101
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Dhar Dwivedi SK, Mustafi SB, Mangala LS, Jiang D, Pradeep S, Rodriguez-Aguayo C, Ling H, Ivan C, Mukherjee P, Calin GA, Lopez-Berestein G, Sood AK, Bhattacharya R. Therapeutic evaluation of microRNA-15a and microRNA-16 in ovarian cancer. Oncotarget 2016; 7:15093-104. [PMID: 26918603 PMCID: PMC4924772 DOI: 10.18632/oncotarget.7618] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 01/23/2016] [Indexed: 12/23/2022] Open
Abstract
Treatment of chemo-resistant ovarian cancer (OvCa) remains clinically challenging and there is a pressing need to identify novel therapeutic strategies. Here we report that multiple mechanisms that promote OvCa progression and chemo-resistance could be inhibited by ectopic expression of miR-15a and miR-16. Significant correlations between low expression of miR-16, high expression of BMI1 and shortened overall survival (OS) were noted in high grade serous (HGS) OvCa patients upon analysis of The Cancer Genome Atlas (TCGA). Targeting BMI1, in vitro with either microRNA reduced clonal growth of OvCa cells. Additionally, epithelial to mesenchymal transition (EMT) as well as expression of the cisplatin transporter ATP7B were inhibited by miR-15a and miR-16 resulting in decreased degradation of the extra-cellular matrix and enhanced sensitization of OvCa cells to cisplatin. Nanoliposomal delivery of the miR-15a and miR-16 combination, in a pre-clinical chemo-resistant orthotopic mouse model of OvCa, demonstrated striking reduction in tumor burden compared to cisplatin alone. Thus, with the advent of miR replacement therapy some of which are in Phase 2 clinical trials, miR-15a and miR-16 represent novel ammunition in the anti-OvCa arsenal.
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Affiliation(s)
- Shailendra Kumar Dhar Dwivedi
- Department of Obstetrics and Gynecology, Stephenson Cancer Center, University of Oklahoma Health Science Center, Oklahoma City, OK, USA
| | - Soumyajit Banerjee Mustafi
- Department of Obstetrics and Gynecology, Stephenson Cancer Center, University of Oklahoma Health Science Center, Oklahoma City, OK, USA
| | - Lingegowda S. Mangala
- Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- The Center for RNA Interference and Non-Coding RNA, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Dahai Jiang
- Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- The Center for RNA Interference and Non-Coding RNA, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sunila Pradeep
- Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Cristian Rodriguez-Aguayo
- The Center for RNA Interference and Non-Coding RNA, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Hui Ling
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Cristina Ivan
- Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Priyabrata Mukherjee
- Department of Pathology, Stephenson Cancer Center, University of Oklahoma Health Science Center, Oklahoma City, OK, USA
| | - George A. Calin
- The Center for RNA Interference and Non-Coding RNA, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Gabriel Lopez-Berestein
- The Center for RNA Interference and Non-Coding RNA, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Anil K. Sood
- Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- The Center for RNA Interference and Non-Coding RNA, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Resham Bhattacharya
- Department of Obstetrics and Gynecology, Stephenson Cancer Center, University of Oklahoma Health Science Center, Oklahoma City, OK, USA
- Department of Cell Biology, University of Oklahoma College of Medicine, Oklahoma City, OK, USA
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102
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Mousavi R, Eftekhari M, Haghighi MG. A new approach to human microRNA target prediction using ensemble pruning and rotation forest. J Bioinform Comput Biol 2016; 13:1550017. [DOI: 10.1142/s0219720015500171] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that have important functions in gene regulation. Since finding miRNA target experimentally is costly and needs spending much time, the use of machine learning methods is a growing research area for miRNA target prediction. In this paper, a new approach is proposed by using two popular ensemble strategies, i.e. Ensemble Pruning and Rotation Forest (EP-RTF), to predict human miRNA target. For EP, the approach utilizes Genetic Algorithm (GA). In other words, a subset of classifiers from the heterogeneous ensemble is first selected by GA. Next, the selected classifiers are trained based on the RTF method and then are combined using weighted majority voting. In addition to seeking a better subset of classifiers, the parameter of RTF is also optimized by GA. Findings of the present study confirm that the newly developed EP-RTF outperforms (in terms of classification accuracy, sensitivity, and specificity) the previously applied methods over four datasets in the field of human miRNA target. Diversity-error diagrams reveal that the proposed ensemble approach constructs individual classifiers which are more accurate and usually diverse than the other ensemble approaches. Given these experimental results, we highly recommend EP-RTF for improving the performance of miRNA target prediction.
