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Cheng YF, Gu XJ, Yang TM, Wei QQ, Cao B, Zhang Y, Shang HF, Chen YP. Signature of miRNAs derived from the circulating exosomes of patients with amyotrophic lateral sclerosis. Front Aging Neurosci 2023; 15:1106497. [PMID: 36845651 PMCID: PMC9951117 DOI: 10.3389/fnagi.2023.1106497] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 01/09/2023] [Indexed: 02/12/2023] Open
Abstract
Background Amyotrophic lateral sclerosis (ALS) is a progressive, fatal neurodegenerative disorder (NDS) with unclear pathophysiology and few therapeutic options. Mutations in SOD1 and C9orf72 are the most common in Asian and Caucasian patients with ALS, respectively. Aberrant (microRNAs) miRNAs found in patients with gene-mutated ALS may be involved in the pathogenesis of gene-specific ALS and sporadic ALS (SALS). The aim of this study was to screen for differentially expressed miRNAs from exosomes in patients with ALS and healthy controls (HCs) and to construct a miRNA-based diagnostic model to classify patients and HCs. Methods We compared circulating exosome-derived miRNAs of patients with ALS and HCs using the following two cohorts: a discovery cohort (three patients with SOD1-mutated ALS, three patients with C9orf72-mutated ALS, and three HCs) analyzed by microarray and a validation cohort (16 patients with gene-mutated ALS, 65 patients with SALS, and 61 HCs) confirmed by RT-qPCR. The support vector machine (SVM) model was used to help diagnose ALS using five differentially expressed miRNAs between SALS and HCs. Results A total of 64 differentially expressed miRNAs in patients with SOD1-mutated ALS and 128 differentially expressed miRNAs in patients with C9orf72-mutated ALS were obtained by microarray compared to HCs. Of these, 11 overlapping dysregulated miRNAs were identified in both groups. Among the 14 top-hit candidate miRNAs validated by RT-qPCR, hsa-miR-34a-3p was specifically downregulated in patients with SOD1-mutated ALS, while hsa-miR-1306-3p was downregulated in ALS patients with both SOD1 and C9orf72 mutations. In addition, hsa-miR-199a-3p and hsa-miR-30b-5p were upregulated significantly in patients with SALS, while hsa-miR-501-3p, hsa-miR-103a-2-5p, and hsa-miR-181d-5p had a trend to be upregulated. The SVM diagnostic model used five miRNAs as features to distinguish ALS from HCs in our cohort with an area under receiver operating characteristic curve (AUC) of 0.80. Conclusion Our study identified aberrant miRNAs from exosomes of SALS and ALS patients with SOD1/C9orf72 mutations and provided additional evidence that aberrant miRNAs were involved in the pathogenesis of ALS regardless of the presence or absence of the gene mutation. The machine learning algorithm had high accuracy in predicting the diagnosis of ALS, shedding light on the foundation for the clinical application of blood tests in the diagnosis of ALS, and revealing the pathological mechanisms of the disease.
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Affiliation(s)
- Yang-Fan Cheng
- Department of Neurology, Laboratory of Neurodegenerative Disorders, Rare Disease Center, West China Hospital, Sichuan University, Chengdu, China,Laboratory of Neurodegenerative Disorders, National Clinical Research Center for Geriatric, West China Hospital, Sichuan University, Chengdu, China
| | - Xiao-Jing Gu
- Department of Neurology, Laboratory of Neurodegenerative Disorders, Rare Disease Center, West China Hospital, Sichuan University, Chengdu, China,Laboratory of Neurodegenerative Disorders, National Clinical Research Center for Geriatric, West China Hospital, Sichuan University, Chengdu, China
| | - Tian-Mi Yang
- Department of Neurology, Laboratory of Neurodegenerative Disorders, Rare Disease Center, West China Hospital, Sichuan University, Chengdu, China
| | - Qian-Qian Wei
- Department of Neurology, Laboratory of Neurodegenerative Disorders, Rare Disease Center, West China Hospital, Sichuan University, Chengdu, China
| | - Bei Cao
- Department of Neurology, Laboratory of Neurodegenerative Disorders, Rare Disease Center, West China Hospital, Sichuan University, Chengdu, China
| | - Yang Zhang
- West China School of Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Hui-Fang Shang
- Department of Neurology, Laboratory of Neurodegenerative Disorders, Rare Disease Center, West China Hospital, Sichuan University, Chengdu, China,Laboratory of Neurodegenerative Disorders, National Clinical Research Center for Geriatric, West China Hospital, Sichuan University, Chengdu, China,*Correspondence: Hui-Fang Shang,
| | - Yong-Ping Chen
- Department of Neurology, Laboratory of Neurodegenerative Disorders, Rare Disease Center, West China Hospital, Sichuan University, Chengdu, China,Laboratory of Neurodegenerative Disorders, National Clinical Research Center for Geriatric, West China Hospital, Sichuan University, Chengdu, China,Yong-Ping Chen,
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2
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Abu-Shahba N, Hegazy E, Khan FM, Elhefnawi M. In Silico Analysis of MicroRNA Expression Data in Liver Cancer. Cancer Inform 2023; 22:11769351231171743. [PMID: 37200943 PMCID: PMC10185868 DOI: 10.1177/11769351231171743] [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: 11/30/2022] [Accepted: 04/04/2023] [Indexed: 05/20/2023] Open
Abstract
Abnormal miRNA expression has been evidenced to be directly linked to HCC initiation and progression. This study was designed to detect possible prognostic, diagnostic, and/or therapeutic miRNAs for HCC using computational analysis of miRNAs expression. Methods: miRNA expression datasets meta-analysis was performed using the YM500v2 server to compare miRNA expression in normal and cancerous liver tissues. The most significant differentially regulated miRNAs in our study undergone target gene analysis using the mirWalk tool to obtain their validated and predicted targets. The combinatorial target prediction tool; miRror Suite was used to obtain the commonly regulated target genes. Functional enrichment analysis was performed on the resulting targets using the DAVID tool. A network was constructed based on interactions among microRNAs, their targets, and transcription factors. Hub nodes and gatekeepers were identified using network topological analysis. Further, we performed patient data survival analysis based on low and high expression of identified hubs and gatekeeper nodes, patients were stratified into low and high survival probability groups. Results: Using the meta-analysis option in the YM500v2 server, 34 miRNAs were found to be significantly differentially regulated (P-value ⩽ .05); 5 miRNAs were down-regulated while 29 were up-regulated. The validated and predicted target genes for each miRNA, as well as the combinatorially predicted targets, were obtained. DAVID enrichment analysis resulted in several important cellular functions that are directly related to the main cancer hallmarks. Among these functions are focal adhesion, cell cycle, PI3K-Akt signaling, insulin signaling, Ras and MAPK signaling pathways. Several hub genes and gatekeepers were found that could serve as potential drug targets for hepatocellular carcinoma. POU2F1 and PPARA showed a significant difference between low and high survival probabilities (P-value ⩽ .05) in HCC patients. Our study sheds light on important biomarker miRNAs for hepatocellular carcinoma along with their target genes and their regulated functions.
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Affiliation(s)
- Nourhan Abu-Shahba
- Department of Medical Molecular Genetics, Human Genetics and Genome Research Institute, National Research Centre, Cairo, Egypt
- Stem Cell Research Group, Medical Research Center of Excellence, National Research Centre, Cairo, Egypt
| | - Elsayed Hegazy
- School of Information Technology and Computer Science, Nile University, Giza, Egypt
| | - Faiz M. Khan
- Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany
| | - Mahmoud Elhefnawi
- Biomedical Informatics and Chemoinformatics Group, Informatics and Systems Department, National Research Centre, Cairo, Egypt
- Mahmoud Elhefnawi, Biomedical Informatics and Chemoinformatics Group, Informatics and Systems Department, National Research Centre, 33, elbohouth street, Cairo 11211, Egypt.
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Wang S, He X, Bao N, Chen M, Ding X, Zhang M, Zhao L, Wang S, Jiang G. Potentials of miR-9-5p in promoting epileptic seizure and improving survival of glioma patients. ACTA EPILEPTOLOGICA 2022. [DOI: 10.1186/s42494-022-00097-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Abstract
Background
Epilepsy affects over 70 million people worldwide; however, the underlying mechanisms remain unclear. MicroRNAs (miRNAs) have essential functions in epilepsy. miRNA-9, a brain-specific/enriched miRNA, plays a role in various nervous system diseases and tumors, but whether miRNA-9 is involved in epilepsy and glioma-associated epilepsy remains unknown. Therefore, we aimed to explore the potential role of miR-9-5p in seizures and its effect on the survival of glioma patients, in order to provide new targets for the treatment of epilepsy and glioma.
