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Shi J, Ding F, Dai D, Song X, Wu X, Yan D, Han X, Tao G, Dai W. Noxa inhibits oncogenesis through ZNF519 in gastric cancer and is suppressed by hsa-miR-200b-3p. Sci Rep 2024; 14:6568. [PMID: 38503887 PMCID: PMC10951337 DOI: 10.1038/s41598-024-57099-7] [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: 11/12/2023] [Accepted: 03/14/2024] [Indexed: 03/21/2024] Open
Abstract
While Phorbol-12-myristate-13-acetate-induced protein 1 (Noxa/PMAIP1) assumes a pivotal role in numerous tumors, its clinical implications and underlying mechanisms of gastric cancer (GC) are yet enigmatic. In this investigation, our primary objective was to scrutinize the clinical relevance and potential mechanisms of Noxa in gastric cancer. Immunohistochemical analysis was conducted on tissue microarrays comprising samples from a meticulously characterized cohort of 84 gastric cancer patients, accompanied by follow-up data, to assess the expression of Noxa. Additionally, Noxa expression levels in gastric cancer clinical samples and cell lines were measured through quantitative real-time polymerase chain reaction (qRT-PCR) and Western blot analysis. The effect of Noxa expression on the prognosis of patients with gastric cancer was evaluated using Kaplan-Meier survival. Further insight into the role of Noxa in driving gastric cancer progression was gained through an array of experimental techniques, including cell viability assays (CCK8), plate cloning assays, transwell assays, scratch assays, and real-time cell analysis (RTCA). Potential upstream microRNAs (miRNAs) that might modulate Noxa were identified through rigorous bioinformatics analysis, substantiated by luciferase reporter assays and Western blot experiments. Additionally, we utilized RNA sequencing, qRT-PCR, and Western blot to identify proteins binding to Noxa and potential downstream target. Finally, we utilized BALB/c nude mice to explore the role of Noxa in vivo. Our investigation unveiled a marked downregulation of Noxa expression in gastric cancer and underscored its significance as a pivotal prognostic factor influencing overall survival (OS). Noxa overexpression exerted a substantial inhibitory effect on the proliferation, migration and invasion of GC cells. Bioinformatic analysis and dual luciferase reporter assays unveiled the capacity of hsa-miR-200b-3p to interact with the 3'-UTR of Noxa mRNA, thereby orchestrating a downregulation of Noxa expression in vitro, consequently promoting tumor progression in GC. Our transcriptome analysis, coupled with mechanistic validation, elucidated a role for Noxa in modulating the expression of ZNF519 in the Mitophagy-animal pathway. The depletion of ZNF519 effectively reversed the oncogenic attributes induced by Noxa. Upregulation of Noxa expression suppressed the tumorigenesis of GC in vivo. The current investigation sheds light on the pivotal role of the hsa-miR-200b-3p/Noxa/ZNF519 axis in elucidating the pathogenesis of gastric cancer, offering a promising avenue for targeted therapeutic interventions in the management of this challenging malignancy.
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Affiliation(s)
- Jin Shi
- Department of Gastrointestinal Surgery, The Affiliated Huaian No. 1 People's Hospital of Nanjing Medical University, Huai'an, Jiangsu, 223300, People's Republic of China
| | - Fan Ding
- Department of Gastrointestinal Surgery, The Affiliated Huaian No. 1 People's Hospital of Nanjing Medical University, Huai'an, Jiangsu, 223300, People's Republic of China
| | - Dezhu Dai
- Department of Gastrointestinal Surgery, The Affiliated Huaian No. 1 People's Hospital of Nanjing Medical University, Huai'an, Jiangsu, 223300, People's Republic of China
| | - Xudong Song
- Department of Gastrointestinal Surgery, The Affiliated Huaian No. 1 People's Hospital of Nanjing Medical University, Huai'an, Jiangsu, 223300, People's Republic of China
| | - Xu Wu
- Department of Vascular, Huaian Hospital Affiliated to Xuzhou Medical University, Huai'an, Jiangsu, 223300, People's Republic of China
| | - Dongsheng Yan
- Department of Gastrointestinal Surgery, The Affiliated Huaian No. 1 People's Hospital of Nanjing Medical University, Huai'an, Jiangsu, 223300, People's Republic of China
| | - Xiao Han
- Department of Gastrointestinal Surgery, The Affiliated Huaian No. 1 People's Hospital of Nanjing Medical University, Huai'an, Jiangsu, 223300, People's Republic of China
| | - Guoquan Tao
- Department of Gastrointestinal Surgery, The Affiliated Huaian No. 1 People's Hospital of Nanjing Medical University, Huai'an, Jiangsu, 223300, People's Republic of China.
| | - Weijie Dai
- Department of Gastroenterology, The Affiliated Huaian No. 1 People's Hospital of Nanjing Medical University, Huai'an, Jiangsu, 223300, People's Republic of China.
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2
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Lucena-Padros H, Bravo-Gil N, Tous C, Rojano E, Seoane-Zonjic P, Fernández RM, Ranea JAG, Antiñolo G, Borrego S. Bioinformatics Prediction for Network-Based Integrative Multi-Omics Expression Data Analysis in Hirschsprung Disease. Biomolecules 2024; 14:164. [PMID: 38397401 PMCID: PMC10886964 DOI: 10.3390/biom14020164] [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: 12/05/2023] [Revised: 01/15/2024] [Accepted: 01/27/2024] [Indexed: 02/25/2024] Open
Abstract
Hirschsprung's disease (HSCR) is a rare developmental disorder in which enteric ganglia are missing along a portion of the intestine. HSCR has a complex inheritance, with RET as the major disease-causing gene. However, the pathogenesis of HSCR is still not completely understood. Therefore, we applied a computational approach based on multi-omics network characterization and clustering analysis for HSCR-related gene/miRNA identification and biomarker discovery. Protein-protein interaction (PPI) and miRNA-target interaction (MTI) networks were analyzed by DPClusO and BiClusO, respectively, and finally, the biomarker potential of miRNAs was computationally screened by miRNA-BD. In this study, a total of 55 significant gene-disease modules were identified, allowing us to propose 178 new HSCR candidate genes and two biological pathways. Moreover, we identified 12 key miRNAs with biomarker potential among 137 predicted HSCR-associated miRNAs. Functional analysis of new candidates showed that enrichment terms related to gene ontology (GO) and pathways were associated with HSCR. In conclusion, this approach has allowed us to decipher new clues of the etiopathogenesis of HSCR, although molecular experiments are further needed for clinical validations.
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Affiliation(s)
- Helena Lucena-Padros
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, 41013 Seville, Spain
| | - Nereida Bravo-Gil
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, 41013 Seville, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), 41013 Seville, Spain
| | - Cristina Tous
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, 41013 Seville, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), 41013 Seville, Spain
| | - Elena Rojano
- Department of Molecular Biology and Biochemistry, University of Malaga, 29010 Malaga, Spain
- Biomedical Research Institute of Malaga, IBIMA, 29010 Malaga, Spain
| | - Pedro Seoane-Zonjic
- Department of Molecular Biology and Biochemistry, University of Malaga, 29010 Malaga, Spain
- Biomedical Research Institute of Malaga, IBIMA, 29010 Malaga, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), 29071 Malaga, Spain
| | - Raquel María Fernández
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, 41013 Seville, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), 41013 Seville, Spain
| | - Juan A. G. Ranea
- Department of Molecular Biology and Biochemistry, University of Malaga, 29010 Malaga, Spain
- Biomedical Research Institute of Malaga, IBIMA, 29010 Malaga, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), 29071 Malaga, Spain
- Spanish National Bioinformatics Institute (INB/ELIXIR-ES), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
| | - Guillermo Antiñolo
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, 41013 Seville, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), 41013 Seville, Spain
| | - Salud Borrego
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, 41013 Seville, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), 41013 Seville, Spain
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3
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Ahirwar SS, Rizwan R, Sethi S, Shahid Z, Malviya S, Khandia R, Agarwal A, Kotnis A. Comparative Analysis of Published Database Predicting MicroRNA Binding in 3'UTR of mRNA in Diverse Species. Microrna 2024; 13:2-13. [PMID: 37929739 DOI: 10.2174/0122115366261005231018070640] [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: 05/06/2023] [Revised: 09/03/2023] [Accepted: 09/15/2023] [Indexed: 11/07/2023]
Abstract
BACKGROUND Micro-RNAs are endogenous non-coding RNA moieties of 22-27 nucleotides that play a crucial role in the regulation of various biological processes and make them useful prognostic and diagnostic biomarkers. Discovery and experimental validation of miRNA is a laborious and time-consuming process. For early prediction, multiple bioinformatics databases are available for miRNA target prediction; however, their utility can confuse amateur researchers in selecting the most appropriate tools for their study. OBJECTIVE This descriptive review aimed to analyse the usability of the existing database based on the following criteria: accessibility, efficiency, interpretability, updatability, and flexibility for miRNA target prediction of 3'UTR of mRNA in diverse species so that the researchers can utilize the database most appropriate to their research. METHODS A systematic literature search was performed in PubMed, Google Scholar and Scopus databases up to November 2022. ≥10,000 articles found online, including ⁓130 miRNA tools, which contain various information on miRNA. Out of them, 31 databases that provide information on validated 3'UTR miRNAs target databases were included and analysed in this review. RESULTS These miRNA database tools are being used in varied areas of biological research to select the most suitable miRNA for their experimental validation. These databases, updated until the year 2021, consist of miRNA-related data from humans, animals, mice, plants, viruses etc. They contain 525-29806351 data entries, and information from most databases is freely available on the online platform. CONCLUSION Reviewed databases provide significant information, but not all information is accurate or up-to-date. Therefore, Diana-TarBase and miRWalk are the most comprehensive and up-to-date databases.
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Affiliation(s)
- Sonu Singh Ahirwar
- Department of Biochemistry, All India Institute of Medical Sciences Bhopal, AIIMS Bhopal, Saket Nagar, Bhopal, MP, India
| | - Rehma Rizwan
- Department of Biochemistry, All India Institute of Medical Sciences Bhopal, AIIMS Bhopal, Saket Nagar, Bhopal, MP, India
| | - Samdish Sethi
- Department of Biochemistry, All India Institute of Medical Sciences Bhopal, AIIMS Bhopal, Saket Nagar, Bhopal, MP, India
| | - Zainab Shahid
- Department of Biochemistry, All India Institute of Medical Sciences Bhopal, AIIMS Bhopal, Saket Nagar, Bhopal, MP, India
| | - Shivani Malviya
- Department of Biochemistry and Genetics, Barkatullah University, Bhopal, Madhya Pradesh, 462026, India
| | - Rekha Khandia
- Department of Biochemistry and Genetics, Barkatullah University, Bhopal, Madhya Pradesh, 462026, India
| | - Amit Agarwal
- Department of Neurosurgery, All India Institute of Medical Sciences Bhopal, Bhopal MP, 462020, India
| | - Ashwin Kotnis
- Department of Biochemistry, All India Institute of Medical Sciences Bhopal, AIIMS Bhopal, Saket Nagar, Bhopal, MP, India
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4
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Simona P, Panneerselvam K, Porras P, Duesbury M, Perfetto L, Licata L, Hermjakob H, Orchard S. The landscape of microRNA interaction annotation: analysis of three rare disorders as a case study. Database (Oxford) 2023; 2023:baad066. [PMID: 37819683 PMCID: PMC10566539 DOI: 10.1093/database/baad066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 08/29/2023] [Accepted: 09/15/2023] [Indexed: 10/13/2023]
Abstract
In recent years, a huge amount of data on ncRNA interactions has been described in scientific papers and databases. Although considerable effort has been made to annotate the available knowledge in public repositories, there are still significant discrepancies in how different resources capture and interpret data on ncRNA functional and physical associations. In the present paper, we present a collection of microRNA-mRNA interactions annotated from the scientific literature following recognized standard criteria and focused on microRNAs, which regulate genes associated with rare diseases as a case study. The list of protein-coding genes with a known role in specific rare diseases was retrieved from the Genome England PanelApp, and associated microRNA-mRNA interactions were annotated in the IntAct database and compared with other datasets. RNAcentral identifiers were used for unambiguous, stable identification of ncRNAs. The information about the interaction was enhanced by a detailed description of the cell types and experimental conditions, providing a computer-interpretable summary of the published data, integrated with the huge amount of protein interactions already gathered in the database. Furthermore, for each interaction, the binding sites of the microRNA are precisely mapped on a well-defined mRNA transcript of the target gene. This information is crucial to conceive and design optimal microRNA mimics or inhibitors to interfere in vivo with a deregulated process. As these approaches become more feasible, high-quality, reliable networks of microRNA interactions are needed to help, for instance, in the selection of the best target to be inhibited and to predict potential secondary off-target effects. Database URL https://www.ebi.ac.uk/intact.
