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Kolenda T, Śmiełowska M, Lipowicz J, Ostapowicz J, Pacześna P, Rosochowicz MA, Poter P, Kozłowska-Masłoń J, Guglas K, Dudek K, Grzejda N, Regulska K, Florczak A, Kazimierczak U, Lamperska K, Teresiak A. The RNA world: from experimental laboratory to "in silico" approach. Part 1: User friendly RNA expression databases portals. Rep Pract Oncol Radiother 2024; 29:245-257. [PMID: 39143966 PMCID: PMC11321768 DOI: 10.5603/rpor.99675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 02/15/2024] [Indexed: 08/16/2024] Open
Abstract
Cellular information about "life instruction" is stored, transferred, and modified using different types of RNA molecules. During the last decades, a growing number of RNA data has been generated thanks to the development of microarray chips and next-generation sequencing (NGS) methods. Improvement of bioinformatics contributed to the discovery of many types of new non-coding RNAs (ncRNAs), mostly with regulatory functions that supplemented the knowledge about the world of RNA. All of it, as well as the Human Genome Project (HGP) and the Cancer Genome Atlas (TCGA) project, has resulted in the formation of data storage and analysis portals which are widely used in cancer research and moved science from in vitro to in silico research. In this review we presented and discussed the data storage and analysis portals used by us, such as cBioPortal, UALCAN, ENCORI, and others. During the revision of these sites, we paid attention to data integration, simplicity of analysis, and results visualization, which are important for users without bioinformatic or statistical skills. In our opinion, the RNA analysis online tools will rapidly develop during the next decade and it seems to be a way for personalization of cancer treatment.
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Affiliation(s)
- Tomasz Kolenda
- Laboratory of Cancer Genetics, Greater Poland Cancer Center, Poznan, Poland
- Greater Poland Cancer Center, Research and Implementation Unit, Poznan, Poland
| | - Marianna Śmiełowska
- Department of Genome Engineering, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Julia Lipowicz
- Department of Histology and Embryology, Poznan University of Medical Sciences, Poznan, Poland
| | - Julia Ostapowicz
- Department of Electroradiology, Poznan University of Medical Sciences, Poznan, Poland
- Radiobiology Laboratory, Department of Medical Physics, Greater Poland Cancer Centre, Poznan, Poland
| | - Paula Pacześna
- Greater Poland Cancer Center, Research and Implementation Unit, Poznan, Poland
| | - Monika Anna Rosochowicz
- Radiobiology Laboratory, Department of Medical Physics, Greater Poland Cancer Centre, Poznan, Poland
- Department of Orthopaedic and Traumatology, W. Dega University Hospital, University of Medical Sciences, Poznań, Poland
| | - Paulina Poter
- Department of Tumor Pathology and Prophylactics, Poznan University of Medical Sciences, Poznan, Poland
- Department of Tumor Pathology, Greater Poland Cancer Center, Poznan, Poland
| | - Joanna Kozłowska-Masłoń
- Laboratory of Cancer Genetics, Greater Poland Cancer Center, Poznan, Poland
- Greater Poland Cancer Center, Research and Implementation Unit, Poznan, Poland
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
| | - Kacper Guglas
- Laboratory of Cancer Genetics, Greater Poland Cancer Center, Poznan, Poland
- Greater Poland Cancer Center, Research and Implementation Unit, Poznan, Poland
- Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warsaw, Poland
| | - Klaudia Dudek
- Laboratory of Cancer Genetics, Greater Poland Cancer Center, Poznan, Poland
- Greater Poland Cancer Center, Research and Implementation Unit, Poznan, Poland
- Poznan University of Life Sciences, Poznan, Poland
| | - Nina Grzejda
- Laboratory of Cancer Genetics, Greater Poland Cancer Center, Poznan, Poland
- Greater Poland Cancer Center, Research and Implementation Unit, Poznan, Poland
- Adam Mickiewicz University in Poznan, Poznan, Poland
| | - Katarzyna Regulska
- Greater Poland Cancer Center, Research and Implementation Unit, Poznan, Poland
- Pharmacy, Greater Poland Cancer Centre, Poznan, Poland
- Department of Clinical Pharmacy and Biopharmacy, Poznan University of Medical Sciences, Poznan, Poland, Collegium Pharmaceuticum, Poznan, Poland
| | - Anna Florczak
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Center, Poznan, Poland
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, Poznan, Poland
| | - Urszula Kazimierczak
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Center, Poznan, Poland
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, Poznan, Poland
| | - Katarzyna Lamperska
- Laboratory of Cancer Genetics, Greater Poland Cancer Center, Poznan, Poland
- Greater Poland Cancer Center, Research and Implementation Unit, Poznan, Poland
| | - Anna Teresiak
- Laboratory of Cancer Genetics, Greater Poland Cancer Center, Poznan, Poland
- Greater Poland Cancer Center, Research and Implementation Unit, Poznan, Poland
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Hu Z, Liu C, Mei Z, Wang X, Ma Y, Liu X, Xu H, Fang G, Liu X, Li R, Wang J, Shi Z, Han C. A-to-I edited miR-154-p13-5p inhibited cell proliferation and migration and induced apoptosis by targeting LIX1L in the bladder cancer. J Cancer 2024; 15:3708-3723. [PMID: 38911375 PMCID: PMC11190776 DOI: 10.7150/jca.93388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 02/14/2024] [Indexed: 06/25/2024] Open
Abstract
With the advancement of RNA sequencing technology, there has been a drive to uncover and elucidate the pivotal role of A-to-I RNA editing events in tumorigenesis. However, A-to-I miRNA editing events have been clearly identified in bladder cancer, the molecular mechanisms underlying their role in bladder cancer remain unclear. In our investigation, we observed a notable under-expression of edited miR-154-p13-5p in bladder cancer (BC) tissues, in contrast to normal counterparts. Remarkably, heightened expression levels of edited miR-154-p13-5p correlated with improved survival outcomes. To assess the impact of modified miR-154-p13-5p, we conducted a string of cell phenotype assays through transfection of the corresponding miRNAs or siRNAs. The results unequivocally demonstrate that edited miR-154-p13-5p exerts a substantial inhibitory influence on proliferation, migration, and induces apoptosis by specifically targeting LIX1L in bladder cancer. Moreover, we observed that the editing of miR-154-p13-5p or LIX1L-siRNAs inhibits the expression of LIX1L, thereby suppressing EMT-related proteins and cell cycle protein CDK2. Simultaneously, an upregulation in the expression levels of Caspase-3 and Cleaved Caspase-3 were also detected. Our research findings suggest that the upregulation of edited miR-154-p13-5p could potentially enhance the prognosis of bladder cancer, thereby presenting molecular biology-based therapeutic strategies.
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Affiliation(s)
- Zhengxiang Hu
- Postgraduate Training Base of Jinzhou Medical University in The Central Hospital of Xuzhou, Jinzhou, Liaoning 121013, China
- Department of Urology, Xuzhou Central Hospital, Xuzhou, Jiangsu 221006, China
| | - Chunhui Liu
- Xuzhou Clinical College of Xuzhou Medical University, Xuzhou 221004, China
| | - Zujun Mei
- Department of Emergency, Jingzhou Central Hospital, Jingzhou, Hubei 434000, China
| | - Xinlei Wang
- Xuzhou Clinical College of Xuzhou Medical University, Xuzhou 221004, China
| | - Yuyang Ma
- Graduate School of Bengbu Medical College, Bengbu, Anhui 233060, China
| | - Xing Liu
- Xuzhou Clinical College of Xuzhou Medical University, Xuzhou 221004, China
| | - Hao Xu
- Graduate School of Bengbu Medical College, Bengbu, Anhui 233060, China
| | - Gaochuan Fang
- School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu 221116, China
| | - Xinyu Liu
- Xuzhou Clinical College of Xuzhou Medical University, Xuzhou 221004, China
| | - Rui Li
- Central Laboratory, Xuzhou Central Hospital, Jiangsu 221006, China
| | - Jie Wang
- Central Laboratory, Xuzhou Central Hospital, Jiangsu 221006, China
| | - Zhenduo Shi
- Department of Urology, Xuzhou Central Hospital, Xuzhou, Jiangsu 221006, China
| | - Conghui Han
- Department of Urology, Xuzhou Central Hospital, Xuzhou, Jiangsu 221006, China
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3
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Hiers NM, Li T, Traugot CM, Xie M. Target-directed microRNA degradation: Mechanisms, significance, and functional implications. WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1832. [PMID: 38448799 PMCID: PMC11098282 DOI: 10.1002/wrna.1832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 01/11/2024] [Accepted: 01/12/2024] [Indexed: 03/08/2024]
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that play a fundamental role in enabling miRNA-mediated target repression, a post-transcriptional gene regulatory mechanism preserved across metazoans. Loss of certain animal miRNA genes can lead to developmental abnormalities, disease, and various degrees of embryonic lethality. These short RNAs normally guide Argonaute (AGO) proteins to target RNAs, which are in turn translationally repressed and destabilized, silencing the target to fine-tune gene expression and maintain cellular homeostasis. Delineating miRNA-mediated target decay has been thoroughly examined in thousands of studies, yet despite these exhaustive studies, comparatively less is known about how and why miRNAs are directed for decay. Several key observations over the years have noted instances of rapid miRNA turnover, suggesting endogenous means for animals to induce miRNA degradation. Recently, it was revealed that certain targets, so-called target-directed miRNA degradation (TDMD) triggers, can "trigger" miRNA decay through inducing proteolysis of AGO and thereby the bound miRNA. This process is mediated in animals via the ZSWIM8 ubiquitin ligase complex, which is recruited to AGO during engagement with triggers. Since its discovery, several studies have identified that ZSWIM8 and TDMD are indispensable for proper animal development. Given the rapid expansion of this field of study, here, we summarize the key findings that have led to and followed the discovery of ZSWIM8-dependent TDMD. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms RNA in Disease and Development > RNA in Development.
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Affiliation(s)
- Nicholas M Hiers
- Department of Biochemistry and Molecular Biology, College of Medicine, UF Health Cancer Center, UF Genetics Institute, University of Florida, Gainesville, Florida, USA
| | - Tianqi Li
- Department of Biochemistry and Molecular Biology, College of Medicine, UF Health Cancer Center, UF Genetics Institute, University of Florida, Gainesville, Florida, USA
| | - Conner M Traugot
- Department of Biochemistry and Molecular Biology, College of Medicine, UF Health Cancer Center, UF Genetics Institute, University of Florida, Gainesville, Florida, USA
| | - Mingyi Xie
- Department of Biochemistry and Molecular Biology, College of Medicine, UF Health Cancer Center, UF Genetics Institute, University of Florida, Gainesville, Florida, USA
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Jones BT, Han J, Zhang H, Hammer RE, Evers BM, Rakheja D, Acharya A, Mendell JT. Target-directed microRNA degradation regulates developmental microRNA expression and embryonic growth in mammals. Genes Dev 2023; 37:661-674. [PMID: 37553261 PMCID: PMC10499020 DOI: 10.1101/gad.350906.123] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 08/01/2023] [Indexed: 08/10/2023]
Abstract
MicroRNAs (miRNAs) are post-transcriptional regulators of gene expression that play critical roles in development and disease. Target-directed miRNA degradation (TDMD), a pathway in which miRNAs that bind to specialized targets with extensive complementarity are rapidly decayed, has emerged as a potent mechanism of controlling miRNA levels. Nevertheless, the biological role and scope of miRNA regulation by TDMD in mammals remains poorly understood. To address these questions, we generated mice with constitutive or conditional deletion of Zswim8, which encodes an essential TDMD factor. Loss of Zswim8 resulted in developmental defects in the heart and lungs, growth restriction, and perinatal lethality. Small RNA sequencing of embryonic tissues revealed widespread miRNA regulation by TDMD and greatly expanded the known catalog of miRNAs regulated by this pathway. These experiments also uncovered novel features of TDMD-regulated miRNAs, including their enrichment in cotranscribed clusters and examples in which TDMD underlies "arm switching," a phenomenon wherein the dominant strand of a miRNA precursor changes in different tissues or conditions. Importantly, deletion of two miRNAs, miR-322 and miR-503, rescued growth of Zswim8-null embryos, directly implicating the TDMD pathway as a regulator of mammalian body size. These data illuminate the broad landscape and developmental role of TDMD in mammals.
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Affiliation(s)
- Benjamin T Jones
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Jaeil Han
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - He Zhang
- Quantitative Biomedical Research Center, Peter O'Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Robert E Hammer
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Bret M Evers
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
- Department of Ophthalmology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Dinesh Rakheja
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Asha Acharya
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Joshua T Mendell
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA;
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
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5
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Jones BT, Han J, Zhang H, Hammer RE, Evers BM, Rakheja D, Acharya A, Mendell JT. Target-directed microRNA degradation regulates developmental microRNA expression and embryonic growth in mammals. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.26.546601. [PMID: 37425885 PMCID: PMC10327180 DOI: 10.1101/2023.06.26.546601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
MicroRNAs (miRNAs) are post-transcriptional regulators of gene expression that play critical roles in development and disease. Target-directed miRNA degradation (TDMD), a pathway in which miRNAs that bind to specialized targets with extensive complementarity are rapidly decayed, has emerged as a potent mechanism of controlling miRNA levels. Nevertheless, the biological role and scope of miRNA regulation by TDMD in mammals remains poorly understood. To address these questions, we generated mice with constitutive or conditional deletion of Zswim8 , which encodes an essential TDMD factor. Loss of Zswim8 resulted in developmental defects in heart and lung, growth restriction, and perinatal lethality. Small RNA sequencing of embryonic tissues revealed widespread miRNA regulation by TDMD and greatly expanded the known catalog of miRNAs regulated by this pathway. These experiments also uncovered novel features of TDMD-regulated miRNAs, including their enrichment in co-transcribed clusters and examples in which TDMD underlies 'arm switching', a phenomenon wherein the dominant strand of a miRNA precursor changes in different tissues or conditions. Importantly, deletion of two miRNAs, miR-322 and miR-503, rescued growth of Zswim8 null embryos, directly implicating the TDMD pathway as a regulator of mammalian body size. These data illuminate the broad landscape and developmental role of TDMD in mammals.
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Affiliation(s)
- Benjamin T Jones
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jaeil Han
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - He Zhang
- Quantitative Biomedical Research Center, Peter O’Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Robert E. Hammer
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Bret M. Evers
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Ophthalmology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Dinesh Rakheja
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Asha Acharya
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Joshua T. Mendell
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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Loganathan T, Doss C GP. Non-coding RNAs in human health and disease: potential function as biomarkers and therapeutic targets. Funct Integr Genomics 2023; 23:33. [PMID: 36625940 PMCID: PMC9838419 DOI: 10.1007/s10142-022-00947-4] [Citation(s) in RCA: 50] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 12/14/2022] [Accepted: 12/15/2022] [Indexed: 01/11/2023]
Abstract
Human diseases have been a critical threat from the beginning of human history. Knowing the origin, course of action and treatment of any disease state is essential. A microscopic approach to the molecular field is a more coherent and accurate way to explore the mechanism, progression, and therapy with the introduction and evolution of technology than a macroscopic approach. Non-coding RNAs (ncRNAs) play increasingly important roles in detecting, developing, and treating all abnormalities related to physiology, pathology, genetics, epigenetics, cancer, and developmental diseases. Noncoding RNAs are becoming increasingly crucial as powerful, multipurpose regulators of all biological processes. Parallel to this, a rising amount of scientific information has revealed links between abnormal noncoding RNA expression and human disorders. Numerous non-coding transcripts with unknown functions have been found in addition to advancements in RNA-sequencing methods. Non-coding linear RNAs come in a variety of forms, including circular RNAs with a continuous closed loop (circRNA), long non-coding RNAs (lncRNA), and microRNAs (miRNA). This comprises specific information on their biogenesis, mode of action, physiological function, and significance concerning disease (such as cancer or cardiovascular diseases and others). This study review focuses on non-coding RNA as specific biomarkers and novel therapeutic targets.
