mimics and pcDNA-STAT4 were transfected into MHCC97H cells, respectively. The MTT assay was used to detect the proliferation of each group of cells, and the Transwell test was used to detect the effect of miR-141 on cell proliferation, migration, and invasion. The interaction between miR-141 and STAT4 was verified by the dual-luciferase reporter experiment, and the expression level of Cyclin D1 and MMP2 was detected by the western blot. Results Compared with normal cell HL7702, the expression level of miR-141 in liver cancer cell lines was relatively low (P < 0.05) and the expression level of STAT4 in liver cancer cell lines was relatively high (P < 0.05) after testing the expression level of STAT4; transfecting miR-141 mimics or Si-SLBP can inhibit cell proliferation, migration, and invasion; dual-luciferase reporter experiments confirmed that miR-141 can specifically bind to the 3′UTR of STAT4; cotransfection of miR-141 mimics and pcDNA-STAT4 can antagonize the effects of miR-141 mimics on cell proliferation, migration, and invasion. Conclusion miR-141 can target the STAT4 gene expression to inhibit the proliferation, migration, and invasion of liver cancer cells.
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24
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Man G, Duan A, Liu W, Cheng J, Liu Y, Song J, Zhou H, Shen K. Circular RNA-Related CeRNA Network and Prognostic Signature for Patients with Osteosarcoma. Cancer Manag Res 2021; 13:7527-7541. [PMID: 34629900 PMCID: PMC8494289 DOI: 10.2147/cmar.s328559] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 09/26/2021] [Indexed: 12/21/2022] Open
Abstract
Introduction Osteosarcoma (OSA) is characterized by its relatively high morbidity in children and adolescents. Patients usually have advanced disease at the time of diagnosis, resulting in poor outcomes. This study focused on building a circular RNA-based ceRNA network to develop a reliable model for OSA risk prediction. Methods We used the Gene Expression Omnibus (GEO) datasets to explore the expression patterns of circRNA, miRNA, and mRNA in OSA. The prognostic value of circRNA host genes was assessed with data from the Therapeutically Applicable Research to Generate Effective Treatments (TARGET) database using Kaplan–Meier survival analysis. We established a circRNA-related ceRNA network and annotated its biological functions. Next, we developed a prognostic risk signature based on mRNAs extracted from the ceRNA network. We also developed a prognostic model and constructed a nomogram to enhance the prediction of OSA prognosis. Results We identified 166 DEcircRNAs, 233 DEmiRNAs, and 1317 DEmRNAs and used them to create a circRNA-related ceRNA network. We then established a prognostic risk model consisting of four genes (MLLT11, TNFRSF11B, SLC7A7, and PARVA). Moreover, we found that inhibition of MLLT11 and SLC7A7 blocked OSA cell proliferation and migration in in vitro experiments. Conclusion Our study identifies crucial prognostic genes and provides a circRNA-related ceRNA network for OSA, which will contribute to the elucidation of the molecular mechanisms underlying the oncogenesis and development of OSA.
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Affiliation(s)
- Gu Man
- Department of Orthopedics, Nanjing Lishui District Traditional Chinese Medicine Hospital, Nanjing, Jiangsu, People's Republic of China
| | - Ao Duan
- Department of Orthopedics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, People's Republic of China
| | - Wanshun Liu
- Department of Orthopedics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, People's Republic of China
| | - Jiangqi Cheng
- Department of Orthopedics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, People's Republic of China
| | - Yu Liu
- Department of Ophthalmology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, People's Republic of China
| | - Jiahang Song
- Department of Radiation Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, People's Republic of China
| | - Haisen Zhou
- Department of Pathology, Nanjing Lishui District Traditional Chinese Medicine Hospital, Nanjing, Jiangsu, People's Republic of China
| | - Kai Shen
- Department of Orthopedics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, People's Republic of China
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25
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De Paolis V, Lorefice E, Orecchini E, Carissimi C, Laudadio I, Fulci V. Epitranscriptomics: A New Layer of microRNA Regulation in Cancer. Cancers (Basel) 2021; 13:3372. [PMID: 34282776 PMCID: PMC8268402 DOI: 10.3390/cancers13133372] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 06/30/2021] [Accepted: 06/30/2021] [Indexed: 12/15/2022] Open
Abstract
MicroRNAs are pervasive regulators of gene expression at the post-transcriptional level in metazoan, playing key roles in several physiological and pathological processes. Accordingly, these small non-coding RNAs are also involved in cancer development and progression. Furthermore, miRNAs represent valuable diagnostic and prognostic biomarkers in malignancies. In the last twenty years, the role of RNA modifications in fine-tuning gene expressions at several levels has been unraveled. All RNA species may undergo post-transcriptional modifications, collectively referred to as epitranscriptomic modifications, which, in many instances, affect RNA molecule properties. miRNAs are not an exception, in this respect, and they have been shown to undergo several post-transcriptional modifications. In this review, we will summarize the recent findings concerning miRNA epitranscriptomic modifications, focusing on their potential role in cancer development and progression.
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Affiliation(s)
| | | | | | - Claudia Carissimi
- Dipartimento di Medicina Molecolare, Sapienza Università di Roma, 00161 Rome, Italy; (V.D.P.); (E.L.); (E.O.); (V.F.)
| | - Ilaria Laudadio
- Dipartimento di Medicina Molecolare, Sapienza Università di Roma, 00161 Rome, Italy; (V.D.P.); (E.L.); (E.O.); (V.F.)
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26
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Dong Z, Gu H, Guo Q, Liang S, Xue J, Yao F, Liu X, Li F, Liu H, Sun L, Zhao K. Profiling of Serum Exosome MiRNA Reveals the Potential of a MiRNA Panel as Diagnostic Biomarker for Alzheimer's Disease. Mol Neurobiol 2021; 58:3084-3094. [PMID: 33629272 DOI: 10.1007/s12035-021-02323-y] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 02/05/2021] [Indexed: 12/14/2022]
Abstract
Alzheimer's disease (AD) is the most common neurodegenerative disease in the older adults. Although much effort has been made in the analyses of diagnostic biomarkers, such as amyloid-β, tau, and neurofilament light chain, identifying peripheral blood-based biomarkers is in extremely urgent need for their minimal invasiveness and more convenience. Here we characterized the miRNA profile by RNA sequencing in human serum exosomes from AD patients and healthy controls (HC) to investigate its potential for AD diagnosis. Subsequently, Gene Ontology analysis and pathway analysis were performed for the targeted genes from the differentially expressed miRNAs. These basic functions were differentially enriched, including cell adhesion, regulation of transcription, and the ubiquitin system. Functional network analysis highlighted the pathways of proteoglycans in cancer, viral carcinogenesis, signaling pathways regulating pluripotency of stem cells, and cellular senescence in AD. A total of 24 miRNAs showed significantly differential expression between AD and HC with more than ± 2.0-fold change at p value < 0.05 and at least 50 reads for each sample. Logistic regression analysis established a model for AD prediction by serum exosomal miR-30b-5p, miR-22-3p, and miR-378a-3p. Sequencing results were validated using quantitative reverse transcription PCR. The data showed that miR-30b-5p, miR-22-3p, and miR-378a-3p were significantly deregulated in AD, with area under the curve (AUC) of 0.668, 0.637, and 0.718, respectively. The combination of the three miRs gained a better diagnostic capability with AUC of 0.880. This finding revealed a miR panel as potential biomarker in the peripheral blood to distinguish AD from HC.