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Affiliation(s)
- Panni Simona
- Dipartimento di Biologia Ecologia e Scienze della Terra, Università della Calabria, Rende 87036, Italy
| | - Kalpana Panneerselvam
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus Hinxton, Cambridge CB10 1SD, UK
| | - Pablo Porras
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus Hinxton, Cambridge CB10 1SD, UK
- Astra Zeneca, Data Office, Data Science and AI, UK Academy House, 136 Hills Road, Cambridge CB2 8PA, UK
| | - Margaret Duesbury
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus Hinxton, Cambridge CB10 1SD, UK
| | - Livia Perfetto
- Department of Biology and Biotechnologies “Charles Darwin”, La Sapienza University, Rome, Italy
| | - Luana Licata
- Department of Biology, University of Tor Vergata, Rome, Italy
| | - Henning Hermjakob
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus Hinxton, Cambridge CB10 1SD, UK
| | - Sandra Orchard
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus Hinxton, Cambridge CB10 1SD, UK
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5
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Kariuki D, Asam K, Aouizerat BE, Lewis KA, Florez JC, Flowers E. Review of databases for experimentally validated human microRNA-mRNA interactions. Database (Oxford) 2023; 2023:7142843. [PMID: 37098414 PMCID: PMC10129384 DOI: 10.1093/database/baad014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 01/13/2023] [Accepted: 03/09/2023] [Indexed: 04/27/2023]
Abstract
MicroRNAs (miRs) may contribute to disease etiology by influencing gene expression. Numerous databases are available for miR target prediction and validation, but their functionality is varied, and outputs are not standardized. The purpose of this review is to identify and describe databases for cataloging validated miR targets. Using Tools4miRs and PubMed, we identified databases with experimentally validated targets, human data, and a focus on miR-messenger RNA (mRNA) interactions. Data were extracted about the number of times each database was cited, the number of miRs, the target genes, the interactions per database, experimental methodology and key features of each database. The search yielded 10 databases, which in order of most cited to least were: miRTarBase, starBase/The Encyclopedia of RNA Interactomes, DIANA-TarBase, miRWalk, miRecords, miRGator, miRSystem, miRGate, miRSel and targetHub. Findings from this review suggest that the information presented within miR target validation databases can be enhanced by adding features such as flexibility in performing queries in multiple ways, downloadable data, ongoing updates and integrating tools for further miR-mRNA target interaction analysis. This review is designed to aid researchers, especially those new to miR bioinformatics tools, in database selection and to offer considerations for future development and upkeep of validation tools. Database URL http://mirtarbase.cuhk.edu.cn/.
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Affiliation(s)
- Dorian Kariuki
- Department of Physiological Nursing, University of California, San Francisco, CA 94143, USA
| | - Kesava Asam
- Bluestone Center for Clinical Research, New York University, New York, CA 10010, USA
| | - Bradley E Aouizerat
- Bluestone Center for Clinical Research, New York University, New York, CA 10010, USA
- Department of Oral and Maxillofacial Surgery, New York University, New York, CA 10010, USA
| | - Kimberly A Lewis
- Department of Physiological Nursing, University of California, San Francisco, CA 94143, USA
| | - Jose C Florez
- Department of Medicine, Center for Genomic Medicine and Diabetes Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute, Cambridge, MA 02142, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Elena Flowers
- Department of Physiological Nursing, University of California, San Francisco, CA 94143, USA
- Institute for Human Genetics, University of California, San Francisco, CA 94143, USA
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6
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Qi G, Xu Z, Dan H, Jia X, Jiang Q, Zhang A, Li Z, Liu X, Ma J, Zheng X, Li Z. A Complex Heterogeneous Network Model of Disease Regulated by Noncoding RNAs: A Case Study of Unstable Angina Pectoris. COMPUTATIONAL INTELLIGENCE AND NEUROSCIENCE 2022; 2022:5852089. [PMID: 36590836 PMCID: PMC9803582 DOI: 10.1155/2022/5852089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 11/27/2022] [Accepted: 12/02/2022] [Indexed: 12/24/2022]
Abstract
MicroRNAs (miRNAs) are important types of noncoding RNAs, and there is a lack of holistic and systematic understanding of the functions they play in disease. We proposed a research strategy, including two parts network analysis and network modelling, to analyze, model, and predict the regulatory network of miRNAs from a network perspective, using unstable angina pectoris as an example. In the network analysis section, we proposed the WGCNA & SimCluster method using both correlation and similarity to find hub miRNAs, and validation on two datasets showed better results than the methods using correlation or similarity alone. In the network modelling section, we used six knowledge graph or graph neural network models for link prediction of three types of edges and multilabel classification of two types of nodes. Comparative experiments showed that the RotatE model was a good model for link prediction, while the RGCN model was the best model for multilabel classification. Potential target genes were predicted for hub miRNAs and validation of hub miRNA-target gene interactions, target genes as biomarkers and target gene functions were performed using a three-step validation approach. In conclusion, our study provides a new strategy to analyze and model miRNA regulatory networks.
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Affiliation(s)
- Guanpeng Qi
- School of Pharmacy, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Ze Xu
- School of Pharmacy, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Hanyu Dan
- School of Medical Devices, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Xiangnan Jia
- School of Medical Devices, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Qiang Jiang
- School of Medical Devices, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Aijun Zhang
- School of Pharmacy, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Zhaohang Li
- School of Pharmacy, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Xin Liu
- School of Life Sciences and Biopharmaceuticals, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Juman Ma
- School of Life Sciences and Biopharmaceuticals, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Xiaosong Zheng
- School of Medical Devices, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Zuojing Li
- School of Medical Devices, Shenyang Pharmaceutical University, Shenyang 110016, China
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7
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Sbirkov Y, Vergov B, Mehterov N, Sarafian V. miRNAs in Lymphocytic Leukaemias-The miRror of Drug Resistance. Int J Mol Sci 2022; 23:ijms23094657. [PMID: 35563051 PMCID: PMC9103677 DOI: 10.3390/ijms23094657] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 04/18/2022] [Accepted: 04/21/2022] [Indexed: 02/04/2023] Open
Abstract
Refractory disease and relapse remain the main causes of cancer therapy failure. Refined risk stratification, treatment regimens and improved early diagnosis and detection of minimal residual disease have increased cure rates in malignancies like childhood acute lymphoblastic leukaemia (ALL) to 90%. Nevertheless, overall survival in the context of drug resistance remains poor. The regulatory role of micro RNAs (miRNAs) in cell differentiation, homeostasis and tumorigenesis has been under extensive investigation in different cancers. There is accumulating data demonstrating the significance of miRNAs for therapy outcomes in lymphoid malignancies and some direct demonstrations of the interplay between these small molecules and drug response. Here, we summarise miRNAs' impact on chemotherapy resistance in adult and paediatric ALL and chronic lymphocytic leukaemia (CLL). The main focus of this review is on the modulation of particular signaling pathways like PI3K-AKT, transcription factors such as NF-κB, and apoptotic mediators, all of which are bona fide and pivotal elements orchestrating the survival of malignant lymphocytic cells. Finally, we discuss the attractive strategy of using mimics, antimiRs and other molecular approaches pointing at miRNAs as promising therapeutic targets. Such novel strategies to circumvent ALL and CLL resistance networks may potentially improve patients' responses and survival rates.
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Affiliation(s)
- Yordan Sbirkov
- Department of Medical Biology, Medical University of Plovdiv, 4002 Plovdiv, Bulgaria; (B.V.); (N.M.)
- Division of Molecular and Regenerative Medicine, Research Institute at Medical University of Plovdiv, 4002 Plovdiv, Bulgaria
- Correspondence: (Y.S.); (V.S.)
| | - Bozhidar Vergov
- Department of Medical Biology, Medical University of Plovdiv, 4002 Plovdiv, Bulgaria; (B.V.); (N.M.)
| | - Nikolay Mehterov
- Department of Medical Biology, Medical University of Plovdiv, 4002 Plovdiv, Bulgaria; (B.V.); (N.M.)
- Division of Molecular and Regenerative Medicine, Research Institute at Medical University of Plovdiv, 4002 Plovdiv, Bulgaria
| | - Victoria Sarafian
- Department of Medical Biology, Medical University of Plovdiv, 4002 Plovdiv, Bulgaria; (B.V.); (N.M.)
- Division of Molecular and Regenerative Medicine, Research Institute at Medical University of Plovdiv, 4002 Plovdiv, Bulgaria
- Correspondence: (Y.S.); (V.S.)
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8
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Huang HY, Lin YCD, Cui S, Huang Y, Tang Y, Xu J, Bao J, Li Y, Wen J, Zuo H, Wang W, Li J, Ni J, Ruan Y, Li L, Chen Y, Xie Y, Zhu Z, Cai X, Chen X, Yao L, Chen Y, Luo Y, LuXu S, Luo M, Chiu CM, Ma K, Zhu L, Cheng GJ, Bai C, Chiang YC, Wang L, Wei F, Lee TY, Huang HD. miRTarBase update 2022: an informative resource for experimentally validated miRNA-target interactions. Nucleic Acids Res 2021; 50:D222-D230. [PMID: 34850920 PMCID: PMC8728135 DOI: 10.1093/nar/gkab1079] [Citation(s) in RCA: 329] [Impact Index Per Article: 109.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/09/2021] [Accepted: 10/25/2021] [Indexed: 12/19/2022] Open
Abstract
MicroRNAs (miRNAs) are noncoding RNAs with 18–26 nucleotides; they pair with target mRNAs to regulate gene expression and produce significant changes in various physiological and pathological processes. In recent years, the interaction between miRNAs and their target genes has become one of the mainstream directions for drug development. As a large-scale biological database that mainly provides miRNA–target interactions (MTIs) verified by biological experiments, miRTarBase has undergone five revisions and enhancements. The database has accumulated >2 200 449 verified MTIs from 13 389 manually curated articles and CLIP-seq data. An optimized scoring system is adopted to enhance this update’s critical recognition of MTI-related articles and corresponding disease information. In addition, single-nucleotide polymorphisms and disease-related variants related to the binding efficiency of miRNA and target were characterized in miRNAs and gene 3′ untranslated regions. miRNA expression profiles across extracellular vesicles, blood and different tissues, including exosomal miRNAs and tissue-specific miRNAs, were integrated to explore miRNA functions and biomarkers. For the user interface, we have classified attributes, including RNA expression, specific interaction, protein expression and biological function, for various validation experiments related to the role of miRNA. We also used seed sequence information to evaluate the binding sites of miRNA. In summary, these enhancements render miRTarBase as one of the most research-amicable MTI databases that contain comprehensive and experimentally verified annotations. The newly updated version of miRTarBase is now available at https://miRTarBase.cuhk.edu.cn/.
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Affiliation(s)
- Hsi-Yuan Huang
- The Genetics Laboratory, Longgang District Maternity & Child Healthcare Hospital of Shenzhen City, Shenzhen, Guangdong518172, China.,School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong518172, China.,Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong518172, China
| | - Yang-Chi-Dung Lin
- The Genetics Laboratory, Longgang District Maternity & Child Healthcare Hospital of Shenzhen City, Shenzhen, Guangdong518172, China.,School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong518172, China.,Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong518172, China
| | - Shidong Cui
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong518172, China.,Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong518172, China
| | - Yixian Huang
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong518172, China.,Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong518172, China
| | - Yun Tang
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong518172, China.,Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong518172, China
| | - Jiatong Xu
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong518172, China.,Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong518172, China
| | - Jiayang Bao
- Division of Biological Sciences, Section of Bioinformatics, University of California, San Diego, San Diego, CA 92093, USA
| | - Yulin Li
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong518172, China.,Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong518172, China
| | - Jia Wen
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong518172, China.,Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong518172, China
| | - Huali Zuo
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong518172, China.,Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong518172, China.,School of Computer Science and Technology, University of Science and Technology of China, Hefei 230027, China
| | - Weijuan Wang
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong518172, China.,Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong518172, China
| | - Jing Li
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong518172, China.,Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong518172, China
| | - Jie Ni
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong518172, China
| | - Yini Ruan
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong518172, China
| | - Liping Li
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong518172, China
| | - Yidan Chen
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong518172, China.,Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong518172, China
| | - Yueyang Xie
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong518172, China
| | - Zihao Zhu
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong518172, China.,Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong518172, China
| | - Xiaoxuan Cai
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong518172, China.,Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong518172, China
| | - Xinyi Chen
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong518172, China.,Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong518172, China
| | - Lantian Yao
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong518172, China.,School of Science and Engineering, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong 518172, China
| | - Yigang Chen
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong518172, China.,Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong518172, China
| | - Yijun Luo
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong518172, China.,Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong518172, China
| | - Shupeng LuXu
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong518172, China.,Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong518172, China
| | - Mengqi Luo
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong518172, China.,Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong518172, China
| | - Chih-Min Chiu
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong518172, China.,Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong518172, China
| | - Kun Ma
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong518172, China
| | - Lizhe Zhu
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong518172, China.,Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong518172, China
| | - Gui-Juan Cheng
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong518172, China.,Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong518172, China
| | - Chen Bai
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong518172, China.,Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong518172, China
| | - Ying-Chih Chiang
- Kobilka Institute of Innovative Drug Discovery, School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong 518172, China
| | - Liping Wang
- Department of Reproductive Medicine Centre, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, Guangdong 518035, China
| | - Fengxiang Wei
- The Genetics Laboratory, Longgang District Maternity & Child Healthcare Hospital of Shenzhen City, Shenzhen, Guangdong518172, China.,Department of Cell Biology, Jiamusi University, Jiamusi, Heilongjiang 154007, China.,Shenzhen Children's Hospital of China Medical University, Shenzhen, Guangdong518172, China
| | - Tzong-Yi Lee
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong518172, China.,Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong518172, China
| | - Hsien-Da Huang
- The Genetics Laboratory, Longgang District Maternity & Child Healthcare Hospital of Shenzhen City, Shenzhen, Guangdong518172, China.,School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong518172, China.,Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong518172, China
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9
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Ballinas-Verdugo MA, Jiménez-Ortega RF, Martínez-Martínez E, Rivas N, Contreras-López EA, Carbó R, Sánchez F, Bojalil R, Márquez-Velasco R, Sánchez-Muñoz F, Alejandre-Aguilar R. Circulating miR-146a as a possible candidate biomarker in the indeterminate phase of Chagas disease. Biol Res 2021; 54:21. [PMID: 34289913 PMCID: PMC8293491 DOI: 10.1186/s40659-021-00345-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 07/11/2021] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Chagas disease is considered important and presents intense inflammatory and fibrotic processes induced by the perpetuation of the parasite in the affected tissues and organs. Therefore, it is necessary to inquire about the host defense and attack mechanisms to have a more detailed knowledge about Chagas disease. MicroRNAs are found in blood, tissues and extracellular vesicles. These small regulators of gene expression are involved in physiological and pathological processes in both mammals and parasites. Several microRNAs have deregulated expression in chagasic heart disease, although little is known about their extracellular expression. Our main objective was to evaluate the involvement of miR-21, miR-146a and miR-155 in several samples from mice infected with the TcI Ninoa strain from the acute and indeterminate phases. We also explored a potential functional association of the selected microRNAs using STRING software. This software identified 23 pathways associated with Trypanosoma cruzi infection. In addition, eleven genes were identified through bioinformatics analysis, and we found that SMAD family member 5 was downregulated in both phases. This gene serves as a mediator in the TGF-β signaling pathway. Thus, forty female mice of the CD1 strain were distributed into 4 groups and the expression levels of miR-21, miR-146a and miR-155 were measured in samples of heart tissue, total plasma and plasma extracellular vesicles by quantitative real-time polymerase chain reaction. RESULTS Overexpression of miR-21, miR-146a and miR-155 was observed in heart and plasma in both phases. Moreover, in extracellular vesicles miR-21 and miR-146a were also overexpressed in the acute phase, whereas in the indeterminate chronic phase we found only miR-146a up-regulated. CONCLUSIONS The expression of inflammatory microRNAs miR-21, miR-146a and miR-155 were up-regulated in each of the samples from acutely and chronically infected mice. The relevant finding was that miR-146a was up-regulated in each sample in both phases; therefore, this miRNA could be a possible candidate biomarker in Chagas disease.