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Affiliation(s)
- Tamizhini Loganathan
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore- 632014, Tamil Nadu, India
| | - George Priya Doss C
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore- 632014, Tamil Nadu, India.
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Dindhoria K, Monga I, Thind AS. Computational approaches and challenges for identification and annotation of non-coding RNAs using RNA-Seq. Funct Integr Genomics 2022; 22:1105-1112. [DOI: 10.1007/s10142-022-00915-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 11/04/2022] [Accepted: 11/04/2022] [Indexed: 11/22/2022]
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Chen J, Lin J, Hu Y, Ye M, Yao L, Wu L, Zhang W, Wang M, Deng T, Guo F, Huang Y, Zhu B, Wang D. RNADisease v4.0: an updated resource of RNA-associated diseases, providing RNA-disease analysis, enrichment and prediction. Nucleic Acids Res 2022; 51:D1397-D1404. [PMID: 36134718 PMCID: PMC9825423 DOI: 10.1093/nar/gkac814] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 09/06/2022] [Accepted: 09/09/2022] [Indexed: 02/06/2023] Open
Abstract
Numerous studies have shown that RNA plays an important role in the occurrence and development of diseases, and RNA-disease associations are not limited to noncoding RNAs in mammals but also exist for protein-coding RNAs. Furthermore, RNA-associated diseases are found across species including plants and nonmammals. To better analyze diseases at the RNA level and facilitate researchers in exploring the pathogenic mechanism of diseases, we decided to update and change MNDR v3.0 to RNADisease v4.0, a repository for RNA-disease association (http://www.rnadisease.org/ or http://www.rna-society.org/mndr/). Compared to the previous version, new features include: (i) expanded data sources and categories of species, RNA types, and diseases; (ii) the addition of a comprehensive analysis of RNAs from thousands of high-throughput sequencing data of cancer samples and normal samples; (iii) the addition of an RNA-disease enrichment tool and (iv) the addition of four RNA-disease prediction tools. In summary, RNADisease v4.0 provides a comprehensive and concise data resource of RNA-disease associations which contains a total of 3 428 058 RNA-disease entries covering 18 RNA types, 117 species and 4090 diseases to meet the needs of biological research and lay the foundation for future therapeutic applications of diseases.
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Affiliation(s)
| | | | | | | | | | - Le Wu
- Department of Bioinformatics, Guangdong Province Key Laboratory of Molecular Tumor Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Wenhai Zhang
- Department of Bioinformatics, Guangdong Province Key Laboratory of Molecular Tumor Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Meiyi Wang
- Department of Bioinformatics, Guangdong Province Key Laboratory of Molecular Tumor Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Tingting Deng
- Department of Bioinformatics, Guangdong Province Key Laboratory of Molecular Tumor Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Feng Guo
- School of Medicine, Tsinghua University, Beijing 100084, China
| | - Yan Huang
- Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Bofeng Zhu
- Correspondence may also be addressed to Bofeng Zhu. Tel: +86 20 61648787; Fax: +86 20 61648787;
| | - Dong Wang
- To whom correspondence should be addressed. Tel: +86 20 61648279; Fax: +86 20 61648279;
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Yao Y, Bade R, Li G, Zhang A, Zhao H, Fan L, Zhu R, Yuan J. Global-Scale Profiling of Differential Expressed Lysine-Lactylated Proteins in the Cerebral Endothelium of Cerebral Ischemia-Reperfusion Injury Rats. Cell Mol Neurobiol 2022:10.1007/s10571-022-01277-6. [PMID: 36030297 DOI: 10.1007/s10571-022-01277-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 08/22/2022] [Indexed: 11/27/2022]
Abstract
Acute ischemic stroke (AIS) is a serious threat to human health. Following AIS, cerebral ischemia-reperfusion injury (CIRI) must be treated to improve prognosis. By combining 4D label-free quantitative proteomics with lactylation modification-specific proteomics analysis, we assessed lysine lactylation (Kla) in cortical proteins of a CIRI rat model. We identified a total of 1003 lactylation sites on 469 proteins in this study, gathering quantitative information (PXD034232) on 660 of 310 proteins, which were further classified by cell composition, molecular function, and biological processes. In addition, we analyzed the metabolic pathways, domains, and protein-protein interaction networks. Lastly, we evaluated differentially expressed lysine lactylation sites, determining 49 upregulated proteins and 99 downregulated proteins with 54 upregulated sites and 54 downregulated sites in the experimental group in comparison with the healthy control group. Moreover, we identified the Kla of Scl25a4 and Slc25a5 in the Ca2+ signaling pathway, but the Kla of Vdac1 was eliminated, as confirmed in vivo. Overall, these results provide new insights into lactylation involved in the underlying mechanism of CIRI because this post-translational modification affects the mitochondrial apoptosis pathway and mediates neuronal death. Therefore, this study may enable us to develop new molecules with therapeutic properties, which have both theoretical significance and broad clinical application prospects. A new model of cerebral ischemia-reperfusion injury (CIRI) induced by lactylation through the regulation of key proteins of the Ca2+ signaling pathway.
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Affiliation(s)
- Yuan Yao
- Department of Neurology, Inner Mongolia People's Hospital, Hohhot, 010017, China.
- Inner Mongolia University People's Hospital, Hohhot, 010017, China.
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China.
| | - Rengui Bade
- Inner Mongolia Key Laboratory of Hypoxic Translational Medicine, Baotou Medical College, Baotou, 014060, China
- Medical College of Neuroscience Institute, School of Medical Technology and Anesthesiology, Baotou Medical College, Baotou, 014060, China
| | - Guotao Li
- Inner Mongolia University People's Hospital, Hohhot, 010017, China
| | - Aoqi Zhang
- Inner Mongolia University People's Hospital, Hohhot, 010017, China
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Haile Zhao
- Inner Mongolia University People's Hospital, Hohhot, 010017, China
- Inner Mongolia Key Laboratory of Hypoxic Translational Medicine, Baotou Medical College, Baotou, 014060, China
| | - Lifei Fan
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Runxiu Zhu
- Department of Neurology, Inner Mongolia People's Hospital, Hohhot, 010017, China.
- Inner Mongolia University People's Hospital, Hohhot, 010017, China.
| | - Jun Yuan
- Department of Neurology, Inner Mongolia People's Hospital, Hohhot, 010017, China.
- Inner Mongolia University People's Hospital, Hohhot, 010017, China.
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Xie GY, Liu CJ, Guo AY. EVAtool: an optimized reads assignment tool for small ncRNA quantification and its application in extracellular vesicle datasets. Brief Bioinform 2022; 23:6651306. [PMID: 35901462 DOI: 10.1093/bib/bbac310] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 07/05/2022] [Accepted: 07/08/2022] [Indexed: 11/13/2022] Open
Abstract
Extracellular vesicles (EVs) carrying various small non-coding RNAs (sncRNAs) play a vital roles in cell communication and diseases. Correct quantification of multiple sncRNA biotypes simultaneously in EVs is a challenge due to the short reads (<30 bp) could be mapped to multiple sncRNA types. To address this question, we developed an optimized reads assignment algorithm (ORAA) to dynamically map multi-mapping reads to the sncRNA type with a higher proportion. We integrated ORAA with reads processing steps into EVAtool Python-package (http://bioinfo.life.hust.edu.cn/EVAtool) to quantify sncRNAs, especially for sncRNA-seq from EV samples. EVAtool allows users to specify interested sncRNA types in advanced mode or use default seven sncRNAs (microRNA, small nucleolar RNA, PIWI-interacting RNAs, small nuclear RNA, ribosomal RNA, transfer RNA and Y RNA). To prove the utilities of EVAtool, we quantified the sncRNA expression profiles for 200 samples from cognitive decline and multiple sclerosis. We found that more than 20% of short reads on average were mapped to multiple sncRNA biotypes in multiple sclerosis. In cognitive decline, the proportion of Y RNA is significantly higher than other sncRNA types. EVAtool is a flexible and extensible tool that would benefit to mine potential biomarkers and functional molecules in EVs.
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Affiliation(s)
- Gui-Yan Xie
- Center for Artificial Intelligence Biology, Hubei Bioinformatics & Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology; Wuhan, 430074, China
| | - Chun-Jie Liu
- Center for Artificial Intelligence Biology, Hubei Bioinformatics & Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology; Wuhan, 430074, China
| | - An-Yuan Guo
- Center for Artificial Intelligence Biology, Hubei Bioinformatics & Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology; Wuhan, 430074, China.,Shenzhen Huazhong University of Science and Technology Research Institute, Shenzhen, China
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11
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Lin YZ, Liu SH, Wu WR, Shen YC, Wang YL, Liao CC, Lin PL, Chang H, Liu LC, Cheng WC, Wang SC. miR-4759 suppresses breast cancer through immune checkpoint blockade. Comput Struct Biotechnol J 2022; 20:241-251. [PMID: 35024096 PMCID: PMC8718579 DOI: 10.1016/j.csbj.2021.12.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Revised: 12/02/2021] [Accepted: 12/12/2021] [Indexed: 12/24/2022] Open
Abstract
Programmed cell death protein 1 (PD-1)/ programmed cell death protein ligand 1 (PD-L1) is the key immune checkpoint governing evasion of advanced cancer from immune surveillance. Immuno-oncology (IO) therapy targeting PD-1/PD-L1 with traditional antibodies is a promising approach to multiple cancer types but to which the response rate remains moderate in breast cancer, calling for the need of exploring alternative IO targeting approaches. A miRNA-gene network was integrated by a bioinformatics approach and corroborated with The Cancer Genome Atlas (TCGA) to screen miRNAs regulating immune checkpoint genes and associated with patient survival. Here we show the identification of a novel microRNA miR-4759 which repressed RNA expression of the PD-L1 gene. miR-4759 targeted the PD-L1 gene through two binding motifs in the 3′ untranslated region (3′-UTR) of PD-L1. Reconstitution of miR-4759 inhibited PD-L1 expression and sensitized breast cancer cells to killing by immune cells. Treatment with miR-4759 suppressed tumor growth of orthotopic xenografts and promoted tumor infiltration of CD8+ T lymphocytes in immunocompetent mice. In contrast, miR-4759 had no effect to tumor growth in immunodeficient mice. In patients with breast cancer, expression of miR-4759 was preferentially downregulated in tumors compared to normal tissues and was associated with poor overall survival. Together, our results demonstrated miR-4759 as a novel non-coding RNA which promotes anti-tumor immunity of breast cancer.
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Affiliation(s)
- You-Zhe Lin
- Graduate Institute of Biomedical Sciences, College of Medicine, China Medical University, Taichung 40402, Taiwan
| | - Shu-Hsuan Liu
- Research Center for Cancer Biology, China Medical University, Taichung 40402, Taiwan
| | - Wan-Rong Wu
- Graduate Institute of Biomedical Sciences, College of Medicine, China Medical University, Taichung 40402, Taiwan
| | - Yi-Chun Shen
- Graduate Institute of Biomedical Sciences, College of Medicine, China Medical University, Taichung 40402, Taiwan
| | - Yuan-Liang Wang
- Graduate Institute of Biomedical Sciences, College of Medicine, China Medical University, Taichung 40402, Taiwan.,Center for Molecular Medicine, China Medical University Hospital, Taichung 40447, Taiwan
| | - Chien-Ching Liao
- Graduate Institute of Biomedical Sciences, College of Medicine, China Medical University, Taichung 40402, Taiwan
| | - Pei-Le Lin
- Graduate Institute of Biomedical Sciences, College of Medicine, China Medical University, Taichung 40402, Taiwan
| | - Han Chang
- Division of Molecular Pathology, Department of Pathology, China Medical University Hospital, Taichung 40447, Taiwan
| | - Liang-Chih Liu
- Department of Surgery, China Medical University Hospital, Taichung 40447, Taiwan
| | - Wei-Chung Cheng
- Graduate Institute of Biomedical Sciences, College of Medicine, China Medical University, Taichung 40402, Taiwan.,Research Center for Cancer Biology, China Medical University, Taichung 40402, Taiwan.,Cancer Biology and Drug Discovery Ph.D. Program, China Medical University, Taichung 40402, Taiwan
| | - Shao-Chun Wang
- Graduate Institute of Biomedical Sciences, College of Medicine, China Medical University, Taichung 40402, Taiwan.,Center for Molecular Medicine, China Medical University Hospital, Taichung 40447, Taiwan.,Center for Molecular Medicine, China Medical University Hospital, Taichung 40447, Taiwan.,Department of Cancer Biology, University of Cincinnati, Cincinnati, OH 45267, USA.,Cancer Biology and Drug Discovery Ph.D. Program, China Medical University, Taichung 40402, Taiwan.,Department of Biotechnology, Asia University, Taichung 41354, Taiwan
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12
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Using bioinformatics approaches to identify survival-related oncomiRs as potential targets of miRNA-based treatments for lung adenocarcinoma. Comput Struct Biotechnol J 2022; 20:4626-4635. [PMID: 36090818 PMCID: PMC9449502 DOI: 10.1016/j.csbj.2022.08.042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 08/17/2022] [Accepted: 08/18/2022] [Indexed: 11/23/2022] Open
Abstract
Lung cancer is a major cause of cancer-associated deaths worldwide, and lung adenocarcinoma (LUAD) is the most common lung cancer subtype. Micro RNAs (miRNAs) regulate the pattern of gene expression in multiple cancer types and have been explored as potential drug development targets. To develop an oncomiR-based panel, we identified miRNA candidates that show differential expression patterns and are relevant to the worse 5-year overall survival outcomes in LUAD patient samples. We further evaluated various combinations of miRNA candidates for association with 5-year overall survival and identified a four-miRNA panel: miR-9-5p, miR-1246, miR-31-3p, and miR-3136-5p. The combination of these four miRNAs outperformed any single miRNA for predicting 5-year overall survival (hazard ratio [HR]: 3.47, log-rank p-value = 0.000271). Experiments were performed on lung cancer cell lines and animal models to validate the effects of these miRNAs. The results showed that singly transfected antagomiRs largely inhibited cell growth, migration, and invasion, and the combination of all four antagomiRs considerably reduced cell numbers, which is twice as effective as any single miRNA-targeted transfected. The in vivo studies revealed that antagomiR-mediated knockdown of all four miRNAs significantly reduced tumor growth and metastatic ability of lung cancer cells compared to the negative control group. The success of these in vivo and in vitro experiments suggested that these four identified oncomiRs may have therapeutic potential.
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13
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Yang CY, Chen YH, Liu PJ, Hu WC, Lu KC, Tsai KW. The emerging role of miRNAs in the pathogenesis of COVID-19: Protective effects of nutraceutical polyphenolic compounds against SARS-CoV-2 infection. Int J Med Sci 2022; 19:1340-1356. [PMID: 35928726 PMCID: PMC9346380 DOI: 10.7150/ijms.76168] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 07/08/2022] [Indexed: 11/05/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection can cause immunosuppression and cytokine storm, leading to lung damage and death. The clinical efficacy of anti-SARS-CoV-2 drugs in preventing viral entry into host cells and suppressing viral replication remains inadequate. MicroRNAs (miRNAs) are crucial to the immune response to and pathogenesis of coronaviruses, such as SARS-CoV-2. However, the specific roles of miRNAs in the life cycle of SARS-CoV-2 remain unclear. miRNAs can participate in SARS-CoV-2 infection and pathogenesis through at least four possible mechanisms: 1. host cell miRNA expression interfering with SARS-CoV-2 cell entry, 2. SARS-CoV-2-derived RNA transcripts acting as competitive endogenous RNAs (ceRNAs) that may attenuate host cell miRNA expression, 3. host cell miRNA expression modulating SARS-CoV-2 replication, and 4. SARS-CoV-2-encoded miRNAs silencing the expression of host protein-coding genes. SARS-CoV-2-related miRNAs may be used as diagnostic or prognostic biomarkers for predicting outcomes among patients with SARS-CoV-2 infection. Furthermore, accumulating evidence suggests that dietary polyphenolic compounds may protect against SARS-CoV-2 infection by modulating host cell miRNA expression. These findings have major implications for the future diagnosis and treatment of COVID-19.