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Affiliation(s)
- Reza Mousavi
- Department of Electrical and Computer Engineering, Graduate University of Advanced Technology, Kerman, Iran
| | - Mahdi Eftekhari
- Department of Computer Engineering, Shahid Bahonar University of Kerman, Iran
| | - Mehdi Ghezelbash Haghighi
- Department of Electrical and Computer Engineering, Graduate University of Advanced Technology, Kerman, Iran
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103
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Louten J, Beach M, Palermino K, Weeks M, Holenstein G. MicroRNAs Expressed during Viral Infection: Biomarker Potential and Therapeutic Considerations. Biomark Insights 2016; 10:25-52. [PMID: 26819546 PMCID: PMC4718089 DOI: 10.4137/bmi.s29512] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 10/22/2015] [Accepted: 10/24/2015] [Indexed: 12/13/2022] Open
Abstract
MicroRNAs (miRNAs) are short sequences of noncoding single-stranded RNAs that exhibit inhibitory effects on complementary target mRNAs. Recently, it has been discovered that certain viruses express their own miRNAs, while other viruses activate the transcription of cellular miRNAs for their own benefit. This review summarizes the viral and/or cellular miRNAs that are transcribed during infection, with a focus on the biomarker and therapeutic potential of miRNAs (or their antagomirs). Several human viruses of clinical importance are discussed, namely, herpesviruses, polyomaviruses, hepatitis B virus, hepatitis C virus, human papillomavirus, and human immunodeficiency virus.
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Affiliation(s)
- Jennifer Louten
- Department of Molecular and Cellular Biology, Kennesaw State University, Kennesaw, GA, USA
| | - Michael Beach
- Department of Molecular and Cellular Biology, Kennesaw State University, Kennesaw, GA, USA
| | - Kristina Palermino
- Department of Molecular and Cellular Biology, Kennesaw State University, Kennesaw, GA, USA
| | - Maria Weeks
- Department of Molecular and Cellular Biology, Kennesaw State University, Kennesaw, GA, USA
| | - Gabrielle Holenstein
- Department of Molecular and Cellular Biology, Kennesaw State University, Kennesaw, GA, USA
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104
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Kulkarni V, Naqvi AR, Uttamani JR, Nares S. MiRNA-Target Interaction Reveals Cell-Specific Post-Transcriptional Regulation in Mammalian Cell Lines. Int J Mol Sci 2016; 17:ijms17010072. [PMID: 26761000 PMCID: PMC4730316 DOI: 10.3390/ijms17010072] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 12/21/2015] [Accepted: 12/31/2015] [Indexed: 12/12/2022] Open
Abstract
MicroRNAs are 18–22 nucleotides long, non-coding RNAs that bind transcripts with complementary sequences leading to either mRNA degradation or translational suppression. However, the inherent differences in preferred mode of miRNA regulation among cells of different origin have not been examined. In our previous transcriptome profiling studies, we observed that post-transcriptional regulation can differ substantially depending on the cell in context. Here we examined mechanistic differences in the regulation of a let-7a targeted (wild type) or resistant (mutant) engineered renilla transcript across various mammalian cell lines of diverse origin. Dual luciferase assays show that compared to mutant (mut), the reporter gene containing wild type (wt) let-7a binding sites was efficiently suppressed upon transfection in various cell lines. Importantly, the strength of miRNA regulation varied across the cell lines. Total RNA analysis demonstrates that wt renilla mRNA was expressed to similar or higher levels compared to mut suggesting that translation repression is a predominant mode of miRNA regulation. Nonetheless, transcript degradation was observed in some cell lines. Ago-2 immunoprecipitation show that miRNA repressed renilla mRNA are associated with functional mi-RISC (miRNA-RNA induced silencing complex). Given the immense potential of miRNA as a therapeutic option, these findings highlight the necessity to thoroughly examine the mode of mRNA regulation in order to achieve the beneficial effects in targeting cells.