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Affiliation(s)
- Martha Alicia Ballinas-Verdugo
- Departamento de Inmunología, Instituto Nacional de Cardiología Ignacio Chávez, Mexico City, CDMX, Mexico. .,Departamento de Parasitología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, CDMX, Mexico.
| | - Rogelio Frank Jiménez-Ortega
- Licenciatura en Nutrición, Plantel Texcoco, Universidad Privada del Estado de México, Texcoco, Estado de México, Mexico
| | | | - Nancy Rivas
- Departamento de Parasitología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, CDMX, Mexico
| | | | - Roxana Carbó
- Departamento de Biomedicina Cardiovascular, Instituto Nacional de Cardiología Ignacio Chávez, Mexico City, CDMX, Mexico
| | - Fausto Sánchez
- División de Ciencias Biológicas y de La Salud, Universidad Autónoma Metropolitana Xochimilco, Mexico City, CDMX, México
| | - Rafael Bojalil
- División de Ciencias Biológicas y de La Salud, Universidad Autónoma Metropolitana Xochimilco, Mexico City, CDMX, México
| | - Ricardo Márquez-Velasco
- Departamento de Inmunología, Instituto Nacional de Cardiología Ignacio Chávez, Mexico City, CDMX, Mexico
| | - Fausto Sánchez-Muñoz
- Departamento de Inmunología, Instituto Nacional de Cardiología Ignacio Chávez, Mexico City, CDMX, Mexico.,Sección de Postgraduados, Instituto Politécnico Nacional, Escuela Superior de Medicina, Mexico City, CDMX, Mexico
| | - Ricardo Alejandre-Aguilar
- Departamento de Parasitología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, CDMX, Mexico.
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10
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Nagaraj S, Want A, Laskowska-Kaszub K, Fesiuk A, Vaz S, Logarinho E, Wojda U. Candidate Alzheimer's Disease Biomarker miR-483-5p Lowers TAU Phosphorylation by Direct ERK1/2 Repression. Int J Mol Sci 2021; 22:ijms22073653. [PMID: 33915734 PMCID: PMC8037306 DOI: 10.3390/ijms22073653] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 03/24/2021] [Accepted: 03/27/2021] [Indexed: 12/13/2022] Open
Abstract
MicroRNAs have been demonstrated as key regulators of gene expression in the etiology of a range of diseases including Alzheimer's disease (AD). Recently, we identified miR-483-5p as the most upregulated miRNA amongst a panel of miRNAs in blood plasma specific to prodromal, early-stage Alzheimer's disease patients. Here, we investigated the functional role of miR-483-5p in AD pathology. Using TargetScan and miRTarBase, we identified the microtubule-associated protein MAPT, often referred to as TAU, and the extracellular signal-regulated kinases 1 and 2 (ERK1 and ERK2), known to phosphorylate TAU, as predicted direct targets of miR-483-5p. Employing several functional assays, we found that miR-483-5p regulates ERK1 and ERK2 at both mRNA and protein levels, resulting in lower levels of phosphorylated forms of both kinases. Moreover, miR-483-5p-mediated repression of ERK1/2 resulted in reduced phosphorylation of TAU protein at epitopes associated with TAU neurofibrillary pathology in AD. These results indicate that upregulation of miR-483-5p can decrease phosphorylation of TAU via ERK pathway, representing a compensatory neuroprotective mechanism in AD pathology. This miR-483-5p/ERK1/TAU axis thus represents a novel target for intervention in AD.
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Affiliation(s)
- Siranjeevi Nagaraj
- Laboratory of Preclinical Testing of Higher Standard, Nencki Institute of Experimental Biology of Polish Academy of Sciences, Pasteur 3, 02-093 Warsaw, Poland; (S.N.); (A.W.); (K.L.-K.); (A.F.)
| | - Andrew Want
- Laboratory of Preclinical Testing of Higher Standard, Nencki Institute of Experimental Biology of Polish Academy of Sciences, Pasteur 3, 02-093 Warsaw, Poland; (S.N.); (A.W.); (K.L.-K.); (A.F.)
| | - Katarzyna Laskowska-Kaszub
- Laboratory of Preclinical Testing of Higher Standard, Nencki Institute of Experimental Biology of Polish Academy of Sciences, Pasteur 3, 02-093 Warsaw, Poland; (S.N.); (A.W.); (K.L.-K.); (A.F.)
| | - Aleksandra Fesiuk
- Laboratory of Preclinical Testing of Higher Standard, Nencki Institute of Experimental Biology of Polish Academy of Sciences, Pasteur 3, 02-093 Warsaw, Poland; (S.N.); (A.W.); (K.L.-K.); (A.F.)
- i3S, Institute for Research and Innovation in Health, University of Porto, 4200-135 Porto, Portugal; (S.V.); (E.L.)
| | - Sara Vaz
- i3S, Institute for Research and Innovation in Health, University of Porto, 4200-135 Porto, Portugal; (S.V.); (E.L.)
| | - Elsa Logarinho
- i3S, Institute for Research and Innovation in Health, University of Porto, 4200-135 Porto, Portugal; (S.V.); (E.L.)
- Aging and Aneuploidy Laboratory, IBMC, Institute of Molecular and Cellular Biology, University of Porto, 4200-135 Porto, Portugal
| | - Urszula Wojda
- Laboratory of Preclinical Testing of Higher Standard, Nencki Institute of Experimental Biology of Polish Academy of Sciences, Pasteur 3, 02-093 Warsaw, Poland; (S.N.); (A.W.); (K.L.-K.); (A.F.)
- Correspondence: ; Tel.: +48-22-5892578
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11
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A novel rationale for targeting FXI: Insights from the hemostatic microRNA targetome for emerging anticoagulant strategies. Pharmacol Ther 2021; 218:107676. [DOI: 10.1016/j.pharmthera.2020.107676] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 09/03/2020] [Indexed: 02/07/2023]
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12
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Shaker F, Nikravesh A, Arezumand R, Aghaee-Bakhtiari SH. Web-based tools for miRNA studies analysis. Comput Biol Med 2020; 127:104060. [DOI: 10.1016/j.compbiomed.2020.104060] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 10/12/2020] [Accepted: 10/12/2020] [Indexed: 02/07/2023]
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13
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Zhao Z, Muth DC, Mulka K, Liao Z, Powell BH, Hancock GV, Metcalf Pate KA, Witwer KW. miRNA profiling of primate cervicovaginal lavage and extracellular vesicles reveals miR-186-5p as a potential antiretroviral factor in macrophages. FEBS Open Bio 2020; 10:2021-2039. [PMID: 33017084 PMCID: PMC7530394 DOI: 10.1002/2211-5463.12952] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 06/03/2020] [Accepted: 08/13/2020] [Indexed: 12/15/2022] Open
Abstract
Cervicovaginal secretions, or their components collected, are referred to as cervicovaginal lavage (CVL). CVL constituents have utility as biomarkers and play protective roles in wound healing and against HIV-1 infection. However, several components of cervicovaginal fluids are less well understood, such as extracellular RNAs and their carriers, for example, extracellular vesicles (EVs). EVs comprise a wide array of double-leaflet membrane extracellular particles and range in diameter from 30 nm to over one micron. The aim of this study was to determine whether differentially regulated CVL microRNAs (miRNAs) might influence retrovirus replication. To this end, we characterized EVs and miRNAs of primate CVL during the menstrual cycle and simian immunodeficiency virus (SIV) infection of macaques. EVs were enriched by stepped ultracentrifugation, and miRNA profiles were assessed with a medium-throughput stem-loop/hydrolysis probe qPCR platform. Whereas hormone cycling was abnormal in infected subjects, EV concentration correlated with progesterone concentration in uninfected subjects. miRNAs were present predominantly in the EV-depleted CVL supernatant. Only a small number of CVL miRNAs changed during the menstrual cycle or SIV infection, for example, miR-186-5p, which was depleted in retroviral infection. This miRNA inhibited HIV replication in infected macrophages in vitro. In silico target prediction and pathway enrichment analyses shed light on the probable functions of miR-186-5p in hindering HIV infections via immunoregulation, T-cell regulation, disruption of viral pathways, etc. These results provide further evidence for the potential of EVs and small RNAs as biomarkers or effectors of disease processes in the reproductive tract.
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Affiliation(s)
- Zezhou Zhao
- Department of Molecular and Comparative PathobiologyThe Johns Hopkins University School of MedicineBaltimoreMDUSA
| | - Dillon C. Muth
- Department of Molecular and Comparative PathobiologyThe Johns Hopkins University School of MedicineBaltimoreMDUSA
| | - Kathleen Mulka
- Department of Molecular and Comparative PathobiologyThe Johns Hopkins University School of MedicineBaltimoreMDUSA
| | - Zhaohao Liao
- Department of Molecular and Comparative PathobiologyThe Johns Hopkins University School of MedicineBaltimoreMDUSA
| | - Bonita H. Powell
- Department of Molecular and Comparative PathobiologyThe Johns Hopkins University School of MedicineBaltimoreMDUSA
| | | | - Kelly A. Metcalf Pate
- Department of Molecular and Comparative PathobiologyThe Johns Hopkins University School of MedicineBaltimoreMDUSA
| | - Kenneth W. Witwer
- Department of Molecular and Comparative PathobiologyThe Johns Hopkins University School of MedicineBaltimoreMDUSA
- Department of NeurologyThe Johns Hopkins University School of MedicineBaltimoreMDUSA
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14
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Herrera-Espejo S, Santos-Zorrozua B, Alvarez-Gonzalez P, Martin-Guerrero I, M de Pancorbo M, Garcia-Orad A, Lopez-Lopez E. A Genome-Wide Study of Single-Nucleotide Polymorphisms in MicroRNAs and Further In Silico Analysis Reveals Their Putative Role in Susceptibility to Late-Onset Alzheimer's Disease. Mol Neurobiol 2020; 58:55-64. [PMID: 32892277 DOI: 10.1007/s12035-020-02103-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 08/27/2020] [Indexed: 02/07/2023]
Abstract
Late-onset Alzheimer's disease (LOAD) is a neurodegenerative disorder of growing relevance in an aging society for which predictive biomarkers are needed. Many genes involved in LOAD are tightly controlled by microRNAs (miRNAs), which can be modulated by single-nucleotide polymorphisms (SNPs). Our aim was to determine the association between SNPs in miRNAs and LOAD. We selected all SNPs in pre-miRNAs with a minor allele frequency (MAF) > 1% and genotyped them in a cohort of 229 individuals diagnosed with LOAD and 237 unrelated healthy controls. In silico analyses were performed to predict the effect of SNPs on miRNA stability and detect downstream pathways. Four SNPs were associated with LOAD risk with a p value < 0.01 (rs74704964 in hsa-miR-518d, rs71363366 in hsa-miR-1283-2, rs11983381 in hsa-miR-4653, and rs10934682 in hsa-miR-544b). In silico analyses support a possible functional effect of those SNPs in miRNA levels and in the regulation of pathways of relevance for the development of LOAD. Although the results are promising, additional studies are needed to validate the association between SNPs in miRNAs and the risk of developing LOAD. Graphical abstract.