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Affiliation(s)
- Zhiwu Dong
- Department of Laboratory Medicine, Jinshan Branch of Shanghai Sixth People's Hospital Affiliated to Shanghai Jiaotong University, 147 Jiankang Road, Jinshan District, Shanghai, 201599, People's Republic of China.
| | - Hongjun Gu
- Shanghai Jinshan Zhongren Aged Care Hospital, Shanghai, 201501, China
| | - Qiang Guo
- Department of Ultrasound Medicine, Jinshan Branch of Shanghai Sixth People's Hospital Affiliated to Shanghai Jiaotong University, Shanghai, 201599, China
| | - Shuang Liang
- Department of Laboratory Medicine, Jinshan Branch of Shanghai Sixth People's Hospital Affiliated to Shanghai Jiaotong University, 147 Jiankang Road, Jinshan District, Shanghai, 201599, People's Republic of China
| | - Jian Xue
- Shanghai Jinshan Zhongren Aged Care Hospital, Shanghai, 201501, China
| | - Feng Yao
- Shanghai Jinshan Zhongren Aged Care Hospital, Shanghai, 201501, China
| | - Xianglu Liu
- Department of Laboratory Medicine, Jinshan Branch of Shanghai Sixth People's Hospital Affiliated to Shanghai Jiaotong University, 147 Jiankang Road, Jinshan District, Shanghai, 201599, People's Republic of China
| | - Feifei Li
- Department of Laboratory Medicine, Jinshan Branch of Shanghai Sixth People's Hospital Affiliated to Shanghai Jiaotong University, 147 Jiankang Road, Jinshan District, Shanghai, 201599, People's Republic of China
| | - Huiling Liu
- Department of Laboratory Medicine, Jinshan Branch of Shanghai Sixth People's Hospital Affiliated to Shanghai Jiaotong University, 147 Jiankang Road, Jinshan District, Shanghai, 201599, People's Republic of China
| | - Li Sun
- Department of Laboratory Medicine, Jinshan Branch of Shanghai Sixth People's Hospital Affiliated to Shanghai Jiaotong University, 147 Jiankang Road, Jinshan District, Shanghai, 201599, People's Republic of China
| | - Kewen Zhao
- Department of Pathophysiology, Shanghai Jiaotong University School of Medicine, Shanghai, 200025, People's Republic of China
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27
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Abstract
Post-synthesis modification of biomolecules is an efficient way of regulating and optimizing their functions. The human epitranscriptome includes a variety of more than 100 modifications known to exist in all RNA subtypes. Modifications of non-coding RNAs are particularly interesting since they can directly affect their structure, stability, interaction and function. Indeed, non-coding RNAs such as tRNA and rRNA are the most modified RNA species in eukaryotic cells. In the last 20 years, new functions of non-coding RNAs have been discovered and their involvement in human disease, including cancer, became clear. In this review, we will present the evidence connecting modifications of different non-coding RNA subtypes and their role in cancer.
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Affiliation(s)
| | | | - Luca Pandolfini
- Corresponding authors: Isaia Barbieri, University of Cambridge, Department of pathology, Division of cellular and molecular pathology, Addenbrooke's hospital, Lab block, level 3 Box 231, CB2 0QQ, Cambridge, UK. Tel.: +44 (0)1223 333917; E-mail: , Luca Pandolfini, Istituto Italiano di Tecnologia, via Enrico Melen 83, Building B, 16152 Genova, Italy. Tel.: +39 010 2897623; E-mail:
| | - Isaia Barbieri
- Corresponding authors: Isaia Barbieri, University of Cambridge, Department of pathology, Division of cellular and molecular pathology, Addenbrooke's hospital, Lab block, level 3 Box 231, CB2 0QQ, Cambridge, UK. Tel.: +44 (0)1223 333917; E-mail: , Luca Pandolfini, Istituto Italiano di Tecnologia, via Enrico Melen 83, Building B, 16152 Genova, Italy. Tel.: +39 010 2897623; E-mail:
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28
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Yu H, Yu Z, Wang X, Wang D. Circular RNA circCLK3 promotes the progression of tongue squamous cell carcinoma via miR-455-5p/PARVA axis. Biotechnol Appl Biochem 2021; 69:431-441. [PMID: 33655541 DOI: 10.1002/bab.2120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 01/29/2021] [Indexed: 12/17/2022]
Abstract
A previous study has elucidated that circular RNA circCLK3 acts as an oncogenic gene in cervical cancer. However, the role and regulatory mechanism of circCLK3 in tongue squamous cell carcinoma (TSCC) remain unknown. Quantitative real-time PCR was used to examine targeted gene expression in different groups. Cell viability and proliferation were investigated by MTT and 5-ethynyl-2'-deoxyuridine assays. Cell migration and invasion were detected by Transwell assays, and cell apoptosis was measured by flow cytometry analysis. The interaction among genes was investigated using luciferase reporter assay, RNA pull-down assay, and RNA immunoprecipitation assay. In the present study, our findings revealed the upregulated expression of circCLK3 in TSCC tissues and cell lines. CircCLK3 knockdown suppressed cell proliferation, migration invasion, and induced cell cycle arrest at G0/G1 phase in TSCC. Moreover, circCLK3 acted as a molecular sponge for miR-455-5p. PARVA was the target gene of miR-455-5p. Furthermore, the negative correlation between expression of miR-455-5p and circCLK3 or PARVA in TSCC tissues was discovered. Rescue assays indicated that PARVA overexpression reversed the circCLK3 knockdown-mediated inhibitory effects on the progression of TSCC. In summary, circCLK3 exerts its carcinogenic effects on TSCC progression via absorbing miR-455-5p to upregulate PARVA, which expands our knowledge on the underlying mechanism of TSCC.
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Affiliation(s)
- Huiming Yu
- Department of Stomatology, The Affiliated Huaian No. 1 People's Hospital of Nanjing Medical University, Huaian, China
| | - Zhifen Yu
- Department of Stomatology, Huaian Maternal and Child Health Hospital, Huaian, China
| | - Xiaowei Wang
- Department of Oncology, The Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, Huaian, China
| | - Dazhao Wang
- Department of Stomatology, The Affiliated Huaian No. 1 People's Hospital of Nanjing Medical University, Huaian, China
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29
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Kurkowiak M, Arcimowicz Ł, Chruściel E, Urban-Wójciuk Z, Papak I, Keegan L, O'Connell M, Kowalski J, Hupp T, Marek-Trzonkowska N. The effects of RNA editing in cancer tissue at different stages in carcinogenesis. RNA Biol 2021; 18:1524-1539. [PMID: 33593231 PMCID: PMC8582992 DOI: 10.1080/15476286.2021.1877024] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
RNA editing is one of the most prevalent and abundant forms of post-transcriptional RNA modification observed in normal physiological processes and often aberrant in diseases including cancer. RNA editing changes the sequences of mRNAs, making them different from the source DNA sequence. Edited mRNAs can produce editing-recoded protein isoforms that are functionally different from the corresponding genome-encoded protein isoforms. The major type of RNA editing in mammals occurs by enzymatic deamination of adenosine to inosine (A-to-I) within double-stranded RNAs (dsRNAs) or hairpins in pre-mRNA transcripts. Enzymes that catalyse these processes belong to the adenosine deaminase acting on RNA (ADAR) family. The vast majority of knowledge on the RNA editing landscape relevant to human disease has been acquired using in vitro cancer cell culture models. The limitation of such in vitro models, however, is that the physiological or disease relevance of results obtained is not necessarily obvious. In this review we focus on discussing in vivo occurring RNA editing events that have been identified in human cancer tissue using samples surgically resected or clinically retrieved from patients. We discuss how RNA editing events occurring in tumours in vivo can identify pathological signalling mechanisms relevant to human cancer physiology which is linked to the different stages of cancer progression including initiation, promotion, survival, proliferation, immune escape and metastasis.