Methods
The YM500v2 database was used to validate the expression of hsa-miR-9-5p in tissues. Moreover, qRT-PCR was performed to investigate the expression of miR-9-5p in temporal lobe epilepsy patients and rats with lithium-pilocarpine-induced seizures. Recombinant adeno-associated virus containing miR-9-5p was constructed to overexpress miR-9-5p in vivo. The effects of miR-9-5p on the behavior and electroencephalographic activities of the lithium-pilocarpine rat model of epilepsy were tested. Bioinformatics analysis was used to predict the targets of miR-9-5p and explore its potential role in epilepsy and glioma-associated epilepsy.
Results
The expression of miR-9-5p increased at 6 h and 7 days after lithium-pilocarpine-induced seizures in rats. Overexpression of miR-9-5p significantly shortened the latency of seizures and increased seizure intensity at 10 min and 20 min after administration of pilocarpine (P < 0.05). Predicted targets of miR-9-5p were abundant and enriched in the brain, and affected various pathways related to epilepsy and tumor. Survival analysis revealed that overexpression of miR-9-5p significantly improved the survival of patients from with low-grade gliomas and glioblastomas. The involvement of miR-9-5p in the glioma-associated epileptic seizures and the improvement of glioma survival may be related to multiple pathways, including the Rho GTPases and hub genes included SH3PXD2B, ARF6, and ANK2.
Conclusions
miR-9-5p may play a key role in promoting epileptic seizures and improving glioma survival, probably through multiple pathways, including GTPases of the Rho family and hub genes including SH3PXD2B, ARF6 and ANK2. Understanding the roles of miR-9-5p in epilepsy and glioma and the underlying mechanisms may provide a theoretical basis for the diagnosis and treatment of patients with epilepsy and glioma.
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Jain CK, Srivastava P, Pandey AK, Singh N, Kumar RS. miRNA therapeutics in precision oncology: a natural premium to nurture. EXPLORATION OF TARGETED ANTI-TUMOR THERAPY 2022; 3:511-532. [PMID: 36071981 PMCID: PMC9446160 DOI: 10.37349/etat.2022.00098] [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: 04/06/2022] [Accepted: 06/02/2022] [Indexed: 11/22/2022] Open
Abstract
The dynamic spectrum of microRNA (miRNA) has grown significantly over the years with its identification and exploration in cancer therapeutics and is currently identified as an important resource for innovative strategies due to its functional behavior for gene regulation and modulation of complex biological networks. The progression of cancer is the consequence of uncontrolled, nonsynchronous procedural faults in the biological system. Diversified and variable cellular response of cancerous cells has always raised challenges in effective cancer therapy. miRNAs, a class of non-coding RNAs (ncRNAs), are the natural genetic gift, responsible to preserve the homeostasis of cell to nurture. The unprecedented significance of endogenous miRNAs has exhibited promising therapeutic potential in cancer therapeutics. Currently, miRNA mimic miR-34, and an antimiR aimed against miR-122 has entered the clinical trials for cancer treatments. This review, highlights the recent breakthroughs, challenges, clinical trials, and advanced delivery vehicles in the administration of miRNA therapies for precision oncology.
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Affiliation(s)
- Chakresh Kumar Jain
- Department of Biotechnology, Jaypee Institute of Information Technology, Noida 201307, India
| | - Poornima Srivastava
- Department of Biotechnology, Jaypee Institute of Information Technology, Noida 201307, India
| | - Amit Kumar Pandey
- Amity Institute of Biotechnology, Amity University Haryana, Panchgaon, Manesar, Haryana 122413, India
| | - Nisha Singh
- Department of Bioinformatics, Gujarat Biotechnology University, Gandhinagar, GIFT city 382355, India
| | - R Suresh Kumar
- Molecular Genetics Lab, Molecular Biology Group, National Institute of Cancer Prevention and Research (ICMR), Noida 201307, India
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ROS-Responsive miR-150-5p Downregulation Contributes to Cigarette Smoke-Induced COPD via Targeting IRE1α. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:5695005. [PMID: 35571237 PMCID: PMC9098354 DOI: 10.1155/2022/5695005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 04/08/2022] [Indexed: 12/12/2022]
Abstract
MicroRNAs (miRNAs) have been reported in human diseases, in which chronic obstructive pulmonary disease (COPD) is included. Herein, we assessed the role along with the possible mechanisms of miR-150-5p in cigarette smoke- (CS-) induced COPD. The plasma miR-150-5p expression was lower in patients with COPD and acute exacerbation of COPD (AECOPD) and was related to disease diagnosis, disease severity, and lung function. Consistently, exposure to CS for 3 months or 3 days reduced miR-150-5p in the plasma and lung tissues of mice, and CS extract (CSE) inhibited miR-150-5p in human bronchial epithelial cells (HBECs) in a concentration along with time-dependent approach. In vitro, miR-150-5p overexpression decreased the contents of inflammatory factors interleukin- (IL-) 6, IL-8 along with cyclooxygenase-2 (COX-2), and endoplasmic reticulum (ER) stress markers glucose-regulated protein (GRP) 78 and C/-EBP homologous protein (CHOP) and promoted cell migrate. Mechanistically, miR-150-5p could bind with the 3′-untranslated region (UTR) of inositol requiring enzyme 1α (IRE1α), while IRE1α overexpression obliterated the impacts of miR-150-5p. Besides, N-acetyl-cysteine (NAC) reversed CSE-induced miR-150-5p downregulation and its downstream effects. In vivo, miR-150-5p overexpression counteracted CS-triggered IRE1α upregulation, inflammation, and ER stress in the lung tissues of mice. In conclusion, our findings illustrated that ROS-mediated downregulation of miR-150-5p led to CS-induced COPD by inhibiting IRE1α expression, suggesting to serve as a useful biomarker for diagnosing and treating COPD.
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6
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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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7
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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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8
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Mahjoubin-Tehran M, Rezaei S, Jalili A, Sahebkar A, Aghaee-Bakhtiari SH. A comprehensive review of online resources for microRNA-diseases associations: the state of the art. Brief Bioinform 2021; 23:6376589. [PMID: 34571538 DOI: 10.1093/bib/bbab381] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 08/07/2021] [Accepted: 08/24/2021] [Indexed: 12/16/2022] Open
Abstract
MicroRNAs (miRNAs) as small 19- to 24-nucleotide noncoding RNAs regulate several mRNA targets and signaling pathways. Therefore, miRNAs are considered key regulators in cellular pathways as well as various pathologies. There is substantial interest in the relationship between disease and miRNAs, which made that one of the important research topics. Interestingly, miRNAs emerged as an attractive approach for clinical application, not only as biomarkers for diagnosis and prognosis or in the prediction of therapy response but also as therapeutic tools. For these purposes, the identification of crucial miRNAs in disease is very important. Databases provided valuable experimental and computational miRNAs-disease information in an accessible and comprehensive manner, such as miRNA target genes, miRNA related in signaling pathways and miRNA involvement in various diseases. In this review, we summarized miRNAs-disease databases in two main categories based on the general or specific diseases. In these databases, researchers could search diseases to identify critical miRNAs and developed that for clinical applications. In another way, by searching particular miRNAs, they could recognize in which disease these miRNAs would be dysregulated. Despite the significant development that has been done in these databases, there are still some limitations, such as not being updated and not providing uniform and detailed information that should be resolved in future databases. This survey can be helpful as a comprehensive reference for choosing a suitable database by researchers and as a guideline for comparing the features and limitations of the database by developer or designer. Short abstract We summarized miRNAs-disease databases that researchers could search disease to identify critical miRNAs and developed that for clinical applications. This survey can help choose a suitable database for researchers.