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Affiliation(s)
- Soraya Herrera-Espejo
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Borja Santos-Zorrozua
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Paula Alvarez-Gonzalez
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Idoia Martin-Guerrero
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU), Leioa, Spain.,BioCruces Bizkaia Health Research Institute, Barakaldo, Spain
| | - Marian M de Pancorbo
- BIOMICs Research Group, Centro de Investigación "Lascaray" Ikergunea, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Africa Garcia-Orad
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU), Leioa, Spain.,BioCruces Bizkaia Health Research Institute, Barakaldo, Spain
| | - Elixabet Lopez-Lopez
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU), Leioa, Spain. .,BioCruces Bizkaia Health Research Institute, Barakaldo, Spain.
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15
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Ibrahimovic M, Franzmann E, Mondul AM, Weh KM, Howard C, Hu JJ, Goodwin WJ, Kresty LA. Disparities in Head and Neck Cancer: A Case for Chemoprevention with Vitamin D. Nutrients 2020; 12:E2638. [PMID: 32872541 PMCID: PMC7551909 DOI: 10.3390/nu12092638] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 08/25/2020] [Accepted: 08/26/2020] [Indexed: 12/13/2022] Open
Abstract
Blacks experience disproportionate head and neck cancer (HNC) recurrence and mortality compared to Whites. Overall, vitamin D status is inversely associated to HNC pointing to a potential protective linkage. Although hypovitaminosis D in Blacks is well documented it has not been investigated in Black HNC patients. Thus, we conducted a prospective pilot study accessing vitamin D status in newly diagnosed HNC patients stratified by race and conducted in vitro studies to investigate mechanisms associated with potential cancer inhibitory effects of vitamin D. Outcome measures included circulating levels of vitamin D, related nutrients, and risk factor characterization as well as dietary and supplemental estimates. Vitamin D-based in vitro assays utilized proteome and microRNA (miR) profiling. Nineteen patients were enrolled, mean circulating vitamin D levels were significantly reduced in Black compared to White HNC patients, 27.3 and 20.0 ng/mL, respectively. Whites also supplemented vitamin D more frequently than Blacks who had non-significantly higher vitamin D from dietary sources. Vitamin D treatment of HNC cell lines revealed five significantly altered miRs regulating genes targeting multiple pathways in cancer based on enrichment analysis (i.e., negative regulation of cell proliferation, angiogenesis, chemokine, MAPK, and WNT signaling). Vitamin D further altered proteins involved in cancer progression, metastasis and survival supporting a potential role for vitamin D in targeted cancer prevention.
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Affiliation(s)
- Mirela Ibrahimovic
- The Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA; (M.I.); (A.M.M.); (K.M.W.); (C.H.)
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Elizabeth Franzmann
- Sylvester Comprehensive Cancer Center, University of Miami School of Medicine, Miami, FL 33136, USA; (E.F.); (J.J.H.); (W.J.G.)
- Department of Otolaryngology, University of Miami School of Medicine, Miami, FL 33136, USA
| | - Alison M. Mondul
- The Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA; (M.I.); (A.M.M.); (K.M.W.); (C.H.)
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Katherine M. Weh
- The Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA; (M.I.); (A.M.M.); (K.M.W.); (C.H.)
- Department of Surgery, Thoracic Surgery Section, University of Michigan, Ann Arbor, MI 48109, USA
| | - Connor Howard
- The Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA; (M.I.); (A.M.M.); (K.M.W.); (C.H.)
- Department of Surgery, Thoracic Surgery Section, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jennifer J. Hu
- Sylvester Comprehensive Cancer Center, University of Miami School of Medicine, Miami, FL 33136, USA; (E.F.); (J.J.H.); (W.J.G.)
- Department of Public Health Sciences, University of Miami School of Medicine, Miami, FL 33136, USA
| | - W. Jarrard Goodwin
- Sylvester Comprehensive Cancer Center, University of Miami School of Medicine, Miami, FL 33136, USA; (E.F.); (J.J.H.); (W.J.G.)
- Department of Public Health Sciences, University of Miami School of Medicine, Miami, FL 33136, USA
| | - Laura A. Kresty
- The Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA; (M.I.); (A.M.M.); (K.M.W.); (C.H.)
- Department of Surgery, Thoracic Surgery Section, University of Michigan, Ann Arbor, MI 48109, USA
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16
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Wang P, Li Q, Sun N, Gao Y, Liu JS, Deng K, He J. MiRACLe: an individual-specific approach to improve microRNA-target prediction based on a random contact model. Brief Bioinform 2020; 22:5868068. [PMID: 34020537 DOI: 10.1093/bib/bbaa117] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 04/30/2020] [Accepted: 05/16/2020] [Indexed: 12/13/2022] Open
Abstract
Deciphering microRNA (miRNA) targets is important for understanding the function of miRNAs as well as miRNA-based diagnostics and therapeutics. Given the highly cell-specific nature of miRNA regulation, recent computational approaches typically exploit expression data to identify the most physiologically relevant target messenger RNAs (mRNAs). Although effective, those methods usually require a large sample size to infer miRNA-mRNA interactions, thus limiting their applications in personalized medicine. In this study, we developed a novel miRNA target prediction algorithm called miRACLe (miRNA Analysis by a Contact modeL). It integrates sequence characteristics and RNA expression profiles into a random contact model, and determines the target preferences by relative probability of effective contacts in an individual-specific manner. Evaluation by a variety of measures shows that fitting TargetScan, a frequently used prediction tool, into the framework of miRACLe can improve its predictive power with a significant margin and consistently outperform other state-of-the-art methods in prediction accuracy, regulatory potential and biological relevance. Notably, the superiority of miRACLe is robust to various biological contexts, types of expression data and validation datasets, and the computation process is fast and efficient. Additionally, we show that the model can be readily applied to other sequence-based algorithms to improve their predictive power, such as DIANA-microT-CDS, miRanda-mirSVR and MirTarget4. MiRACLe is publicly available at https://github.com/PANWANG2014/miRACLe.
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Affiliation(s)
- Pan Wang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Qi Li
- Center for Statistical Science & Department of Industry Engineering, Tsinghua University, Beijing, China
| | - Nan Sun
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yibo Gao
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jun S Liu
- Department of Statistics, Harvard University, Cambridge, MA, USA
| | - Ke Deng
- Center for Statistical Science & Department of Industry Engineering, Tsinghua University, Beijing, China
| | - Jie He
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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17
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Huang HY, Lin YCD, Li J, Huang KY, Shrestha S, Hong HC, Tang Y, Chen YG, Jin CN, Yu Y, Xu JT, Li YM, Cai XX, Zhou ZY, Chen XH, Pei YY, Hu L, Su JJ, Cui SD, Wang F, Xie YY, Ding SY, Luo MF, Chou CH, Chang NW, Chen KW, Cheng YH, Wan XH, Hsu WL, Lee TY, Wei FX, Huang HD. miRTarBase 2020: updates to the experimentally validated microRNA-target interaction database. Nucleic Acids Res 2020; 48:D148-D154. [PMID: 31647101 PMCID: PMC7145596 DOI: 10.1093/nar/gkz896] [Citation(s) in RCA: 592] [Impact Index Per Article: 148.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 09/30/2019] [Accepted: 10/22/2019] [Indexed: 12/15/2022] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs (typically consisting of 18–25 nucleotides) that negatively control expression of target genes at the post-transcriptional level. Owing to the biological significance of miRNAs, miRTarBase was developed to provide comprehensive information on experimentally validated miRNA–target interactions (MTIs). To date, the database has accumulated >13,404 validated MTIs from 11,021 articles from manual curations. In this update, a text-mining system was incorporated to enhance the recognition of MTI-related articles by adopting a scoring system. In addition, a variety of biological databases were integrated to provide information on the regulatory network of miRNAs and its expression in blood. Not only targets of miRNAs but also regulators of miRNAs are provided to users for investigating the up- and downstream regulations of miRNAs. Moreover, the number of MTIs with high-throughput experimental evidence increased remarkably (validated by CLIP-seq technology). In conclusion, these improvements promote the miRTarBase as one of the most comprehensively annotated and experimentally validated miRNA–target interaction databases. The updated version of miRTarBase is now available at http://miRTarBase.cuhk.edu.cn/.
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Affiliation(s)
- Hsi-Yuan Huang
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong Province 518172, China.,Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong Province 518172, China
| | - Yang-Chi-Dung Lin
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong Province 518172, China.,Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong Province 518172, China
| | - Jing Li
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong Province 518172, China.,Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong Province 518172, China
| | - Kai-Yao Huang
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong Province 518172, China.,Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong Province 518172, China
| | - Sirjana Shrestha
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu 300, Taiwan
| | - Hsiao-Chin Hong
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong Province 518172, China.,Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong Province 518172, China
| | - Yun Tang
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong Province 518172, China.,Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong Province 518172, China
| | - Yi-Gang Chen
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong Province 518172, China
| | - Chen-Nan Jin
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong Province 518172, China
| | - Yuan Yu
- School of Science and Engineering, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong Province 518172, China
| | - Jia-Tong Xu
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong Province 518172, China
| | - Yue-Ming Li
- School of Science and Engineering, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong Province 518172, China
| | - Xiao-Xuan Cai
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong Province 518172, China
| | - Zhen-Yu Zhou
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong Province 518172, China
| | - Xiao-Hang Chen
- The Genetics Laboratory, Longgang District Maternity & Child Healthcare Hospital of Shenzhen City, Shenzhen, Guangdong Province 518172, China
| | - Yuan-Yuan Pei
- The Genetics Laboratory, Longgang District Maternity & Child Healthcare Hospital of Shenzhen City, Shenzhen, Guangdong Province 518172, China
| | - Liang Hu
- The Genetics Laboratory, Longgang District Maternity & Child Healthcare Hospital of Shenzhen City, Shenzhen, Guangdong Province 518172, China
| | - Jin-Jiang Su
- The Genetics Laboratory, Longgang District Maternity & Child Healthcare Hospital of Shenzhen City, Shenzhen, Guangdong Province 518172, China.,Department of Cell Biology, Jiamusi University, Jiamusi, Heilongjiang Province 154007, China
| | - Shi-Dong Cui
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong Province 518172, China
| | - Fei Wang
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong Province 518172, China.,Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong Province 518172, China
| | - Yue-Yang Xie
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong Province 518172, China
| | - Si-Yuan Ding
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong Province 518172, China
| | - Meng-Fan Luo
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong Province 518172, China
| | - Chih-Hung Chou
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu 300, Taiwan.,Center for Intelligent Drug Systems and Smart Bio-devices (IDS2B), National Chiao Tung University, Hsinchu, Taiwan
| | - Nai-Wen Chang
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei 106, Taiwan
| | - Kai-Wen Chen
- Institute of Molecular Medicine and Bioengineering, National Chiao Tung University, Hsinchu 300, Taiwan
| | - Yu-Hsiang Cheng
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu 300, Taiwan
| | - Xin-Hong Wan
- The Genetics Laboratory, Longgang District Maternity & Child Healthcare Hospital of Shenzhen City, Shenzhen, Guangdong Province 518172, China
| | - Wen-Lian Hsu
- Institute of Information Science, Academia Sinica, Taipei 115, Taiwan
| | - Tzong-Yi Lee
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong Province 518172, China.,Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong Province 518172, China
| | - Feng-Xiang Wei
- The Genetics Laboratory, Longgang District Maternity & Child Healthcare Hospital of Shenzhen City, Shenzhen, Guangdong Province 518172, China.,Department of Cell Biology, Jiamusi University, Jiamusi, Heilongjiang Province 154007, China.,Department of Pathogenic Microorganisms, Zunyi Medical University, Zunyi, Guizhong Province 563006, China
| | - Hsien-Da Huang
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong Province 518172, China.,Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong Province 518172, China.,Department of Biological Science and Technology, National Chiao Tung University, Hsinchu 300, Taiwan
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18
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Hrovatin K, Kunej T, Dolžan V. Genetic variability of serotonin pathway associated with schizophrenia onset, progression, and treatment. Am J Med Genet B Neuropsychiatr Genet 2020; 183:113-127. [PMID: 31674148 DOI: 10.1002/ajmg.b.32766] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Revised: 09/11/2019] [Accepted: 10/07/2019] [Indexed: 12/22/2022]
Abstract
Schizophrenia (SZ) onset and treatment outcome have important genetic components, however individual genes do not have strong effects on SZ phenotype. Therefore, it is important to use the pathway-based approach and study metabolic and signaling pathways, such as dopaminergic and serotonergic. Serotonin pathway has an important role in brain signaling, nevertheless, its role in SZ is not as thoroughly examined as that of dopamine pathway. In this study, we reviewed serotonin pathway genes and genetic variations associated with SZ, including variations at DNA, RNA, and epigenetic level. We obtained 30 serotonin pathway genes from Kyoto encyclopedia of genes and genomes and used these genes for the literature review. We extracted 20 protein coding serotonin pathway genes with genetic variations associated with SZ onset, development, and treatment from 31 research papers. Genes associated with SZ are present on all levels of serotonin pathway: serotonin synthesis, transport, receptor binding, intracellular signaling, and reuptake; however, regulatory genes are poorly researched. We summarized common challenges of genetic association studies and presented some solutions. The analysis of reported serotonin pathway-SZ associations revealed lack of information about certain serotonin pathway genes potentially associated with SZ. Furthermore, it is becoming clear that interactions among serotonin pathway genes and their regulators may bring further knowledge about their involvement in SZ.