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Affiliation(s)
- Chih-Yun Yang
- Division of Chest Medicine, Kaohsiung Municipal Min-Sheng Hospital, Kaohsiung, Taiwan, ROC
| | - Yu-Hsuan Chen
- Division of Chest Medicine, Department of Internal Medicine, CHENG HSIN General Hospital, Taipei, Taiwan, ROC
| | - Pei-Jung Liu
- Division of Chest Medicine, Department of Internal Medicine, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan, ROC
| | - Wan-Chung Hu
- Department of Clinical Pathology and Medical Research, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, New Taipei City, Taiwan, ROC
| | - Kuo-Cheng Lu
- Division of Nephrology, Department of Medicine, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, New Taipei City, Taiwan, ROC.,Division of Nephrology, Department of Medicine, Fu-Jen Catholic University Hospital, School of Medicine, Fu-Jen Catholic University, New Taipei City, Taiwan, ROC
| | - Kuo-Wang Tsai
- Department of Research, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, New Taipei City, Taiwan, ROC
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14
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A computational approach on studying the regulation of TGF-β1-stimulated Runx2 expression by MicroRNAs in human breast cancer cells. Comput Biol Med 2021; 137:104823. [PMID: 34492519 DOI: 10.1016/j.compbiomed.2021.104823] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 08/15/2021] [Accepted: 08/29/2021] [Indexed: 01/20/2023]
Abstract
BACKGROUND Transforming growth factor-beta1 (TGF-β1) acts as a most effective growth inhibitor for normal epithelial cells. Loss of this anti-proliferative factor in breast tissues favors invasion and development of osteolytic metastases, aided by a master transcription factor, runt-related transcription factor 2 (Runx2). Several reports identified Runx2 regulation with the help of non-coding RNAs such as microRNAs (miRNAs) under physiological and pathological conditions. METHODS Using bioinformatics tools such as miRDB, STarMir, Venny, TarBase, a unique list of miRNAs that putatively target the 3' UTR Runx2 was identified. Further, the expression patterns of those miRNAs at the precursor and mature levels were studied by RT-qPCR analyses. Following this, computational analyses using software like TransmiR and bc-GenExMiner v4.6 were done to speculate the miRNA's other target genes that indirectly regulate Runx2 activity in breast cancer. RESULTS There were 13 miRNAs that putatively target Runx2 identified using bioinformatics tools. Among these miRNAs, miR-5703 expression was significantly downregulated at both precursor and mature levels upon TGF-β1-treatment in human breast cancer cells. Computational analyses speculated an indirect targeting of Runx2 by miR-5703 by influencing multiple Runx2 regulatory signaling pathways including Jak/Stat, MAPK, Wnt/β-Catenin, Notch, BMP, and PKA pathways. Furthermore, a correlation of the expression profiles of the speculated genes and Runx2 with miR-5703 was depicted in triple-negative breast cancer patients. CONCLUSION Identification of miR-5703 and its network for Runx2 regulation directly or indirectly in breast cancer cells could significantly advance our understanding of breast cancer-mediated bone metastasis. In addition, it would potentially pave the way for miRNAs to be used as biomarkers and therapeutic agents in cancer research.
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15
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Liu SH, Hsu KW, Lai YL, Lin YF, Chen FH, Peng PH, Lin LJ, Wu HH, Li CY, Wang SC, Wu MZ, Sher YP, Cheng WC. Systematic identification of clinically relevant miRNAs for potential miRNA-based therapy in lung adenocarcinoma. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 25:1-10. [PMID: 34141460 PMCID: PMC8181588 DOI: 10.1016/j.omtn.2021.04.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 04/28/2021] [Indexed: 12/21/2022]
Abstract
Lung adenocarcinoma (LUAD), the most common histological type of non-small cell lung cancer, is one of the most malignant and deadly diseases. Current treatments for advanced LUAD patients are far from ideal and require further improvements. Here, we utilized a systematic integrative analysis of LUAD microRNA sequencing (miRNA-seq) and RNA-seq data from The Cancer Genome Atlas (TCGA) to identify clinically relevant tumor suppressor miRNAs. Three miRNA candidates (miR-195-5p, miR-101-3p, and miR-338-5p) were identified based on their differential expressions, survival significance levels, correlations with targets, and an additive effect on survival among them. We further evaluated mimics of the three miRNAs to determine their therapeutic potential in inhibiting cancer progression. The results showed not only that each of the miRNA mimics alone but also the three miRNA mimics in combination were efficient at inhibiting tumor growth and progression with equal final concentrations, meaning that the three miRNA mimics in combination were more effective than the single miRNA mimics. Moreover, the combined miRNA mimics provided significant therapeutic effects in terms of reduced tumor volume and metastasis nodules in lung tumor animal models. Hence, our findings show the potential of using the three miRNAs in combination to treat LUAD patients with poor survival outcomes.
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Affiliation(s)
- Shu-Hsuan Liu
- Research Center for Cancer Biology, China Medical University, Taichung 40402, Taiwan
| | - Kai-Wen Hsu
- Institute of New Drug Development, Drug Development Center, China Medical University, Taichung 40402, Taiwan
| | - Yo-Liang Lai
- Department of Radiation Oncology, China Medical University Hospital, Taichung 40447, Taiwan.,Graduate Institute of Biomedical Science, China Medical University, Taichung 40402, Taiwan
| | - Yu-Feng Lin
- Department of Biotechnology, College of Medical and Health Science, Asia University, Taichung 41354, Taiwan.,Department of Medical Laboratory Science and Biotechnology, College of Medical and Health Science, Asia University, Taichung 41354, Taiwan
| | - Fang-Hsin Chen
- Department of Medical Imaging and Radiological Sciences, Chang Gung University, Taoyuan 33302, Taiwan.,Department of Radiation Oncology, Chang Gung Memorial Hospital at Linkou, Taoyuan 33305, Taiwan.,Institute for Radiological Research, Chang Gung University and Chang Gung Memorial Hospital, Taoyuan 33302, Taiwan
| | - Pei-Hwa Peng
- Cancer Genome Research Center, Chang Gung Memorial Hospital at Linkou, Taoyuan 33305, Taiwan
| | - Li-Jie Lin
- The Ph.D. program for Cancer Biology and Drug Discovery, China Medical University and Academia Sinica, Taichung 40402, Taiwan
| | - Heng-Hsiung Wu
- The Ph.D. program for Cancer Biology and Drug Discovery, China Medical University and Academia Sinica, Taichung 40402, Taiwan.,Research Center for Cancer Biology, China Medical University, Taichung 40402, Taiwan
| | - Chia-Yang Li
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Shu-Chi Wang
- Department of Medical Laboratory Science and Biotechnology, College of Health Sciences, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Min-Zu Wu
- AbbVie Biotherapeutics Inc., Redwood City, CA 94063, USA
| | - Yuh-Pyng Sher
- Graduate Institute of Biomedical Science, China Medical University, Taichung 40402, Taiwan.,Center for Molecular Medicine, China Medical University Hospital, Taichung 40402, Taiwan
| | - Wei-Chung Cheng
- Research Center for Cancer Biology, China Medical University, Taichung 40402, Taiwan.,The Ph.D. program for Cancer Biology and Drug Discovery, China Medical University and Academia Sinica, Taichung 40402, Taiwan
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16
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Circulating miRNAs Act as Diagnostic Biomarkers for Bladder Cancer in Urine. Int J Mol Sci 2021; 22:ijms22084278. [PMID: 33924142 PMCID: PMC8074331 DOI: 10.3390/ijms22084278] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/16/2021] [Accepted: 04/19/2021] [Indexed: 02/06/2023] Open
Abstract
MicroRNAs (miRNAs) can be secreted into body fluids and have thus been reported as a new type of cancer biomarker. This study aimed to determine whether urinary miRNAs act as noninvasive biomarkers for diagnosing bladder cancer. Small RNA profiles from urine were generated for 10 patients with bladder cancer and 10 healthy controls by using next-generation sequencing. We identified 50 urinary miRNAs that were differentially expressed in bladder cancer compared with controls, comprising 44 upregulated and six downregulated miRNAs. Pathway enrichment analysis revealed that the biological role of these differentially expressed miRNAs might be involved in cancer-associated signaling pathways. Further analysis of the public database revealed that let-7b-5p, miR-149-5p, miR-146a-5p, miR-193a-5p, and miR-423-5p were significantly increased in bladder cancer compared with corresponding adjacent normal tissues. Furthermore, high miR-149-5p and miR-193a-5p expression was significantly correlated with poor overall survival in patients with bladder cancer. The qRT-PCR approach revealed that the expression levels of let-7b-5p, miR-149-5p, miR-146a-5p and miR-423-5p were significantly increased in the urine of patients with bladder cancer compared with those of controls. Although our results indicated that urinary miRNAs are promising biomarkers for diagnosing bladder cancer, this must be validated in larger cohorts in the future.
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17
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Identification and validation of a miRNA-based prognostic signature for cervical cancer through an integrated bioinformatics approach. Sci Rep 2020; 10:22270. [PMID: 33335254 PMCID: PMC7747620 DOI: 10.1038/s41598-020-79337-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 12/02/2020] [Indexed: 12/15/2022] Open
Abstract
Cervical cancer is the fourth most common cancer in women worldwide. Increasing evidence has shown that miRNAs are related to the progression of cervical cancer. However, the mechanisms that affect the prognosis of cancer are still largely unknown. In the present study, we sought to identify miRNAs associated with poor prognosis of patient with cervical cancer, as well as the possible mechanisms regulated by them. The miRNA expression profiles and relevant clinical information of patients with cervical cancer were obtained from The Cancer Genome Atlas (TCGA). The selection of prognostic miRNAs was carried out through an integrated bioinformatics approach. The most effective miRNAs with synergistic and additive effects were selected for validation through in vitro experiments. Three miRNAs (miR-216b-5p, miR-585-5p, and miR-7641) were identified as exhibiting good performance in predicting poor prognosis through additive effects analysis. The functional enrichment analysis suggested that not only pathways traditionally involved in cancer but also immune system pathways might be important in regulating the outcome of the disease. Our findings demonstrated that a synergistic combination of three miRNAs may be associated, through their regulation of specific pathways, with very poor survival rates for patients with cervical cancer.
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18
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Liu SH, Shen PC, Chen CY, Hsu AN, Cho YC, Lai YL, Chen FH, Li CY, Wang SC, Chen M, Chung IF, Cheng WC. DriverDBv3: a multi-omics database for cancer driver gene research. Nucleic Acids Res 2020; 48:D863-D870. [PMID: 31701128 PMCID: PMC7145679 DOI: 10.1093/nar/gkz964] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 10/09/2019] [Accepted: 11/06/2019] [Indexed: 12/13/2022] Open
Abstract
An integrative multi-omics database is needed urgently, because focusing only on analysis of one-dimensional data falls far short of providing an understanding of cancer. Previously, we presented DriverDB, a cancer driver gene database that applies published bioinformatics algorithms to identify driver genes/mutations. The updated DriverDBv3 database (http://ngs.ym.edu.tw/driverdb) is designed to interpret cancer omics’ sophisticated information with concise data visualization. To offer diverse insights into molecular dysregulation/dysfunction events, we incorporated computational tools to define CNV and methylation drivers. Further, four new features, CNV, Methylation, Survival, and miRNA, allow users to explore the relations from two perspectives in the ‘Cancer’ and ‘Gene’ sections. The ‘Survival’ panel offers not only significant survival genes, but gene pairs synergistic effects determine. A fresh function, ‘Survival Analysis’ in ‘Customized-analysis,’ allows users to investigate the co-occurring events in user-defined gene(s) by mutation status or by expression in a specific patient group. Moreover, we redesigned the web interface and provided interactive figures to interpret cancer omics’ sophisticated information, and also constructed a Summary panel in the ‘Cancer’ and ‘Gene’ sections to visualize the features on multi-omics levels concisely. DriverDBv3 seeks to improve the study of integrative cancer omics data by identifying driver genes and contributes to cancer biology.
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Affiliation(s)
- Shu-Hsuan Liu
- Graduate Institute of Biomedical Science, China Medical University, Taichung 40403, Taiwan
| | - Pei-Chun Shen
- Graduate Institute of Biomedical Science, China Medical University, Taichung 40403, Taiwan
| | - Chen-Yang Chen
- Cytoaurora Biotechnologies, Inc. Hsinchu Science Park, Hsinchu 30261, Taiwan
| | - An-Ni Hsu
- Graduate Institute of Biomedical Science, China Medical University, Taichung 40403, Taiwan
| | - Yi-Chun Cho
- Graduate Institute of Biomedical Science, China Medical University, Taichung 40403, Taiwan
| | - Yo-Liang Lai
- Graduate Institute of Biomedical Science, China Medical University, Taichung 40403, Taiwan.,Department of Radiation Oncology, China Medical University Hospital, Taichung 40403, Taiwan
| | - Fang-Hsin Chen
- Department of Medical Imaging and Radiological Sciences, Chang Gung University, Taoyuan 33302, Taiwan.,Department of Radiation Oncology, Chang Gung Memorial Hospital at Linkou, Taoyuan 33302, Taiwan.,Institute for Radiological Research, Chang Gung University and Chang Gung Memorial Hospital, Taoyuan 33302, Taiwan
| | - Chia-Yang Li
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Shu-Chi Wang
- Department of Medical Laboratory Science and Biotechnology, College of Health Sciences, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Ming Chen
- Center for Medical Genetics, Changhua Christian Hospital, Changhua 50006, Taiwan
| | - I-Fang Chung
- Institute of BioMedical Informatics, National Yang-Ming University, Taipei 11221, Taiwan
| | - Wei-Chung Cheng
- Graduate Institute of Biomedical Science, China Medical University, Taichung 40403, Taiwan.,Research Center for Tumor Medical Science, China Medical University, Taichung 40403, Taiwan
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19
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Yang C, Yang W, Wong Y, Wang K, Teng Y, Chang M, Liao K, Nian F, Chao C, Tsai J, Hwang W, Lin M, Tzeng T, Wang P, Campbell M, Chen L, Tsai T, Chang P, Kung H. Muscle atrophy-related myotube-derived exosomal microRNA in neuronal dysfunction: Targeting both coding and long noncoding RNAs. Aging Cell 2020; 19:e13107. [PMID: 32233025 PMCID: PMC7253071 DOI: 10.1111/acel.13107] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 12/17/2019] [Accepted: 01/05/2020] [Indexed: 12/27/2022] Open
Abstract
In mammals, microRNAs can be actively secreted from cells to blood. miR‐29b‐3p has been shown to play a pivotal role in muscle atrophy, but its role in intercellular communication is largely unknown. Here, we showed that miR‐29b‐3p was upregulated in normal and premature aging mouse muscle and plasma. miR‐29b‐3p was also upregulated in the blood of aging individuals, and circulating levels of miR‐29b‐3p were negatively correlated with relative appendicular skeletal muscle. Consistently, miR‐29b‐3p was observed in exosomes isolated from long‐term differentiated atrophic C2C12 cells. When C2C12‐derived miR‐29b‐3p‐containing exosomes were uptaken by neuronal SH‐SY5Y cells, increased miR‐29b‐3p levels in recipient cells were observed. Moreover, miR‐29b‐3p overexpression led to downregulation of neuronal‐related genes and inhibition of neuronal differentiation. Interestingly, we identified HIF1α‐AS2 as a novel c‐FOS targeting lncRNA that is induced by miR‐29b‐3p through down‐modulation of c‐FOS and is required for miR‐29b‐3p‐mediated neuronal differentiation inhibition. Our results suggest that atrophy‐associated circulating miR‐29b‐3p may mediate distal communication between muscle cells and neurons.