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Affiliation(s)
- Maryam Mahjoubin-Tehran
- Bioinformatics Research Group, Mashhad University of Medical Sciences, Mashhad, Iran and Department of Medical Biotechnology and Nanotechnology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Samaneh Rezaei
- Bioinformatics Research Group, Mashhad University of Medical Sciences, Mashhad, Iran and Department of Medical Biotechnology and Nanotechnology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Amin Jalili
- Bioinformatics Research Group, Mashhad University of Medical Sciences, Mashhad, Iran and Department of Medical Biotechnology and Nanotechnology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Amirhossein Sahebkar
- Bioinformatics Research Group, Mashhad University of Medical Sciences, Mashhad, Iran and Department of Medical Biotechnology and Nanotechnology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
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Patil AH, Halushka MK. miRge3.0: a comprehensive microRNA and tRF sequencing analysis pipeline. NAR Genom Bioinform 2021; 3:lqab068. [PMID: 34308351 PMCID: PMC8294687 DOI: 10.1093/nargab/lqab068] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 07/02/2021] [Accepted: 07/15/2021] [Indexed: 12/12/2022] Open
Abstract
MicroRNAs and tRFs are classes of small non-coding RNAs, known for their roles in translational regulation of genes. Advances in next-generation sequencing (NGS) have enabled high-throughput small RNA-seq studies, which require robust alignment pipelines. Our laboratory previously developed miRge and miRge2.0, as flexible tools to process sequencing data for annotation of miRNAs and other small-RNA species and further predict novel miRNAs using a support vector machine approach. Although miRge2.0 is a leading analysis tool in terms of speed with unique quantifying and annotation features, it has a few limitations. We present miRge3.0 that provides additional features along with compatibility to newer versions of Cutadapt and Python. The revisions of the tool include the ability to process Unique Molecular Identifiers (UMIs) to account for PCR duplicates while quantifying miRNAs in the datasets, correct erroneous single base substitutions in miRNAs with miREC and an accurate mirGFF3 formatted isomiR tool. miRge3.0 also has speed improvements benchmarked to miRge2.0, Chimira and sRNAbench. Finally, miRge3.0 output integrates into other packages for a streamlined analysis process and provides a cross-platform Graphical User Interface (GUI). In conclusion miRge3.0 is our third generation small RNA-seq aligner with improvements in speed, versatility and functionality over earlier iterations.
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Affiliation(s)
- Arun H Patil
- Department of Pathology, Division of Cardiovascular Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Marc K Halushka
- Department of Pathology, Division of Cardiovascular Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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10
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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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11
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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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12
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Bai F, Yu Z, Gao X, Gong J, Fan L, Liu F. Simvastatin induces breast cancer cell death through oxidative stress up-regulating miR-140-5p. Aging (Albany NY) 2020; 11:3198-3219. [PMID: 31138773 PMCID: PMC6555469 DOI: 10.18632/aging.101974] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 05/12/2019] [Indexed: 12/22/2022]
Abstract
Statins, a class of hyperlipidemic drugs, are widely used cholesterol lowering drugs that selectively inhibit 3-hydroxy-3-methylglutaryl CoA reductase, which is the rate-limiting enzyme in cholesterol biosynthesis, leading to decreasing of cholesterol biosynthesis. Statins exert anti-tumoral effects on various cancer, including breast cancer. However, the molecular mechanisms for the actions were not fully elucidated. The purpose of this study was to elucidate the effects of statins on proliferation and apoptosis in the ER-negative breast cancer cell line MDA-MB-231. Our results showed that simvastatin increased the expression of miR-140-5p in a dose dependent manner via activating transcription factor NRF1, reduced cell proliferation and induced apoptosis, and we also found that SLC2A1 was a new target of miR-140-5p. In conclusion, data in this study shed light on the potential anti-tumoral effects of simvastatin in breast cancer and presents a highly promising therapeutic option, using drug and miRNA for combined treating cancers.
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Affiliation(s)
- Fuliang Bai
- Lubin Environmental Protection Technology (Shanghai) Co., Ltd, Shanghai, China
| | - Ze Yu
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Xin Gao
- Department of the Second General Surgery, Jixi Mine Hospital of Heilongjiang, Jixi, China
| | - Jiawei Gong
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Lizhi Fan
- Department of Geratology, The First Hospital of Harbin in Heilongjiang, Harbin, China
| | - Feifei Liu
- Department of Medical Records, Hongqi Hospital Affiliated to Mudanjiang Medical College, Mudanjiang City, China
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13
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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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14
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Fromm B, Domanska D, Høye E, Ovchinnikov V, Kang W, Aparicio-Puerta E, Johansen M, Flatmark K, Mathelier A, Hovig E, Hackenberg M, Friedländer MR, Peterson KJ. MirGeneDB 2.0: the metazoan microRNA complement. Nucleic Acids Res 2020; 48:D132-D141. [PMID: 31598695 PMCID: PMC6943042 DOI: 10.1093/nar/gkz885] [Citation(s) in RCA: 155] [Impact Index Per Article: 38.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 09/18/2019] [Accepted: 10/01/2019] [Indexed: 02/07/2023] Open
Abstract
Small non-coding RNAs have gained substantial attention due to their roles in animal development and human disorders. Among them, microRNAs are special because individual gene sequences are conserved across the animal kingdom. In addition, unique and mechanistically well understood features can clearly distinguish bona fide miRNAs from the myriad other small RNAs generated by cells. However, making this distinction is not a common practice and, thus, not surprisingly, the heterogeneous quality of available miRNA complements has become a major concern in microRNA research. We addressed this by extensively expanding our curated microRNA gene database - MirGeneDB - to 45 organisms, encompassing a wide phylogenetic swath of animal evolution. By consistently annotating and naming 10,899 microRNA genes in these organisms, we show that previous microRNA annotations contained not only many false positives, but surprisingly lacked >2000 bona fide microRNAs. Indeed, curated microRNA complements of closely related organisms are very similar and can be used to reconstruct ancestral miRNA repertoires. MirGeneDB represents a robust platform for microRNA-based research, providing deeper and more significant insights into the biology and evolution of miRNAs as well as biomedical and biomarker research. MirGeneDB is publicly and freely available at http://mirgenedb.org/.
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Affiliation(s)
- Bastian Fromm
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden.,Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Diana Domanska
- Center for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway.,Department of Pathology, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Eirik Høye
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Vladimir Ovchinnikov
- School of Life Sciences, Faculty of Health and Life Sciences, University of Nottingham, UK.,Department of Human and Animal Genetics, The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
| | - Wenjing Kang
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | | | - Morten Johansen
- Center for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway
| | - Kjersti Flatmark
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Department of Gastroenterological Surgery, The Norwegian Radium Hospital, Oslo University Hospital, Nydalen, Oslo, Norway
| | - Anthony Mathelier
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, Oslo, Norway.,Department of Cancer Genetics, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital Radiumhospitalet, Oslo, Norway
| | - Eivind Hovig
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway.,Center for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway
| | - Michael Hackenberg
- Department of Genetics, Faculty of Sciences, University of Granada, Granada, Spain
| | - Marc R Friedländer
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Kevin J Peterson
- Department of Biological Sciences, Dartmouth College, Hanover, NH, USA
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15
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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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16
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Zhu L, Kandasamy SK, Fukunaga R. Dicer partner protein tunes the length of miRNAs using base-mismatch in the pre-miRNA stem. Nucleic Acids Res 2019; 46:3726-3741. [PMID: 29373753 PMCID: PMC5909426 DOI: 10.1093/nar/gky043] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 01/17/2018] [Indexed: 12/19/2022] Open
Abstract
Dicer partner proteins Drosophila Loquacious-PB (Loqs-PB) and human TRBP tune the length of miRNAs produced by Dicer from a subset of pre-miRNAs and thereby alter their target repertoire, by an unknown mechanism. Here, we developed a novel high-throughput method that we named Dram-seq (Dice randomized pre-miRNA pool and seq) to study length distributions of miRNAs produced from thousands of different pre-miRNA variants. Using Dram-seq, we found that a base-mismatch in the pre-miRNA stem can alter the length of miRNAs compared with a base-pair at the same position in both Drosophila and human, and is important for the miRNA length tuning by Loqs-PB. Loqs-PB directly bound base-mismatched nucleotides in the pre-miRNA stem. We speculate that Loqs-PB tunes miRNA length by changing the conformation of base-mismatched nucleotides in the pre-miRNA stem to that of base-paired ones and thereby altering the distance of the pre-miRNA stem.