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Affiliation(s)
- Karin Hrovatin
- University of Ljubljana, Biotechnical Faculty, Department of Animal Science, Ljubljana, Slovenia
| | - Tanja Kunej
- University of Ljubljana, Biotechnical Faculty, Department of Animal Science, Ljubljana, Slovenia
| | - Vita Dolžan
- University of Ljubljana, Faculty of Medicine, Institute of Biochemistry, Pharmacogenetics Laboratory, Ljubljana, Slovenia
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19
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Bajan S, Hutvagner G. RNA-Based Therapeutics: From Antisense Oligonucleotides to miRNAs. Cells 2020; 9:E137. [PMID: 31936122 PMCID: PMC7016530 DOI: 10.3390/cells9010137] [Citation(s) in RCA: 236] [Impact Index Per Article: 59.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 12/23/2019] [Accepted: 12/30/2019] [Indexed: 02/07/2023] Open
Abstract
The first therapeutic nucleic acid, a DNA oligonucleotide, was approved for clinical use in 1998. Twenty years later, in 2018, the first therapeutic RNA-based oligonucleotide was United States Food and Drug Administration (FDA) approved. This promises to be a rapidly expanding market, as many emerging biopharmaceutical companies are developing RNA interference (RNAi)-based, and RNA-based antisense oligonucleotide therapies. However, miRNA therapeutics are noticeably absent. miRNAs are regulatory RNAs that regulate gene expression. In disease states, the expression of many miRNAs is measurably altered. The potential of miRNAs as therapies and therapeutic targets has long been discussed and in the context of a wide variety of infections and diseases. Despite the great number of studies identifying miRNAs as potential therapeutic targets, only a handful of miRNA-targeting drugs (mimics or inhibitors) have entered clinical trials. In this review, we will discuss whether the investment in finding potential miRNA therapeutic targets has yielded feasible and practicable results, the benefits and obstacles of miRNAs as therapeutic targets, and the potential future of the field.
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Affiliation(s)
- Sarah Bajan
- Faculty of Science, University of Technology Sydney, Sydney, NSW 2000, Australia
- Health and Sport Science, University of Sunshine Coast, Sunshine Coast, QLD 4556, Australia
| | - Gyorgy Hutvagner
- School of Biomedical Engineering Faculty of Engineering and Information Technology, University of Technology Sydney, Sydney, NSW 2000, Australia
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20
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Licursi V, Conte F, Fiscon G, Paci P. MIENTURNET: an interactive web tool for microRNA-target enrichment and network-based analysis. BMC Bioinformatics 2019; 20:545. [PMID: 31684860 PMCID: PMC6829817 DOI: 10.1186/s12859-019-3105-x] [Citation(s) in RCA: 202] [Impact Index Per Article: 40.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 09/20/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND miRNAs regulate the expression of several genes with one miRNA able to target multiple genes and with one gene able to be simultaneously targeted by more than one miRNA. Therefore, it has become indispensable to shorten the long list of miRNA-target interactions to put in the spotlight in order to gain insight into understanding the regulatory mechanism orchestrated by miRNAs in various cellular processes. A reasonable solution is certainly to prioritize miRNA-target interactions to maximize the effectiveness of the downstream analysis. RESULTS We propose a new and easy-to-use web tool MIENTURNET (MicroRNA ENrichment TURned NETwork) that receives in input a list of miRNAs or mRNAs and tackles the problem of prioritizing miRNA-target interactions by performing a statistical analysis followed by a fully featured network-based visualization and analysis. The statistics is used to assess the significance of an over-representation of miRNA-target interactions and then MIENTURNET filters based on the statistical significance associated with each miRNA-target interaction. In addition, the holistic approach of the network theory is used to infer possible evidences of miRNA regulation by capturing emergent properties of the miRNA-target regulatory network that would be not evident through a pairwise analysis of the individual components. CONCLUSION MIENTURNET offers the possibility to consistently perform both statistical and network-based analyses by using only a single tool leading to a more effective prioritization of the miRNA-target interactions. This has the potential to avoid researchers without computational and informatics skills to navigate multiple websites and thus to independently investigate miRNA activity in every cellular process of interest in an easy and at the same time exhaustive way thanks to the intuitive web interface. The web application along with a well-documented and comprehensive user guide are freely available at http://userver.bio.uniroma1.it/apps/mienturnet/ without any login requirement.
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Affiliation(s)
- Valerio Licursi
- Institute for Systems Analysis and Computer Science “Antonio Ruberti”, National Research Council, Via dei Taurini 19, Rome, 00185 Italy
- Department of Biology and Biotechnology “Charles Darwin”, “Sapienza” University of Rome, Via dei Sardi 70, Rome, 00185 Italy
| | - Federica Conte
- Institute for Systems Analysis and Computer Science “Antonio Ruberti”, National Research Council, Via dei Taurini 19, Rome, 00185 Italy
| | - Giulia Fiscon
- Institute for Systems Analysis and Computer Science “Antonio Ruberti”, National Research Council, Via dei Taurini 19, Rome, 00185 Italy
| | - Paola Paci
- Institute for Systems Analysis and Computer Science “Antonio Ruberti”, National Research Council, Via dei Taurini 19, Rome, 00185 Italy
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21
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Oliveira AC, Bovolenta LA, Alves L, Figueiredo L, Ribeiro AO, Campos VF, Lemke N, Pinhal D. Understanding the Modus Operandi of MicroRNA Regulatory Clusters. Cells 2019; 8:cells8091103. [PMID: 31540501 PMCID: PMC6770051 DOI: 10.3390/cells8091103] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 07/06/2019] [Accepted: 07/09/2019] [Indexed: 12/24/2022] Open
Abstract
MicroRNAs (miRNAs) are non-coding RNAs that regulate a wide range of biological pathways by post-transcriptionally modulating gene expression levels. Given that even a single miRNA may simultaneously control several genes enrolled in multiple biological functions, one would expect that these tiny RNAs have the ability to properly sort among distinctive cellular processes to drive protein production. To test this hypothesis, we scrutinized previously published microarray datasets and clustered protein-coding gene expression profiles according to the intensity of fold-change levels caused by the exogenous transfection of 10 miRNAs (miR-1, miR-7, miR-9, miR-124, miR-128a, miR-132, miR-133a, miR-142, miR-148b, miR-181a) in a human cell line. Through an in silico functional enrichment analysis, we discovered non-randomic regulatory patterns, proper of each cluster identified. We demonstrated that miRNAs are capable of equivalently modulate the expression signatures of target genes in regulatory clusters according to the biological function they are assigned to. Moreover, target prediction analysis applied to ten vertebrate species, suggest that such miRNA regulatory modus operandi is evolutionarily conserved within vertebrates. Overall, we discovered a complex regulatory cluster-module strategy driven by miRNAs, which relies on the controlled intensity of the repression over distinct targets under specific biological contexts. Our discovery helps to clarify the mechanisms underlying the functional activity of miRNAs and makes it easier to take the fastest and most accurate path in the search for the functions of miRNAs in any distinct biological process of interest.
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Affiliation(s)
- Arthur C Oliveira
- Institute of Biosciences of Botucatu, Department of Genetics, Sao Paulo State University (UNESP), Botucatu, Sao Paulo 18618-689, Brazil.
| | - Luiz A Bovolenta
- Department of Physics and Biophysics, Sao Paulo State University (UNESP), Botucatu, Sao Paulo 18618-689, Brazil.
| | - Lucas Alves
- Institute of Biosciences of Botucatu, Department of Genetics, Sao Paulo State University (UNESP), Botucatu, Sao Paulo 18618-689, Brazil.
| | - Lucas Figueiredo
- Institute of Biosciences of Botucatu, Department of Genetics, Sao Paulo State University (UNESP), Botucatu, Sao Paulo 18618-689, Brazil.
| | - Amanda O Ribeiro
- Institute of Biosciences of Botucatu, Department of Genetics, Sao Paulo State University (UNESP), Botucatu, Sao Paulo 18618-689, Brazil.
| | - Vinicius F Campos
- Laboratory of Structural Genomics (GenEstrut), Technology Developmental Center, Graduate Program of Biotechnology, Federal University of Pelotas, Pelotas, Rio Grande do Sul 96010-610, Brazil.
| | - Ney Lemke
- Department of Physics and Biophysics, Sao Paulo State University (UNESP), Botucatu, Sao Paulo 18618-689, Brazil.
| | - Danillo Pinhal
- Institute of Biosciences of Botucatu, Department of Genetics, Sao Paulo State University (UNESP), Botucatu, Sao Paulo 18618-689, Brazil.
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22
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Chou CH, Shrestha S, Yang CD, Chang NW, Lin YL, Liao KW, Huang WC, Sun TH, Tu SJ, Lee WH, Chiew MY, Tai CS, Wei TY, Tsai TR, Huang HT, Wang CY, Wu HY, Ho SY, Chen PR, Chuang CH, Hsieh PJ, Wu YS, Chen WL, Li MJ, Wu YC, Huang XY, Ng FL, Buddhakosai W, Huang PC, Lan KC, Huang CY, Weng SL, Cheng YN, Liang C, Hsu WL, Huang HD. miRTarBase update 2018: a resource for experimentally validated microRNA-target interactions. Nucleic Acids Res 2019; 46:D296-D302. [PMID: 29126174 PMCID: PMC5753222 DOI: 10.1093/nar/gkx1067] [Citation(s) in RCA: 1264] [Impact Index Per Article: 252.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 10/25/2017] [Indexed: 01/16/2023] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs of ∼ 22 nucleotides that are involved in negative regulation of mRNA at the post-transcriptional level. Previously, we developed miRTarBase which provides information about experimentally validated miRNA-target interactions (MTIs). Here, we describe an updated database containing 422 517 curated MTIs from 4076 miRNAs and 23 054 target genes collected from over 8500 articles. The number of MTIs curated by strong evidence has increased ∼1.4-fold since the last update in 2016. In this updated version, target sites validated by reporter assay that are available in the literature can be downloaded. The target site sequence can extract new features for analysis via a machine learning approach which can help to evaluate the performance of miRNA-target prediction tools. Furthermore, different ways of browsing enhance user browsing specific MTIs. With these improvements, miRTarBase serves as more comprehensively annotated, experimentally validated miRNA-target interactions databases in the field of miRNA related research. miRTarBase is available at http://miRTarBase.mbc.nctu.edu.tw/.
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Affiliation(s)
- Chih-Hung Chou
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan.,Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Sirjana Shrestha
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Chi-Dung Yang
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan.,Institute of Population Health Sciences, National Health Research Institutes, Miaoli, 350, Taiwan
| | - Nai-Wen Chang
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, 106, Taiwan
| | - Yu-Ling Lin
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan.,Center for Bioinformatics Research, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Kuang-Wen Liao
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan.,Institute of Molecular Medicine and Bioengineering, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Wei-Chi Huang
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan.,Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Ting-Hsuan Sun
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Siang-Jyun Tu
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Wei-Hsiang Lee
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan.,Clinical Research Center, Chung Shan Medical University Hospital, Taichung, 402, Taiwan
| | - Men-Yee Chiew
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Chun-San Tai
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Ting-Yen Wei
- Interdisciplinary Program of Life Science, National Tsing Hua University, Hsinchu, 300, Taiwan
| | - Tzi-Ren Tsai
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Hsin-Tzu Huang
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Chung-Yu Wang
- Institute of Molecular Medicine and Bioengineering, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Hsin-Yi Wu
- Institute of Molecular Medicine and Bioengineering, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Shu-Yi Ho
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Pin-Rong Chen
- Institute of Molecular Medicine and Bioengineering, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Cheng-Hsun Chuang
- Institute of Molecular Medicine and Bioengineering, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Pei-Jung Hsieh
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Yi-Shin Wu
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Wen-Liang Chen
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Meng-Ju Li
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan.,Department of Pediatrics, National Taiwan University Hospital Hsinchu Branch, Hsinchu, 300, Taiwan
| | - Yu-Chun Wu
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Xin-Yi Huang
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Fung Ling Ng
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Waradee Buddhakosai
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Pei-Chun Huang
- Delivery Room, Department of Nursing, National Taiwan University Hospital Hsinchu Branch, Hsinchu, 300, Taiwan
| | - Kuan-Chun Lan
- Institute of Molecular Medicine and Bioengineering, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Chia-Yen Huang
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan.,Gynecologic Cancer Center, Department of Obstetrics and Gynecology, Cathay General Hospital, Taipei, 106, Taiwan
| | - Shun-Long Weng
- Department of Obstetrics and Gynecology, Hsinchu Mackay Memorial Hospital, Hsinchu, 300, Taiwan.,Mackay Medicine, Nursing and Management College, Taipei, 112, Taiwan.,Department of Medicine, Mackay Medical College, New Taipei City, 252, Taiwan
| | - Yeong-Nan Cheng
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Chao Liang
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Wen-Lian Hsu
- Institute of Information Science, Academia Sinica, Taipei, 115, Taiwan
| | - Hsien-Da Huang
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan.,Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan.,Warshel Institute for Computational Biology, The Chinese University of Hong Kong (Shenzhen), Shenzhen, Guangdong Province, 518172, China.,School of Science and Engineering, The Chinese University of Hong Kong (Shenzhen), Shenzhen, Guangdong Province, 518172, China
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23
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Borgmästars E, de Weerd HA, Lubovac-Pilav Z, Sund M. miRFA: an automated pipeline for microRNA functional analysis with correlation support from TCGA and TCPA expression data in pancreatic cancer. BMC Bioinformatics 2019; 20:393. [PMID: 31311505 PMCID: PMC6636046 DOI: 10.1186/s12859-019-2974-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 06/28/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND MicroRNAs (miRNAs) are small RNAs that regulate gene expression at a post-transcriptional level and are emerging as potentially important biomarkers for various disease states, including pancreatic cancer. In silico-based functional analysis of miRNAs usually consists of miRNA target prediction and functional enrichment analysis of miRNA targets. Since miRNA target prediction methods generate a large number of false positive target genes, further validation to narrow down interesting candidate miRNA targets is needed. One commonly used method correlates miRNA and mRNA expression to assess the regulatory effect of a particular miRNA. The aim of this study was to build a bioinformatics pipeline in R for miRNA functional analysis including correlation analyses between miRNA expression levels and its targets on mRNA and protein expression levels available from the cancer genome atlas (TCGA) and the cancer proteome atlas (TCPA). TCGA-derived expression data of specific mature miRNA isoforms from pancreatic cancer tissue was used. RESULTS Fifteen circulating miRNAs with significantly altered expression levels detected in pancreatic cancer patients were queried separately in the pipeline. The pipeline generated predicted miRNA target genes, enriched gene ontology (GO) terms and Kyoto encyclopedia of genes and genomes (KEGG) pathways. Predicted miRNA targets were evaluated by correlation analyses between each miRNA and its predicted targets. MiRNA functional analysis in combination with Kaplan-Meier survival analysis suggest that hsa-miR-885-5p could act as a tumor suppressor and should be validated as a potential prognostic biomarker in pancreatic cancer. CONCLUSIONS Our miRNA functional analysis (miRFA) pipeline can serve as a valuable tool in biomarker discovery involving mature miRNAs associated with pancreatic cancer and could be developed to cover additional cancer types. Results for all mature miRNAs in TCGA pancreatic adenocarcinoma dataset can be studied and downloaded through a shiny web application at https://emmbor.shinyapps.io/mirfa/ .