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Affiliation(s)
- Chia‐Pei Yang
- Institute of Microbiology and Immunology National Yang‐Ming University Taipei Taiwan
| | - Wan‐Shan Yang
- Institute of Microbiology and Immunology National Yang‐Ming University Taipei Taiwan
| | - Yu‐Hui Wong
- Brain Research Center National Yang‐Ming University Taipei Taiwan
| | - Kai‐Hsuan Wang
- Institute of Molecular and Genomic Medicine National Health Research Institutes Zhunan Taiwan
| | - Yuan‐Chi Teng
- Program in Molecular Medicine School of Life Sciences National Yang‐Ming University and Academia Sinica Taipei Taiwan
- Department of Life Sciences Institute of Genome Sciences National Yang‐Ming University Taipei Taiwan
| | - Ming‐Hsuan Chang
- Institute of Microbiology and Immunology National Yang‐Ming University Taipei Taiwan
| | - Ko‐Hsun Liao
- Institute of Microbiology and Immunology National Yang‐Ming University Taipei Taiwan
| | - Fang‐Shin Nian
- Institute of Brain Science National Yang‐Ming University Taipei Taiwan
- Program in Molecular Medicine National Yang‐Ming University and Academia Sinica Taipei Taiwan
| | - Chuan‐Chuan Chao
- The Ph.D. Program for Cancer Molecular Biology and Drug Discovery College of Medical Science and Technology Taipei Medical University Taipei Taiwan
| | - Jin‐Wu Tsai
- Institute of Brain Science National Yang‐Ming University Taipei Taiwan
| | - Wei‐Lun Hwang
- Department of Biotechnology and Laboratory Science in Medicine National Yang‐Ming University Taipei Taiwan
| | - Ming‐Wei Lin
- Institute of Public Health National Yang‐Ming University Taipei Taiwan
| | - Tsai‐Yu Tzeng
- Cancer Progression Research Center National Yang‐Ming University Taipei Taiwan
| | - Pei‐Ning Wang
- Brain Research Center National Yang‐Ming University Taipei Taiwan
- Department of Neurology Neurological InstituteTaipei Veterans General Hospital Taipei Taiwan
- Aging and Health Research Center National Yang‐Ming University Taipei Taiwan
| | - Mel Campbell
- UC Davis Comprehensive Cancer CenterUniversity of California Davis CA USA
| | - Liang‐Kung Chen
- Aging and Health Research Center National Yang‐Ming University Taipei Taiwan
- Department of Geriatric Medicine School of Medicine National Yang Ming University Taipei Taiwan
- Center for Geriatrics and Gerontology Taipei Veterans General Hospital Taipei Taiwan
| | - Ting‐Fen Tsai
- Institute of Molecular and Genomic Medicine National Health Research Institutes Zhunan Taiwan
- Program in Molecular Medicine School of Life Sciences National Yang‐Ming University and Academia Sinica Taipei Taiwan
- Department of Life Sciences Institute of Genome Sciences National Yang‐Ming University Taipei Taiwan
- Aging and Health Research Center National Yang‐Ming University Taipei Taiwan
| | - Pei‐Ching Chang
- Institute of Microbiology and Immunology National Yang‐Ming University Taipei Taiwan
- Cancer Progression Research Center National Yang‐Ming University Taipei Taiwan
| | - Hsing‐Jien Kung
- Institute of Molecular and Genomic Medicine National Health Research Institutes Zhunan Taiwan
- The Ph.D. Program for Cancer Molecular Biology and Drug Discovery College of Medical Science and Technology Taipei Medical University Taipei Taiwan
- UC Davis Comprehensive Cancer CenterUniversity of California Davis CA USA
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20
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Ma M, Yin Z, Zhong H, Liang T, Guo L. Analysis of the expression, function, and evolution of miR-27 isoforms and their responses in metabolic processes. Genomics 2019; 111:1249-1257. [DOI: 10.1016/j.ygeno.2018.08.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 07/31/2018] [Accepted: 08/08/2018] [Indexed: 12/13/2022]
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21
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Shi X, Li Y, Yan P, Shi Y, Lai J. Weighted gene co-expression network analysis to explore the mechanism of heroin addiction in human nucleus accumbens. J Cell Biochem 2019; 121:1870-1879. [PMID: 31692007 DOI: 10.1002/jcb.29422] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 10/08/2019] [Indexed: 12/29/2022]
Abstract
Heroin dependence is a complex behavioral disease, and a chronic encephalopathy with the important feature of relapse. The purpose of the study was to identify the regulatory mechanism of the nucleus accumbens (NAc) in heroin dependence. We used weighted gene co-expression network analysis to analyze the GSE87823 data package, which included 27 heroin users and 22 controls of human NAc tissue. Modules were correlated with basic information of samples and enrichment analyses used to identify biological function and transcription factors and online tools were used to perform the gene ontology of significant genes. We identified one gene module from the total data (blue) and the male data (turquoise), respectively. The overlap genes of top 10 hub genes in significant modules (PRR11, SLC35E1, LPP, ZNF721, ZNF611, LRRFIP1) were selected to identify as candidate genes in the regulation mechanism of NAc in heroin dependence. Then, we accorded the results to further explore that miRNA-hsa-miR-155-5p in male and total may be a potential marker. The candidate genes may serve as novel prognostic markers and treatment targets. Hsa-miR-155-5p may be a promising regulatory point for the treatment of heroin addiction.
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Affiliation(s)
- Xugang Shi
- Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University, Ministry of Education, Xi'an, China.,College of Forensic Science, Key Laboratory of Public Health for Forensic Science, Xi'an Jiaotong University, Xi'an, China
| | - Yunxiao Li
- Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University, Ministry of Education, Xi'an, China.,College of Forensic Science, Key Laboratory of Public Health for Forensic Science, Xi'an Jiaotong University, Xi'an, China
| | - Peng Yan
- Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University, Ministry of Education, Xi'an, China.,College of Forensic Science, Key Laboratory of Public Health for Forensic Science, Xi'an Jiaotong University, Xi'an, China
| | - Yuhui Shi
- Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University, Ministry of Education, Xi'an, China.,College of Forensic Science, Key Laboratory of Public Health for Forensic Science, Xi'an Jiaotong University, Xi'an, China
| | - Jianghua Lai
- Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University, Ministry of Education, Xi'an, China.,College of Forensic Science, Key Laboratory of Public Health for Forensic Science, Xi'an Jiaotong University, Xi'an, China
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22
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Hsieh TH, Liu YR, Chang TY, Liang ML, Chen HH, Wang HW, Yen Y, Wong TT. Global DNA methylation analysis reveals miR-214-3p contributes to cisplatin resistance in pediatric intracranial nongerminomatous malignant germ cell tumors. Neuro Oncol 2019; 20:519-530. [PMID: 29036598 DOI: 10.1093/neuonc/nox186] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Background Pediatric central nervous system germ cell tumors (CNSGCTs) are rare and heterogeneous neoplasms, which can be divided into germinomas and nongerminomatous germ cell tumors (NGGCTs). NGGCTs are further subdivided into mature teratomas and nongerminomatous malignant GCTs (NGMGCTs). Clinical outcomes suggest that NGMGCTs have poor prognosis and survival and that they require more extensive radiotherapy and adjuvant chemotherapy. However, the mechanisms underlying this difference are still unclear. DNA methylation alteration is generally acknowledged to cause therapeutic resistance in cancers. We hypothesized that the pediatric NGMGCTs exhibit a different genome-wide DNA methylation pattern, which is involved in the mechanism of its therapeutic resistance. Methods We performed methylation and hydroxymethylation DNA immunoprecipitation sequencing, mRNA expression microarray, and small RNA sequencing (smRNA-seq) to determine methylation-regulated genes, including microRNAs (miRNAs). Results The expression levels of 97 genes and 8 miRNAs were correlated with promoter DNA methylation and hydroxymethylation status, such as the miR-199/-214 cluster, and treatment with DNA demethylating agent 5-aza-2'-deoxycytidine elevated its expression level. Furthermore, smRNA-seq analysis showed 27 novel miRNA candidates with differential expression between germinomas and NGMGCTs. Overexpresssion of miR-214-3p in NCCIT cells leads to reduced expression of the pro-apoptotic protein BCL2-like 11 and induces cisplatin resistance. Conclusions We interrogated the differential DNA methylation patterns between germinomas and NGMGCTs and proposed a mechanism for chemoresistance in NGMGCTs. In addition, our sequencing data provide a roadmap for further pediatric CNSGCT research and potential targets for the development of new therapeutic strategies.
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Affiliation(s)
- Tsung-Han Hsieh
- Joint Biobank, Office of Human Research, Taipei Medical University, Taipei, Taiwan.,Research Center of Cancer Translational Medicine, Taipei Medical University, Taipei, Taiwan
| | - Yun-Ru Liu
- Joint Biobank, Office of Human Research, Taipei Medical University, Taipei, Taiwan.,Comprehensive Cancer Center of Taipei Medical University, Taipei Medical University, Taipei, Taiwan
| | - Ting-Yu Chang
- Comprehensive Cancer Center of Taipei Medical University, Taipei Medical University, Taipei, Taiwan.,Research Center of Cancer Translational Medicine, Taipei Medical University, Taipei, Taiwan
| | - Muh-Lii Liang
- Division of Pediatric Neurosurgery, Neurological Institute, Taipei Veterans General Hospital (VGH-TPE), Taipei, Taiwan
| | - Hsin-Hung Chen
- Division of Pediatric Neurosurgery, Neurological Institute, Taipei Veterans General Hospital (VGH-TPE), Taipei, Taiwan
| | - Hsei-Wei Wang
- Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan
| | - Yun Yen
- Comprehensive Cancer Center of Taipei Medical University, Taipei Medical University, Taipei, Taiwan.,Program for Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Tai-Tong Wong
- Comprehensive Cancer Center of Taipei Medical University, Taipei Medical University, Taipei, Taiwan.,Institutes of Clinical Medicine, Taipei Medical University, Taipei, Taiwan.,Department of Neurosurgery, Taipei Medical University Hospital, Taipei Medical University, Taipei, Taiwan.,Neuroscience Research Center, Taipei Medical University Hospital, Taipei, Taiwan
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23
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Abstract
One of the most important resources for researchers of noncoding RNAs is the information available in public databases spread over the internet. However, the effective exploration of this data can represent a daunting task, given the large amount of databases available and the variety of stored data. This chapter describes a classification of databases based on information source, type of RNA, source organisms, data formats, and the mechanisms for information retrieval, detailing the relevance of each of these classifications and its usability by researchers. This classification is used to update a 2012 review, indexing now more than 229 public databases. This review will include an assessment of the new trends for ncRNA research based on the information that is being offered by the databases. Additionally, we will expand the previous analysis focusing on the usability and application of these databases in pathogen and disease research. Finally, this chapter will analyze how currently available database schemas can help the development of new and improved web resources.
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24
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Wu CW, Evans JM, Huang S, Mahoney DW, Dukek BA, Taylor WR, Yab TC, Smyrk TC, Jen J, Kisiel JB, Ahlquist DA. A Comprehensive Approach to Sequence-oriented IsomiR annotation (CASMIR): demonstration with IsomiR profiling in colorectal neoplasia. BMC Genomics 2018; 19:401. [PMID: 29801434 PMCID: PMC5970459 DOI: 10.1186/s12864-018-4794-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 05/14/2018] [Indexed: 01/14/2023] Open
Abstract
Background MicroRNA (miRNA) profiling is an important step in studying biological associations and identifying marker candidates. miRNA exists in isoforms, called isomiRs, which may exhibit distinct properties. With conventional profiling methods, limitations in assay and analysis platforms may compromise isomiR interrogation. Results We introduce a comprehensive approach to sequence-oriented isomiR annotation (CASMIR) to allow unbiased identification of global isomiRs from small RNA sequencing data. In this approach, small RNA reads are maintained as independent sequences instead of being summarized under miRNA names. IsomiR features are identified through step-wise local alignment against canonical forms and precursor sequences. Through customizing the reference database, CASMIR is applicable to isomiR annotation across species. To demonstrate its application, we investigated isomiR profiles in normal and neoplastic human colorectal epithelia. We also ran miRDeep2, a popular miRNA analysis algorithm to validate isomiRs annotated by CASMIR. With CASMIR, specific and biologically relevant isomiR patterns could be identified. We note that specific isomiRs are often more abundant than their canonical forms. We identify isomiRs that are commonly up-regulated in both colorectal cancer and advanced adenoma, and illustrate advantages in targeting isomiRs as potential biomarkers over canonical forms. Conclusions Studying miRNAs at the isomiR level could reveal new insight into miRNA biology and inform assay design for specific isomiRs. CASMIR facilitates comprehensive annotation of isomiR features in small RNA sequencing data for isomiR profiling and differential expression analysis. Electronic supplementary material The online version of this article (10.1186/s12864-018-4794-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chung Wah Wu
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Jared M Evans
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA
| | - Shengbing Huang
- Division of Bioinformatics and Computational Biology, University of Minnesota Rochester, Rochester, MN, USA
| | - Douglas W Mahoney
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA
| | - Brian A Dukek
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - William R Taylor
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Tracy C Yab
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Thomas C Smyrk
- Division of Anatomic Pathology, Mayo Clinic, Rochester, MN, USA
| | - Jin Jen
- Genome Analysis Core, Medical Genome Facility, Mayo Clinic, Rochester, MN, USA.,Division of Experimental Pathology, Mayo Clinic, Rochester, MN, USA
| | - John B Kisiel
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - David A Ahlquist
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA.
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25
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Lin MH, Chen YZ, Lee MY, Weng KP, Chang HT, Yu SY, Dong BJ, Kuo FR, Hung LT, Liu LF, Chen WS, Tsai KW. Comprehensive identification of microRNA arm selection preference in lung cancer: miR-324-5p and -3p serve oncogenic functions in lung cancer. Oncol Lett 2018; 15:9818-9826. [PMID: 29844840 PMCID: PMC5958786 DOI: 10.3892/ol.2018.8557] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 11/16/2017] [Indexed: 12/31/2022] Open
Abstract
MicroRNA (miRNA/miR) dysfunction is a hallmark of lung cancer, and results in the dysregulation of tumor suppressors and oncogenes during lung cancer progression. Selection of the 5p and 3p arms of miRNA is a mechanism that improves the modulation of miRNA biological functions and complicates the regulatory network in human types of cancer. However, the involvement of arm selection preference of miRNA in lung cancer remains unclear. In the present study, changes in miRNA arm selection preference were comprehensively identified in lung cancer and corresponding adjacent normal tissues by analyzing The Cancer Genome Atlas. Arm selection was revealed to be consistent in the majority of miRNAs in lung cancer. Only a few miRNAs had significantly altered arm selection preference in lung cancer. Among these, the biological functions of the individual arms of miR-324 were investigated further. The data revealed that miR-324-5p and -3p were significantly overexpressed in lung cancer cells. Ectopic expression of miR-324-5p significantly promoted cell proliferation and invasion in lung cancer cells, while miR-324-3p overexpression significantly increased cell proliferation but did not alter the invasion of lung cancer cells. In conclusion, the arm selection preference of miRNA may be an additional mechanism through which biological functions are modulated. The results of the present study provide a novel insight into the underlying mechanisms of lung cancer and may direct research into future therapies.