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Affiliation(s)
- Li Zhu
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, 725 North Wolfe Street, 521A Physiology Building, Baltimore, MD 21205, USA
| | - Suresh K Kandasamy
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, 725 North Wolfe Street, 521A Physiology Building, Baltimore, MD 21205, USA
| | - Ryuya Fukunaga
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, 725 North Wolfe Street, 521A Physiology Building, Baltimore, MD 21205, USA
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17
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Computational Resources for Prediction and Analysis of Functional miRNA and Their Targetome. Methods Mol Biol 2019; 1912:215-250. [PMID: 30635896 DOI: 10.1007/978-1-4939-8982-9_9] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
microRNAs are evolutionarily conserved, endogenously produced, noncoding RNAs (ncRNAs) of approximately 19-24 nucleotides (nts) in length known to exhibit gene silencing of complementary target sequence. Their deregulated expression is reported in various disease conditions and thus has therapeutic implications. In the last decade, various computational resources are published in this field. In this chapter, we have reviewed bioinformatics resources, i.e., miRNA-centered databases, algorithms, and tools to predict miRNA targets. First section has enlisted more than 75 databases, which mainly covers information regarding miRNA registries, targets, disease associations, differential expression, interactions with other noncoding RNAs, and all-in-one resources. In the algorithms section, we have compiled about 140 algorithms from eight subcategories, viz. for the prediction of precursor (pre-) and mature miRNAs. These algorithms are developed on various sequence, structure, and thermodynamic based features incorporated into different machine learning techniques (MLTs). In addition, computational identification of miRNAs from high-throughput next generation sequencing (NGS) data and their variants, viz. isomiRs, differential expression, miR-SNPs, and functional annotation, are discussed. Prediction and analysis of miRNAs and their associated targets are also evaluated under miR-targets section providing knowledge regarding novel miRNA targets and complex host-pathogen interactions. In conclusion, we have provided comprehensive review of in silico resources published in miRNA research to help scientific community be updated and choose the appropriate tool according to their needs.
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18
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Li T, Liu X, Gong X, E Q, Zhang X, Zhang X. microRNA 92b-3p regulates primordial follicle assembly by targeting TSC1 in neonatal mouse ovaries. Cell Cycle 2019; 18:824-833. [PMID: 30880550 PMCID: PMC6527271 DOI: 10.1080/15384101.2019.1593648] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 12/18/2018] [Accepted: 02/15/2019] [Indexed: 01/17/2023] Open
Abstract
The primordial follicle pool, providing all oocytes available to a female throughout her reproductive life, is established perinatally. The formation of primordial follicle pool is regulated by precise transcriptional and post-transcriptional mechanisms. Recent studies have identified several microRNAs as post-transcriptional regulatory factors in the process of primordial follicle assembly. Here, we showed that miR-92b-3p was significantly upregulated in the stage of primordial follicle assembly in newborn mouse ovaries. Inhibiting miR-92b-3p suppressed the formation of primordial follicles, while overexpression of miR-92b-3p accelerated the processes of cyst breakdown and the following primordial follicle assembly. Accordingly, the expression of follicular development-related genes was reduced upon inhibiting of miR-92b-3p and increased under miR-92b-3p overexpression. Mechanistic studies identified TSC1 as a direct target of miR-92b-3p. miR-92b-3p could activate mTOR/Rps6 signaling through targeting and inhibiting TSC1 expression. In addition, knockdown of TSC1 showed an identical phenotype with that of miR-92b-3p overexpression in accelerating processes of cyst breakdown and primordial follicle formation. Thus, our work demonstrates that miR-92b-3p is a novel regulator of primordial follicle assembly by negatively regulating TSC1 in mTOR/Rps6 signaling.
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Affiliation(s)
- Tingting Li
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
- Department of Reproductive Medicine, Maternal and Child Health Care Hospital of Nantong City, Nantong, China
| | - Xiaoqiu Liu
- Key Laboratory of Pathogen Biology of Jiangsu Province, Nanjing Medical University, Nanjing, China
- Department of Microbiology, Nanjing Medical University, Nanjing, China
| | - Xuefeng Gong
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Qiukai E
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Xiaoqian Zhang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Xuesen Zhang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
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19
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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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20
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Tang CT, Liang Q, Yang L, Lin XL, Wu S, Chen Y, Zhang XT, Gao YJ, Ge ZZ. RAB31 Targeted by MiR-30c-2-3p Regulates the GLI1 Signaling Pathway, Affecting Gastric Cancer Cell Proliferation and Apoptosis. Front Oncol 2018; 8:554. [PMID: 30534536 PMCID: PMC6275292 DOI: 10.3389/fonc.2018.00554] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 11/08/2018] [Indexed: 12/13/2022] Open
Abstract
Background: Gastric cancer (GC), one of the most common cancers worldwide, is highly malignant and fatal. Ras-related protein in brain 31 (RAB31), a member of the RAB family of oncogenes, participates in the process of carcinogenesis and cancer development; however, its role in GC progression is unknown. Methods: In our study, 90 pairs of tissue microarrays were used to measure the levels of RAB31 protein by immunochemistry, and 22 pairs of fresh tissue were used to measure the levels of RAB31 mRNA by quantitative PCR. We also investigated the effects of RAB31 on tumor growth both in vitro and in vivo. Results: RAB31 was overexpressed in GC tissues, and its overexpression predicted poor survival in patients. In a nude mouse model, depletion of RAB31 inhibited tumor growth. In vitro, silencing of RAB31 suppressed cell viability, promoted cell cycle arrest, enhanced apoptosis, and affected the expression of cell cycle and apoptotic proteins; these effects were mediated by glioma-associated oncogene homolog 1 (GLI1). Co-immunoprecipitation and immunofluorescence assays confirmed that RAB31 interacted with GLI1. In addition, luciferase reporter assays and Western blotting showed that microRNA-30c-2-3p modulated the RAB31/GLI1 pathway by targeting the 3′-untranslated region of RAB31. Conclusions: Collectively, these data show that RAB31 is regulated by microRNA-30c-2-3p, and functions as an oncogene in GC tumorigenesis and development by interacting with GLI1. Therefore, targeting the miR-30c-2-3p/RAB31/GLI1 axis may be a therapeutic intervention for gastric cancer.
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Affiliation(s)
- Chao-Tao Tang
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Shanghai Institute of Digestive Disease, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Qian Liang
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Shanghai Institute of Digestive Disease, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Li Yang
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Shanghai Institute of Digestive Disease, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiao-Lu Lin
- Department of Digestive Endoscopy, Provincial Clinic Medical College, Fujian Medical University, Fujian Provincial Hospital, Fuzhou, China
| | - Shan Wu
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Shanghai Institute of Digestive Disease, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yong Chen
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Shanghai Institute of Digestive Disease, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xin-Tian Zhang
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Shanghai Institute of Digestive Disease, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yun-Jie Gao
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Shanghai Institute of Digestive Disease, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Zhi-Zheng Ge
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Shanghai Institute of Digestive Disease, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
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21
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Finotti A, Allegretti M, Gasparello J, Giacomini P, Spandidos DA, Spoto G, Gambari R. Liquid biopsy and PCR-free ultrasensitive detection systems in oncology (Review). Int J Oncol 2018; 53:1395-1434. [PMID: 30085333 PMCID: PMC6086621 DOI: 10.3892/ijo.2018.4516] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 07/31/2018] [Indexed: 02/07/2023] Open
Abstract
In oncology, liquid biopsy is used in the detection of next-generation analytes, such as tumor cells, cell-free nucleic acids and exosomes in peripheral blood and other body fluids from cancer patients. It is considered one of the most advanced non-invasive diagnostic systems to enable clinically relevant actions and implement precision medicine. Medical actions include, but are not limited to, early diagnosis, staging, prognosis, anticipation (lead time) and the prediction of therapy responses, as well as follow-up. Historically, the applications of liquid biopsy in cancer have focused on circulating tumor cells (CTCs). More recently, this analysis has been extended to circulating free DNA (cfDNA) and microRNAs (miRNAs or miRs) associated with cancer, with potential applications for development into multi-marker diagnostic, prognostic and therapeutic signatures. Liquid biopsies avoid some key limitations of conventional tumor tissue biopsies, including invasive tumor sampling, under-representation of tumor heterogeneity and poor description of clonal evolution during metastatic dissemination, strongly reducing the need for multiple sampling. On the other hand, this approach suffers from important drawbacks, i.e., the fragmentation of cfDNA, the instability of RNA, the low concentrations of certain analytes in body fluids and the confounding presence of normal, as well as aberrant DNAs and RNAs. For these reasons, the analysis of cfDNA has been mostly focused on mutations arising in, and pathognomonicity of, tumor DNA, while the analysis of cfRNA has been mostly focused on miRNA patterns strongly associated with neoplastic transformation/progression. This review lists some major applicative areas, briefly addresses how technology is bypassing liquid biopsy limitations, and places a particular emphasis on novel, PCR-free platforms. The ongoing collaborative efforts of major international consortia are reviewed. In addition to basic and applied research, we will consider technological transfer, including patents, patent applications and available information on clinical trials aimed at verifying the potential of liquid biopsy in cancer.