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Affiliation(s)
- Emmy Borgmästars
- Department of Surgical and Perioperative Sciences, Umeå University, Umeå, Sweden
| | - Hendrik Arnold de Weerd
- School of bioscience, Systems Biology Research Centre, University of Skövde, Skövde, Sweden
- Department of Physics, Chemistry and Biology, Bioinformatics, Linköping University, Linköping, Sweden
| | - Zelmina Lubovac-Pilav
- School of bioscience, Systems Biology Research Centre, University of Skövde, Skövde, Sweden
| | - Malin Sund
- Department of Surgical and Perioperative Sciences, Umeå University, Umeå, Sweden
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24
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McGrory CL, Ryan KM, Kolshus E, McLoughlin DM. Peripheral blood E2F1 mRNA in depression and following electroconvulsive therapy. Prog Neuropsychopharmacol Biol Psychiatry 2019; 89:380-385. [PMID: 30365982 DOI: 10.1016/j.pnpbp.2018.10.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 10/19/2018] [Accepted: 10/21/2018] [Indexed: 12/28/2022]
Abstract
The E2F transcription factors are a group of proteins that bind to the promotor region of the adenovirus E2 gene. E2F1, the first family member to be cloned, is linked to functions including cell proliferation and apoptosis, DNA repair, cell senescence and metabolism. We recently performed a deep sequencing study of micro-RNA changes in whole blood following ECT. Two micro-RNAs (miR-126-3p and miR-106a-5p) were identified and gene targeting analysis identified E2F1 as a shared target of these miRNAs. To our knowledge, no studies have examined E2F1 mRNA levels in patients with depression. Peripheral blood E2F1 mRNA levels were therefore examined in patients with depression, compared to healthy controls, and the effects of a course of ECT on peripheral blood E2F1 mRNA was investigated. Depressed patient and healthy control groups were balanced on the basis of age and sex. E2F1 mRNA levels were significantly lower in depressed patients in comparison to controls (p = .009) but did not change with ECT. There was no relationship between baseline E2F1 levels and depression severity, response to treatment, presence of psychosis or polarity of depression. There were no significant correlations between E2F1 levels and mood scores based on the HAM-D24. These results indicate that reduced peripheral blood E2F1 mRNA could be a trait feature of depression.
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Affiliation(s)
- Claire L McGrory
- Trinity College Institute of Neuroscience, Trinity College Dublin, Dublin 2, Ireland; Department of Psychiatry, Trinity College Dublin, St Patrick's University Hospital, Dublin 8, Ireland
| | - Karen M Ryan
- Trinity College Institute of Neuroscience, Trinity College Dublin, Dublin 2, Ireland; Department of Psychiatry, Trinity College Dublin, St Patrick's University Hospital, Dublin 8, Ireland
| | - Erik Kolshus
- Trinity College Institute of Neuroscience, Trinity College Dublin, Dublin 2, Ireland; Department of Psychiatry, Trinity College Dublin, St Patrick's University Hospital, Dublin 8, Ireland
| | - Declan M McLoughlin
- Trinity College Institute of Neuroscience, Trinity College Dublin, Dublin 2, Ireland; Department of Psychiatry, Trinity College Dublin, St Patrick's University Hospital, Dublin 8, Ireland.
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25
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Evolutionary Patterns of Non-Coding RNA in Cardiovascular Biology. Noncoding RNA 2019; 5:ncrna5010015. [PMID: 30709035 PMCID: PMC6468844 DOI: 10.3390/ncrna5010015] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 01/26/2019] [Accepted: 01/29/2019] [Indexed: 12/15/2022] Open
Abstract
Cardiovascular diseases (CVDs) affect the heart and the vascular system with a high prevalence and place a huge burden on society as well as the healthcare system. These complex diseases are often the result of multiple genetic and environmental risk factors and pose a great challenge to understanding their etiology and consequences. With the advent of next generation sequencing, many non-coding RNA transcripts, especially long non-coding RNAs (lncRNAs), have been linked to the pathogenesis of CVD. Despite increasing evidence, the proper functional characterization of most of these molecules is still lacking. The exploration of conservation of sequences across related species has been used to functionally annotate protein coding genes. In contrast, the rapid evolutionary turnover and weak sequence conservation of lncRNAs make it difficult to characterize functional homologs for these sequences. Recent studies have tried to explore other dimensions of interspecies conservation to elucidate the functional role of these novel transcripts. In this review, we summarize various methodologies adopted to explore the evolutionary conservation of cardiovascular non-coding RNAs at sequence, secondary structure, syntenic, and expression level.
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26
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Zhang J, Xu Y, Liu H, Pan Z. MicroRNAs in ovarian follicular atresia and granulosa cell apoptosis. Reprod Biol Endocrinol 2019; 17:9. [PMID: 30630485 PMCID: PMC6329178 DOI: 10.1186/s12958-018-0450-y] [Citation(s) in RCA: 122] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 12/17/2018] [Indexed: 12/13/2022] Open
Abstract
MicroRNAs (miRNAs) are short, noncoding RNAs that posttranscriptionally regulate gene expression. In the past decade, studies on miRNAs in ovaries have revealed the key roles of miRNAs in ovarian development and function. In this review, we first introduce the development of follicular atresia research and then summarize genome-wide studies on the ovarian miRNA profiles of different mammalian species. Differentially expressed miRNA profiles during atresia and other biological processes are herein compared. In addition, current knowledge on confirmed functional miRNAs during the follicular atresia process, which is mostly indicated by granulosa cell (GC) apoptosis, is presented. The main miRNA families and clusters, including the let-7 family, miR-23-27-24 cluster, miR-183-96-182 cluster and miR-17-92 cluster, and related pathways that are involved in follicular atresia are thoroughly summarized. A deep understanding of the roles of miRNA networks will not only help elucidate the mechanisms of GC apoptosis, follicular development, atresia and their disorders but also offer new diagnostic and treatment strategies for infertility and other ovarian dysfunctions.
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Affiliation(s)
- Jinbi Zhang
- 0000 0000 9750 7019grid.27871.3bCollege of Animal Science and Technology, Nanjing Agriculture University, Nanjing, 210095 People’s Republic of China
| | - Yinxue Xu
- 0000 0000 9750 7019grid.27871.3bCollege of Animal Science and Technology, Nanjing Agriculture University, Nanjing, 210095 People’s Republic of China
| | - Honglin Liu
- 0000 0000 9750 7019grid.27871.3bCollege of Animal Science and Technology, Nanjing Agriculture University, Nanjing, 210095 People’s Republic of China
| | - Zengxiang Pan
- 0000 0000 9750 7019grid.27871.3bCollege of Animal Science and Technology, Nanjing Agriculture University, Nanjing, 210095 People’s Republic of China
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27
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Gutierrez-Camino Á, Umerez M, Lopez-Lopez E, Santos-Zorrozua B, Martin-Guerrero I, de Andoin NG, Ana S, Navajas A, Astigarraga I, Garcia-Orad A. Involvement of miRNA polymorphism in mucositis development in childhood acute lymphoblastic leukemia treatment. Pharmacogenomics 2018; 19:1403-1412. [DOI: 10.2217/pgs-2018-0113] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Aim: Mucositis, linked to methotrexate, daunorubicin or cyclophosphamide, is a frequent childhood acute lymphoblastic leukemia (ALL) therapy side effect. miRNAs regulate the expression of pharmacokinetic/pharmacodynamic pathway genes. SNPs in miRNAs could affect their levels or function, and affect their pharmacokinetic/pharmacodynamic pathway target genes. Our aim was to determine the association between miRNA genetic variants targeting mucositis-related genes and mucositis-developing risk. Patients & methods: We analyzed 160 SNPs in 179 Spanish children with B-cell precursor ALL homogeneously treated with LAL/SHOP protocols. Results: We identified three SNPs in miR-4268, miR-4751 and miR-3117 associated with mucositis, diarrhea and vomiting, respectively. Conclusion: The effect of these SNPs on genes related to drug pharmacokinetics/pharmacodynamics could explain mucositis, diarrhea and vomiting development during ALL therapy.
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Affiliation(s)
- Ángela Gutierrez-Camino
- Department of Genetics, Physic Anthropology & Animal Physiology, University of the Basque Country, UPV/EHU, Leioa, 48940, Spain
- BioCruces Health Research Institute, Barakaldo, 48903, Spain
| | - Maitane Umerez
- Department of Genetics, Physic Anthropology & Animal Physiology, University of the Basque Country, UPV/EHU, Leioa, 48940, Spain
| | - Elixabet Lopez-Lopez
- Department of Genetics, Physic Anthropology & Animal Physiology, University of the Basque Country, UPV/EHU, Leioa, 48940, Spain
- BioCruces Health Research Institute, Barakaldo, 48903, Spain
| | - Borja Santos-Zorrozua
- Department of Genetics, Physic Anthropology & Animal Physiology, University of the Basque Country, UPV/EHU, Leioa, 48940, Spain
| | - Idoia Martin-Guerrero
- Department of Genetics, Physic Anthropology & Animal Physiology, University of the Basque Country, UPV/EHU, Leioa, 48940, Spain
- BioCruces Health Research Institute, Barakaldo, 48903, Spain
| | - Nagore García de Andoin
- Department of Pediatrics, University Hospital Donostia, San Sebastian, 20014, Spain
- Department of Pediatrics, University of the Basque Country, UPV/EHU, Leioa, 48940, Spain
| | - Sastre Ana
- Department of Oncohematology, University Hospital La Paz, Madrid, 28046, Spain
| | - Aurora Navajas
- BioCruces Health Research Institute, Barakaldo, 48903, Spain
- Department of Pediatrics, University Hospital Cruces, Barakaldo, 48903, Spain
| | - Itziar Astigarraga
- BioCruces Health Research Institute, Barakaldo, 48903, Spain
- Department of Pediatrics, University of the Basque Country, UPV/EHU, Leioa, 48940, Spain
- Department of Pediatrics, University Hospital Cruces, Barakaldo, 48903, Spain
| | - Africa Garcia-Orad
- Department of Genetics, Physic Anthropology & Animal Physiology, University of the Basque Country, UPV/EHU, Leioa, 48940, Spain
- BioCruces Health Research Institute, Barakaldo, 48903, Spain
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28
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Huntley RP, Kramarz B, Sawford T, Umrao Z, Kalea A, Acquaah V, Martin MJ, Mayr M, Lovering RC. Expanding the horizons of microRNA bioinformatics. RNA (NEW YORK, N.Y.) 2018; 24:1005-1017. [PMID: 29871895 PMCID: PMC6049505 DOI: 10.1261/rna.065565.118] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 06/01/2018] [Indexed: 06/08/2023]
Abstract
MicroRNA regulation of key biological and developmental pathways is a rapidly expanding area of research, accompanied by vast amounts of experimental data. This data, however, is not widely available in bioinformatic resources, making it difficult for researchers to find and analyze microRNA-related experimental data and define further research projects. We are addressing this problem by providing two new bioinformatics data sets that contain experimentally verified functional information for mammalian microRNAs involved in cardiovascular-relevant, and other, processes. To date, our resource provides over 4400 Gene Ontology annotations associated with over 500 microRNAs from human, mouse, and rat and over 2400 experimentally validated microRNA:target interactions. We illustrate how this resource can be used to create microRNA-focused interaction networks with a biological context using the known biological role of microRNAs and the mRNAs they regulate, enabling discovery of associations between gene products, biological pathways and, ultimately, diseases. This data will be crucial in advancing the field of microRNA bioinformatics and will establish consistent data sets for reproducible functional analysis of microRNAs across all biological research areas.