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Affiliation(s)
- Min-Hsi Lin
- Division of Chest Medicine, Kaohsiung Veterans General Hospital, Kaohsiung 813, Taiwan, R.O.C.,School of Medicine, National Yang-Ming University, Taipei 112, Taiwan, R.O.C
| | - You-Zuo Chen
- Department of Medical Education and Research, Kaohsiung Veterans General Hospital, Kaohsiung 813, Taiwan, R.O.C
| | - Mei-Yu Lee
- Department of Medical Education and Research, Kaohsiung Veterans General Hospital, Kaohsiung 813, Taiwan, R.O.C.,Department of Biological Science and Technology, I-Shou University, Kaohsiung 813, Taiwan, R.O.C
| | - Ken-Pen Weng
- School of Medicine, National Yang-Ming University, Taipei 112, Taiwan, R.O.C.,Department of Pediatrics, Kaohsiung Veterans General Hospital, Kaohsiung 813, Taiwan, R.O.C.,Department of Physical Therapy, Shu-Zen College of Medicine and Management, Kaohsiung 813, Taiwan, R.O.C
| | - Hong-Tai Chang
- Center for Geriatrics and Gerontology, Kaohsiung Veterans General Hospital, Kaohsiung 813, Taiwan, R.O.C.,Department of Surgery, Kaohsiung Veterans General Hospital, Kaohsiung 813, Taiwan, R.O.C
| | - Shou-Yu Yu
- Department of Medical Education and Research, Kaohsiung Veterans General Hospital, Kaohsiung 813, Taiwan, R.O.C
| | - Bo-Jhu Dong
- Department of Chemical Biology, National Pingtung University of Education, Pingtung 900, Taiwan, R.O.C
| | - Fan-Rong Kuo
- Department of Chemical Biology, National Pingtung University of Education, Pingtung 900, Taiwan, R.O.C
| | - Li-Tzu Hung
- Department of Chemical Biology, National Pingtung University of Education, Pingtung 900, Taiwan, R.O.C
| | - Li-Feng Liu
- Department of Biological Science and Technology, I-Shou University, Kaohsiung 813, Taiwan, R.O.C
| | - Wei-Shone Chen
- School of Medicine, National Yang-Ming University, Taipei 112, Taiwan, R.O.C.,Department of Surgery, Veterans General Hospital, Taipei 112, Taiwan, R.O.C
| | - Kuo-Wang Tsai
- Department of Medical Education and Research, Kaohsiung Veterans General Hospital, Kaohsiung 813, Taiwan, R.O.C.,Department of Chemical Biology, National Pingtung University of Education, Pingtung 900, Taiwan, R.O.C.,Institute of Biomedical Sciences, National Sun Yat-sen University, Kaohsiung 813, Taiwan, R.O.C
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26
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Panwar B, Omenn GS, Guan Y. miRmine: a database of human miRNA expression profiles. Bioinformatics 2018; 33:1554-1560. [PMID: 28108447 DOI: 10.1093/bioinformatics/btx019] [Citation(s) in RCA: 102] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 01/17/2017] [Indexed: 12/17/2022] Open
Abstract
Motivation MicroRNAs (miRNAs) are small non-coding RNAs that are involved in post-transcriptional regulation of gene expression. In this high-throughput sequencing era, a tremendous amount of RNA-seq data is accumulating, and full utilization of publicly available miRNA data is an important challenge. These data are useful to determine expression values for each miRNA, but quantification pipelines are in a primitive stage and still evolving; there are many factors that affect expression values significantly. Results We used 304 high-quality microRNA sequencing (miRNA-seq) datasets from NCBI-SRA and calculated expression profiles for different tissues and cell-lines. In each miRNA-seq dataset, we found an average of more than 500 miRNAs with higher than 5x coverage, and we explored the top five highly expressed miRNAs in each tissue and cell-line. This user-friendly miRmine database has options to retrieve expression profiles of single or multiple miRNAs for a specific tissue or cell-line, either normal or with disease information. Results can be displayed in multiple interactive, graphical and downloadable formats. Availability and Implementation http://guanlab.ccmb.med.umich.edu/mirmine. Contact bharatpa@umich.edu. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Bharat Panwar
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Gilbert S Omenn
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.,Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA.,Department of Human Genetics and School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Yuanfang Guan
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.,Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA.,Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI, USA
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27
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Chang TY, Tsai WC, Huang TS, Su SH, Chang CY, Ma HY, Wu CH, Yang CY, Lin CH, Huang PH, Cheng CC, Cheng SM, Wang HW. Dysregulation of endothelial colony-forming cell function by a negative feedback loop of circulating miR-146a and -146b in cardiovascular disease patients. PLoS One 2017; 12:e0181562. [PMID: 28727754 PMCID: PMC5519171 DOI: 10.1371/journal.pone.0181562] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2017] [Accepted: 07/03/2017] [Indexed: 11/19/2022] Open
Abstract
Functional impairment of endothelial colony-forming cells (ECFCs), a specific cell lineage of endothelial progenitor cells (EPCs) is highly associated with the severity of coronary artery disease (CAD), the most common type of cardiovascular disease (CVD). Emerging evidence show that circulating microRNAs (miRNAs) in CAD patients’ body fluid hold a great potential as biomarkers. However, our knowledge of the role of circulating miRNA in regulating the function of ECFCs and the progression of CAD is still in its infancy. We showed that when ECFCs from healthy volunteers were incubated with conditioned medium or purified exosomes of cultured CAD ECFCs, the secretory factors from CAD ECFCs dysregulated migration and tube formation ability of healthy ECFCs. It is known that exosomes influence the physiology of recipient cells by introducing RNAs including miRNAs. By using small RNA sequencing (smRNA-seq), we deciphered the circulating miRNome in the plasma of healthy individual and CAD patients, and found that the plasma miRNA spectrum from CAD patients was significantly different from that of healthy control. Interestingly, smRNA-seq of both healthy and CAD ECFCs showed that twelve miRNAs that had a higher expression in the plasma of CAD patients also showed higher expression in CAD ECFCs when compared with healthy control. This result suggests that these miRNAs may be involved in the regulation of ECFC functions. For identification of potential mRNA targets of the differentially expressed miRNA in CAD patients, cDNA microarray analysis was performed to identify the angiogenesis-related genes that were down-regulated in CAD ECFCs and Pearson’s correlation were used to identify miRNAs that were negatively correlated with the identified angiogenesis-related genes. RT-qPCR analysis of the five miRNAs that negatively correlated with the down-regulated angiogenesis-related genes in plasma and ECFC of CAD patients showed miR-146a-5p and miR-146b-5p up-regulation compared to healthy control. Knockdown of miR-146a-5p or miR-146b-5p in CAD ECFCs enhanced migration and tube formation activity in diseased ECFCs. Contrarily, overexpression of miR-146a-5p or miR-146b-5p in healthy ECFC repressed migration and tube formation in ECFCs. TargetScan analysis showed that miR-146a-5p and miR-146b-5p target many of the angiogenesis-related genes that were down-regulated in CAD ECFCs. Knockdown of miR-146a-5p or miR-146b-5p restores CAV1 and RHOJ levels in CAD ECFCs. Reporter assays confirmed the direct binding and repression of miR-146a-5p and miR-146b-5p to the 3’-UTR of mRNA of RHOJ, a positive regulator of angiogenic potential in endothelial cells. Consistently, RHOJ knockdown inhibited the migration and tube formation ability in ECFCs. Collectively, we discovered the dysregulation of miR-146a-5p/RHOJ and miR-146b-5p/RHOJ axis in the plasma and ECFCs of CAD patients that could be used as biomarkers or therapeutic targets for CAD and other angiogenesis-related diseases.
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Affiliation(s)
- Ting-Yu Chang
- Research Center of Translational Medicine, Taipei Medical University, Taipei, Taiwan
| | - Wei-Chi Tsai
- Division of Cardiology, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
- Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan
| | - Tse-Shun Huang
- Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan
- Institute of Engineering in Medicine, University of California, San Diego, United States of America
| | - Shu-Han Su
- Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan
| | - Chih-Young Chang
- Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan
| | - Hsiu-Yen Ma
- Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan
| | - Chun-Hsien Wu
- Division of Cardiology, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
- Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan
| | - Chih-Yung Yang
- Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan
| | - Chi-Hung Lin
- Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan
| | - Po-Hsun Huang
- Cardiovascular Research Center, National Yang-Ming University, Taipei, Taiwan
- Division of Cardiology, Department of Medicine, Taipei Veterans General Hospital and Institute of Clinical Medicine, Taipei, Taiwan
| | - Cheng-Chung Cheng
- Division of Cardiology, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Shu-Meng Cheng
- Division of Cardiology, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
- * E-mail:
| | - Hsei-Wei Wang
- Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan
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28
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Pisignano G, Napoli S, Magistri M, Mapelli SN, Pastori C, Di Marco S, Civenni G, Albino D, Enriquez C, Allegrini S, Mitra A, D'Ambrosio G, Mello-Grand M, Chiorino G, Garcia-Escudero R, Varani G, Carbone GM, Catapano CV. A promoter-proximal transcript targeted by genetic polymorphism controls E-cadherin silencing in human cancers. Nat Commun 2017; 8:15622. [PMID: 28555645 PMCID: PMC5459991 DOI: 10.1038/ncomms15622] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2016] [Accepted: 04/12/2017] [Indexed: 02/06/2023] Open
Abstract
Long noncoding RNAs are emerging players in the epigenetic machinery with key roles in development and diseases. Here we uncover a complex network comprising a promoter-associated noncoding RNA (paRNA), microRNA and epigenetic regulators that controls transcription of the tumour suppressor E-cadherin in epithelial cancers. E-cadherin silencing relies on the formation of a complex between the paRNA and microRNA-guided Argonaute 1 that, together, recruit SUV39H1 and induce repressive chromatin modifications in the gene promoter. A single nucleotide polymorphism (rs16260) linked to increased cancer risk alters the secondary structure of the paRNA, with the risk allele facilitating the assembly of the microRNA-guided Argonaute 1 complex and gene silencing. Collectively, these data demonstrate the role of a paRNA in E-cadherin regulation and the impact of a noncoding genetic variant on its function. Deregulation of paRNA-based epigenetic networks may contribute to cancer and other diseases making them promising targets for drug discovery.
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Affiliation(s)
- Giuseppina Pisignano
- Tumor Biology and Experimental Therapeutics Program, Institute of Oncology Research (IOR), and Oncology Institute of Southern Switzerland (IOSI), Bellinzona 6500, Switzerland
| | - Sara Napoli
- Tumor Biology and Experimental Therapeutics Program, Institute of Oncology Research (IOR), and Oncology Institute of Southern Switzerland (IOSI), Bellinzona 6500, Switzerland
| | - Marco Magistri
- Tumor Biology and Experimental Therapeutics Program, Institute of Oncology Research (IOR), and Oncology Institute of Southern Switzerland (IOSI), Bellinzona 6500, Switzerland
| | - Sarah N Mapelli
- Tumor Biology and Experimental Therapeutics Program, Institute of Oncology Research (IOR), and Oncology Institute of Southern Switzerland (IOSI), Bellinzona 6500, Switzerland
| | - Chiara Pastori
- Tumor Biology and Experimental Therapeutics Program, Institute of Oncology Research (IOR), and Oncology Institute of Southern Switzerland (IOSI), Bellinzona 6500, Switzerland
| | - Stefano Di Marco
- Tumor Biology and Experimental Therapeutics Program, Institute of Oncology Research (IOR), and Oncology Institute of Southern Switzerland (IOSI), Bellinzona 6500, Switzerland
| | - Gianluca Civenni
- Tumor Biology and Experimental Therapeutics Program, Institute of Oncology Research (IOR), and Oncology Institute of Southern Switzerland (IOSI), Bellinzona 6500, Switzerland
| | - Domenico Albino
- Tumor Biology and Experimental Therapeutics Program, Institute of Oncology Research (IOR), and Oncology Institute of Southern Switzerland (IOSI), Bellinzona 6500, Switzerland
| | - Claudia Enriquez
- Tumor Biology and Experimental Therapeutics Program, Institute of Oncology Research (IOR), and Oncology Institute of Southern Switzerland (IOSI), Bellinzona 6500, Switzerland
| | - Sara Allegrini
- Tumor Biology and Experimental Therapeutics Program, Institute of Oncology Research (IOR), and Oncology Institute of Southern Switzerland (IOSI), Bellinzona 6500, Switzerland
| | - Abhishek Mitra
- Tumor Biology and Experimental Therapeutics Program, Institute of Oncology Research (IOR), and Oncology Institute of Southern Switzerland (IOSI), Bellinzona 6500, Switzerland
| | | | | | - Giovanna Chiorino
- Laboratory of Cancer Genomics, Fondo Edo Tempia, Biella 13900, Italy
| | - Ramon Garcia-Escudero
- Tumor Biology and Experimental Therapeutics Program, Institute of Oncology Research (IOR), and Oncology Institute of Southern Switzerland (IOSI), Bellinzona 6500, Switzerland.,Molecular Oncology Unit, CIEMAT and Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid 28040, Spain
| | - Gabriele Varani
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700, USA
| | - Giuseppina M Carbone
- Tumor Biology and Experimental Therapeutics Program, Institute of Oncology Research (IOR), and Oncology Institute of Southern Switzerland (IOSI), Bellinzona 6500, Switzerland
| | - Carlo V Catapano
- Tumor Biology and Experimental Therapeutics Program, Institute of Oncology Research (IOR), and Oncology Institute of Southern Switzerland (IOSI), Bellinzona 6500, Switzerland.,Department of Oncology, Faculty of Biology and Medicine, University of Lausanne, Lausanne 1066, Switzerland
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29
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Yang K, Sablok G, Qiao G, Nie Q, Wen X. isomiR2Function: An Integrated Workflow for Identifying MicroRNA Variants in Plants. FRONTIERS IN PLANT SCIENCE 2017; 8:322. [PMID: 28377776 PMCID: PMC5359237 DOI: 10.3389/fpls.2017.00322] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2016] [Accepted: 02/22/2017] [Indexed: 05/28/2023]
Abstract
In plants, post transcriptional regulation by non-coding RNAs (ncRNAs), in particular miRNAs (19-24 nt) has been involved in modulating the transcriptional landscape in developmental, biotic and abiotic interactions. In past few years, considerable focus has been leveraged on delineating and deciphering the role of miRNAs and their canonical isomiRs in plants. However, proper classification and accurate prediction of plant isomiRs taking into account the relative features by which we define isomiRs, such as templated or non-templated is still lacking. In the present research, we present isomiR2Function, a standalone easily deployable tool that allows for the robust and high-throughput discovery of templated and non-templated isomiRs. Additionally, isomiR2Function allows for identification of differentially expressed isomiRs and in parallel target prediction based on both transcripts or PARE-Seq either using Targetfinder or Cleaveland. isomiR2Function allows for the functional enrichment of the detected targets using TopGO package. Benchmarking of isomiR2Function revealed highly accurate prediction and classification of isomiRs as compared to the previously developed isomiR prediction tools. Additionally, the downstream implementation of additional features allows isomiR2Function to be classified as a single standalone tool for isomiR profiling from discovery to functional roles. All in all, isomiR2Function allows the streamline processing of the miRNA-seq for the identification and characterization of isomiRs with minimal efforts. isomiR2Function can be accessed through: https://github.com/347033139/isomiR2Function.