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Affiliation(s)
- Alessia Finotti
- Department of Life Sciences and Biotechnology, Ferrara University, 44121 Ferrara, Italy
| | - Matteo Allegretti
- Oncogenomics and Epigenetic Unit, IRCCS Regina Elena National Cancer Institute, 00144 Rome, Italy
| | - Jessica Gasparello
- Department of Life Sciences and Biotechnology, Ferrara University, 44121 Ferrara, Italy
| | - Patrizio Giacomini
- Oncogenomics and Epigenetic Unit, IRCCS Regina Elena National Cancer Institute, 00144 Rome, Italy
| | - Demetrios A Spandidos
- Laboratory of Clinical Virology, Medical School, University of Crete, 71003 Heraklion, Crete, Greece
| | - Giuseppe Spoto
- Department of Chemistry, Catania University, 95125 Catania, Italy
| | - Roberto Gambari
- Department of Life Sciences and Biotechnology, Ferrara University, 44121 Ferrara, Italy
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22
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Shukla V, Varghese VK, Kabekkodu SP, Mallya S, Satyamoorthy K. A compilation of Web-based research tools for miRNA analysis. Brief Funct Genomics 2018; 16:249-273. [PMID: 28334134 DOI: 10.1093/bfgp/elw042] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Since the discovery of microRNAs (miRNAs), a class of noncoding RNAs that regulate the gene expression posttranscriptionally in sequence-specific manner, there has been a release of number of tools useful for both basic and advanced applications. This is because of the significance of miRNAs in many pathophysiological conditions including cancer. Numerous bioinformatics tools that have been developed for miRNA analysis have their utility for detection, expression, function, target prediction and many other related features. This review provides a comprehensive assessment of web-based tools for the miRNA analysis that does not require prior knowledge of any computing languages.
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23
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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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24
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MacLeod AR, Crooke ST. RNA Therapeutics in Oncology: Advances, Challenges, and Future Directions. J Clin Pharmacol 2018; 57 Suppl 10:S43-S59. [PMID: 28921648 DOI: 10.1002/jcph.957] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 05/08/2017] [Indexed: 12/18/2022]
Abstract
RNA-based therapeutic technologies represent a rapidly expanding class of therapeutic opportunities with the power to modulate cellular biology in ways never before possible. With RNA-targeted therapeutics, inhibitors of previously undruggable proteins, gene expression modulators, and even therapeutic proteins can be rationally designed based on sequence information alone, something that is not possible with other therapeutic modalities. The most advanced RNA therapeutic modalities are antisense oligonucleotides (ASOs) and small interfering RNAs. Particularly with ASOs, recent clinical data have demonstrated proof of mechanism and clinical benefit with these approaches across several nononcology disease areas by multiple routes of administration. In cancer, next-generation ASOs have recently demonstrated single-agent activity in patients with highly refractory cancers. Here we discuss advances in RNA therapeutics for the treatment of cancer and the challenges that remain to solidify these as mainstay therapeutic modalities to bridge the pharmacogenomic divide that remains in cancer drug discovery.
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Affiliation(s)
- A Robert MacLeod
- Vice President, Oncology Discovery, Ionis Pharmaceuticals, Carlsbad, CA, USA
| | - Stanley T Crooke
- CEO and Chairman of the Board, Ionis Pharmaceuticals, Carlsbad, CA, USA
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25
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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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26
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Zou ZC, Dai M, Huang ZY, Lu Y, Xie HP, Li YF, Li Y, Tan Y, Wang FL. MicroRNA-139-3p Suppresses Tumor Growth and Metastasis in Hepatocellular Carcinoma by Repressing ANXA2R. Oncol Res 2018; 26:1391-1399. [PMID: 29422116 PMCID: PMC7844686 DOI: 10.3727/096504018x15178798885361] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The direct roles of miR-139-3p on hepatocellular carcinoma (HCC) cell growth and metastasis remain poorly understood. We attempted to demonstrate the regulatory role of miR-139-3p in HCC progression and its underlying mechanisms. Here we showed that miR-139-3p expression was significantly reduced in the HCC tissues compared to paratumor tissues. Exogenous overexpression of miR-139-3p inhibited the migration and invasion of HCC cells, whereas downregulation of miR-139-3p was able to induce HCC HepG2 and SNU-449 cell migration and invasion. In addition, miR-139-3p inhibited HCC growth and lung metastasis in an in vivo mouse model, which is mainly regulated by annexin A2 receptor (ANXA2R). Finally, we identified that the expression of miR-139-3p was inversely correlated with ANXA2R expression in human HCC tissue. All these results demonstrated that miR-139-3p inhibited the metastasis process in HCC by downregulating ANXA2R expression.
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Affiliation(s)
- Zeng Cheng Zou
- Department of Integrated Traditional and Western Medicine, The Third Affiliated Hospital of SunYat-sen University, Guangzhou, P.R. China
| | - Min Dai
- Department of Integrated Traditional and Western Medicine, The Third Affiliated Hospital of SunYat-sen University, Guangzhou, P.R. China
| | - Zeng Yin Huang
- Department of Oncology Guangdong Provincial Hospital of Traditional Chinese Medicine, Guangzhou, P.R. China
| | - Yi Lu
- Department of Hepatobiliary Surgery, The Third Affiliated Hospital of SunYat-sen University, Guangzhou, P.R. China
| | - He Ping Xie
- Department of Integrated Traditional and Western Medicine, The Third Affiliated Hospital of SunYat-sen University, Guangzhou, P.R. China
| | - Yi Fang Li
- Department of Acupuncture, Guangdong Provincial Hospital of Traditional Chinese Medicine, Guangzhou, P.R. China
| | - Yue Li
- Department of Integrated Traditional and Western Medicine, The Third Affiliated Hospital of SunYat-sen University, Guangzhou, P.R. China
| | - Ying Tan
- Department of Infertility and Sterility, Guangdong Provincial Family Planning Research Institute, Guangzhou, P.R. China
| | - Feng Lin Wang
- Department of Integrated Traditional and Western Medicine, The Third Affiliated Hospital of SunYat-sen University, Guangzhou, P.R. China
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27
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Xu FF, Xie WF, Zha GQ, Chen HW, Deng L. MiR-520f promotes cell aggressiveness by regulating fibroblast growth factor 16 in hepatocellular carcinoma. Oncotarget 2017; 8:109546-109558. [PMID: 29312628 PMCID: PMC5752541 DOI: 10.18632/oncotarget.22726] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 11/02/2017] [Indexed: 12/13/2022] Open
Abstract
Cancer metastasis is a multistep cellular process, which has be confirmed one of mainly causes of cancer associated-death in hepatocellular carcinoma (HCC). MicroRNAs (miRNAs) participate in tumorigenesis function as either tumor suppressor genes or oncogenes. In order to elaborate the critical miRNAs and their targets in HCC, we compared the differential expression of miRNA between HCC tissues and normal tissues. Microarray analysis revealed there were several significantly up-expression miRNAs in HCC, compared to normal solid tissue. Among them, the expression of miR-520f was the most over-expression in HCC cell lines than that in human normal liver cells LO2, as well as up-regulated in HCC than that in the corresponding normal tissues. Moreover, Kaplan Meier-plotter analyses revealed that higher miR-520f levels were negatively correlated with poor overall survival. By applying bioinformatics methods to identify the targeting genes of miRNA, we demonstrated that fibroblast growth factor 16 (FGF16) was the miR-520f-targeted gene. Meanwhile, FGF16 exhibited similar expression patterns to miR-520f in HCC. Forced miR-520f expression accelerated HCC cells proliferation and aggressiveness in vitro and in vivo, whereas down-regulation of miR-520f caused an opposite outcome. Moreover, over-expression of FGF16 was closely related to the metastatic potential of HCC cells. Herein, we also confirmed that ectopic expression of FGF16 in HCC cells promoted proliferation, colony formation, and increased migration, invasion of HCC cells in vitro. Collectively, our results indicated that over-expression of miR-520f and FGF16 was positively associated with aggressive phenotypes and poor survival of patients with HCC, and miR-520f promoted HCC aggressive phenotypes by regulating the expression of FGF16. MiR-520f may be employed as a prognostic factor and therapeutic target for HCC.