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Affiliation(s)
- Małgorzata Kurkowiak
- International Centre for Cancer Vaccine Science (ICCVS), University of Gdańsk, Gdańsk, Poland
| | - Łukasz Arcimowicz
- International Centre for Cancer Vaccine Science (ICCVS), University of Gdańsk, Gdańsk, Poland
| | - Elżbieta Chruściel
- International Centre for Cancer Vaccine Science (ICCVS), University of Gdańsk, Gdańsk, Poland
| | - Zuzanna Urban-Wójciuk
- International Centre for Cancer Vaccine Science (ICCVS), University of Gdańsk, Gdańsk, Poland
| | - Ines Papak
- International Centre for Cancer Vaccine Science (ICCVS), University of Gdańsk, Gdańsk, Poland
| | - Liam Keegan
- CEITEC Masaryk University, Brno, CZ, Czech Republic
| | | | - Jacek Kowalski
- International Centre for Cancer Vaccine Science (ICCVS), University of Gdańsk, Gdańsk, Poland.,Department of Pathomorphology, Medical University of Gdańsk, Gdańsk, Poland
| | - Ted Hupp
- International Centre for Cancer Vaccine Science (ICCVS), University of Gdańsk, Gdańsk, Poland.,University of Edinburgh, Edinburgh Cancer Research Centre, Edinburgh, Scotland, UK
| | - Natalia Marek-Trzonkowska
- International Centre for Cancer Vaccine Science (ICCVS), University of Gdańsk, Gdańsk, Poland.,Laboratory of Immunoregulation and Cellular Therapies, Department of Family Medicine, Medical University of Gdańsk, Gdańsk, Poland
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30
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Huang C, Shen Q, Song G, He S, Zhou L. Downregulation of PARVA promotes metastasis by modulating integrin-linked kinase activity and regulating MAPK/ERK and MLC2 signaling in prostate cancer. Transl Androl Urol 2021; 10:915-928. [PMID: 33718092 PMCID: PMC7947443 DOI: 10.21037/tau-21-108] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Background Metastasis is the predominant cause of mortality in prostate cancer (PCa); however, the underlying mechanisms are largely uncharted. Here, we found that Parvin alpha (PARVA) is downregulated in PCa and its loss is associated with clinical metastasis. We further explored the mechanistic basis of this finding. Methods The mRNA expression of PARVA was identified by analysis of the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) data sets. Immunohistochemistry (IHC) analysis was performed to evaluate the PARVA expression pattern in 198 PCa tissues, and 36 metastatic lymph node tissues. The function and molecular mechanism by which PARVA affects PCa were investigated in vitro using knockdown and overexpression cell lines. The effect of PARVA in cell proliferation, migration, and invasion in PCa cells was detected by MTS assay and Transwell assay. Real-time polymerase chain reaction (PCR) and Western blot analysis were used to assess the gene expression in mRNA and protein level. Results The microarray data analysis indicated that PARVA was drastically downregulated in primary and metastatic PCa compared with normal and primary samples, respectively (all P<0.001). Multivariate Cox regression analysis suggested that downregulation of PARVA in PCa was an independent prognostic factor for poor biochemical recurrence (BCR)-free survival (P<0.01). IHC analysis confirmed that PARVA was frequently downregulated in metastatic and primary PCa tissues (All P<0.001). Furthermore, PARVA expression was found to be associated with Gleason score, pathological stage, extracapsular extension, and lymph node invasion (All P<0.05). Knockdown of PARVA triggered cell migration and invasion in vitro, whereas overexpression of PARVA reverted the invasive phenotypes. Mechanistic investigations identified that overexpression of PARVA repressed the mitogen-activated protein kinase (MAPK)/extracellular signal-regulated kinase (ERK) phosphorylation via inhibiting the integrin-linked kinase (ILK) biological function. With knockdown of ILK, the downregulated MAPK/ERK phosphorylation and Myosin Light Chain 2 (MLC2) expression by PARVA overexpression were abolished, indicating that the PARVA effect on PCa is ILK/MAPK/ERK pathway dependent. Conclusions Our study revealed that loss of PARVA expression in PCa promotes metastasis by releasing the inhibition of ILK activity, followed by the activation of MAPK/ERK and MLC2 signaling.
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Affiliation(s)
- Cong Huang
- Department of Urology, Peking University First Hospital, Beijing, China.,Institute of Urology, Peking University, Beijing, China.,National Urological Cancer Center of China, Beijing, China
| | - Qi Shen
- Department of Urology, Peking University First Hospital, Beijing, China.,Institute of Urology, Peking University, Beijing, China.,National Urological Cancer Center of China, Beijing, China
| | - Gang Song
- Department of Urology, Peking University First Hospital, Beijing, China.,Institute of Urology, Peking University, Beijing, China.,National Urological Cancer Center of China, Beijing, China
| | - Shiming He
- Department of Urology, Peking University First Hospital, Beijing, China.,Institute of Urology, Peking University, Beijing, China.,National Urological Cancer Center of China, Beijing, China
| | - Liqun Zhou
- Department of Urology, Peking University First Hospital, Beijing, China.,Institute of Urology, Peking University, Beijing, China.,National Urological Cancer Center of China, Beijing, China
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31
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Mao Y, Li W, Hua B, Gu X, Pan W, Chen Q, Xu B, Lu C, Wang Z. Circular RNA_PDHX Promotes the Proliferation and Invasion of Prostate Cancer by Sponging MiR-378a-3p. Front Cell Dev Biol 2021; 8:602707. [PMID: 33634097 PMCID: PMC7901981 DOI: 10.3389/fcell.2020.602707] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 12/02/2020] [Indexed: 12/12/2022] Open
Abstract
The dysregulation of circular RNAs (circRNAs) is implicated in the pathogenesis of prostate cancer (PCa). However, the underlying mechanisms by which hsa_circ_0003768 (circPDHX) contributes to PCa remain elusive. The differentially expressed circRNAs between PCa and normal tissues were identified by Gene Expression Omnibus dataset. The association of circPDHX and miR-378a-3p expression with the clinicopathological parameters and prognosis in patients with PCa was analyzed by fluorescence in situ hybridization and The Cancer Genome Atlas dataset. 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) and Transwell assays as well as a xenograft tumor model were used to assess the role of circPDHX in PCa cells. circPDHX-specific binding with miR-378a-3p was validated by bioinformatic analysis, luciferase gene reporter, and RNA immunoprecipitation assays. As a result, we found that increased expression of circPDHX was associated with Gleason score (P = 0.001) and pathogenic T stage (P = 0.01) and acted as an independent prognostic factor of poor survival (P = 0.036) in patients with PCa. Knockdown of circPDHX inhibited cell proliferation and invasion in vitro and in vivo, but ectopic expression of circPDHX reversed these effects. Furthermore, circPDHX could sponge miR-378a-3p to promote cell proliferation, but miR-378a-3p counteracted circPDHX-induced cell proliferation and insulin-like growth factor 1 receptor (IGF1R) expression in PCa cells. In conclusion, our findings demonstrated that circPDHX facilitated the proliferation and invasion of PCa cells by sponging miR-378a-3p.
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Affiliation(s)
- Yuanshen Mao
- Department of Urology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wenfeng Li
- Department of Urology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Bao Hua
- Department of Urology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xin Gu
- Department of Urology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Weixin Pan
- Department of Urology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qi Chen
- Department of Urology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Bin Xu
- Department of Urology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chao Lu
- Department of Urology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhong Wang
- Department of Urology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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Torsin LI, Petrescu GED, Sabo AA, Chen B, Brehar FM, Dragomir MP, Calin GA. Editing and Chemical Modifications on Non-Coding RNAs in Cancer: A New Tale with Clinical Significance. Int J Mol Sci 2021; 22:ijms22020581. [PMID: 33430133 PMCID: PMC7827606 DOI: 10.3390/ijms22020581] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 12/29/2020] [Accepted: 12/30/2020] [Indexed: 12/11/2022] Open
Abstract
Currently, for seemingly every type of cancer, dysregulated levels of non-coding RNAs (ncRNAs) are reported and non-coding transcripts are expected to be the next class of diagnostic and therapeutic tools in oncology. Recently, alterations to the ncRNAs transcriptome have emerged as a novel hallmark of cancer. Historically, ncRNAs were characterized mainly as regulators and little attention was paid to the mechanisms that regulate them. The role of modifications, which can control the function of ncRNAs post-transcriptionally, only recently began to emerge. Typically, these modifications can be divided into reversible (i.e., chemical modifications: m5C, hm5C, m6A, m1A, and pseudouridine) and non-reversible (i.e., editing: ADAR dependent, APOBEC dependent and ADAR/APOBEC independent). The first research papers showed that levels of these modifications are altered in cancer and can be part of the tumorigenic process. Hence, the aim of this review paper is to describe the most common regulatory modifications (editing and chemical modifications) of the traditionally considered “non-functional” ncRNAs (i.e., microRNAs, long non-coding RNAs and circular RNAs) in the context of malignant disease. We consider that only by understanding this extra regulatory layer it is possible to translate the knowledge about ncRNAs and their modifications into clinical practice.
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Affiliation(s)
- Ligia I. Torsin
- Department of Anesthesiology and Critical Care, Elias Clinical Emergency Hospital, 011461 Bucharest, Romania;
| | - George E. D. Petrescu
- Department of Neurosurgery, Carol Davila University of Medicine and Pharmacy, 020021 Bucharest, Romania; (G.E.D.P.); (F.M.B.)