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Affiliation(s)
- Rachael P Huntley
- Institute of Cardiovascular Science, University College London, London WC1E 6JF, United Kingdom
| | - Barbara Kramarz
- Institute of Cardiovascular Science, University College London, London WC1E 6JF, United Kingdom
| | - Tony Sawford
- European Bioinformatics Institute, European Molecular Biology Laboratory (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge CB10 1SD, United Kingdom
| | - Zara Umrao
- Institute of Cardiovascular Science, University College London, London WC1E 6JF, United Kingdom
| | - Anastasia Kalea
- Institute of Cardiovascular Science, University College London, London WC1E 6JF, United Kingdom
| | - Vanessa Acquaah
- Institute of Cardiovascular Science, University College London, London WC1E 6JF, United Kingdom
| | - Maria J Martin
- European Bioinformatics Institute, European Molecular Biology Laboratory (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge CB10 1SD, United Kingdom
| | - Manuel Mayr
- King's British Heart Foundation Centre, King's College London, London SE5 9NU, United Kingdom
| | - Ruth C Lovering
- Institute of Cardiovascular Science, University College London, London WC1E 6JF, United Kingdom
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29
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Wang F, Dai M, Chen H, Li Y, Zhang J, Zou Z, Yang H. Prognostic value of hsa-mir-299 and hsa-mir-7706 in hepatocellular carcinoma. Oncol Lett 2018; 16:815-820. [PMID: 29963149 PMCID: PMC6019942 DOI: 10.3892/ol.2018.8710] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 04/17/2018] [Indexed: 12/12/2022] Open
Abstract
This study aimed to investigate the expression of microRNA (miRNA) 299 and miRNA-7706 in patients with hepatocellular carcinoma (HCC), and to explore their effects on proliferation of SK-HEP-1 HCC cells. Expression of miRNA-299 and miRNA-7706 in tumor tissue (HCC group) and adjacent healthy tissue (>30 mm away from the tumor tissue) of 179 patients with HCC was determined by real-time polymerase chain reaction (qRT-PCR). miR-299 mimics and miR-7706 mimics were transfected into SK-HEP-1 HCC cells by RNA transfection. The proliferation and invasion of SK-HEP-1 cells were detected by CCK-8 kit and Transwell kit, respectively. Compared with adjacent tissues, expression levels of miRNA-299 and miRNA-7706 in HCC group were significantly downregulated. Analyses on the correlation between the expression of miRNA-299 and miRNA-7706 and clinical factors showed that expression levels of miRNA-299 and miRNA-7706 were significantly correlated with pathological stages and lymph node metastasis. ROC curve analysis showed that the areas under the curve were 0.837 and 0.845 for miRNA-299 and miRNA-7706 in the prediction of HCC, respectively. Survival analysis showed that the 5-year overall survival rate of patients with high expression levels of miRNA-299 and miRNA-7706 was significantly different from that of patients with low expression levels (P=0.016). Compared with cells transfected with scramble mimics, proliferation and invasion abilities of SK-HEP-1 cells transfected with miR-299 mimics and miRNA-7706 were significantly weakened. Results suggested that downregulation of miRNA-299 and miRNA-7706 can inhibit the proliferation of HCC cells and can be used as a new target for the treatment of HCC.
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Affiliation(s)
- Fenglin Wang
- Department of Traditional Chinese Medicine, The Third Affiliated Hospital of Sun Yet-sen University, Guangzhou, Guangdong 510000, P.R. China
| | - Min Dai
- Department of Traditional Chinese Medicine, The Third Affiliated Hospital of Sun Yet-sen University, Guangzhou, Guangdong 510000, P.R. China
| | - Hongjie Chen
- Department of Traditional Chinese Medicine, The Third Affiliated Hospital of Sun Yet-sen University, Guangzhou, Guangdong 510000, P.R. China
| | - Yue Li
- Department of Traditional Chinese Medicine, The Third Affiliated Hospital of Sun Yet-sen University, Guangzhou, Guangdong 510000, P.R. China
| | - Jiongshan Zhang
- Department of Traditional Chinese Medicine, The Third Affiliated Hospital of Sun Yet-sen University, Guangzhou, Guangdong 510000, P.R. China
| | - Zengcheng Zou
- Department of Traditional Chinese Medicine, The Third Affiliated Hospital of Sun Yet-sen University, Guangzhou, Guangdong 510000, P.R. China
| | - Hongzhi Yang
- Department of Traditional Chinese Medicine, The Third Affiliated Hospital of Sun Yet-sen University, Guangzhou, Guangdong 510000, P.R. China
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30
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Gutierrez-Camino A, Martin-Guerrero I, Dolzan V, Jazbec J, Carbone-Bañeres A, Garcia de Andoin N, Sastre A, Astigarraga I, Navajas A, Garcia-Orad A. Involvement of SNPs in miR-3117 and miR-3689d2 in childhood acute lymphoblastic leukemia risk. Oncotarget 2018; 9:22907-22914. [PMID: 29796161 PMCID: PMC5955428 DOI: 10.18632/oncotarget.25144] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 04/02/2018] [Indexed: 12/24/2022] Open
Abstract
Acute lymphoblastic leukemia (ALL) is the most common cancer in children. Numerous studies have shown that microRNAs (miRNAs) could play a role in this disease. Nowadays, more than 2500 miRNAs have been described, that regulate more than 50% of genes, including those involved in B-cell maturation, differentiation and proliferation. Genetic variants in miRNAs can alter their own levels or function, affecting their target gene expression, and then, may affect ALL risk. Therefore, the aim of this study was to determine the role of miRNA genetic variants in B-ALL susceptibility. We analyzed all variants in pre-miRNAs (MAF > 1%) in two independent cohorts from Spain and Slovenia and inferred their functional effect by in silico analysis. SNPs rs12402181 in miR-3117 and rs62571442 in miR-3689d2 were associated with ALL risk in both cohorts, possibly through their effect on MAPK signalling pathway. These SNPs could be novel markers for ALL susceptibility.
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Affiliation(s)
- Angela Gutierrez-Camino
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country, UPV/EHU, Leioa, Spain
| | - Idoia Martin-Guerrero
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country, UPV/EHU, Leioa, Spain
| | - Vita Dolzan
- Institute of Biochemistry, Faculty of Medicine, Ljubljana, Slovenia
| | - Janez Jazbec
- Department of Oncology and Haematology, University Children's Hospital, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Ana Carbone-Bañeres
- Department of Paediatrics, University Hospital Miguel Servet, Zaragoza, Spain
| | - Nagore Garcia de Andoin
- Department of Paediatrics, University Hospital Donostia, San Sebastian, Spain.,BioDonostia Health Research Institute, San Sebastian, Spain
| | - Ana Sastre
- Department of Oncohematology, University Hospital La Paz, Madrid, Spain
| | - Itziar Astigarraga
- Department of Paediatrics, University Hospital Cruces, Barakaldo, Spain.,BioCruces Health Research Institute, Barakaldo, Spain
| | | | - Africa Garcia-Orad
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country, UPV/EHU, Leioa, Spain.,BioCruces Health Research Institute, Barakaldo, Spain
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31
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Abstract
miRNA regulome is whole set of regulatory elements that regulate miRNA expression or are under control of miRNAs. Its understanding is vital for comprehension of miRNA functions. Classification of miRNA-related genetic variability is challenging because miRNA interact with different genomic elements and are studied at different omics levels. In the present study, miRNA-associated genetic variability is presented at three levels: miRNA genes and their upstream regulation, miRNA silencing machinery and miRNA targets. Several types of miRNA-associated genetic variations are known, including short and structural polymorphisms and epimutations. Differential expression can also affect miRNA regulome function. Classification of miRNA-associated genetic variability presents a baseline for complementing sequence variant nomenclature, planning of experiments, protocols for multi-omics data integration and development of biomarkers.
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Affiliation(s)
- Karin Hrovatin
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domžale, 1230, Slovenia
| | - Tanja Kunej
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domžale, 1230, Slovenia
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32
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Johansson K, Weidner J, Rådinger M. MicroRNAs in type 2 immunity. Cancer Lett 2018; 425:116-124. [PMID: 29604393 DOI: 10.1016/j.canlet.2018.03.036] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 03/22/2018] [Accepted: 03/23/2018] [Indexed: 12/15/2022]
Abstract
Type 2 immunity drives the pathology of allergic diseases and is necessary for expulsion of parasitic worms as well as having important implications in tumor progression. Over the last decade, a new research field has emerged describing a significant link between type 2 immunity and cancer development, called AllergoOncology. Thus, type 2 immune responses must be carefully regulated to mediate effective protection against damaging environmental factors, yet avoid excessive activation and immunopathology. Regulation of gene expression by microRNAs is required for normal behavior of most mammalian cells and has been studied extensively in the context of cancer. Although microRNA regulation of the immune system in cancer is well established and includes type 2 immune reactions in the tumor microenvironment, the involvement of microRNAs in these responses initiated by allergens, parasites or other environmental factors is just emerging. In this review, we focus on recent advances which increase the understanding of microRNA-mediated regulation of key mechanisms of type 2 immunity.
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Affiliation(s)
- Kristina Johansson
- Krefting Research Centre, Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Julie Weidner
- Krefting Research Centre, Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Madeleine Rådinger
- Krefting Research Centre, Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden.
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33
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Mir-pharmacogenetics of Vincristine and peripheral neurotoxicity in childhood B-cell acute lymphoblastic leukemia. THE PHARMACOGENOMICS JOURNAL 2017; 18:704-712. [PMID: 29282364 DOI: 10.1038/s41397-017-0003-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2017] [Revised: 07/11/2017] [Accepted: 09/18/2017] [Indexed: 12/17/2022]
Abstract
Vincristine (VCR), an important component of childhood acute lymphoblastic leukemia (ALL) therapy, can cause sensory and motor neurotoxicity. This neurotoxicity could lead to dose reduction or treatment discontinuation, which could in turn reduce survival. In this line, several studies associated peripheral neurotoxicity and polymorphisms in genes involved in pharmacokinetics (PK) and pharmacodynamics (PD) of VCR. Nowadays, it is well known that these genes are regulated by microRNAs (miRNAs) and SNPs in miRNAs could modify their levels or function. Therefore, the aim of this study was to determine whether SNPs in miRNAs could be associated with VCR-induced neurotoxicity. To achieve this aim, we analyzed all the SNPs in miRNAs (minor allele frequency (MAF) ≥ 0.01) which could regulate VCR-related genes in a large cohort of Spanish children with B-cell precursor ALL (B-ALL) homogeneously treated with LAL/SHOP protocols. We identified the A allele of rs12402181 in the seed region of miR-3117-3p, that could affect the binding with ABCC1 and RALBP1 gene, and C allele of rs7896283 in pre-mature sequence of miR-4481, which could be involved in peripheral nerve regeneration, significantly associated with VCR-induced neurotoxicity. These findings point out the possible involvement of two SNPs in miRNA associated with VCR-related neurotoxicity.
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34
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Kolshus E, Ryan KM, Blackshields G, Smyth P, Sheils O, McLoughlin DM. Peripheral blood microRNA and VEGFA mRNA changes following electroconvulsive therapy: implications for psychotic depression. Acta Psychiatr Scand 2017; 136:594-606. [PMID: 28975998 DOI: 10.1111/acps.12821] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/18/2017] [Indexed: 12/26/2022]
Abstract
OBJECTIVE MicroRNAs are short, non-coding molecules that regulate gene expression. Here, we investigate the role of microRNAs in depression and electroconvulsive therapy (ECT). METHODS We performed three studies: a deep sequencing discovery-phase study of miRNA changes in whole blood following ECT (n = 16), followed by a validation study in a separate cohort of patients pre-/post-ECT (n = 37) and matched healthy controls (n = 34). Changes in an experimentally validated gene target (VEGFA) were then analysed in patients pre-/post-ECT (n = 97) and in matched healthy controls (n = 53). RESULTS In the discovery-phase study, we found no statistically significant differences in miRNA expression from baseline to end of treatment in the group as a whole, but post hoc analysis indicated a difference in patients with psychotic depression (n = 3). In a follow-up validation study, patients with psychotic depression (n = 7) had elevated baseline levels of miR-126-3p (t = 3.015, P = 0.006) and miR-106a-5p (t = 2.598, P = 0.025) compared to healthy controls. Following ECT, these differences disappeared. Baseline VEGFA levels were significantly higher in depressed patients compared to healthy controls (F(1,144) = 27.688, P = <0.001). Following ECT, there was a significant change in VEGFA levels in the psychotic group only (t = 2.915, P = 0.010). CONCLUSION Molecular differences (miRNA and VEGFA) may exist between psychotic and non-psychotic depression treated with ECT.