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Affiliation(s)
- Feng Feng Xu
- Department II of General Surgery, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou 510700, China
| | - Wen Feng Xie
- Department of Intensive Care Unit, The Eastern Hospital of the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510700, China
| | - Guo Qing Zha
- Upper Limb Department Of Orthopedics, The Eastern Hospital of the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510700, China
| | - Hong Wu Chen
- Department of Emergency, The Eastern Hospital of the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510700, China
| | - Liang Deng
- Department of Hepatobiliary Surgery, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen 518107, China
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28
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Liang ML, Hsieh TH, Ng KH, Tsai YN, Tsai CF, Chao ME, Liu DJ, Chu SS, Chen W, Liu YR, Liu RS, Lin SC, Ho DMT, Wong TT, Yang MH, Wang HW. Downregulation of miR-137 and miR-6500-3p promotes cell proliferation in pediatric high-grade gliomas. Oncotarget 2017; 7:19723-37. [PMID: 26933822 PMCID: PMC4991414 DOI: 10.18632/oncotarget.7736] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 02/18/2016] [Indexed: 01/22/2023] Open
Abstract
Pediatric high-grade gliomas (pHGGs) are aggressive brain tumors affecting children, and outcomes have remained dismal, even with access to new multimodal therapies. In this study, we compared the miRNomes and transcriptomes of pediatric low- (pLGGs) and high-grade gliomas (pHGGs) using small RNA sequencing (smRNA-Seq) and gene expression microarray, respectively. Through integrated bioinformatics analyses and experimental validation, we identified miR-137 and miR-6500-3p as significantly downregulated in pHGGs. miR-137 or miR-6500-3p overexpression reduced cell proliferation in two pHGG cell lines, SF188 and UW479. CENPE, KIF14 and NCAPG levels were significantly higher in pHGGs than pLGGs, and were direct targets of miR-137 or miR-6500-3p. Furthermore, knockdown of CENPE, KIF14 or NCAPG combined with temozolomide treatment resulted in a combined suppressive effect on pHGG cell proliferation. In summary, our results identify novel mRNA/miRNA interactions that contribute to pediatric glioma malignancy and represent potential targets for the development of new therapeutic strategies.
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Affiliation(s)
- Muh-Lii Liang
- Institutes of Clinical Medicine, National Yang-Ming University, Taipei, Taiwan.,Division of Pediatric Neurosurgery, Neurological Institute, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Tsung-Han Hsieh
- PhD Program for Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan.,Comprehensive Cancer Center of Taipei Medical University, Taipei Medical University, Taipei, Taiwan
| | - Kim-Hai Ng
- Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan
| | - Ya-Ni Tsai
- Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan
| | - Cheng-Fong Tsai
- Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan
| | - Meng-En Chao
- Institutes of Clinical Medicine, Taipei Medical University, Taipei, Taiwan.,Department of Neurosurgery, Taipei Medical University Hospital, Taipei Medical University, Taipei, Taiwan
| | - Da-Jung Liu
- Division of Pediatric Neurosurgery, Neurological Institute, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Shing-Shiung Chu
- Institutes of Clinical Medicine, Taipei Medical University, Taipei, Taiwan.,Department of Neurosurgery, Taipei Medical University Hospital, Taipei Medical University, Taipei, Taiwan
| | - Wan Chen
- Institutes of Clinical Medicine, Taipei Medical University, Taipei, Taiwan.,Department of Neurosurgery, Taipei Medical University Hospital, Taipei Medical University, Taipei, Taiwan
| | - Yun-Ru Liu
- Comprehensive Cancer Center of Taipei Medical University, Taipei Medical University, Taipei, Taiwan.,Joint Biobank, Office of Human Research, Taipei Medical University, Taipei, Taiwan
| | - Ren-Shyan Liu
- School of Medicine, National Yang-Ming University, Taipei, Taiwan.,National PET/Cyclotron Center, Department of Nuclear Medicine, Taipei Veterans General Hospital, Taipei, Taiwan.,Molecular and Genetic Imaging Core/Taiwan Mouse Clinic National Comprehensive Mouse Phenotyping and Drug Testing Center, Taipei, Taiwan
| | - Shih-Chieh Lin
- Department of Pathology and Laboratory Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Donald Ming-Tak Ho
- School of Medicine, National Yang-Ming University, Taipei, Taiwan.,Department of Pathology and Laboratory Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Tai-Tong Wong
- Division of Pediatric Neurosurgery, Neurological Institute, Taipei Veterans General Hospital, Taipei, Taiwan.,Institutes of Clinical Medicine, Taipei Medical University, Taipei, Taiwan.,Department of Neurosurgery, Taipei Medical University Hospital, Taipei Medical University, Taipei, Taiwan.,Joint Biobank, Office of Human Research, Taipei Medical University, Taipei, Taiwan
| | - Muh-Hwa Yang
- Institutes of Clinical Medicine, National Yang-Ming University, Taipei, Taiwan.,Cancer Research Center & Genome Research Center, National Yang-Ming University, Taipei, Taiwan.,Division of Hematology-Oncology, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan.,Immunity and Inflammation Research Center, National Yang-Ming University, Taipei, Taiwan.,Genomic Research Center, Academia Sinica, Taipei, Taiwan
| | - Hsei-Wei Wang
- Institutes of Clinical Medicine, National Yang-Ming University, Taipei, Taiwan.,Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan.,Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan.,Cancer Research Center & Genome Research Center, National Yang-Ming University, Taipei, Taiwan
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29
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McCall MN, Kim MS, Adil M, Patil AH, Lu Y, Mitchell CJ, Leal-Rojas P, Xu J, Kumar M, Dawson VL, Dawson TM, Baras AS, Rosenberg AZ, Arking DE, Burns KH, Pandey A, Halushka MK. Toward the human cellular microRNAome. Genome Res 2017; 27:1769-1781. [PMID: 28877962 PMCID: PMC5630040 DOI: 10.1101/gr.222067.117] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 08/07/2017] [Indexed: 12/26/2022]
Abstract
MicroRNAs are short RNAs that serve as regulators of gene expression and are essential components of normal development as well as modulators of disease. MicroRNAs generally act cell-autonomously, and thus their localization to specific cell types is needed to guide our understanding of microRNA activity. Current tissue-level data have caused considerable confusion, and comprehensive cell-level data do not yet exist. Here, we establish the landscape of human cell-specific microRNA expression. This project evaluated 8 billion small RNA-seq reads from 46 primary cell types, 42 cancer or immortalized cell lines, and 26 tissues. It identified both specific and ubiquitous patterns of expression that strongly correlate with adjacent superenhancer activity. Analysis of unaligned RNA reads uncovered 207 unknown minor strand (passenger) microRNAs of known microRNA loci and 495 novel putative microRNA loci. Although cancer cell lines generally recapitulated the expression patterns of matched primary cells, their isomiR sequence families exhibited increased disorder, suggesting DROSHA- and DICER1-dependent microRNA processing variability. Cell-specific patterns of microRNA expression were used to de-convolute variable cellular composition of colon and adipose tissue samples, highlighting one use of these cell-specific microRNA expression data. Characterization of cellular microRNA expression across a wide variety of cell types provides a new understanding of this critical regulatory RNA species.