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Affiliation(s)
- Varun Kulkarni
- Department of Periodontics, College of Dentistry, University of Illinois at Chicago, 458 Dent MC 859, 801 S. Paulina, Chicago, IL 60612, USA.
| | - Afsar Raza Naqvi
- Department of Periodontics, College of Dentistry, University of Illinois at Chicago, 458 Dent MC 859, 801 S. Paulina, Chicago, IL 60612, USA.
| | - Juhi Raju Uttamani
- Department of Periodontics, College of Dentistry, University of Illinois at Chicago, 458 Dent MC 859, 801 S. Paulina, Chicago, IL 60612, USA.
| | - Salvador Nares
- Department of Periodontics, College of Dentistry, University of Illinois at Chicago, 458 Dent MC 859, 801 S. Paulina, Chicago, IL 60612, USA.
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105
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Makino T, Jinnin M. Genetic and epigenetic abnormalities in systemic sclerosis. J Dermatol 2016; 43:10-8. [DOI: 10.1111/1346-8138.13221] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 10/15/2015] [Indexed: 12/12/2022]
Affiliation(s)
- Takamitsu Makino
- Department of Dermatology and Plastic Surgery; Faculty of Life Sciences; Kumamoto University; Kumamoto Japan
| | - Masatoshi Jinnin
- Department of Dermatology and Plastic Surgery; Faculty of Life Sciences; Kumamoto University; Kumamoto Japan
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106
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Maragkakis M, Alexiou P, Nakaya T, Mourelatos Z. CLIPSeqTools--a novel bioinformatics CLIP-seq analysis suite. RNA (NEW YORK, N.Y.) 2016; 22:1-9. [PMID: 26577377 PMCID: PMC4691824 DOI: 10.1261/rna.052167.115] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 10/18/2015] [Indexed: 05/22/2023]
Abstract
Immunoprecipitation of RNA binding proteins (RBPs) after in vivo crosslinking, coupled with sequencing of associated RNA footprints (HITS-CLIP, CLIP-seq), is a method of choice for the identification of RNA targets and binding sites for RBPs. Compared with RNA-seq, CLIP-seq analysis is widely diverse and depending on the RBPs that are analyzed, the approaches vary significantly, necessitating the development of flexible and efficient informatics tools. In this study, we present CLIPSeqTools, a novel, highly flexible computational suite that can perform analysis from raw sequencing data with minimal user input. It contains a wide array of tools to provide an in-depth view of CLIP-seq data sets. It supports extensive customization and promotes improvization, a critical virtue, since CLIP-seq analysis is rarely well defined a priori. To highlight CLIPSeqTools capabilities, we used the suite to analyze Ago-miRNA HITS-CLIP data sets that we prepared from human brains.
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Affiliation(s)
- Manolis Maragkakis
- Department of Pathology and Laboratory Medicine, Division of Neuropathology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA PENN Genome Frontiers Institute, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Panagiotis Alexiou
- Department of Pathology and Laboratory Medicine, Division of Neuropathology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA PENN Genome Frontiers Institute, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Tadashi Nakaya
- Laboratory of Neuroscience, Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Zissimos Mourelatos
- Department of Pathology and Laboratory Medicine, Division of Neuropathology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA PENN Genome Frontiers Institute, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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107
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Zhu X, Zhao H, Lin Z, Zhang G. Functional studies of miR-130a on the inhibitory pathways of apoptosis in patients with chronic myeloid leukemia. Cancer Gene Ther 2015; 22:573-80. [PMID: 26494558 DOI: 10.1038/cgt.2015.50] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 08/27/2015] [Accepted: 09/03/2015] [Indexed: 02/05/2023]
Abstract
The p53 mutation in chronic myeloid leukemia (CML) led to decreased overall survival and therapy resistance which was also closely correlated with the downstream proto-oncogenes BCL-2, TCL-1 and MCL-1. We in this study aimed to investigate the function of miR130a in p53 tumor suppressor signaling pathway. We performed microRNA (miRNA) expression profile analysis in CML cancer stem cells of 38 cases and extracted total RNA from peripheral blood of 143 cases. Standard curves of U6 and miRNA were made from 10-fold serial dilutions of the cDNA, which were quantified using real-time quantitative PCR with SYBR Green by ABI 7300. The p53 mutations and BCR/ABL mutation status analysis in CML patients were detected by PCR and direct sequencing. Candidate targets of miR130a of putative relevance in CML pathogenesis were analyzed by bioinformatics approach. We then used dual-luciferase activity assay to verify the target genes of miR130a and used western blot analysis to elucidate the mechanism of miR130a on modulating drug resistance. The levels of miR-130a expression in CML were significantly lower in poor prognostic subgroups, defined by prognostic factors including mutated BCR/ABL status, p53 and ATM deletions and p53 mutations. Furthermore, underexpression of miR-130a was significantly associated with shorter overall survival and treatment-free survival in CML patients. We demonstrated that miR130a function as tumor suppressors by inhibiting multiple anti-apoptosis proteins, including BCL-2, MCL-1 and XIAP. This was a direct effect because miR130a negatively regulated expression of a BCL-2/MCL-1/XIAP 3'untranslated region-based reporter construct. Transfection of miR130a mimics into CML cells from 30 patients without p53 aberrations led to significant increases in apoptosis compared with transfection with the miRNA control. Besides, enforced expression of miR130a had no significant drug-sensitization effect in CML cells from p53-attenuated patients. MiR-130a may have an important role in the pathogenesis of CML and may be useful for assessing prognosis in patients with CML. Moreover, miR130a may provide a possible therapeutic avenue and a sensitive indicator of the activity of the p53 in CML.