- Department of Neurosurgery, Bagdasar-Arseni Clinical Emergency Hospital, 041915 Bucharest, Romania
| | - Alexandru A. Sabo
- Zentrum für Kinder, Jugend und Frauenmedizin, Pediatrics 2 (General and Special Pediatrics), Klinikum Stuttgart, Olgahospital, 70174 Stuttgart, Germany;
| | - Baoqing Chen
- State Key Laboratory of Oncology in South China, Department of Radiation Oncology, Collaborative Innovation Center of Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China;
- Guangdong Esophageal Cancer Research Institute, Guangzhou 510060, China
| | - Felix M. Brehar
- Department of Neurosurgery, Carol Davila University of Medicine and Pharmacy, 020021 Bucharest, Romania; (G.E.D.P.); (F.M.B.)
- Department of Neurosurgery, Bagdasar-Arseni Clinical Emergency Hospital, 041915 Bucharest, Romania
| | - Mihnea P. Dragomir
- Institute of Pathology, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
- Correspondence: or (M.P.D.); (G.A.C.); Tel.: +40-254-219-493 (M.P.D.); +1-713-792-5461 (G.A.C.)
| | - George A. Calin
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
- Correspondence: or (M.P.D.); (G.A.C.); Tel.: +40-254-219-493 (M.P.D.); +1-713-792-5461 (G.A.C.)
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Tassinari V, Cesarini V, Silvestris DA, Scafidi A, Cucina L, Gallo A. MicroRNA Editing Detection and Function: A Combined In Silico and Experimental Approach for the Identification and Validation of Putative Oncogenic Targets. Methods Mol Biol 2021; 2181:253-267. [PMID: 32729085 DOI: 10.1007/978-1-0716-0787-9_15] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
MicroRNAs (miRNAs) are a class of ~22 nt noncoding RNAs playing essential roles in the post-transcriptional regulation of gene expression, cell proliferation, and cell differentiation and are often found deregulated in several diseases including cancer.The A-to-I RNA editing, mediated by ADAR enzymes, is a diffuse post-transcriptional mechanism that converts the genetically coded adenosine (A) into inosine (I) at the RNA level. Among different RNA targets, the ADAR enzymes can also edit miRNA precursors. Specifically, a single nucleotide change (A/I) lying within the mature miRNA can alter the miRNA binding specificity and redirect the edited miRNA to a different mRNA target. In several cancer types a consistent deregulation of A-to-I RNA editing machinery also involves important miRNAs (either oncomiRs or tumor-suppressor miRNAs). Herein we describe a combined in silico and experimental approach for the detection of edited miRNAs and the identification and validation of their target genes potentially involved in cancer progression or invasion.
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Affiliation(s)
- Valentina Tassinari
- RNA Editing Lab, Oncohaematology Department, IRCCS Ospedale Pediatrico "Bambino Gesù", Rome, Italy
| | - Valeriana Cesarini
- RNA Editing Lab, Oncohaematology Department, IRCCS Ospedale Pediatrico "Bambino Gesù", Rome, Italy
| | | | - Andrea Scafidi
- RNA Editing Lab, Oncohaematology Department, IRCCS Ospedale Pediatrico "Bambino Gesù", Rome, Italy
| | - Lorenzo Cucina
- RNA Editing Lab, Oncohaematology Department, IRCCS Ospedale Pediatrico "Bambino Gesù", Rome, Italy
| | - Angela Gallo
- RNA Editing Lab, Oncohaematology Department, IRCCS Ospedale Pediatrico "Bambino Gesù", Rome, Italy.
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Erdmann EA, Mahapatra A, Mukherjee P, Yang B, Hundley HA. To protect and modify double-stranded RNA - the critical roles of ADARs in development, immunity and oncogenesis. Crit Rev Biochem Mol Biol 2020; 56:54-87. [PMID: 33356612 DOI: 10.1080/10409238.2020.1856768] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Adenosine deaminases that act on RNA (ADARs) are present in all animals and function to both bind double-stranded RNA (dsRNA) and catalyze the deamination of adenosine (A) to inosine (I). As inosine is a biological mimic of guanosine, deamination by ADARs changes the genetic information in the RNA sequence and is commonly referred to as RNA editing. Millions of A-to-I editing events have been reported for metazoan transcriptomes, indicating that RNA editing is a widespread mechanism used to generate molecular and phenotypic diversity. Loss of ADARs results in lethality in mice and behavioral phenotypes in worm and fly model systems. Furthermore, alterations in RNA editing occur in over 35 human pathologies, including several neurological disorders, metabolic diseases, and cancers. In this review, a basic introduction to ADAR structure and target recognition will be provided before summarizing how ADARs affect the fate of cellular RNAs and how researchers are using this knowledge to engineer ADARs for personalized medicine. In addition, we will highlight the important roles of ADARs and RNA editing in innate immunity and cancer biology.
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Affiliation(s)
- Emily A Erdmann
- Department of Biology, Indiana University, Bloomington, IN, USA
| | | | - Priyanka Mukherjee
- Medical Sciences Program, Indiana University School of Medicine-Bloomington, Bloomington, IN, USA
| | - Boyoon Yang
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN, USA
| | - Heather A Hundley
- Medical Sciences Program, Indiana University School of Medicine-Bloomington, Bloomington, IN, USA
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Chen S, Zhang J, Chen Q, Cheng J, Chen X, Mao Y, Chen W, Liu C, Wu H, Lv Y, Lin Y. MicroRNA-200a and microRNA-141 have a synergetic effect on the suppression of epithelial-mesenchymal transition in liver cancer by targeting STAT4. Oncol Lett 2020; 21:137. [PMID: 33552256 PMCID: PMC7798046 DOI: 10.3892/ol.2020.12398] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 11/24/2020] [Indexed: 02/06/2023] Open
Abstract
MicroRNAs (miRNAs or miRs) are non-coding small RNAs that target specific messenger RNAs to inhibit protein translation. miR-200a and miR-141 function as tumor suppressors by targeting STAT4. These two miRNAs belong to the same family, and their expression is often decreased in various cancer types, but are located on different chromosomes of the human genome. The present study showed that the expression levels of miR-141 and miR-200a in serum and cells of liver cancer are significantly downregulated. The expression levels of miR-141 and miR-200a are closely associated with clinicopathological features of liver cancer, especially metastasis and invasion. It is first reported that STAT4 is the new common target gene of miR-141 and miR-200a. In the present study, miR-141 and miR-200a were confirmed to inhibit the expression of E-cadherin and vimentin synergistically during epithelial-mesenchymal transition to regulate the proliferation, migration and invasion of liver cancer cells by targeting STAT4. Simultaneous overexpression of miR-200a and miR-141 resulted in stronger effects compared with each miRNA alone. In addition, overexpression of STAT4 significantly reversed the tumor suppressive roles of miR-200a and miR-141 in liver cancer cells. These findings enrich the tumor suppressor mechanisms of the miR-200 family, and may also provide new experimental and theoretical basis for the use of miRNAs for early diagnosis, prognosis and thorough treatment of liver cancer.