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Affiliation(s)
- E Kolshus
- Trinity College Institute of Neuroscience, Trinity College Dublin, Dublin 2, Ireland.,Department of Psychiatry, Trinity College Dublin, St Patrick's University Hospital, Dublin 8, Ireland
| | - K M Ryan
- Trinity College Institute of Neuroscience, Trinity College Dublin, Dublin 2, Ireland.,Department of Psychiatry, Trinity College Dublin, St Patrick's University Hospital, Dublin 8, Ireland
| | - G Blackshields
- Department of Histopathology, Trinity College Dublin, St James's Hospital, Dublin 8, Ireland
| | - P Smyth
- Department of Histopathology, Trinity College Dublin, St James's Hospital, Dublin 8, Ireland
| | - O Sheils
- Department of Histopathology, Trinity College Dublin, St James's Hospital, Dublin 8, Ireland
| | - D M McLoughlin
- Trinity College Institute of Neuroscience, Trinity College Dublin, Dublin 2, Ireland.,Department of Psychiatry, Trinity College Dublin, St Patrick's University Hospital, Dublin 8, Ireland
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35
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Coding and small non-coding transcriptional landscape of tuberous sclerosis complex cortical tubers: implications for pathophysiology and treatment. Sci Rep 2017; 7:8089. [PMID: 28808237 PMCID: PMC5556011 DOI: 10.1038/s41598-017-06145-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 06/08/2017] [Indexed: 12/21/2022] Open
Abstract
Tuberous Sclerosis Complex (TSC) is a rare genetic disorder that results from a mutation in the TSC1 or TSC2 genes leading to constitutive activation of the mechanistic target of rapamycin complex 1 (mTORC1). TSC is associated with autism, intellectual disability and severe epilepsy. Cortical tubers are believed to represent the neuropathological substrates of these disabling manifestations in TSC. In the presented study we used high-throughput RNA sequencing in combination with systems-based computational approaches to investigate the complexity of the TSC molecular network. Overall we detected 438 differentially expressed genes and 991 differentially expressed small non-coding RNAs in cortical tubers compared to autopsy control brain tissue. We observed increased expression of genes associated with inflammatory, innate and adaptive immune responses. In contrast, we observed a down-regulation of genes associated with neurogenesis and glutamate receptor signaling. MicroRNAs represented the largest class of over-expressed small non-coding RNA species in tubers. In particular, our analysis revealed that the miR-34 family (including miR-34a, miR-34b and miR-34c) was significantly over-expressed. Functional studies demonstrated the ability of miR-34b to modulate neurite outgrowth in mouse primary hippocampal neuronal cultures. This study provides new insights into the TSC transcriptomic network along with the identification of potential new treatment targets.
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36
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Singh NK. miRNAs target databases: developmental methods and target identification techniques with functional annotations. Cell Mol Life Sci 2017; 74:2239-2261. [PMID: 28204845 PMCID: PMC11107700 DOI: 10.1007/s00018-017-2469-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 01/09/2017] [Accepted: 01/18/2017] [Indexed: 12/13/2022]
Abstract
PURPOSE microRNA (miRNA) regulates diverse biological mechanisms and metabolisms in plants and animals. Thus, the discoveries of miRNA has revolutionized the life sciences and medical research.The miRNA represses and cleaves the targeted mRNA by binding perfect or near perfect or imperfect complementary base pairs by RNA-induced silencing complex (RISC) formation during biogenesis process. One miRNA interacts with one or more mRNA genes and vice versa, hence takes part in causing various diseases. In this paper, the different microRNA target databases and their functional annotations developed by various researchers have been reviewed. The concurrent research review aims at comprehending the significance of miRNA and presenting the existing status of annotated miRNA target resources built by researchers henceforth discovering the knowledge for diagnosis and prognosis. METHODS AND RESULTS This review discusses the applications and developmental methodologies for constructing target database as well as the utility of user interface design. An integrated architecture is drawn and a graphically comparative study of present status of miRNA targets in diverse diseases and various biological processes is performed. These databases comprise of information such as miRNA target-associated disease, transcription factor binding sites (TFBSs) in miRNA genomic locations, polymorphism in miRNA target, A-to-I edited target, Gene Ontology (GO), genome annotations, KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways, target expression analysis, TF-miRNA and miRNA-mRNA interaction networks, drugs-targets interactions, etc. CONCLUSION miRNA target databases contain diverse experimentally and computationally predicted target through various algorithms. The comparison of various miRNA target database has been performed on various parameters. The computationally predicted target databases suffer from false positive information as there is no common theory for prediction of miRNA targets. The review conclusion emphasizes the need of more intelligent computational improvement for the miRNA target identification, their functional annotations and datasbase development.
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Affiliation(s)
- Nagendra Kumar Singh
- Department of Biological Science and Engineering, Maulana Azad National Institute of Technology, Bhopal, 462003, India.
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Piletič K, Kunej T. Minimal Standards for Reporting microRNA:Target Interactions. ACTA ACUST UNITED AC 2017; 21:197-206. [DOI: 10.1089/omi.2017.0023] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Klara Piletič
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domzale, Slovenia
| | - Tanja Kunej
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domzale, Slovenia
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Sherafatian M, Mowla SJ. The origins and evolutionary history of human non-coding RNA regulatory networks. J Bioinform Comput Biol 2017; 15:1750005. [PMID: 28274175 DOI: 10.1142/s0219720017500056] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The evolutionary history and origin of the regulatory function of animal non-coding RNAs are not well understood. Lack of conservation of long non-coding RNAs and small sizes of microRNAs has been major obstacles in their phylogenetic analysis. In this study, we tried to shed more light on the evolution of ncRNA regulatory networks by changing our phylogenetic strategy to focus on the evolutionary pattern of their protein coding targets. We used available target databases of miRNAs and lncRNAs to find their protein coding targets in human. We were able to recognize evolutionary hallmarks of ncRNA targets by phylostratigraphic analysis. We found the conventional 3'-UTR and lesser known 5'-UTR targets of miRNAs to be enriched at three consecutive phylostrata. Firstly, in eukaryata phylostratum corresponding to the emergence of miRNAs, our study revealed that miRNA targets function primarily in cell cycle processes. Moreover, the same overrepresentation of the targets observed in the next two consecutive phylostrata, opisthokonta and eumetazoa, corresponded to the expansion periods of miRNAs in animals evolution. Coding sequence targets of miRNAs showed a delayed rise at opisthokonta phylostratum, compared to the 3' and 5' UTR targets of miRNAs. LncRNA regulatory network was the latest to evolve at eumetazoa.
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Affiliation(s)
- Masih Sherafatian
- 1 Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Seyed Javad Mowla
- 1 Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
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MiR-pharmacogenetics of methotrexate in childhood B-cell acute lymphoblastic leukemia. Pharmacogenet Genomics 2016; 26:517-525. [DOI: 10.1097/fpc.0000000000000245] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Witwer KW, Halushka MK. Toward the promise of microRNAs - Enhancing reproducibility and rigor in microRNA research. RNA Biol 2016; 13:1103-1116. [PMID: 27645402 DOI: 10.1080/15476286.2016.1236172] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The fields of applied and translational microRNA research have exploded in recent years as microRNAs have been implicated across a spectrum of diseases. MicroRNA biomarkers, microRNA therapeutics, microRNA regulation of cellular physiology and even xenomiRs have stimulated great interest, which have brought many researchers into the field. Despite many successes in determining general mechanisms of microRNA generation and function, the application of microRNAs in translational areas has not had as much success. It has been a challenge to localize microRNAs to a given cell type within tissues and assay them reliably. At supraphysiologic levels, microRNAs may regulate hosts of genes that are not the physiologic biochemical targets. Thus the applied and translational microRNA literature is filled with pitfalls and claims that are neither scientifically rigorous nor reproducible. This review is focused on increasing awareness of the challenges of working with microRNAs in translational research and recommends better practices in this area of discovery.
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Affiliation(s)
- Kenneth W Witwer
- a Department of Molecular and Comparative Pathobiology , The Johns Hopkins University School of Medicine , Baltimore , MD , USA.,b Department of Neurology , The Johns Hopkins University School of Medicine , Baltimore , MD , USA
| | - Marc K Halushka
- c Department of Pathology , The Johns Hopkins University School of Medicine , Baltimore , MD , USA
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Fritz JV, Heintz-Buschart A, Ghosal A, Wampach L, Etheridge A, Galas D, Wilmes P. Sources and Functions of Extracellular Small RNAs in Human Circulation. Annu Rev Nutr 2016; 36:301-36. [PMID: 27215587 PMCID: PMC5479634 DOI: 10.1146/annurev-nutr-071715-050711] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Various biotypes of endogenous small RNAs (sRNAs) have been detected in human circulation, including microRNAs, transfer RNAs, ribosomal RNA, and yRNA fragments. These extracellular sRNAs (ex-sRNAs) are packaged and secreted by many different cell types. Ex-sRNAs exhibit differences in abundance in several disease states and have, therefore, been proposed for use as effective biomarkers. Furthermore, exosome-borne ex-sRNAs have been reported to elicit physiological responses in acceptor cells. Exogenous ex-sRNAs derived from diet (most prominently from plants) and microorganisms have also been reported in human blood. Essential issues that remain to be conclusively addressed concern the (a) presence and sources of exogenous ex-sRNAs in human bodily fluids, (b) detection and measurement of ex-sRNAs in human circulation, (c) selectivity of ex-sRNA export and import, (d) sensitivity and specificity of ex-sRNA delivery to cellular targets, and (e) cell-, tissue-, organ-, and organism-wide impacts of ex-sRNA-mediated cell-to-cell communication. We survey the present state of knowledge of most of these issues in this review.
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MESH Headings
- Animals
- Biological Transport
- Biomarkers/blood
- Cell Communication
- Diet
- Gastrointestinal Microbiome/immunology
- Gene Expression Regulation
- Host-Parasite Interactions
- Host-Pathogen Interactions
- Humans
- Immunity, Innate
- MicroRNAs/blood
- MicroRNAs/metabolism
- Models, Biological
- RNA, Bacterial/blood
- RNA, Bacterial/metabolism
- RNA, Plant/blood
- RNA, Plant/metabolism
- RNA, Ribosomal/blood
- RNA, Ribosomal/metabolism
- RNA, Small Interfering/blood
- RNA, Small Interfering/metabolism
- RNA, Small Untranslated/blood
- RNA, Small Untranslated/metabolism
- RNA, Transfer/blood
- RNA, Transfer/metabolism
- RNA, Viral/blood
- RNA, Viral/metabolism
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Affiliation(s)
- Joëlle V Fritz
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Campus Belval, L-4367 Belvaux, Luxembourg; ,
| | - Anna Heintz-Buschart
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Campus Belval, L-4367 Belvaux, Luxembourg; ,
| | - Anubrata Ghosal
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Linda Wampach
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Campus Belval, L-4367 Belvaux, Luxembourg; ,
| | - Alton Etheridge
- Pacific Northwest Diabetes Research Institute, Seattle, Washington 98122
| | - David Galas
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Campus Belval, L-4367 Belvaux, Luxembourg; ,
- Pacific Northwest Diabetes Research Institute, Seattle, Washington 98122
| | - Paul Wilmes
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Campus Belval, L-4367 Belvaux, Luxembourg; ,
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Understanding the CREB1-miRNA feedback loop in human malignancies. Tumour Biol 2016; 37:8487-502. [PMID: 27059735 DOI: 10.1007/s13277-016-5050-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 04/01/2016] [Indexed: 02/07/2023] Open
Abstract
cAMP response element binding protein 1 (CREB1, CREB) is a key transcription factor that mediates transcriptional responses to a variety of growth factors and stress signals. CREB1 has been shown to play a critical role in development and progression of tumors. MicroRNAs (miRNAs) are a class of non-coding RNAs. They post-transcriptionally regulate gene expression through pairing with the 3'-UTR of their target mRNAs and thus regulate initiation and progression of various types of human cancers. Recent studies have demonstrated that a number of miRNAs can be transcriptionally regulated by CREB1. Interestingly, CREB1 expression can also be modulated by miRNAs, thus forming a feedback loop. This review outlines the functional roles of CREB1, miRNA, and their interactions in human malignancies. This will help to define a relationship between CREB1 and miRNA in human cancer and develop novel therapeutic strategies.
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Krishna CV, Singh J, Thangavel C, Rattan S. Role of microRNAs in gastrointestinal smooth muscle fibrosis and dysfunction: novel molecular perspectives on the pathophysiology and therapeutic targeting. Am J Physiol Gastrointest Liver Physiol 2016; 310:G449-59. [PMID: 26822916 PMCID: PMC4824177 DOI: 10.1152/ajpgi.00445.2015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 01/20/2016] [Indexed: 01/31/2023]
Abstract
MicroRNAs (miRNAs) belong to a group of short noncoding RNA molecules with important roles in cellular biology. miRNAs regulate gene expression by repressing translation or degrading the target mRNA. Recently, a growing body of evidence suggests that miRNAs are implicated in many diseases and could be potential biomarkers. Fibrosis and/smooth muscle (SM) dysfunction contributes to the morbidity and mortality associated with several diseases of the gastrointestinal tract (GIT). Currently available therapeutic modalities are unsuccessful in efficiently blocking or reversing fibrosis and/or SM dysfunction. Recent understanding of the role of miRNAs in signaling pathway of fibrogenesis and SM phenotype switch has provided a new insight into translational research. However, much is still unknown about the molecular targets and therapeutic potential of miRNAs in the GIT. This review discusses miRNA biology, pathophysiology of fibrosis, and aging- associated SM dysfunction in relation to the deregulation of miRNAs in the GIT. We also highlight the role of selected miRNAs associated with fibrosis and SM dysfunction-related diseases of the GIT.
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Affiliation(s)
| | - Jagmohan Singh
- 2Department of Medicine, Division of Gastroenterology & Hepatology, Sidney Kimmel Medical College of Thomas Jefferson University, Philadelphia, Pennsylvania; and
| | - Chellappagounder Thangavel
- 3Department of Radiation Oncology, Sidney Kimmel Cancer Center (TC), Sidney Kimmel Medical College of Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Satish Rattan
- 2Department of Medicine, Division of Gastroenterology & Hepatology, Sidney Kimmel Medical College of Thomas Jefferson University, Philadelphia, Pennsylvania; and
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