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MESH Headings
- Apoptosis
- Ataxia Telangiectasia Mutated Proteins/genetics
- Female
- Fusion Proteins, bcr-abl
- Gene Expression
- Gene Expression Regulation, Leukemic
- Humans
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/diagnosis
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/metabolism
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/physiopathology
- Male
- MicroRNAs/genetics
- Middle Aged
- Mutation
- Prognosis
- Signal Transduction
- Tumor Suppressor Protein p53/genetics
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Affiliation(s)
- X Zhu
- Cancer Center, Beijing Shijitan Hospital, Capital Medical Hospital, Beijing, China
| | - H Zhao
- Clinical Department, Capital Medical University, Beijing, China
| | - Z Lin
- Clinical Research Center, Affiliated Hospital of Guangdong Medical College, Guangdong, China
| | - G Zhang
- The Breast Center, Cancer Hospital, Shantou University Medical College, Shantou, China
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108
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Cui Y, Huang T, Zhang X. RNA editing of microRNA prevents RNA-induced silencing complex recognition of target mRNA. Open Biol 2015; 5:150126. [PMID: 26674414 PMCID: PMC4703055 DOI: 10.1098/rsob.150126] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 11/17/2015] [Indexed: 12/20/2022] Open
Abstract
MicroRNAs (miRNAs) integrate with Argonaut (Ago) to create the RNA-induced silencing complex, and regulate gene expression by silencing target mRNAs. RNA editing of miRNA may affect miRNA processing, assembly of the Ago complex and target mRNA binding. However, the function of edited miRNA, assembled within the Ago complex, has not been extensively investigated. In this study, sequence analysis of the Ago complex of Marsupenaeus japonicus shrimp infected with white spot syndrome virus (WSSV) revealed that host ADAR (adenosine deaminase acting on RNA) catalysed A-to-I RNA editing of a viral miRNA (WSSV-miR-N12) at the +16 site. This editing of the non-seed sequence did not affect association of the edited miRNA with the Ago protein, but inhibited interaction between the miRNA and its target gene (wsv399). The WSSV early gene wsv399 inhibited WSSV infection. As a result, the RNA editing of miRNA caused virus latency. Our results highlight a novel example of miRNA editing in the miRNA-induced silencing complex.
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Affiliation(s)
- Yalei Cui
- College of Life Sciences, Zhejiang University, Hangzhou 310058, People's Republic of China
| | - Tianzhi Huang
- College of Life Sciences, Zhejiang University, Hangzhou 310058, People's Republic of China
| | - Xiaobo Zhang
- College of Life Sciences, Zhejiang University, Hangzhou 310058, People's Republic of China
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109
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Ben-Hamo R, Efroni S. MicroRNA regulation of molecular pathways as a generic mechanism and as a core disease phenotype. Oncotarget 2015; 6:1594-604. [PMID: 25593195 PMCID: PMC4359317 DOI: 10.18632/oncotarget.2734] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Accepted: 11/12/2014] [Indexed: 12/21/2022] Open
Abstract
The role of microRNAs as key regulators of a wide variety of fundamental cellular processes, such as apoptosis, differentiation, proliferation and cell cycle is increasingly recognized in most aspects of biology and biomedicine. Accretion of results from multiple microRNA studies over multiple pathway networks, led us to hypothesize that microRNAs target molecular pathways. As we show here, this is a network-wide phenomenon. The work presented, uses statistical tools that show how single microRNAs target molecular pathways. We demonstrate that this targeting could not be the result of random associations and cannot be the result of the sheer numeracy of microRNA targets. Furthermore, the strongest evidence for the association microRNA-pathway, is in a demonstration of the way by which these associations are disease-relevant. In our analyses we study ten different types of cancer involving thousands of samples, and show that the identified microRNA–pathway associations demonstrate a clinical affiliation and an ability to stratify patients. The work presented here shows the first evidence for a mechanism of microRNAs-pathway generic regulation. This regulation is tightly associated with clinical phenotype. The presented approach may catalyze targeted treatment through exposure of hidden regulatory mechanisms and a systems-medicine view of clinical observation.