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Affiliation(s)
- Shuying Chen
- Department of Laboratory Medicine, Huashan Hospital, Fudan University, Shanghai 200040, P.R. China
| | - Jingjun Zhang
- Department of Rehabilitation, Huashan Hospital, Fudan University, Shanghai 200040, P.R. China
| | - Qiudan Chen
- Department of Central Laboratory, Clinical Laboratory, Jingan District Central Hospital, Fudan University, Shanghai 200040, P.R. China
| | - Juan Cheng
- Department of Clinical Laboratory, The Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230601, P.R. China
| | - Xiaotong Chen
- Department of Laboratory Medicine, Huashan Hospital, Fudan University, Shanghai 200040, P.R. China
| | - Yinqi Mao
- School of Medicine, Shanghai Jiao Tong University, Shanghai 200025, P.R. China
| | - Wei Chen
- School of Medicine, Shanghai Jiao Tong University, Shanghai 200025, P.R. China
| | - Chenbin Liu
- School of Medicine, Shanghai Jiao Tong University, Shanghai 200025, P.R. China
| | - Han Wu
- School of Medicine, Shanghai Jiao Tong University, Shanghai 200025, P.R. China
| | - Yuan Lv
- Department of Laboratory Medicine, Huashan Hospital, Fudan University, Shanghai 200040, P.R. China
| | - Yong Lin
- Department of Laboratory Medicine, Huashan Hospital, Fudan University, Shanghai 200040, P.R. China
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Zhu J, Deng J, Zhang L, Zhao J, Zhou F, Liu N, Cai R, Wu J, Shu B, Qi S. Reconstruction of lncRNA-miRNA-mRNA network based on competitive endogenous RNA reveals functional lncRNAs in skin cutaneous melanoma. BMC Cancer 2020; 20:927. [PMID: 32993558 PMCID: PMC7523354 DOI: 10.1186/s12885-020-07302-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 08/16/2020] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Human skin cutaneous melanoma is the most common and dangerous skin tumour, but its pathogenesis is still unclear. Although some progress has been made in genetic research, no molecular indicators related to the treatment and prognosis of melanoma have been found. In various diseases, dysregulation of lncRNA is common, but its role has not been fully elucidated. In recent years, the birth of the "competitive endogenous RNA" theory has promoted our understanding of lncRNAs. METHODS To identify the key lncRNAs in melanoma, we reconstructed a global triple network based on the "competitive endogenous RNA" theory. Gene Ontology and KEGG pathway analysis were performed using DAVID (Database for Annotation, Visualization, and Integration Discovery). Our findings were validated through qRT-PCR assays. Moreover, to determine whether the identified hub gene signature is capable of predicting the survival of cutaneous melanoma patients, a multivariate Cox regression model was performed. RESULTS According to the "competitive endogenous RNA" theory, 898 differentially expressed mRNAs, 53 differentially expressed lncRNAs and 16 differentially expressed miRNAs were selected to reconstruct the competitive endogenous RNA network. MALAT1, LINC00943, and LINC00261 were selected as hub genes and are responsible for the tumorigenesis and prognosis of cutaneous melanoma. CONCLUSIONS MALAT1, LINC00943, and LINC00261 may be closely related to tumorigenesis in cutaneous melanoma. In addition, MALAT1 and LINC00943 may be independent risk factors for the prognosis of patients with this condition and might become predictive molecules for the long-term treatment of melanoma and potential therapeutic targets.
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Affiliation(s)
- Junyou Zhu
- Department of Burn, The First Affiliated Hospital, Sun yat-sen University, Guangzhou, Guangdong 510080 People’s Republic of China
| | - Jin Deng
- Department of Radiation Oncology, Cancer Center of Guangzhou Medical University, Guangzhou, Guangdong 510095 People’s Republic of China
| | - Lijun Zhang
- Department of Burn, The First Affiliated Hospital, Sun yat-sen University, Guangzhou, Guangdong 510080 People’s Republic of China
| | - Jingling Zhao
- Department of Burn, The First Affiliated Hospital, Sun yat-sen University, Guangzhou, Guangdong 510080 People’s Republic of China
| | - Fei Zhou
- Department of Burn, The First Affiliated Hospital, Sun yat-sen University, Guangzhou, Guangdong 510080 People’s Republic of China
| | - Ning Liu
- Department of Burn, The First Affiliated Hospital, Sun yat-sen University, Guangzhou, Guangdong 510080 People’s Republic of China
| | - Ruizhao Cai
- Department of Burn, The First Affiliated Hospital, Sun yat-sen University, Guangzhou, Guangdong 510080 People’s Republic of China
| | - Jun Wu
- Department of Burn, The First Affiliated Hospital, Sun yat-sen University, Guangzhou, Guangdong 510080 People’s Republic of China
| | - Bin Shu
- Department of Burn, The First Affiliated Hospital, Sun yat-sen University, Guangzhou, Guangdong 510080 People’s Republic of China
| | - Shaohai Qi
- Department of Burn, The First Affiliated Hospital, Sun yat-sen University, Guangzhou, Guangdong 510080 People’s Republic of China
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Zhang C, Wu S. microRNA -378a-3p Restrains the Proliferation of Retinoblastoma Cells but Promotes Apoptosis of Retinoblastoma Cells via Inhibition of FOXG1. Invest Ophthalmol Vis Sci 2020; 61:31. [PMID: 32428232 PMCID: PMC7405766 DOI: 10.1167/iovs.61.5.31] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Purpose More recently, literature has emerged providing findings about the novelty of microRNAs (miR)-targeted therapeutics in the treatment of retinoblastoma (RB). The prime objective of this study was to identify the potential role of miR-378a-3p and its regulation in RB cells via forkhead box G1 (FOXG1). Methods The expression of miR-378a-3p and FOXG1 in the clinical RB tissues was determined using RNA quantitation and Western blot assays. The interaction between miR-378a-3p and FOXG1 was identified using dual luciferase reporter gene assay. The potential effects of miR-378a-3p on the RB cell biological processes were evaluated by conducting gain- and loss-of-function studies of miR-378a-3p and FOXG1, followed by cell viability, cell cycle progression, and apoptosis measurements. Furthermore, experiments were performed in nude mice to assess its effects on tumor formation. Results miR-378a-3p was poorly expressed, whereas FOXG1 was highly expressed in RB tissues and cells. miR-378a-3p bound to the FOXG1 3′ untranslated region and negatively modulated its expression. The overexpression of miR-378a-3p was found to decrease RB cell viability and to promote cell apoptosis in vitro, whereas overexpressed FOXG1 reversed the regulatory effects of miR-378a-3p on RB cellular behaviors. In nude mice, the restoration of miR-378a-3p by miR-378a-3p agomir was shown to play a role in the reduction of tumor volume and size relative to nude mice injected with negative control-agomir. Conclusions Our findings identified that increased miR-378a-3p exerted an inhibitory effect on RB cell proliferation by targeting FOXG1, suggesting the role of miR-378a-3p as a novel therapeutic target for RB.
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van der Kwast RVCT, Parma L, van der Bent ML, van Ingen E, Baganha F, Peters HAB, Goossens EAC, Simons KH, Palmen M, de Vries MR, Quax PHA, Nossent AY. Adenosine-to-Inosine Editing of Vasoactive MicroRNAs Alters Their Targetome and Function in Ischemia. MOLECULAR THERAPY-NUCLEIC ACIDS 2020; 21:932-953. [PMID: 32814251 PMCID: PMC7452086 DOI: 10.1016/j.omtn.2020.07.020] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 06/30/2020] [Accepted: 07/14/2020] [Indexed: 12/17/2022]
Abstract
Adenosine-to-inosine (A-to-I) editing in the seed sequence of microRNAs can shift the microRNAs’ targetomes and thus their function. Using public RNA-sequencing data, we identified 35 vasoactive microRNAs that are A-to-I edited. We quantified A-to-I editing of the primary (pri-)microRNAs in vascular fibroblasts and endothelial cells. Nine pri-microRNAs were indeed edited, and editing consistently increased under ischemia. We determined mature microRNA editing for the highest expressed microRNAs, i.e., miR-376a-3p, miR-376c-3p, miR-381-3p, and miR-411-5p. All four mature microRNAs were edited in their seed sequence. We show that both ADAR1 and ADAR2 (adenosine deaminase acting on RNA 1 and RNA 2) can edit pri-microRNAs in a microRNA-specific manner. MicroRNA editing also increased under ischemia in vivo in a murine hindlimb ischemia model and ex vivo in human veins. For each edited microRNA, we confirmed a shift in targetome. Expression of the edited microRNA targetomes, not the wild-type targetomes, was downregulated under ischemia in vivo. Furthermore, microRNA editing enhanced angiogenesis in vitro and ex vivo. In conclusion, we show that microRNA A-to-I editing is a widespread phenomenon, induced by ischemia. Each editing event results in a novel microRNA with a unique targetome, leading to increased angiogenesis.
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Affiliation(s)
- Reginald V C T van der Kwast
- Department of Surgery, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands; Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Laura Parma
- Department of Surgery, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands; Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - M Leontien van der Bent
- Department of Surgery, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands; Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Eva van Ingen
- Department of Surgery, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands; Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Fabiana Baganha
- Department of Surgery, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands; Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Hendrika A B Peters
- Department of Surgery, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands; Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Eveline A C Goossens
- Department of Surgery, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands; Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Karin H Simons
- Department of Surgery, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands; Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Meindert Palmen
- Department of Cardiothoracic Surgery, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Margreet R de Vries
- Department of Surgery, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands; Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Paul H A Quax
- Department of Surgery, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands; Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - A Yaël Nossent
- Department of Surgery, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands; Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands; Department of Laboratory Medicine, Medical University of Vienna, 1090 Vienna, Austria; Department of Internal Medicine II, Medical University of Vienna, 1090 Vienna, Austria.