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Affiliation(s)
- Kun Yang
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region – Ministry of Education, Institute of Agro-bioengineering, Guizhou UniversityGuiyang, China
- College of Life Sciences, Guizhou UniversityGuiyang, China
| | - Gaurav Sablok
- Climate Change Cluster (C3), University of Technology SydneySydney, NSW, Australia
| | - Guang Qiao
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region – Ministry of Education, Institute of Agro-bioengineering, Guizhou UniversityGuiyang, China
- College of Life Sciences, Guizhou UniversityGuiyang, China
| | - Qiong Nie
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region – Ministry of Education, Institute of Agro-bioengineering, Guizhou UniversityGuiyang, China
- College of Life Sciences, Guizhou UniversityGuiyang, China
| | - Xiaopeng Wen
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region – Ministry of Education, Institute of Agro-bioengineering, Guizhou UniversityGuiyang, China
- College of Life Sciences, Guizhou UniversityGuiyang, China
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30
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Liu Y, Liu R, Yang F, Cheng R, Chen X, Cui S, Gu Y, Sun W, You C, Liu Z, Sun F, Wang Y, Fu Z, Ye C, Zhang C, Li J, Chen X. miR-19a promotes colorectal cancer proliferation and migration by targeting TIA1. Mol Cancer 2017; 16:53. [PMID: 28257633 PMCID: PMC5336638 DOI: 10.1186/s12943-017-0625-8] [Citation(s) in RCA: 135] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 02/26/2017] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Colorectal cancer (CRC) is a major worldwide health problem due to its high prevalence and mortality rate. T-cell intracellular antigen 1 (TIA1) is an important tumor suppressor involved in many aspects of carcinogenesis and cancer development. How TIA1 expression is regulated during CRC development remains to be carefully elucidated. METHODS In CRC tissue sample pairs, TIA1 protein and mRNA levels were monitored by Western blot and qRT-PCR, respectively. Combining meta-analysis and miRNA target prediction software, we could predict microRNAs that targeted TIA1. Next, three CRC cell lines (SW480, Caco2 and HT29) were used to demonstrate the direct targeting of TIA1 by miR-19a. In addition, we investigated the biological effects of TIA1 inhibition by miR-19a both in vitro by CCK-8, EdU, Transwell, Ki67 immunofluorescence and Colony formation assays and in vivo by a xenograft mice model. RESULTS In colorectal cancer (CRC), we found that TIA1 protein, but not its mRNA, was downregulated. We predicted that TIA1 was a target of miR-19a and validated that miR-19a binded directly to the 3'-UTR of TIA1 mRNA. miR-19a could promote cell proliferation and migration in CRC cells and accelerated tumor growth in xenograft mice by targeting TIA1. CONCLUSIONS This study highlights an oncomiR role for miR-19a in regulating TIA1 in CRC and suggests that miR-19a may be a novel molecular therapeutic target for CRC.
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Affiliation(s)
- Yanqing Liu
- State Key Laboratory of Pharmaceutical Biotechnology, Collaborative Innovation Center of Chemistry for Life Sciences, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute for Life Sciences (NAILS), School of Life Sciences, Nanjing University, 163 Xianlin Road, Nanjing, Jiangsu, 210046, China
| | - Rui Liu
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, 300060, China
| | - Fei Yang
- State Key Laboratory of Pharmaceutical Biotechnology, Collaborative Innovation Center of Chemistry for Life Sciences, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute for Life Sciences (NAILS), School of Life Sciences, Nanjing University, 163 Xianlin Road, Nanjing, Jiangsu, 210046, China
| | - Rongjie Cheng
- State Key Laboratory of Pharmaceutical Biotechnology, Collaborative Innovation Center of Chemistry for Life Sciences, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute for Life Sciences (NAILS), School of Life Sciences, Nanjing University, 163 Xianlin Road, Nanjing, Jiangsu, 210046, China
| | - Xiaorui Chen
- State Key Laboratory of Pharmaceutical Biotechnology, Collaborative Innovation Center of Chemistry for Life Sciences, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute for Life Sciences (NAILS), School of Life Sciences, Nanjing University, 163 Xianlin Road, Nanjing, Jiangsu, 210046, China
| | - Shufang Cui
- State Key Laboratory of Pharmaceutical Biotechnology, Collaborative Innovation Center of Chemistry for Life Sciences, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute for Life Sciences (NAILS), School of Life Sciences, Nanjing University, 163 Xianlin Road, Nanjing, Jiangsu, 210046, China
| | - Yuanyuan Gu
- State Key Laboratory of Pharmaceutical Biotechnology, Collaborative Innovation Center of Chemistry for Life Sciences, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute for Life Sciences (NAILS), School of Life Sciences, Nanjing University, 163 Xianlin Road, Nanjing, Jiangsu, 210046, China
| | - Wu Sun
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, 300060, China
| | - Chaoying You
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, 300060, China
| | - Zhijian Liu
- Department of Gastrointestinal Surgery, Nanjing Drum Tower Hospital Clinical College of Nanjing Medical University, 321 Zhongshan Road, Nanjing, Jiangsu, 210008, China
| | - Feng Sun
- Department of Gastrointestinal Surgery, Nanjing Drum Tower Hospital Clinical College of Nanjing Medical University, 321 Zhongshan Road, Nanjing, Jiangsu, 210008, China
| | - Yanbo Wang
- State Key Laboratory of Pharmaceutical Biotechnology, Collaborative Innovation Center of Chemistry for Life Sciences, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute for Life Sciences (NAILS), School of Life Sciences, Nanjing University, 163 Xianlin Road, Nanjing, Jiangsu, 210046, China
| | - Zheng Fu
- State Key Laboratory of Pharmaceutical Biotechnology, Collaborative Innovation Center of Chemistry for Life Sciences, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute for Life Sciences (NAILS), School of Life Sciences, Nanjing University, 163 Xianlin Road, Nanjing, Jiangsu, 210046, China
| | - Chao Ye
- State Key Laboratory of Pharmaceutical Biotechnology, Collaborative Innovation Center of Chemistry for Life Sciences, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute for Life Sciences (NAILS), School of Life Sciences, Nanjing University, 163 Xianlin Road, Nanjing, Jiangsu, 210046, China
| | - Chenyu Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, Collaborative Innovation Center of Chemistry for Life Sciences, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute for Life Sciences (NAILS), School of Life Sciences, Nanjing University, 163 Xianlin Road, Nanjing, Jiangsu, 210046, China.
| | - Jing Li
- State Key Laboratory of Pharmaceutical Biotechnology, Collaborative Innovation Center of Chemistry for Life Sciences, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute for Life Sciences (NAILS), School of Life Sciences, Nanjing University, 163 Xianlin Road, Nanjing, Jiangsu, 210046, China.
| | - Xi Chen
- State Key Laboratory of Pharmaceutical Biotechnology, Collaborative Innovation Center of Chemistry for Life Sciences, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute for Life Sciences (NAILS), School of Life Sciences, Nanjing University, 163 Xianlin Road, Nanjing, Jiangsu, 210046, China.
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Su SH, Wu CH, Chiu YL, Chang SJ, Lo HH, Liao KH, Tsai CF, Tsai TN, Lin CH, Cheng SM, Cheng CC, Wang HW. Dysregulation of Vascular Endothelial Growth Factor Receptor-2 by Multiple miRNAs in Endothelial Colony-Forming Cells of Coronary Artery Disease. J Vasc Res 2017; 54:22-32. [PMID: 28122380 DOI: 10.1159/000449202] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 08/13/2016] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND/AIMS Endothelial colony-forming cells (ECFCs) have the potential to be used in regenerative medicine. Dysfunction of ECFCs is correlated with the onset of cardiovascular disorders, especially coronary artery disease (CAD). Binding of vascular endothelial growth factor A (VEGFA) to vascular endothelial growth factor receptor-2 (VEGFR2) triggers cell motility and angiogenesis of ECFCs, which are crucial to vascular repair. METHODS To identify the miRNA-VEGFR2-dependent regulation of ECFC functions, ECFCs isolated from peripheral blood of disease-free and CAD individuals were subjected to small RNA sequencing for identification of anti-VEGFR2 miRNAs. The angiogenic activities of the miRNAs were determined in both in vitro and in vivo mice models. RESULTS Three miRNAs, namely miR-410-3p, miR-497-5p, and miR-2355-5p, were identified to be upregulated in CAD-ECFCs, and VEGFR2 was their common target gene. Knockdown of these miRNAs not only restored the expression of VEGFR2 and increased angiogenic activities of CAD-ECFCs in vitro, but also promoted blood flow recovery in ischemic limbs in vivo. miR-410-3p, miR-497-5p, and miR-2355-5p could serve as potential biomarkers for CAD detection as they are highly expressed in the plasma of CAD patients. CONCLUSIONS This modulation could help develop new therapeutic modalities for cardiovascular diseases and other vascular dysregulated diseases, especially tumor angiogenesis.
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Affiliation(s)
- Shu-Han Su
- Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan, ROC
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32
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Guo L, Liang T. MicroRNAs and their variants in an RNA world: implications for complex interactions and diverse roles in an RNA regulatory network. Brief Bioinform 2016; 19:245-253. [DOI: 10.1093/bib/bbw124] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Indexed: 01/09/2023] Open
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Chung IF, Chang SJ, Chen CY, Liu SH, Li CY, Chan CH, Shih CC, Cheng WC. YM500v3: a database for small RNA sequencing in human cancer research. Nucleic Acids Res 2016; 45:D925-D931. [PMID: 27899625 PMCID: PMC5210564 DOI: 10.1093/nar/gkw1084] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 10/24/2016] [Accepted: 10/26/2016] [Indexed: 12/15/2022] Open
Abstract
We previously presented the YM500 database, which contains >8000 small RNA sequencing (smRNA-seq) data sets and integrated analysis results for various cancer miRNome studies. In the updated YM500v3 database (http://ngs.ym.edu.tw/ym500/) presented herein, we not only focus on miRNAs but also on other functional small non-coding RNAs (sncRNAs), such as PIWI-interacting RNAs (piRNAs), tRNA-derived fragments (tRFs), small nuclear RNAs (snRNAs) and small nucleolar RNAs (snoRNAs). There is growing knowledge of the role of sncRNAs in gene regulation and tumorigenesis. We have also incorporated >10 000 cancer-related RNA-seq and >3000 more smRNA-seq data sets into the YM500v3 database. Furthermore, there are two main new sections, ‘Survival' and ‘Cancer', in this updated version. The ‘Survival’ section provides the survival analysis results in all cancer types or in a user-defined group of samples for a specific sncRNA. The ‘Cancer’ section provides the results of differential expression analyses, miRNA–gene interactions and cancer miRNA-related pathways. In the ‘Expression’ section, sncRNA expression profiles across cancer and sample types are newly provided. Cancer-related sncRNAs hold potential for both biotech applications and basic research.
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Affiliation(s)
- I-Fang Chung
- Institute of Biomedical Informatics, National Yang-Ming University, Taipei 11221, Taiwan
| | - Shing-Jyh Chang
- Department of Obstetrics and Gynecology, Hsinchu MacKay Memorial Hospital, Hsinchu City 30071, Taiwan
| | - Chen-Yang Chen
- Institute of Biomedical Informatics, National Yang-Ming University, Taipei 11221, Taiwan
| | - Shu-Hsuan Liu
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, 40402, Taiwan
- Research Center for Tumour Medical Science, China Medical University, Taichung, 40402, Taiwan
| | - Chia-Yang Li
- Department of Genome Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Center for Infectious Disease and Cancer Research, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Chia-Hao Chan
- Department of Obstetrics and Gynecology, Hsinchu MacKay Memorial Hospital, Hsinchu City 30071, Taiwan
| | - Chuan-Chi Shih
- Department of Obstetrics and Gynecology, Hsinchu MacKay Memorial Hospital, Hsinchu City 30071, Taiwan
| | - Wei-Chung Cheng
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, 40402, Taiwan
- Research Center for Tumour Medical Science, China Medical University, Taichung, 40402, Taiwan
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Tsai KW, Leung CM, Lo YH, Chen TW, Chan WC, Yu SY, Tu YT, Lam HC, Li SC, Ger LP, Liu WS, Chang HT. Arm Selection Preference of MicroRNA-193a Varies in Breast Cancer. Sci Rep 2016; 6:28176. [PMID: 27307030 PMCID: PMC4910092 DOI: 10.1038/srep28176] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 05/31/2016] [Indexed: 01/28/2023] Open
Abstract
MicroRNAs (miRNAs) are short noncoding RNAs derived from the 3′ and 5′ ends of the same precursor. However, the biological function and mechanism of miRNA arm expression preference remain unclear in breast cancer. We found significant decreases in the expression levels of miR-193a-5p but no significant differences in those of miR-193a-3p in breast cancer. MiR-193a-3p suppressed breast cancer cell growth and migration and invasion abilities, whereas miR-193a-5p suppressed cell growth but did not influence cell motility. Furthermore, NLN and CCND1, PLAU, and SEPN1 were directly targeted by miR-193a-5p and miR-193a-3p, respectively, in breast cancer cells. The endogenous levels of miR-193a-5p and miR-193a-3p were significantly increased by transfecting breast cancer cells with the 3′UTR of their direct targets. Comprehensive analysis of The Cancer Genome Atlas database revealed significant differences in the arm expression preferences of several miRNAs between breast cancer and adjacent normal tissues. Our results collectively indicate that the arm expression preference phenomenon may be attributable to the target gene amount during breast cancer progression. The miRNA arm expression preference may be a means of modulating miRNA function, further complicating the mRNA regulatory network. Our findings provide a new insight into miRNA regulation and an application for breast cancer therapy.
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Affiliation(s)
- Kuo-Wang Tsai
- Department of Medical Education and Research, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan.,Department of Chemical Biology, National Pingtung University of Education, Pingtung, Taiwan
| | - Chung-Man Leung
- Department of Radiation Oncology, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Yi-Hao Lo
- Department of Family Medicine, Zuoying Branch of Kaohsiung Armed Forces General Hospital, Kaohsiung, Taiwan
| | - Ting-Wen Chen
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan.,Bioinformatics Center, Chang Gung University, Taoyuan, Taiwan
| | - Wen-Ching Chan
- Genomics &Proteomics Core Laboratory, Department of medical research, Kaohsiung, Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Shou-Yu Yu
- Department of Medical Education and Research, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Ya-Ting Tu
- Department of Medical Education and Research, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Hing-Chung Lam
- Center For Geriatrics and Gerontology, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Sung-Chou Li
- Genomics &Proteomics Core Laboratory, Department of medical research, Kaohsiung, Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Luo-Ping Ger
- Department of Medical Education and Research, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan.,Institute of Biomedical Sciences, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | - Wen-Shan Liu
- Department of Radiation Oncology, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan.,Department of Radiation Oncology, Tri-Service General Hospital, Taipei, Twiwan
| | - Hong-Tai Chang
- Center For Geriatrics and Gerontology, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan.,Department of Surgery, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
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35
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Guo L, Yu J, Liang T, Zou Q. miR-isomiRExp: a web-server for the analysis of expression of miRNA at the miRNA/isomiR levels. Sci Rep 2016; 6:23700. [PMID: 27009551 PMCID: PMC4806314 DOI: 10.1038/srep23700] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 03/09/2016] [Indexed: 12/22/2022] Open
Abstract
MicroRNA (miRNA) locus has been found that can generate a series of varied isomiR sequences. Most studies always focus on determining miRNA level, however, the canonical miRNA sequence is only a specific member in the multiple isomiRs. Some studies have shown that isomiR sequences play versatile roles in biological progress, and the analysis and research should be simultaneously performed at the miRNA/isomiR levels. Based on the biological characteristics of miRNA and isomiR, we developed miR-isomiRExp to analyze expression pattern of miRNA at the miRNA/isomiR levels, provide insights into tracking miRNA/isomiR maturation and processing mechanisms, and reveal functional characteristics of miRNA/isomiR. Simultaneously, we also performed expression analysis of specific human diseases using public small RNA sequencing datasets based on the analysis platform, which may help in surveying the potential deregulated miRNA/isomiR expression profiles, especially sequence and function-related isomiRs for further interaction analysis and study. The miR-isomiRExp platform provides miRNA/isomiR expression patterns and more information to study deregulated miRNA loci and detailed isomiR sequences. This comprehensive analysis will enrich experimental miRNA studies. miR-isomiRExp is available at http://server.malab.cn/miRisomiRExp/.