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Affiliation(s)
- Rotem Ben-Hamo
- The Mina and Everard Goodman Faculty of Life Science, Bar Ilan University, Ramat-Gan, 52900, Israel
| | - Sol Efroni
- The Mina and Everard Goodman Faculty of Life Science, Bar Ilan University, Ramat-Gan, 52900, Israel
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110
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Abstract
Bone is increasingly viewed as an endocrine organ with key biological functions. The skeleton produces hormones and cytokines, such as FGF23 and osteocalcin, which regulate an extensive list of homoeostatic functions. Some of these functions include glucose metabolism, male fertility, blood cell production and calcium/phosphate metabolism. Many of the genes regulating these functions are specific to bone cells. Some of these genes can be wrongly expressed by other malfunctioning cells, driving the generation of disease. The miRNAs are a class of non-coding RNA molecules that are powerful regulators of gene expression by suppressing and fine-tuning target mRNAs. Expression of one such miRNA, miR-140, is ubiquitous in chondrocyte cells during embryonic bone development. Activity in cells found in the adult breast, colon and lung tissue can silence genes required for tumour suppression. The realization that the same miRNA can be both normal and detrimental, depending on the cell, tissue and time point, provides a captivating twist to the study of whole-organism functional genomics. With the recent interest in miRNAs in bone biology and RNA-based therapeutics on the horizon, we present a review on the role of miR-140 in the molecular events that govern bone formation in the embryo. Cellular pathways involving miR-140 may be reactivated or inhibited when treating skeletal injury or disorder in adulthood. These pathways may also provide a novel model system when studying cancer biology of other cells and tissues.
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111
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Zhao J, Luo R, Xu X, Zou Y, Zhang Q, Pan W. High-throughput sequencing of RNAs isolated by cross-linking immunoprecipitation (HITS-CLIP) reveals Argonaute-associated microRNAs and targets in Schistosoma japonicum. Parasit Vectors 2015; 8:589. [PMID: 26577460 PMCID: PMC4650335 DOI: 10.1186/s13071-015-1203-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2015] [Accepted: 11/10/2015] [Indexed: 02/07/2023] Open
Abstract
Background Schistosomiasis, caused by schistosomes, is one of the most prevalent and serious parasitic diseases in tropical and subtropical countries. This pathogen has a complex life cycle and harbors a unique repertoire of genes expressed at different life-stages. Understanding the gene regulation of schistosomes will contribute to identification of novel drug targets and vaccine candidates. Some conserved and novel microRNAs (miRNAs) have been identified in schistosomes as key transcriptional and post-transcriptional regulators in the past few years; however, little is known about their specific targets. Methods High-throughput sequencing of RNAs isolated by cross-linking immunoprecipitation (HITS-CLIP) was used to covalently crosslink native Argonaute protein-RNA complexes in Schistosoma japonicum. An antibody against S.japonicum Argonaute proteins, was generated and used for immunoprecipitation of the crosslinked SjAgo-RNA complex from soluble adult worm extract. Small RNAs, including miRNAs and their target mRNAs associated with the native SjAgo in adult parasites, were enriched and extracted for library construction. Results High-throughput sequencing produced a total of ~7.4 million high-quality reads, of which approximately 45.07 % were composed of 769 miRNAs and 35.54 % were composed of 11,854 mRNAs target sites. Further bioinformatics analysis identified 43 conserved known miRNAs and 256 novel miRNAs in the SjAgo-associated small RNA population. An average of approximately 15 target sites were predicted for each miRNA. Moreover, a positive rate of 50 % has been achieved in a small-scale verification test of the putative target sites of miRNA1. Conclusion In this study, we isolated and identified small RNAs including miRNAs and their targets associated with the S. japonicum Argonaute proteins, by the HITS-CLIP method combined with bioinformatics and biologic experimental analysis. These data reveal a genome-wide miRNA-mRNA interaction map in S. japonicum in vivo, which will help us understand the complex gene regulatory network in this pathogen and thereby facilitate the development of novel drug approaches against schistosomiasis. Electronic supplementary material The online version of this article (doi:10.1186/s13071-015-1203-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jing Zhao
- Institute for Infectious Diseases and Vaccine Development, Tongji University School of Medicine, Shanghai, China.