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Non-Coding RNA Editing in Cancer Pathogenesis. Cancers (Basel) 2020; 12:cancers12071845. [PMID: 32650588 PMCID: PMC7408896 DOI: 10.3390/cancers12071845] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 07/05/2020] [Accepted: 07/06/2020] [Indexed: 12/19/2022] Open
Abstract
In the last two decades, RNA post-transcriptional modifications, including RNA editing, have been the subject of increasing interest among the scientific community. The efforts of the Human Genome Project combined with the development of new sequencing technologies and dedicated bioinformatic approaches created to detect and profile RNA transcripts have served to further our understanding of RNA editing. Investigators have determined that non-coding RNA (ncRNA) A-to-I editing is often deregulated in cancer. This discovery has led to an increased number of published studies in the field. However, the eventual clinical application for these findings remains a work in progress. In this review, we provide an overview of the ncRNA editing phenomenon in cancer. We discuss the bioinformatic strategies for RNA editing detection as well as the potential roles for ncRNA A to I editing in tumor immunity and as clinical biomarkers.
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microRNA-378a-5p iS a novel positive regulator of melanoma progression. Oncogenesis 2020; 9:22. [PMID: 32060259 PMCID: PMC7021836 DOI: 10.1038/s41389-020-0203-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 01/20/2020] [Accepted: 01/24/2020] [Indexed: 02/07/2023] Open
Abstract
Evaluating the expression levels of miR-378a-5p both in a large melanoma patient cohort from The Cancer Genome Atlas database and in melanoma patients from our Institute, we found that miR-378a-5p is upregulated in metastatic melanoma specimens. miR-378a-5p expression was also increased in melanoma cells resistant to target therapy, and decreased in response to drug treatment. We also demonstrated that overexpression of miR-378a-5p enhances in vitro cell invasion and migration, and facilitates the ability of melanoma cells to form de novo vasculogenic structures. While performing downstream targeting studies, we confirmed the ability of miR-378a-5p to modulate the expression of known target genes, such as SUFU, FUS-1, and KLF9. Luciferase-3′UTR experiments also identified STAMBP and HOXD10 as new miR-378a-5p target genes. MMP2 and uPAR, two HOXD10 target genes, were positively regulated by miR-378a-5p. Genetic and pharmacologic approaches inhibiting uPAR expression and activity evidenced that the in vitro tumor-promoting functions of miR-378a-5p, were in part mediated by uPAR. Of note miR-378a-5p was also able to increase VEGF, as well as in vitro and in vivo angiogenesis. Finally, genetic and pharmacologic modulation of Bcl-2 evidenced Bcl-2 ability to regulate miR-378a-5p expression. In conclusion, to the best of our knowledge, this is the first study demonstrating that miR-378a-5p acts as an oncogenic microRNA in melanoma.
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Chong H, Wei Z, Na M, Sun G, Zheng S, Zhu X, Xue Y, Zhou Q, Guo S, Xu J, Wang H, Cui L, Zhang CY, Jiang X, Wang D. The PGC-1α/NRF1/miR-378a axis protects vascular smooth muscle cells from FFA-induced proliferation, migration and inflammation in atherosclerosis. Atherosclerosis 2020; 297:136-145. [PMID: 32120345 DOI: 10.1016/j.atherosclerosis.2020.02.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 01/19/2020] [Accepted: 02/07/2020] [Indexed: 01/26/2023]
Abstract
BACKGROUND AND AIMS Atherosclerosis (AS) is the leading cause of cardiovascular diseases. PGC-1α is a key regulator of cellular energy homeostasis, but its role in AS remains debatable. METHODS AND RESULTS In our study, PGC-1α was shown to be significantly decreased in the media of human atherosclerotic vessels. To explore whether miRNAs might be regulated by PGC-1α in vascular smooth muscle cells (VSMCs), microarray analysis was performed. Microarray and Pearson's correlation analysis showed that PGC-1α and miR-378a were positively correlated in vivo and in vitro. As an upstream co-activator, PGC-1α was found to regulate miR-378a through binding to the transcriptional factor NRF1 in VSMCs. Therefore, the decreased expression of PGC-1α might account for suppression of miR-378a in VSMCs in AS. Furthermore, IGF1 and TLR8, two genes known to be aberrantly up-regulated in atherogenic vessels, were identified as direct targets of miR-378a. In vitro up-regulation of miR-378a markedly inhibited free fatty acid (FFA)-induced VSMC proliferation, migration and inflammation through targeting IGF1 and TLR8. CONCLUSIONS These findings highlight the protective role of the PGC-1α/NRF1/miR-378a regulatory axis in AS progression and suggest miR-378a as potential therapeutic target for AS treatment.
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Affiliation(s)
- Hoshun Chong
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Thoracic and Cardiovascular Surgery, Nanjing Drum Tower Hospital, Medical School of Nanjing University, China; State Key Laboratory of Pharmaceutical Biotechnology, Collaborative Innovation Center of Chemistry for Life Sciences, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute for Life Sciences (NAILS), School of Life Sciences, Nanjing University, China
| | - Zhe Wei
- State Key Laboratory of Pharmaceutical Biotechnology, Collaborative Innovation Center of Chemistry for Life Sciences, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute for Life Sciences (NAILS), School of Life Sciences, Nanjing University, China
| | - Muhan Na
- State Key Laboratory of Pharmaceutical Biotechnology, Collaborative Innovation Center of Chemistry for Life Sciences, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute for Life Sciences (NAILS), School of Life Sciences, Nanjing University, China
| | - Gongrui Sun
- State Key Laboratory of Pharmaceutical Biotechnology, Collaborative Innovation Center of Chemistry for Life Sciences, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute for Life Sciences (NAILS), School of Life Sciences, Nanjing University, China
| | - Shasha Zheng
- State Key Laboratory of Pharmaceutical Biotechnology, Collaborative Innovation Center of Chemistry for Life Sciences, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute for Life Sciences (NAILS), School of Life Sciences, Nanjing University, China
| | - Xiyu Zhu
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Thoracic and Cardiovascular Surgery, Nanjing Drum Tower Hospital, Medical School of Nanjing University, China
| | - Yunxing Xue
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Thoracic and Cardiovascular Surgery, Nanjing Drum Tower Hospital, Medical School of Nanjing University, China
| | - Qing Zhou
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Thoracic and Cardiovascular Surgery, Nanjing Drum Tower Hospital, Medical School of Nanjing University, China
| | - Shanjun Guo
- State Key Laboratory of Pharmaceutical Biotechnology, Collaborative Innovation Center of Chemistry for Life Sciences, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute for Life Sciences (NAILS), School of Life Sciences, Nanjing University, China
| | - Jinhong Xu
- State Key Laboratory of Pharmaceutical Biotechnology, Collaborative Innovation Center of Chemistry for Life Sciences, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute for Life Sciences (NAILS), School of Life Sciences, Nanjing University, China
| | - Haoquan Wang
- State Key Laboratory of Pharmaceutical Biotechnology, Collaborative Innovation Center of Chemistry for Life Sciences, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute for Life Sciences (NAILS), School of Life Sciences, Nanjing University, China
| | - Le Cui
- State Key Laboratory of Pharmaceutical Biotechnology, Collaborative Innovation Center of Chemistry for Life Sciences, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute for Life Sciences (NAILS), School of Life Sciences, Nanjing University, China
| | - Chen-Yu Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, Collaborative Innovation Center of Chemistry for Life Sciences, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute for Life Sciences (NAILS), School of Life Sciences, Nanjing University, China
| | - Xiaohong Jiang
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Thoracic and Cardiovascular Surgery, Nanjing Drum Tower Hospital, Medical School of Nanjing University, China; State Key Laboratory of Pharmaceutical Biotechnology, Collaborative Innovation Center of Chemistry for Life Sciences, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute for Life Sciences (NAILS), School of Life Sciences, Nanjing University, China.
| | - Dongjin Wang
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Thoracic and Cardiovascular Surgery, Nanjing Drum Tower Hospital, Medical School of Nanjing University, China; State Key Laboratory of Pharmaceutical Biotechnology, Collaborative Innovation Center of Chemistry for Life Sciences, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute for Life Sciences (NAILS), School of Life Sciences, Nanjing University, China; Institute of Cardiothoracic Vascular Disease, Nanjing University, China.