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Affiliation(s)
- Li Guo
- Department of Bioinformatics, School of Geographic and Biologic Information, Nanjing University of Posts and Telecommunications, Nanjing, 210023, China
| | - Jiafeng Yu
- Shandong Provincial Key Laboratory of Functional Macromolecular Biophysics, Institute of Biophysics, Dezhou University, Dezhou, 253023, China
| | - Tingming Liang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, 210023, China
| | - Quan Zou
- School of Computer Science and Technology, Tianjin University, Tianjin, 300072, China
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36
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Tsai CH, Liao KH, Shih CC, Chan CH, Hsieh JY, Tsai CF, Wang HW, Chang SJ. Small RNA and RNA-IP Sequencing Identifies and Validates Novel MicroRNAs in Human Mesenchymal Stem Cells. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2016; 20:191-8. [PMID: 26910904 DOI: 10.1089/omi.2015.0136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Organ regeneration therapies using multipotent mesenchymal stem cells (MSCs) are currently being investigated for a variety of common complex diseases. Understanding the molecular regulation of MSC biology will benefit regenerative medicine. MicroRNAs (miRNAs) act as regulators in MSC stemness. There are approximately 2500 currently known human miRNAs that have been recorded in the miRBase v21 database. In the present study, we identified novel microRNAs involved in MSC stemness and differentiation by obtaining the global microRNA expression profiles (miRNomes) of MSCs from two anatomical locations bone marrow (BM-MSCs) and umbilical cord Wharton's jelly (WJ-MSCs) and from osteogenically and adipogenically differentiated progenies of BM-MSCs. Small RNA sequencing (smRNA-seq) and bioinformatics analyses predicted that 49 uncharacterized miRNA candidates had high cellular expression values in MSCs. Another independent batch of Ago1/2-based RNA immunoprecipitation (RNA-IP) sequencing datasets validated the existence of 40 unreported miRNAs in cells and their associations with the RNA-induced silencing complex (RISC). Nine of these 40 new miRNAs were universally overexpressed in both MSC types; nine others were overexpressed in differentiated cells. A novel miRNA (UNI-118-3p) was specifically expressed in BM-MSCs, as verified using RT-qPCR. Taken together, this report offers comprehensive miRNome profiles for two MSC types, as well as cells differentiated from BM-MSCs. MSC transplantation has the potential to ameliorate degenerative disorders and repair damaged tissues. Interventions involving the above 40 new microRNA members in transplanted MSCs may potentially guide future clinical applications.
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Affiliation(s)
- Chin-Han Tsai
- 1 Department of Obstetrics and Gynecology, Hsinchu Mackay Memorial Hospital , Hsinchu, Taiwan
| | | | - Chuan-Chi Shih
- 1 Department of Obstetrics and Gynecology, Hsinchu Mackay Memorial Hospital , Hsinchu, Taiwan
| | - Chia-Hao Chan
- 1 Department of Obstetrics and Gynecology, Hsinchu Mackay Memorial Hospital , Hsinchu, Taiwan
| | | | | | - Hsei-Wei Wang
- 2 Institute of Microbiology and Immunology.,3 VGH-YM Genome Research Center, National Yang-Ming University , Taipei, Taiwan .,4 Departments of Education and Research, Taipei City Hospital , Taipei, Taiwan
| | - Shing-Jyh Chang
- 1 Department of Obstetrics and Gynecology, Hsinchu Mackay Memorial Hospital , Hsinchu, Taiwan
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37
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Wang HW, Su SH, Wang YL, Chang ST, Liao KH, Lo HH, Chiu YL, Hsieh TH, Huang TS, Lin CS, Cheng SM, Cheng CC. MicroRNA-134 Contributes to Glucose-Induced Endothelial Cell Dysfunction and This Effect Can Be Reversed by Far-Infrared Irradiation. PLoS One 2016; 11:e0147067. [PMID: 26799933 PMCID: PMC4723308 DOI: 10.1371/journal.pone.0147067] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 12/27/2015] [Indexed: 12/19/2022] Open
Abstract
Diabetes mellitus (DM) is a metabolic disease that is increasing worldwide. Furthermore, it is associated with the deregulation of vascular-related functions, which can develop into major complications among DM patients. Endothelial colony forming cells (ECFCs) have the potential to bring about medical repairs because of their post-natal angiogenic activities; however, such activities are impaired by high glucose- (HG) and the DM-associated conditions. Far-infrared radiation (FIR) transfers energy as heat that is perceived by the thermoreceptors in human skin. Several studies have revealed that FIR improves vascular endothelial functioning and boost angiogenesis. FIR has been used as anti-inflammatory therapy and as a clinical treatment for peripheral circulation improvement. In addition to vascular repair, there is increasing evidence to show that FIR can be applied to a variety of diseases, including cardiovascular disorders, hypertension and arthritis. Yet mechanism of action of FIR and the biomarkers that indicate FIR effects remain unclear. MicroRNA-134 (miR-134-5p) was identified by small RNA sequencing as being increased in high glucose (HG) treated dfECFCs (HG-dfECFCs). Highly expressed miR-134 was also validated in dmECFCs by RT-qPCR and it is associated with impaired angiogenic activities of ECFCs. The functioning of ECFCs is improved by FIR treatment and this occurs via a reduction in the level of miR-134 and an increase in the NRIP1 transcript, a direct target of miR-134. Using a mouse ischemic hindlimb model, the recovery of impaired blood flow in the presence of HG-dfECFCs was improved by FIR pretreatment and this enhanced functionality was decreased when there was miR-134 overexpression in the FIR pretreated HG-dfECFCs. In conclusion, our results reveal that the deregulation of miR-134 is involved in angiogenic defects found in DM patients. FIR treatment improves the angiogenic activity of HG-dfECFCs and dmECFCs and FIR has potential as a treatment for DM. Detection of miR-134 expression in FIR-treated ECFCs should help us to explore further the effectiveness of FIR therapy.
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Affiliation(s)
- Hsei-Wei Wang
- Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan
- VGH-YM Genome Research Center, National Yang-Ming University, Taipei, Taiwan
- Department of Education and Research, Taipei City Hospital, Taipei, Taiwan
| | - Shu-Han Su
- Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan
- Program in Molecular Medicine, National Yang-Ming University and Academia Sinica, Taipei, Taiwan
| | - Yen-Li Wang
- Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan
| | - Shih-Ting Chang
- Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan
| | - Ko-Hsun Liao
- Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan
| | - Hung-Hao Lo
- Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan
| | - Ya-Lin Chiu
- Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan
| | - Tsung-Han Hsieh
- Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan
| | - Tse-Shun Huang
- Institute of Engineering in Medicine, University of California, San Diego, La Jolla, California, United States of America
| | - Chin-Sheng Lin
- Division of Cardiology, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Shu-Meng Cheng
- Division of Cardiology, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Cheng-Chung Cheng
- Division of Cardiology, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
- * E-mail:
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38
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Gong J, Wu Y, Zhang X, Liao Y, Sibanda VL, Liu W, Guo AY. Comprehensive analysis of human small RNA sequencing data provides insights into expression profiles and miRNA editing. RNA Biol 2015; 11:1375-85. [PMID: 25692236 DOI: 10.1080/15476286.2014.996465] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
MicroRNAs (miRNAs) play key regulatory roles in various biological processes and diseases. A comprehensive analysis of large scale small RNA sequencing data (smRNA-seq) will be very helpful to explore tissue or disease specific miRNA markers and uncover miRNA variants. Here, we systematically analyzed 410 human smRNA-seq datasets, which samples are from 24 tissue/disease/cell lines. We tested the mapping strategies and found that it was necessary to make multiple-round mappings with different mismatch parameters. miRNA expression profiles revealed that on average ∼70% of known miRNAs were expressed at low level or not expressed (RPM < 1) in a sample and only ∼9% of known miRNAs were relatively highly expressed (RPM > 100). About 30% known miRNAs were not expressed in all of our used samples. The miRNA expression profiles were compiled into an online database (HMED, http://bioinfo.life.hust.edu.cn/smallRNA/). Dozens of tissue/disease specific miRNAs, disease/control dysregulated miRNAs and miRNAs with arm switching events were discovered. Further, we identified some highly confident editing sites including 24 A-to-I sites and 23 C-to-U sites. About half of them were widespread miRNA editing sites in different tissues. We characterized that the 2 types of editing sites have different features with regard to location, editing level and frequency. Our analyses for expression profiles, specific miRNA markers, arm switching, and editing sites, may provide valuable information for further studies of miRNA function and biomarker finding.
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Affiliation(s)
- Jing Gong
- a Hubei Bioinformatics & Molecular Imaging Key Laboratory; Department of Biomedical Engineering; Key Laboratory of Molecular Biophysics of the Ministry of Education; College of Life Science and Technology ; Huazhong University of Science and Technology ; Wuhan , China
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39
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Kaushik A, Saraf S, Mukherjee SK, Gupta D. miRMOD: a tool for identification and analysis of 5' and 3' miRNA modifications in Next Generation Sequencing small RNA data. PeerJ 2015; 3:e1332. [PMID: 26623179 PMCID: PMC4662591 DOI: 10.7717/peerj.1332] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 09/27/2015] [Indexed: 12/27/2022] Open
Abstract
In the past decade, the microRNAs (miRNAs) have emerged to be important regulators of gene expression across various species. Several studies have confirmed different types of post-transcriptional modifications at terminal ends of miRNAs. The reports indicate that miRNA modifications are conserved and functionally significant as it may affect miRNA stability and ability to bind mRNA targets, hence affecting target gene repression. Next Generation Sequencing (NGS) of the small RNA (sRNA) provides an efficient and reliable method to explore miRNA modifications. The need for dedicated software, especially for users with little knowledge of computers, to determine and analyze miRNA modifications in sRNA NGS data, motivated us to develop miRMOD. miRMOD is a user-friendly, Microsoft Windows and Graphical User Interface (GUI) based tool for identification and analysis of 5′ and 3′ miRNA modifications (non-templated nucleotide additions and trimming) in sRNA NGS data. In addition to identification of miRNA modifications, the tool also predicts and compares the targets of query and modified miRNAs. In order to compare binding affinities for the same target, miRMOD utilizes minimum free energies of the miRNA:target and modified-miRNA:target interactions. Comparisons of the binding energies may guide experimental exploration of miRNA post-transcriptional modifications. The tool is available as a stand-alone package to overcome large data transfer problems commonly faced in web-based high-throughput (HT) sequencing data analysis tools. miRMOD package is freely available at http://bioinfo.icgeb.res.in/miRMOD.
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Affiliation(s)
- Abhinav Kaushik
- Bioinformatics Laboratory, SCB Group, International Centre for Genetic Engineering & Biotechnology, New Delhi, India
| | - Shradha Saraf
- Bioinformatics Laboratory, SCB Group, International Centre for Genetic Engineering & Biotechnology, New Delhi, India
| | - Sunil K Mukherjee
- Department of Genetics, University of Delhi, South Campus, Delhi, India
| | - Dinesh Gupta
- Bioinformatics Laboratory, SCB Group, International Centre for Genetic Engineering & Biotechnology, New Delhi, India
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Evolutionary and expression analysis of miR-#-5p and miR-#-3p at the miRNAs/isomiRs levels. BIOMED RESEARCH INTERNATIONAL 2015; 2015:168358. [PMID: 26075215 PMCID: PMC4436453 DOI: 10.1155/2015/168358] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Revised: 09/27/2014] [Accepted: 09/29/2014] [Indexed: 11/18/2022]
Abstract
We mainly discussed miR-#-5p and miR-#-3p under three aspects: (1) primary evolutionary analysis of human miRNAs; (2) evolutionary analysis of miRNAs from different arms across the typical 10 vertebrates; (3) expression pattern analysis of miRNAs at the miRNA/isomiR levels using public small RNA sequencing datasets. We found that no bias can be detected between the numbers of 5p-miRNA and 3p-miRNA, while miRNAs from miR-#-5p and miR-#-3p show variable nucleotide compositions. IsomiR expression profiles from the two arms are always stable, but isomiR expressions in diseased samples are prone to show larger degree of dispersion. miR-#-5p and miR-#-3p have relative independent evolution/expression patterns and datasets of target mRNAs, which might also contribute to the phenomena of arm selection and/or arm switching. Simultaneously, miRNA/isomiR expression profiles may be regulated via arm selection and/or arm switching, and the dynamic miRNAome and isomiRome will adapt to functional and/or evolutionary pressures. A comprehensive analysis and further experimental study at the miRNA/isomiR levels are quite necessary for miRNA study.
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Cheng WC, Chung IF, Tsai CF, Huang TS, Chen CY, Wang SC, Chang TY, Sun HJ, Chao JYC, Cheng CC, Wu CW, Wang HW. YM500v2: a small RNA sequencing (smRNA-seq) database for human cancer miRNome research. Nucleic Acids Res 2014; 43:D862-7. [PMID: 25398902 PMCID: PMC4383957 DOI: 10.1093/nar/gku1156] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
We previously presented YM500, which is an integrated database for miRNA quantification, isomiR identification, arm switching discovery and novel miRNA prediction from 468 human smRNA-seq datasets. Here in this updated YM500v2 database (http://ngs.ym.edu.tw/ym500/), we focus on the cancer miRNome to make the database more disease-orientated. New miRNA-related algorithms developed after YM500 were included in YM500v2, and, more significantly, more than 8000 cancer-related smRNA-seq datasets (including those of primary tumors, paired normal tissues, PBMC, recurrent tumors, and metastatic tumors) were incorporated into YM500v2. Novel miRNAs (miRNAs not included in the miRBase R21) were not only predicted by three independent algorithms but also cleaned by a new in silico filtration strategy and validated by wetlab data such as Cross-Linked ImmunoPrecipitation sequencing (CLIP-seq) to reduce the false-positive rate. A new function 'Meta-analysis' is additionally provided for allowing users to identify real-time differentially expressed miRNAs and arm-switching events according to customer-defined sample groups and dozens of clinical criteria tidying up by proficient clinicians. Cancer miRNAs identified hold the potential for both basic research and biotech applications.