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Affiliation(s)
- Matthew N McCall
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, New York 14642, USA
| | - Min-Sik Kim
- Department of Applied Chemistry, Kyung Hee University, Yongin, Gyeonggi 17104, South Korea 3
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Mohammed Adil
- Department School of Life Sciences, B.S. Abdur Rahman University, Chennai, 600048, India
| | - Arun H Patil
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
- School of Biotechnology, KIIT University, Bhubaneswar, Odisha, 751024, India
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India
- YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore, 575018, India
| | - Yin Lu
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | | | - Pamela Leal-Rojas
- Center of Excellence in Translational Medicine (CEMT) & Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, 4810296 Temuco, Chile
| | - Jinchong Xu
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Manoj Kumar
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Valina L Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Ted M Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Alexander S Baras
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Avi Z Rosenberg
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Dan E Arking
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Kathleen H Burns
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Akhilesh Pandey
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Marc K Halushka
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
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30
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Quan W, Yao Y, Xianhua C, Xiaodong P, Qi H, Dong W, Youcai D, Xiaohui L, Jun Y, Jihong Z. Competing endogenous RNA screening based on long noncoding RNA-messenger RNA co-expression profile in Hepatitis B virus-associated hepatocarcinogenesis. J TRADIT CHIN MED 2017. [DOI: 10.1016/s0254-6272(17)30158-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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31
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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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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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Newie I, Søkilde R, Persson H, Jacomasso T, Gorbatenko A, Borg Å, de Hoon M, Pedersen SF, Rovira C. HER2-encoded mir-4728 forms a receptor-independent circuit with miR-21-5p through the non-canonical poly(A) polymerase PAPD5. Sci Rep 2016; 6:35664. [PMID: 27752128 PMCID: PMC5067774 DOI: 10.1038/srep35664] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 10/04/2016] [Indexed: 12/24/2022] Open
Abstract
We previously reported that the human HER2 gene encodes the intronic microRNA mir-4728, which is overexpressed together with its oncogenic host gene and may act independently of the HER2 receptor. More recently, we also reported that the oncogenic miR-21-5p is regulated by 3' tailing and trimming by the non-canonical poly(A) polymerase PAPD5 and the ribonuclease PARN. Here we demonstrate a dual function for the HER2 locus in upregulation of miR-21-5p; while HER2 signalling activates transcription of mir-21, miR-4728-3p specifically stabilises miR-21-5p through inhibition of PAPD5. Our results establish a new and unexpected oncogenic role for the HER2 locus that is not currently being targeted by any anti-HER2 therapy.
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Affiliation(s)
- Inga Newie
- Department of Clinical Sciences, Lund, Division of Oncology and Pathology, Lund University Cancer Center, Lund, Sweden.,BioCARE, Strategic Cancer Research Program, Lund, Sweden
| | - Rolf Søkilde
- Department of Clinical Sciences, Lund, Division of Oncology and Pathology, Lund University Cancer Center, Lund, Sweden.,BioCARE, Strategic Cancer Research Program, Lund, Sweden
| | - Helena Persson
- Department of Clinical Sciences, Lund, Division of Oncology and Pathology, Lund University Cancer Center, Lund, Sweden
| | - Thiago Jacomasso
- Department of Clinical Sciences, Lund, Division of Oncology and Pathology, Lund University Cancer Center, Lund, Sweden
| | - Andrej Gorbatenko
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Åke Borg
- Department of Clinical Sciences, Lund, Division of Oncology and Pathology, Lund University Cancer Center, Lund, Sweden.,BioCARE, Strategic Cancer Research Program, Lund, Sweden.,CREATE Health, Strategic Centre for Translational Cancer Research, Lund, Sweden
| | - Michiel de Hoon
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan
| | - Stine F Pedersen
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Carlos Rovira
- Department of Clinical Sciences, Lund, Division of Oncology and Pathology, Lund University Cancer Center, Lund, Sweden.,BioCARE, Strategic Cancer Research Program, Lund, Sweden.,CREATE Health, Strategic Centre for Translational Cancer Research, Lund, Sweden
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Peng F, Xiong L, Tang H, Peng C, Chen J. Regulation of epithelial-mesenchymal transition through microRNAs: clinical and biological significance of microRNAs in breast cancer. Tumour Biol 2016; 37:14463-14477. [DOI: 10.1007/s13277-016-5334-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2016] [Accepted: 09/06/2016] [Indexed: 12/16/2022] Open
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Targeting oncomiRNAs and mimicking tumor suppressor miRNAs: Νew trends in the development of miRNA therapeutic strategies in oncology (Review). Int J Oncol 2016; 49:5-32. [PMID: 27175518 PMCID: PMC4902075 DOI: 10.3892/ijo.2016.3503] [Citation(s) in RCA: 164] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 04/29/2016] [Indexed: 12/16/2022] Open
Abstract
MicroRNA (miRNA or miR) therapeutics in cancer are based on targeting or mimicking miRNAs involved in cancer onset, progression, angiogenesis, epithelial-mesenchymal transition and metastasis. Several studies conclusively have demonstrated that miRNAs are deeply involved in tumor onset and progression, either behaving as tumor-promoting miRNAs (oncomiRNAs and metastamiRNAs) or as tumor suppressor miRNAs. This review focuses on the most promising examples potentially leading to the development of anticancer, miRNA-based therapeutic protocols. The inhibition of miRNA activity can be readily achieved by the use of miRNA inhibitors and oligomers, including RNA, DNA and DNA analogues (miRNA antisense therapy), small molecule inhibitors, miRNA sponges or through miRNA masking. On the contrary, the enhancement of miRNA function (miRNA replacement therapy) can be achieved by the use of modified miRNA mimetics, such as plasmid or lentiviral vectors carrying miRNA sequences. Combination strategies have been recently developed based on the observation that i) the combined administration of different antagomiR molecules induces greater antitumor effects and ii) some anti-miR molecules can sensitize drug-resistant tumor cell lines to therapeutic drugs. In this review, we discuss two additional issues: i) the combination of miRNA replacement therapy with drug administration and ii) the combination of antagomiR and miRNA replacement therapy. One of the solid results emerging from different independent studies is that miRNA replacement therapy can enhance the antitumor effects of the antitumor drugs. The second important conclusion of the reviewed studies is that the combination of anti-miRNA and miRNA replacement strategies may lead to excellent results, in terms of antitumor effects.
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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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Karali M, Persico M, Mutarelli M, Carissimo A, Pizzo M, Singh Marwah V, Ambrosio C, Pinelli M, Carrella D, Ferrari S, Ponzin D, Nigro V, di Bernardo D, Banfi S. High-resolution analysis of the human retina miRNome reveals isomiR variations and novel microRNAs. Nucleic Acids Res 2016; 44:1525-40. [PMID: 26819412 PMCID: PMC4770244 DOI: 10.1093/nar/gkw039] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 01/13/2016] [Indexed: 01/14/2023] Open
Abstract
MicroRNAs play a fundamental role in retinal development and function. To characterise the miRNome of the human retina, we carried out deep sequencing analysis on sixteen individuals. We established the catalogue of retina-expressed miRNAs, determined their relative abundance and found that a small number of miRNAs accounts for almost 90% of the retina miRNome. We discovered more than 3000 miRNA variants (isomiRs), encompassing a wide range of sequence variations, which include seed modifications that are predicted to have an impact on miRNA action. We demonstrated that a seed-modifying isomiR of the retina-enriched miR-124-3p was endowed with different targeting properties with respect to the corresponding canonical form. Moreover, we identified 51 putative novel, retina-specific miRNAs and experimentally validated the expression for nine of them. Finally, a parallel analysis of the human Retinal Pigment Epithelium (RPE)/choroid, two tissues that are known to be crucial for retina homeostasis, yielded notably distinct miRNA enrichment patterns compared to the retina. The generated data are accessible through an ad hoc database. This study is the first to reveal the complexity of the human retina miRNome at nucleotide resolution and constitutes a unique resource to assess the contribution of miRNAs to the pathophysiology of the human retina.