| | - Rong Luo
- Institute for Infectious Diseases and Vaccine Development, Tongji University School of Medicine, Shanghai, China.
| | - Xindong Xu
- Institute for Infectious Diseases and Vaccine Development, Tongji University School of Medicine, Shanghai, China.
| | - Ying Zou
- Institute for Infectious Diseases and Vaccine Development, Tongji University School of Medicine, Shanghai, China.
| | - Qingfeng Zhang
- Institute for Infectious Diseases and Vaccine Development, Tongji University School of Medicine, Shanghai, China.
| | - Weiqing Pan
- Institute for Infectious Diseases and Vaccine Development, Tongji University School of Medicine, Shanghai, China. .,Department of Tropical Infectious Diseases, Second Military Medical University, Shanghai, China.
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112
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Zhang H, Artiles KL, Fire AZ. Functional relevance of "seed" and "non-seed" sequences in microRNA-mediated promotion of C. elegans developmental progression. RNA (NEW YORK, N.Y.) 2015; 21:1980-1992. [PMID: 26385508 PMCID: PMC4604436 DOI: 10.1261/rna.053793.115] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2012] [Accepted: 08/05/2015] [Indexed: 06/05/2023]
Abstract
The founding heterochronic microRNAs, lin-4 and let-7, together with their validated targets and well-characterized phenotypes in C. elegans, offer an opportunity to test functionality of microRNAs in a developmental context. In this study, we defined sequence requirements at the microRNA level for these two microRNAs, evaluating lin-4 and let-7 mutant microRNAs for their ability to support temporal development under conditions where the wild-type lin-4 and let-7 gene products are absent. For lin-4, we found a strong requirement for seed sequences, with function drastically affected by several central mutations in the seed sequence, while rescue was retained by a set of mutations peripheral to the seed. let-7 rescuing activity was retained to a surprising degree by a variety of central seed mutations, while several non-seed mutant effects support potential noncanonical contributions to let-7 function. Taken together, this work illustrates both the functional partnership between seed and non-seed sequences in mediating C. elegans temporal development and a diversity among microRNA effectors in the contributions of seed and non-seed regions to activity.
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Affiliation(s)
- Huibin Zhang
- Stanford University School of Medicine, Stanford, California 94305, USA
| | - Karen L Artiles
- Stanford University School of Medicine, Stanford, California 94305, USA
| | - Andrew Z Fire
- Stanford University School of Medicine, Stanford, California 94305, USA
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113
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Coexpression Network Analysis of miRNA-142 Overexpression in Neuronal Cells. BIOMED RESEARCH INTERNATIONAL 2015; 2015:921517. [PMID: 26539539 PMCID: PMC4619910 DOI: 10.1155/2015/921517] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Revised: 01/26/2015] [Accepted: 01/28/2015] [Indexed: 01/14/2023]
Abstract
MicroRNAs are small noncoding RNA molecules, which are differentially expressed in diverse biological processes and are also involved in the regulation of multiple genes. A number of sites in the 3′ untranslated regions (UTRs) of different mRNAs allow complimentary binding for a microRNA, leading to their posttranscriptional regulation. The miRNA-142 is one of the microRNAs overexpressed in neurons that is found to regulate SIRT1 and MAOA genes. Differential analysis of gene expression data, which is focused on identifying up- or downregulated genes, ignores many relationships between genes affected by miRNA-142 overexpression in a cell. Thus, we applied a correlation network model to identify the coexpressed genes and to study the impact of miRNA-142 overexpression on this network. Combining multiple sources of knowledge is useful to infer meaningful relationships in systems biology. We applied coexpression model on the data obtained from wild type and miR-142 overexpression neuronal cells and integrated miRNA seed sequence mapping information to identify genes greatly affected by this overexpression. Larger differences in the enriched networks revealed that the nervous system development related genes such as TEAD2, PLEKHA6, and POGLUT1 were greatly impacted due to miRNA-142 overexpression.