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42
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Xu X, Wang Y, Mojumdar K, Zhou Z, Jeong KJ, Mangala LS, Yu S, Tsang YH, Rodriguez-Aguayo C, Lu Y, Lopez-Berestein G, Sood AK, Mills GB, Liang H. A-to-I-edited miRNA-379-5p inhibits cancer cell proliferation through CD97-induced apoptosis. J Clin Invest 2019; 129:5343-5356. [PMID: 31682236 PMCID: PMC6877318 DOI: 10.1172/jci123396] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 05/29/2019] [Indexed: 12/26/2022] Open
Abstract
Both miRNAs and A-to-I RNA editing, a widespread nucleotide modification mechanism, have recently emerged as key players in cancer pathophysiology. However, the functional impact of RNA editing of miRNAs in cancer remains largely unexplored. Here, we focused on an ADAR2-catalyzed RNA editing site within the miR-379-5p seed region. This site was under-edited in tumors relative to normal tissues, with a high editing level being correlated with better patient survival times across cancer types. We demonstrated that in contrast to wild-type miRNA, edited miR-379-5p inhibited cell proliferation and promoted apoptosis in diverse tumor contexts in vitro, which was due to the ability of edited but not wild-type miR-379-5p to target CD97. Importantly, through nanoliposomal delivery, edited miR-379-5p mimics significantly inhibited tumor growth and extended survival of mice. Our study indicates a role of RNA editing in diversifying miRNA function during cancer progression and highlights the translational potential of edited miRNAs as a new class of cancer therapeutics.
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Affiliation(s)
- Xiaoyan Xu
- Department of Pathophysiology, College of Basic Medical Science, China Medical University, Shenyang, Liaoning Province, China
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Yumeng Wang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, Texas, USA
| | - Kamalika Mojumdar
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Zhicheng Zhou
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Department of Systems Biology
| | | | - Lingegowda S. Mangala
- Department of Gynecologic Oncology and Reproductive Medicine, and
- Center for RNA Interference and Non–Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | | | - Yiu Huen Tsang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Cristian Rodriguez-Aguayo
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | | | - Gabriel Lopez-Berestein
- Center for RNA Interference and Non–Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Anil K. Sood
- Department of Gynecologic Oncology and Reproductive Medicine, and
- Center for RNA Interference and Non–Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | | | - Han Liang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, Texas, USA
- Department of Systems Biology
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43
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Zhang Y, Qian H, Xu J, Gao W. ADAR, the carcinogenesis mechanisms of ADAR and related clinical applications. ANNALS OF TRANSLATIONAL MEDICINE 2019; 7:686. [PMID: 31930087 DOI: 10.21037/atm.2019.11.06] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Adenosine deaminases acting on RNA (ADARs) catalyze the conversion of adenosine (A) to inosine (I) in double-stranded RNA, which can change the codons after transcription. Abnormal ADAR editing is present in a variety of cancers. However, the study of the biological effects of ADARs in cancer is not very deep. Here, we review current important ADAR-mediated editing events, related carcinogenic mechanisms and applications in clinical medicine. Further exploration in ADARs can provide a new direction for cancer treatment.
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Affiliation(s)
- Yue Zhang
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Huizhu Qian
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Jing Xu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Wen Gao
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
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44
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Gatsiou A, Stellos K. Dawn of Epitranscriptomic Medicine. CIRCULATION-GENOMIC AND PRECISION MEDICINE 2019; 11:e001927. [PMID: 30354331 DOI: 10.1161/circgen.118.001927] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Medicine is at the crossroads of expanding disciplines. Prompt adaptation of medicine to each rapidly advancing research field, bridging bench to bedside, is a key step toward health improvement. Cardiovascular disease still ranks first among the mortality causes in the Western world, indicating a poor adaptation rate of cardiovascular medicine, albeit the gigantic scientific breakthroughs of this century. This urges the cardiovascular research field to explore novel concepts with promising prognostic and therapeutic potential. This review attempts to introduce the newly emerging field of epitranscriptome (or else known as RNA epigenetics) to cardiovascular researchers and clinicians summarizing its applications on health and disease. The traditionally perceived, intermediate carrier of genetic information or as contemporary revised as, occasionally, even the final product of gene expression, RNA, is dynamically subjected to >140 different kinds of chemical modifications determining its fate, which may profoundly impact the cellular responses and thus both health and disease course. Which are the most prevalent types of these RNA modifications, how are they catalyzed, how are they regulated, which role may they play in health and disease, and which are the implications for the cardiovascular medicine are few important questions that are discussed in the present review.
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Affiliation(s)
- Aikaterini Gatsiou
- Institute of Cardiovascular Regeneration, Center of Molecular Medicine, Goethe University Frankfurt, Frankfurt am Main, Germany (A.G., K.S.).,Department of Cardiology, Center of Internal Medicine, Goethe University Frankfurt, Germany (A.G., K.S.).,German Center of Cardiovascular Research, Rhein-Main Partner Site, Frankfurt (A.G., K.S.)
| | - Konstantinos Stellos
- Institute of Cardiovascular Regeneration, Center of Molecular Medicine, Goethe University Frankfurt, Frankfurt am Main, Germany (A.G., K.S.).,Department of Cardiology, Center of Internal Medicine, Goethe University Frankfurt, Germany (A.G., K.S.).,German Center of Cardiovascular Research, Rhein-Main Partner Site, Frankfurt (A.G., K.S.).,Cardiovascular Research Centre, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom (K.S.).,Department of Cardiology, Freeman Hospital, Newcastle upon Tyne Hospitals National Health System Foundation Trust, United Kingdom (K.S.)
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45
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Bavelloni A, Focaccia E, Piazzi M, Raffini M, Cesarini V, Tomaselli S, Orsini A, Ratti S, Faenza I, Cocco L, Gallo A, Blalock WL. AKT-dependent phosphorylation of the adenosine deaminases ADAR-1 and -2 inhibits deaminase activity. FASEB J 2019; 33:9044-9061. [PMID: 31095429 DOI: 10.1096/fj.201800490rr] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Murine thymoma viral oncogene homolog (AKT) kinases target both cytosolic and nuclear substrates for phosphorylation. Whereas the cytosolic substrates are known to be closely associated with the regulation of apoptosis and autophagy or metabolism and protein synthesis, the nuclear substrates are, for the most part, poorly understood. To better define the role of nuclear AKT, potential AKT substrates were isolated from the nuclear lysates of leukemic cell lines using a phosphorylated AKT substrate antibody and identified in tandem mass spectrometry. Among the proteins identified was adenosine deaminase acting on RNA (ADAR)1p110, the predominant nuclear isoform of the adenosine deaminase acting on double-stranded RNA. Coimmunoprecipitation studies and in vitro kinase assays revealed that AKT-1, -2, and -3 interact with both ADAR1p110 and ADAR2 and phosphorylate these RNA editases. Using site-directed mutagenesis of suspected AKT phosphorylation sites, AKT was found to primarily phosphorylate ADAR1p110 and ADAR2 on T738 and T553, respectively, and overexpression of the phosphomimic mutants ADAR1p110 (T738D) and ADAR2 (T553D) resulted in a 50-100% reduction in editase activity. Thus, activation of AKT has a direct and major impact on RNA editing.-Bavelloni, A., Focaccia, E., Piazzi, M., Raffini, M., Cesarini, V., Tomaselli, S., Orsini, A., Ratti, S., Faenza, I., Cocco, L., Gallo, A., Blalock, W. L. AKT-dependent phosphorylation of the adenosine deaminases ADAR-1 and -2 inhibits deaminase activity.