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Affiliation(s)
- Marianthi Karali
- Telethon Institute of Genetics and Medicine, via Campi Flegrei 34, 80078 Pozzuoli (NA), Italy Department of Biochemistry, Biophysics and General Pathology, Second University of Naples, via Luigi De Crecchio 7, 80138 Naples (NA), Italy
| | - Maria Persico
- Telethon Institute of Genetics and Medicine, via Campi Flegrei 34, 80078 Pozzuoli (NA), Italy
| | - Margherita Mutarelli
- Telethon Institute of Genetics and Medicine, via Campi Flegrei 34, 80078 Pozzuoli (NA), Italy
| | - Annamaria Carissimo
- Telethon Institute of Genetics and Medicine, via Campi Flegrei 34, 80078 Pozzuoli (NA), Italy
| | - Mariateresa Pizzo
- Telethon Institute of Genetics and Medicine, via Campi Flegrei 34, 80078 Pozzuoli (NA), Italy
| | - Veer Singh Marwah
- Telethon Institute of Genetics and Medicine, via Campi Flegrei 34, 80078 Pozzuoli (NA), Italy
| | - Concetta Ambrosio
- Telethon Institute of Genetics and Medicine, via Campi Flegrei 34, 80078 Pozzuoli (NA), Italy
| | - Michele Pinelli
- Telethon Institute of Genetics and Medicine, via Campi Flegrei 34, 80078 Pozzuoli (NA), Italy
| | - Diego Carrella
- Telethon Institute of Genetics and Medicine, via Campi Flegrei 34, 80078 Pozzuoli (NA), Italy
| | - Stefano Ferrari
- Eye Bank of Venice, Padiglione Rama, via Paccagnella 11, 30174 Zelarino (VE), Italy
| | - Diego Ponzin
- Eye Bank of Venice, Padiglione Rama, via Paccagnella 11, 30174 Zelarino (VE), Italy
| | - Vincenzo Nigro
- Telethon Institute of Genetics and Medicine, via Campi Flegrei 34, 80078 Pozzuoli (NA), Italy Department of Biochemistry, Biophysics and General Pathology, Second University of Naples, via Luigi De Crecchio 7, 80138 Naples (NA), Italy
| | - Diego di Bernardo
- Telethon Institute of Genetics and Medicine, via Campi Flegrei 34, 80078 Pozzuoli (NA), Italy Department of Chemical, Materials and Production Engineering, University of Naples 'Federico II', via Claudio 21, 80125 Naples (NA), Italy
| | - Sandro Banfi
- Telethon Institute of Genetics and Medicine, via Campi Flegrei 34, 80078 Pozzuoli (NA), Italy Department of Biochemistry, Biophysics and General Pathology, Second University of Naples, via Luigi De Crecchio 7, 80138 Naples (NA), Italy
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Chang HC, Hsieh TH, Lee YW, Tsai CF, Tsai YN, Cheng CC, Wang HW. c-Myc and viral cofactor Kaposin B co-operate to elicit angiogenesis through modulating miRNome traits of endothelial cells. BMC SYSTEMS BIOLOGY 2016; 10 Suppl 1:1. [PMID: 26817819 PMCID: PMC4895700 DOI: 10.1186/s12918-015-0242-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
BACKGROUND MicroRNAs (miRNAs) have emerged as master regulators of angiogenesis and other cancer-related events. Discovering new angiogenesis-regulating microRNAs (angiomiRs) will eventually help in developing new therapeutic strategies for tumor angiogenesis and cardiovascular diseases. Kaposi's sarcoma (KS), which is induced by the etiological infectious agent KS-associated herpesvirus (KSHV), is a peculiar neoplasm that expresses both blood and lymphatic endothelial markers and possesses extensive neovasculature. Using KSHV and its proteins as baits will be an efficient way to discover new angiomiRs in endothelial cells. Kaposin B is one of the latent viral genes and is expressed in all KSHV tumor cells. Since Kaposin B is a nuclear protein with no DNA-binding domain, it may regulate gene expression by incorporating itself into a transcription complex. RESULTS We demonstrated that c-Myc and Kaposin B form a transcription complex and bind to the miR-221/-222 promoter, thereby affecting their expression and anti-angiogenic ability. By small RNA sequencing (smRNA-Seq), we revealed that 72.1% (173/240) of Kaposin B up-regulated and 46.5% (113/243) of Kaposin B down-regulated known miRNAs were regulated by c-Myc. We also found that 77 novel miRNA were up-regulated and 28 novel miRNAs were down-regulated in cells expressing both c-Myc and Kaposin B compared with cells expressing Kaposin B only. The result was confirmed by RNA-IP-seq data. CONCLUSIONS Our study identifies known and novel c-Myc-regulated microRNAs and reveals that a c-Myc-oriented program is coordinated by Kaposin B in KSHV-infected cells.
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Affiliation(s)
- Hsin-Chuan Chang
- 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.
| | - Yi-Wei Lee
- Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan.
| | - Cheng-Fong Tsai
- Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan.
| | - Ya-Ni Tsai
- Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan.
| | - Cheng-Chung Cheng
- Division of Cardiology, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan.
| | - Hsei-Wei Wang
- Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan. .,Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan. .,VGH-YM Genome Research Center, National Yang-Ming University, Taipei, Taiwan.
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40
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Zielezinski A, Dolata J, Alaba S, Kruszka K, Pacak A, Swida-Barteczka A, Knop K, Stepien A, Bielewicz D, Pietrykowska H, Sierocka I, Sobkowiak L, Lakomiak A, Jarmolowski A, Szweykowska-Kulinska Z, Karlowski WM. mirEX 2.0 - an integrated environment for expression profiling of plant microRNAs. BMC PLANT BIOLOGY 2015; 15:144. [PMID: 26141515 PMCID: PMC4490709 DOI: 10.1186/s12870-015-0533-2] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 05/23/2015] [Indexed: 05/19/2023]
Abstract
BACKGROUND MicroRNAs are the key post-transcriptional regulators of gene expression in development and stress responses. Thus, precisely quantifying the level of each particular microRNA is of utmost importance when studying the biology of any organism. DESCRIPTION The mirEX 2.0 web portal ( http://www.combio.pl/mirex ) provides a comprehensive platform for the exploration of microRNA expression data based on quantitative Real Time PCR and NGS sequencing experiments, covering various developmental stages, from wild-type to mutant plants. The portal includes mature and pri-miRNA expression levels detected in three plant species (Arabidopsis thaliana, Hordeum vulgare and Pellia endiviifolia), and in A. thaliana miRNA biogenesis pathway mutants. In total, the database contains information about the expression of 461 miRNAs representing 268 families. The data can be explored through the use of advanced web tools, including (i) a graphical query builder system allowing a combination of any given species, developmental stages and tissues, (ii) a modular presentation of the results in the form of thematic windows, and (iii) a number of user-friendly utilities such as a community-building discussion system and extensive tutorial documentation (e.g., tooltips, exemplary videos and presentations). All data contained within the mirEX 2.0 database can be downloaded for use in further applications in a context-based way from the result windows or from a dedicated web page. CONCLUSIONS The mirEX 2.0 portal provides the plant research community with easily accessible data and powerful tools for application in multi-conditioned analyses of miRNA expression from important plant species in different biological and developmental backgrounds.
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Affiliation(s)
- Andrzej Zielezinski
- Department of Computational Biology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland.
| | - Jakub Dolata
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland.
| | - Sylwia Alaba
- Department of Computational Biology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland.
| | - Katarzyna Kruszka
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland.
| | - Andrzej Pacak
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland.
| | - Aleksandra Swida-Barteczka
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland.
| | - Katarzyna Knop
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland.
| | - Agata Stepien
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland.
| | - Dawid Bielewicz
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland.
| | - Halina Pietrykowska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland.
| | - Izabela Sierocka
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland.
| | - Lukasz Sobkowiak
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland.
| | - Alicja Lakomiak
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland.
| | - Artur Jarmolowski
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland.
| | - Zofia Szweykowska-Kulinska
- Department of Computational Biology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland.
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland.
| | - Wojciech M Karlowski
- Department of Computational Biology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland.
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Cammaerts S, Strazisar M, De Rijk P, Del Favero J. Genetic variants in microRNA genes: impact on microRNA expression, function, and disease. Front Genet 2015; 6:186. [PMID: 26052338 PMCID: PMC4439572 DOI: 10.3389/fgene.2015.00186] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 05/05/2015] [Indexed: 12/21/2022] Open
Abstract
MicroRNAs (miRNAs) are important regulators of gene expression and like any other gene, their coding sequences are subject to genetic variation. Variants in miRNA genes can have profound effects on miRNA functionality at all levels, including miRNA transcription, maturation, and target specificity, and as such they can also contribute to disease. The impact of variants in miRNA genes is the focus of the present review. To put these effects into context, we first discuss the requirements of miRNA transcripts for maturation. In the last part an overview of available databases and tools and experimental approaches to investigate miRNA variants related to human disease is presented.
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Affiliation(s)
- Sophia Cammaerts
- Applied Molecular Genomics Unit, Department of Molecular Genetics, VIB, University of Antwerp Antwerp, Belgium
| | - Mojca Strazisar
- Applied Molecular Genomics Unit, Department of Molecular Genetics, VIB, University of Antwerp Antwerp, Belgium
| | - Peter De Rijk
- Applied Molecular Genomics Unit, Department of Molecular Genetics, VIB, University of Antwerp Antwerp, Belgium
| | - Jurgen Del Favero
- Applied Molecular Genomics Unit, Department of Molecular Genetics, VIB, University of Antwerp Antwerp, Belgium ; Multiplicom N.V., Niel Belgium
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