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114
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Vorozheykin PS, Titov II. Web server for prediction of miRNAs and their precursors and binding sites. Mol Biol 2015. [DOI: 10.1134/s0026893315050192] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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115
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MicroRNA dynamics during human embryonic stem cell differentiation to pancreatic endoderm. Gene 2015; 574:359-70. [PMID: 26297998 DOI: 10.1016/j.gene.2015.08.027] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 08/12/2015] [Indexed: 11/23/2022]
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that have emerged as critical regulators of human embryonic stem cell (hESC) pluripotency and differentiation. Despite the wealth of information about the role individual that miRNAs play in these two processes, there has yet to be a large-scale temporal analysis of the dynamics of miRNA expression as hESCs move from pluripotency into defined lineages. In this report, we used Next Generation Sequencing (NGS) to map temporal expression of miRNAs over ten 24-hour intervals as pluripotent cells were differentiated into pancreatic endoderm. Of the 2042 known human miRNAs, 694 had non-zero expression on all 11 days. Of these 694 miRNAs, 494 showed statistically significant changes in expression during differentiation. Clusters of miRNAs were identified, each displaying unique expression profiles distributed over multiple days. Selected miRNAs associated with pluripotency/differentiation (miR-302/367 and miR-371/372/373) and development/growth (miR-21, miR-25, miR-103, miR-9, and miR-92a) were found to have distinct expression profiles correlated with changes in media used to drive the differentiation process. Taken together, the clustering of miRNAs to identify expression dynamics that occur over longer periods of time (days vs. hours) provides unique insight into specific stages of differentiation. Major shifts in defined stages of hESC differentiation appear to be heavily dependent upon changes in external environmental factors, rather than intrinsic conditions in the cells.
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Ding M, Li J, Yu Y, Liu H, Yan Z, Wang J, Qian Q. Integrated analysis of miRNA, gene, and pathway regulatory networks in hepatic cancer stem cells. J Transl Med 2015; 13:259. [PMID: 26259570 PMCID: PMC4531430 DOI: 10.1186/s12967-015-0609-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 07/17/2015] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is one of the most common malignancies worldwide. HCC has a poor prognosis associated with tumor recurrence and drug resistance, which has been attributed to the existence of hepatic cancer stem cells (HCSCs). However, the characteristics and regulatory mechanisms of HCSCs remain unclear. We therefore established a novel system to enrich HCSCs and we demonstrate that these HCSCs exhibit cancer stem cell properties. METHODS We used miRNA and mRNA high-throughput sequencing data sets to determine molecular signatures and regulatory mechanisms in HCSCs. Paired miRNA and gene deep sequencing data in HCSCs versus HCC cells were used to identify candidate biomarkers of HCSCs. Using network analysis, we studied the relationship between miRNA and gene biomarkers, and KEGG pathway enrichment analysis was performed to study the function of candidate biomarkers. RESULTS We identified 9 up- and 9 down-regulated miRNAs and 115 up- and 402 down-regulated genes in HCSCs compared with HCC cells. A miRNA-gene network was constructed using 651 miRNA-gene interactions (between 7 up-regulated miRNAs and 274 down-regulated genes), and 103 miRNA-gene interactions (between 9 down-regulated miRNAs and 62 up-regulated genes). Pathway enrichment analysis identified five tumor invasion- and metastasis-related pathways and MAPK signaling associated with HCSCs. We further discovered two novel pathways that likely play a role in the regulation of HCSCs. CONCLUSIONS We identified a molecular expression signature and pathway regulatory mechanisms in HCSCs with potential diagnostic and therapeutic value.