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Affiliation(s)
| | - Enrico Focaccia
- IRCSS Istituto Ortopedico Rizzoli (IOR), Bologna, Italy.,National Research Council (CNR) of Italy, Institute of Molecular Genetics (IGM), Bologna, Italy
| | - Manuela Piazzi
- IRCSS Istituto Ortopedico Rizzoli (IOR), Bologna, Italy.,National Research Council (CNR) of Italy, Institute of Molecular Genetics (IGM), Bologna, Italy
| | - Mirco Raffini
- IRCSS Istituto Ortopedico Rizzoli (IOR), Bologna, Italy
| | - Valeriana Cesarini
- Oncohaematology Department, RNA Editing Laboratory, IRCCS-Ospedale Pediatrico Bambino Gesù, Rome, Italy; and
| | - Sara Tomaselli
- Oncohaematology Department, RNA Editing Laboratory, IRCCS-Ospedale Pediatrico Bambino Gesù, Rome, Italy; and
| | - Arianna Orsini
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Stefano Ratti
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Irene Faenza
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Lucio Cocco
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Angela Gallo
- Oncohaematology Department, RNA Editing Laboratory, IRCCS-Ospedale Pediatrico Bambino Gesù, Rome, Italy; and
| | - William L Blalock
- IRCSS Istituto Ortopedico Rizzoli (IOR), Bologna, Italy.,National Research Council (CNR) of Italy, Institute of Molecular Genetics (IGM), Bologna, Italy
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46
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Xiang Y, Li C, Liao Y, Wu J. An integrated mRNA-lncRNA signature for relapse prediction in laryngeal cancer. J Cell Biochem 2019; 120:15883-15890. [PMID: 31062433 DOI: 10.1002/jcb.28859] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 01/25/2019] [Accepted: 01/28/2019] [Indexed: 01/13/2023]
Abstract
Patients with laryngeal cancer with early relapse usually have a poor prognosis. In this study, we aimed to identify a multi-gene signature to improve the relapse prediction in laryngeal cancer. One microarray data set GSE27020 (training set, N = 109) and one RNA-sequencing data set (validation set, N = 85) were included into the analysis. In the training set, the microarray expression profile was re-annotated into an mRNA-long noncoding RNA (lncRNA) biphasic profile. Then, LASSO Cox regression model identified nine relapse-related RNA (eight mRNA and one lncRNA), and a risk score was calculated for each sample according to the model coefficients. Patients with high-risk showed poorer relapse-free survival than patients with low risk (hazard ratios (HR): 6.189, 95% confidence interval (CI): 3.075-12.460, P < 0.0001). The risk score demonstrated good accuracy in predicting the relapse (area under time-dependent receiver-operating characteristic (AUC): 0.859 at 1 year, 0.822 at 3 years, and 0.815 at 5 years). The results were validated in the validation set (HR: 3.762, 95% CI: 1.594-8.877, P = 0.011; AUC: 0.770 at 1 year, 0.769 at 3 years, and 0.728 at 5 years). The multivariate analysis reached consistent results after adjustment by multiple confounders. When compared with a 27-gene signature, a 2-lncRNA signature, and Tumor-Node-Metastasis stage, the risk score also showed better performance (P < 0.05). In conclusion, we successfully developed a robust mRNA-lncRNA signature that can accurately predict the relapse in laryngeal cancer.
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Affiliation(s)
- Yuandi Xiang
- Department of Otorhinolaryngology, Wuhan No.1 Hospital, Wuhan, China
| | - Chunli Li
- Department of Otorhinolaryngology, Wuhan No.1 Hospital, Wuhan, China
| | - Yong Liao
- Department of Otorhinolaryngology, University Hospital of Hubei University for Nationalities, Enshi, China
| | - Juan Wu
- Department of Dermatology, Wuhan No.1 Hospital, Wuhan, China
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47
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Weston WW, Ganey T, Temple HT. The Relationship between Exosomes and Cancer: Implications for Diagnostics and Therapeutics. BioDrugs 2019; 33:137-158. [DOI: 10.1007/s40259-019-00338-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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48
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Abstract
Noncoding RNAs (ncRNAs) have received much attention due to their central role in gene expression and translational regulation as well as due to their involvement in several biological processes and disease development. Small noncoding RNAs (sncRNAs), such as microRNAs and piwiRNAs, have been thoroughly investigated and functionally characterized. Long noncoding RNAs (lncRNAs), known to play an important role in chromatin-interacting transcription regulation, posttranscriptional regulation, cell-to-cell signaling, and protein regulation, are also being investigated to further elucidate their functional roles.Next-generation sequencing (NGS) technologies have greatly aided in characterizing the ncRNAome. Moreover, the coupling of NGS technology together with bioinformatics tools has been essential to the genome-wide detection of RNA modifications in ncRNAs. RNA editing, a common human co-transcriptional and posttranscriptional modification, is a dynamic biological phenomenon able to alter the sequence and the structure of primary transcripts (both coding and noncoding RNAs) during the maturation process, consequently influencing the biogenesis, as well as the function, of ncRNAs. In particular, the dysregulation of the RNA editing machineries have been associated with the onset of human diseases.In this chapter we discuss the potential functions of ncRNA editing and describe the knowledge base and bioinformatics resources available to investigate such phenomenon.
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49
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Riefolo M, Porcellini E, Dika E, Broseghini E, Ferracin M. Interplay between small and long non-coding RNAs in cutaneous melanoma: a complex jigsaw puzzle with missing pieces. Mol Oncol 2019; 13:74-98. [PMID: 30499222 PMCID: PMC6322194 DOI: 10.1002/1878-0261.12412] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Revised: 10/20/2018] [Accepted: 10/23/2018] [Indexed: 12/12/2022] Open
Abstract
The incidence of cutaneous melanoma (CM) has increased in the past few decades. The biology of melanoma is characterized by a complex interaction between genetic, environmental and phenotypic factors. A greater understanding of the molecular mechanisms that promote melanoma cell growth and dissemination is crucial to improve diagnosis, prognostication, and treatment of CM. Both small and long non-coding RNAs (lncRNAs) have been identified to play a role in melanoma biology; microRNA and lncRNA expression is altered in transformed melanocytes and this in turn has functional effects on cell proliferation, apoptosis, invasion, metastasis, and immune response. Moreover, specific dysregulated ncRNAs were shown to have a diagnostic or prognostic role in melanoma and to drive the establishment of drug resistance. Here, we review the current literature on small and lncRNAs with a role in melanoma, with the aim of putting into some order this complex jigsaw puzzle.
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Affiliation(s)
- Mattia Riefolo
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES)University of BolognaItaly
| | - Elisa Porcellini
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES)University of BolognaItaly
| | - Emi Dika
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES)University of BolognaItaly
| | - Elisabetta Broseghini
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES)University of BolognaItaly
| | - Manuela Ferracin
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES)University of BolognaItaly
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50
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Tassinari V, Cesarini V, Silvestris DA, Gallo A. The adaptive potential of RNA editing-mediated miRNA-retargeting in cancer. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1862:291-300. [PMID: 30605729 DOI: 10.1016/j.bbagrm.2018.12.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 12/20/2018] [Accepted: 12/20/2018] [Indexed: 12/18/2022]
Abstract
A-to-I RNA editing is a post-transcriptional mechanism that converts the genomically coded Adenosine (A) into Inosine (I) at the RNA level. This type of RNA editing is the most frequent in humans and is mediated by the ADAR enzymes. RNA editing can alter the genetic code of mRNAs, but also affect the functions of noncoding RNAs such as miRNAs. Recent studies have identified thousands of microRNA editing events in different cancer types. However, the important role played by miRNA-editing in cancer has been reported for just a few microRNAs. Herein, we recapitulate the current studies on cancer-related microRNA editing and discuss their importance in tumor growth and progression. This article is part of a Special Issue entitled: mRNA modifications in gene expression control edited by Dr. Soller Matthias and Dr. Fray Rupert.
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Affiliation(s)
- Valentina Tassinari
- RNA Editing Laboratory, Oncohaematology Department, IRCCS Ospedale Pediatrico Bambino Gesù (OPBG), Viale di San Paolo, 15, 00146 Rome, Italy
| | - Valeriana Cesarini
- RNA Editing Laboratory, Oncohaematology Department, IRCCS Ospedale Pediatrico Bambino Gesù (OPBG), Viale di San Paolo, 15, 00146 Rome, Italy
| | - Domenico Alessandro Silvestris
- RNA Editing Laboratory, Oncohaematology Department, IRCCS Ospedale Pediatrico Bambino Gesù (OPBG), Viale di San Paolo, 15, 00146 Rome, Italy
| | - Angela Gallo
- RNA Editing Laboratory, Oncohaematology Department, IRCCS Ospedale Pediatrico Bambino Gesù (OPBG), Viale di San Paolo, 15, 00146 Rome, Italy.
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