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Affiliation(s)
- Wei-Chung Cheng
- Research Center for Tumor Medical Science, China Medical University, Taichung 40402, Taiwan
| | - I-Fang Chung
- Institute of Biomedical Informatics, National Yang-Ming University, Taipei 11221, Taiwan
| | - Cheng-Fong Tsai
- Institute of Biomedical Informatics, National Yang-Ming University, Taipei 11221, Taiwan VGH-YM Genomic Research Center, National Yang-Ming University, Taipei 11221, Taiwan
| | - Tse-Shun Huang
- Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Chen-Yang Chen
- Institute of Biomedical Informatics, National Yang-Ming University, Taipei 11221, Taiwan VGH-YM Genomic Research Center, National Yang-Ming University, Taipei 11221, Taiwan
| | - Shao-Chuan Wang
- Institute of Biomedical Informatics, National Yang-Ming University, Taipei 11221, Taiwan
| | - Ting-Yu Chang
- VGH-YM Genomic Research Center, National Yang-Ming University, Taipei 11221, Taiwan
| | - Hsing-Jen Sun
- Institute of Biomedical Informatics, National Yang-Ming University, Taipei 11221, Taiwan
| | - Jeffrey Yung-Chuan Chao
- Institute of Clinical Medicine, Medical College, National Yang-Ming University, Taipei 11221, Taiwan Department of Radiation Oncology, Taichung Veterans' General Hospital, Taichung 40705, Taiwan
| | - Cheng-Chung Cheng
- Division of Cardiology, Department of Internal Medicine, Tri-Service General Hospital, National Defence Medical Center, Taipei 11490, Taiwan
| | - Cheng-Wen Wu
- Institute of Clinical Medicine, Medical College, National Yang-Ming University, Taipei 11221, Taiwan Institute of Biomedical Science, Academia Sinica, Taipei 11529, Taiwan Institute of Biochemistry and Molecular Biology, National Yang Ming University, Taipei 11221, Taiwan
| | - Hsei-Wei Wang
- Institute of Biomedical Informatics, National Yang-Ming University, Taipei 11221, Taiwan VGH-YM Genomic Research Center, National Yang-Ming University, Taipei 11221, Taiwan Institute of Clinical Medicine, Medical College, National Yang-Ming University, Taipei 11221, Taiwan Institute of Microbiology and Immunology, National Yang-Ming University, Taipei 11221, Taiwan Department of Education and Research, Taipei City Hospital, Taipei 10341, Taiwan
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Zhang H, Yang S, Guo L, Zhao Y, Shao F, Chen F. Comparisons of isomiR patterns and classification performance using the rank-based MANOVA and 10-fold cross-validation. Gene 2014; 569:21-6. [PMID: 25447923 DOI: 10.1016/j.gene.2014.11.026] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Revised: 11/07/2014] [Accepted: 11/11/2014] [Indexed: 12/29/2022]
Abstract
Next generation sequencing technology has identified a series of miRNA variants (named "isomiRs"), which might be associated with cancer progression. We provide a new strategy to reanalyze the miR-seq datasets through a view of the isomiR spectrum. Firstly, differentially expressed (DE) isomiRs were detected with the DESeq algorithm based on negative binomial distribution. Secondly, the rank-based MANOVA was adopted to compare the isomiR patterns between normal and tumor tissues. Moreover, a comprehensive survey on classification performance of three features was conducted, including the logistic regression, k-nearest neighbors and Random Forest. Finally, functional enrichment analysis was performed with the putative targets of specific isomiRs to elucidate their biological functions. Furthermore, the methods were applied to the downloaded miR-seq datasets of breast invasive carcinoma from TCGA. We found that the expression levels of multiple isomiRs derived from the same miRNA locus showed significant inconsistency between normal and tumor samples. In most cases, logistic regression with multiple DE isomiRs was superior to the others, with highest AUC and lowest AIC. Similarly, DE isomiRs performed best in the average accuracy of standard classifiers. Integrated targets were significantly enriched in some cancer-related pathways, including MAPK signaling pathway, and focal adhesion. Collectively, we could recommend the rank-based MANOVA for comparing different isomiR patterns, and further investigation on isomiRs needs to be considered in miRNA sequencing research.
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Affiliation(s)
- Hui Zhang
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Sheng Yang
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Li Guo
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Yang Zhao
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Fang Shao
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Feng Chen
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing 211166, China.
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Chang TY, Huang TS, Wang HW, Chang SJ, Lo HH, Chiu YL, Wang YL, Hsiao CD, Tsai CH, Chan CH, You RI, Wu CH, Tsai TN, Cheng SM, Cheng CC. miRNome traits analysis on endothelial lineage cells discloses biomarker potential circulating microRNAs which affect progenitor activities. BMC Genomics 2014; 15:802. [PMID: 25236949 PMCID: PMC4176563 DOI: 10.1186/1471-2164-15-802] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Accepted: 08/26/2014] [Indexed: 01/12/2023] Open
Abstract
Background Endothelial progenitor cells (EPCs) play a fundamental role in not only blood vessel development but also post-natal vascular repair. Currently EPCs are defined as early and late EPCs based on their biological properties and their time of appearance during in vitro culture. Both EPC types assist angiogenesis and have been linked to ischemia-related disorders, including coronary artery disease (CAD). Results We found late EPCs are more mobile than early EPCs and matured endothelial cells (ECs). To pinpoint the mechanism, microRNA profiles of early EPCs late EPCs, and ECs were deciphered by small RNA sequencing. Obtained signatures made up of both novel and known microRNAs, in which anti-angiogenic microRNAs such as miR-221 and miR-222 are more abundant in matured ECs than in late EPCs. Overexpression of miR-221 and miR-222 resulted in the reduction of genes involved in hypoxia response, metabolism, TGF-beta signalling, and cell motion. Not only hamper late EPC activities in vitro, both microRNAs (especially miR-222) also hindered in vivo vasculogenesis in a zebrafish model. Reporter assays showed that miR-222, but not miR-221, targets the angiogenic factor ETS1. In contrast, PIK3R1 is the target of miR-221, but not miR-222 in late EPCs. Clinically, both miR-221-PIK3R1 and miR-222-ETS1 pairs are deregulated in late EPCs of CAD patients. Conclusions Our results illustrate EPCs and ECs exploit unique miRNA modalities to regulate angiogenic features, and explain why late EPC levels and activities are reduced in CAD patients. These data will further help to develop new plasma biomarkers and therapeutic approaches for ischemia-related diseases or tumor angiogenesis. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-802) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Cheng-Chung Cheng
- Division of Cardiology, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan.
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Omer A, Singh P, Yadav NK, Singh RK. microRNAs: role in leukemia and their computational perspective. WILEY INTERDISCIPLINARY REVIEWS-RNA 2014; 6:65-78. [PMID: 25132152 DOI: 10.1002/wrna.1256] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Revised: 06/19/2014] [Accepted: 06/26/2014] [Indexed: 12/22/2022]
Abstract
MicroRNAs (miRNAs) belong to the family of noncoding RNAs (ncRNAs) and had gained importance due to its role in complex biochemical pathways. Changes in the expression of protein coding genes are the major cause of leukemia. Role of miRNAs as tumor suppressors has provided a new insight in the field of leukemia research. Particularly, the miRNAs mediated gene regulation involves the modulation of multiple mRNAs and cooperative action of different miRNAs to regulate a particular gene expression. This highly complex array of regulatory pathway network indicates the great possibility in analyzing and identifying novel findings. Owing to the conventional, slow experimental identification process of miRNAs and their targets, the last decade has witnessed the development of a large amount of computational approaches to deal with the complex interrelations present within biological systems. This article describes the various roles played by miRNAs in regulating leukemia and the role of computational approaches in exploring new possibilities.
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Affiliation(s)
- Ankur Omer
- Division of Toxicology, CSIR-Central Drug Research Institute, Lucknow, India; Academy of Scientific & Innovative Research (AcSIR), New Delhi, India
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Dysregulated miR-361-5p/VEGF axis in the plasma and endothelial progenitor cells of patients with coronary artery disease. PLoS One 2014; 9:e98070. [PMID: 24865854 PMCID: PMC4035317 DOI: 10.1371/journal.pone.0098070] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2014] [Accepted: 04/24/2014] [Indexed: 02/07/2023] Open
Abstract
Dysfunction and reduction of circulating endothelial progenitor cell (EPC) is correlated with the onset of cardiovascular disorders including coronary artery disease (CAD). VEGF is a known mitogen for EPC to migrate out of bone marrow to possess angiogenic activities, and the plasma levels of VEGF are inversely correlated to the progression of CAD. Circulating microRNAs (miRNAs) in patient body fluids have recently been considered to hold the potential of being novel disease biomarkers and drug targets. However, how miRNAs and VEGF cooperate to regulate CAD progression is still unclear. Through the small RNA sequencing (smRNA-seq), we deciphered the miRNome patterns of EPCs with different angiogenic activities, hypothesizing that miRNAs targeting VEGF must be more abundant in EPCs with lower angiogenic activities. Candidates of anti-VEGF miRNAs, including miR-361-5p and miR-484, were enriched in not only diseased EPCs but also the plasma of CAD patients. However, we found out only miR-361-5p, but not miR-484, was able to suppress VEGF expression and EPC activities. Reporter assays confirmed the direct binding and repression of miR-361-5p to the 3′-UTR of VEGF mRNA. Knock down of miR-361-5p not only restored VEGF levels and angiogenic activities of diseased EPCs in vitro, but further promoted blood flow recovery in ischemic limbs of mice. Collectively, we discovered a miR-361-5p/VEGF-dependent regulation that could help to develop new therapeutic modalities not only for ischemia-related diseases but also for tumor angiogenesis.
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Hsieh TH, Chien CL, Lee YH, Lin CI, Hsieh JY, Chao ME, Liu DJ, Chu SS, Chen W, Lin SC, Ho DMT, Liu RS, Lin CH, Wong TT, Wang HW. Downregulation of SUN2, a novel tumor suppressor, mediates miR-221/222-induced malignancy in central nervous system embryonal tumors. Carcinogenesis 2014; 35:2164-74. [DOI: 10.1093/carcin/bgu105] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
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47
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A challenge for miRNA: multiple isomiRs in miRNAomics. Gene 2014; 544:1-7. [PMID: 24768184 DOI: 10.1016/j.gene.2014.04.039] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2014] [Revised: 04/11/2014] [Accepted: 04/18/2014] [Indexed: 11/22/2022]
Abstract
Accumulating evidence suggests that a single microRNA (miRNA) locus can generate a series of sequences during miRNA maturation process. These multiple sequences, called miRNA variants, or isomiRs, have different lengths and different 5' and 3' ends. Some of these isomiRs are detected as varied nucleotides and 3' additional non-template nucleotides. As physiological miRNA isoforms, they have drawn attention for possible regulatory biological roles. The present work mainly reviews miRNA/isomiR biogenesis, isomiR expression patterns, and functional and evolutionary implications, especially between isomiRs from homologous and clustered miRNA loci. The phenomenon of multiple isomiRs and their biological roles indicates that analysis performed at the miRNA and isomiR levels should be included in miRNA studies. This may enrich and complicate miRNA biogenesis and coding-non-coding RNA regulatory networks.
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48
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Abstract
A mature miRNA may be generated from 5p or 3p arm of a hairpin precursor. The selection may be flexible via "arm switching". However, accumulating evidences suggest that both arms of many pre-miRNAs can yield mature functional miRNAs. Herein, we attempted to compare the isomiR expression profiles between the two arms through analyzing in-house and published small RNA deep sequencing datasets. Although many miR-#-5p and miR-#-3p have been reported as functional miRNAs, fewer miRNA pairs (11 and 6 pairs are collected in tumor and normal cells, respectively) are simultaneously identified as abundant miRNA species. According to isomiR types and dominant isomiR species, miR-#-5p and miR-#-3p show various isomiR expression profiles as well as diverse enrichment levels. IsomiR profiles of non-dominant arm are not well-conserved in 5' ends as well as isomiR profiles of dominant arm. If both the miR-#-5p and miR-#-3p are abundantly expressed, their isomiR expression profiles are always stable across different samples. Similar to diverse enrichment levels of miR-#-5p and miR-#-3p, the isomiR expression patterns may also be influenced by the phenomenon of "arm switching". The diverged isomiR expression profiles further enrich the complexity of multiple isomiRs, and complicate the coding-non-coding RNA regulatory network.
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49
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Ezzine S, Vassaux G, Pitard B, Barteau B, Malinge JM, Midoux P, Pichon C, Baril P. RILES, a novel method for temporal analysis of the in vivo regulation of miRNA expression. Nucleic Acids Res 2013; 41:e192. [PMID: 24013565 PMCID: PMC3814383 DOI: 10.1093/nar/gkt797] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Novel methods are required to investigate the complexity of microRNA (miRNA) biology and particularly their dynamic regulation under physiopathological conditions. Herein, a novel plasmid-based RNAi-Inducible Luciferase Expression System (RILES) was engineered to monitor the activity of endogenous RNAi machinery. When RILES is transfected in a target cell, the miRNA of interest suppresses the expression of a transcriptional repressor and consequently switch-ON the expression of the luciferase reporter gene. Hence, miRNA expression in cells is signed by the emission of bioluminescence signals that can be monitored using standard bioluminescence equipment. We validated this approach by monitoring in mice the expression of myomiRs-133, −206 and −1 in skeletal muscles and miRNA-122 in liver. Bioluminescence experiments demonstrated robust qualitative and quantitative data that correlate with the miRNA expression pattern detected by quantitative RT-PCR (qPCR). We further demonstrated that the regulation of miRNA-206 expression during the development of muscular atrophy is individual-dependent, time-regulated and more complex than the information generated by qPCR. As RILES is simple and versatile, we believe that this methodology will contribute to a better understanding of miRNA biology and could serve as a rationale for the development of a novel generation of regulatable gene expression systems with potential therapeutic applications.
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Affiliation(s)
- Safia Ezzine
- Centre de Biophysique Moléculaire, CNRS UPR4301, Université d'Orléans and Inserm, Orléans, France, UMRE 4320, Faculté de Médecine, Université de Nice-Sophia-Antipolis, Nice, France, Inserm UMR 1087/CNRS UMR 6291, Université de Nantes, Faculté de médecine, L'institut du Thorax, Nantes F-44000 and In-Cell-Art, Nantes F44200, France
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Hsieh JY, Huang TS, Cheng SM, Lin WS, Tsai TN, Lee OK, Wang HW. miR-146a-5p circuitry uncouples cell proliferation and migration, but not differentiation, in human mesenchymal stem cells. Nucleic Acids Res 2013; 41:9753-63. [PMID: 23963696 PMCID: PMC3834804 DOI: 10.1093/nar/gkt666] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Administration of mesenchymal stem cells (MSCs) has the potential to ameliorate degenerative disorders and to repair damaged tissues. The homing of transplanted MSCs to injured sites is a critical property of engraftment. Our aim was to identify microRNAs involved in controlling MSC proliferation and migration. MSCs can be isolated from bone marrow and umbilical cord Wharton’s jelly (BM-MSCs and WJ-MSCs, respectively), and WJ-MSCs show poorer motility yet have a better amplification rate compared with BM-MSCs. Small RNA sequencing revealed that miR-146a-5p is significantly overexpressed and has high abundance in WJ-MSCs. Knockdown of miR-146a-5p in WJ-MSCs inhibited their proliferation yet enhanced their migration, whereas overexpression of miR-146a-5p in BM-MSCs did not influence their osteogenic and adipogenic potentials. Chemokine (C-X-C motif) ligand 12 (CXCL12), together with SIKE1, which is an I-kappa-B kinase epsilon (IKKε) suppressor, is a direct target of miR-146a-5p in MSCs. Knockdown of miR-146a-5p resulted in the down-regulation of nuclear factor kappa-B (NF-κB) activity, which is highly activated in WJ-MSCs and is known to activate miR-146a-5p promoter. miR-146a-5p is also downstream of CXCL12, and a negative feedback loop is therefore formed in MSCs. These findings suggest that miR-146a-5p is critical to the uncoupling of motility and proliferation of MSCs. Our miRNome data also provide a roadmap for further understanding MSC biology.
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Affiliation(s)
- Jui-Yu Hsieh
- Department of Life Sciences, Institute of Microbiology and Immunology, National Yang-Ming University, Linong St. Taipei, Taiwan 11221, Division of Cardiology, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Chenggong Rd. Taipei, Taiwan 11490, Department of Medical Research and Education, Taipei Veteran General Hospital, Shipai Rd., Taipei, Taiwan 11217, Stem Cell Research Center, National Yang-Ming University, Linong St. Taipei, Taiwan 11221, Institute of Clinical Medicine, National Yang-Ming University, Taipei, Taiwan, Veteran General Hospital-Yang Ming Genome Research Center, National Yang-Ming University, Linong St. Taipei, Taiwan 11221, Department of Education and Research, Taipei City Hospital, Zhengzhou Rd. Taipei, Taiwan 10341 and Cancer Research Center and Genome Research Center, National Yang-Ming University, Linong St. Taipei, Taiwan 11221
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