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Affiliation(s)
- Min Ding
- Department of Viral and Gene Therapy, Eastern Hepatobiliary Surgery Hospital, The Second Military Medical University, Shanghai, 200438, People's Republic of China.
| | - Jiang Li
- Department of Viral and Gene Therapy, Eastern Hepatobiliary Surgery Hospital, The Second Military Medical University, Shanghai, 200438, People's Republic of China.
| | - Yong Yu
- The First Department of Biliary Surgery, Eastern Hepatobiliary Surgical Hospital, The Second Military Medical University, Shanghai, 200438, People's Republic of China.
| | - Hui Liu
- Department of Viral and Gene Therapy, Eastern Hepatobiliary Surgery Hospital, The Second Military Medical University, Shanghai, 200438, People's Republic of China.
| | - Zi Yan
- Department of Viral and Gene Therapy, Eastern Hepatobiliary Surgery Hospital, The Second Military Medical University, Shanghai, 200438, People's Republic of China.
| | - Jinghan Wang
- The First Department of Biliary Surgery, Eastern Hepatobiliary Surgical Hospital, The Second Military Medical University, Shanghai, 200438, People's Republic of China.
| | - Qijun Qian
- Department of Viral and Gene Therapy, Eastern Hepatobiliary Surgery Hospital, The Second Military Medical University, Shanghai, 200438, People's Republic of China.
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Tang Y, Zhang L, Forsyth CB, Shaikh M, Song S, Keshavarzian A. The Role of miR-212 and iNOS in Alcohol-Induced Intestinal Barrier Dysfunction and Steatohepatitis. Alcohol Clin Exp Res 2015. [PMID: 26207424 DOI: 10.1111/acer.12813] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
BACKGROUND Alcoholic liver disease is commonly associated with intestinal barrier dysfunction. Alcohol-induced dysregulation of intestinal tight junction proteins, such as Zonula Occludens-1 (ZO-1), plays an important role in alcohol-induced gut leakiness. However, the mechanism of alcohol-induced disruption of tight junction proteins is not well established. The goal of this study was to elucidate this mechanism by studying the role of microRNA 212 (miR-212) and inducible nitric oxide synthase (iNOS) in alcohol-induced gut leakiness. METHODS The permeability of the Caco-2 monolayer was assessed by transepithelial electrical resistance and flux of fluorescein sulfonic acid. miR-212 was measured by real-time polymerase chain reaction. The wild-type, iNOS knockout, and miR-212 knockdown mice were fed with alcohol diet (29% of total calories, 4.5% v/v) for 8 weeks. The LNA-anti-miR-212 was used to inhibit miR-212 expression in mice. The alcohol-induced intestinal permeability, miR-212 expression, and liver injuries in mice were measured. RESULTS Our in vitro monolayer and in vivo mice studies showed that: (i) alcohol-induced overexpression of the intestinal miR-212 and intestinal hyperpermeability is prevented using miR-212 knockdown techniques; and (ii) iNOS is up-regulated in the intestine by alcohol and that iNOS signaling is required for alcohol-induced miR-212 overexpression, ZO-1 disruption, gut leakiness, and steatohepatitis. CONCLUSIONS These studies thus support a novel miR-212 mechanism for alcohol-induced gut leakiness and a potential target that could be exploited for therapeutic intervention to prevent leaky gut and liver injury in alcoholics.
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Affiliation(s)
- Yueming Tang
- Division of Digestive Diseases and Nutrition, Department of Internal Medicine, Section of Gastroenterology, Rush University Medical Center, Chicago, Illinois
| | - Lijuan Zhang
- Division of Digestive Diseases and Nutrition, Department of Internal Medicine, Section of Gastroenterology, Rush University Medical Center, Chicago, Illinois
| | - Christopher B Forsyth
- Division of Digestive Diseases and Nutrition, Department of Internal Medicine, Section of Gastroenterology, Rush University Medical Center, Chicago, Illinois
| | - Maliha Shaikh
- Division of Digestive Diseases and Nutrition, Department of Internal Medicine, Section of Gastroenterology, Rush University Medical Center, Chicago, Illinois
| | - Shiwen Song
- Division of Digestive Diseases and Nutrition, Department of Internal Medicine, Section of Gastroenterology, Rush University Medical Center, Chicago, Illinois
| | - Ali Keshavarzian
- Division of Digestive Diseases and Nutrition, Department of Internal Medicine, Section of Gastroenterology, Rush University Medical Center, Chicago, Illinois
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Chen Y, Wang S, Zhang L, Xie T, Song S, Huang J, Zhang Y, Ouyang L, Liu B. Identification of ULK1 as a novel biomarker involved in miR-4487 and miR-595 regulation in neuroblastoma SH-SY5Y cell autophagy. Sci Rep 2015; 5:11035. [PMID: 26183158 PMCID: PMC4505320 DOI: 10.1038/srep11035] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 05/11/2015] [Indexed: 02/05/2023] Open
Abstract
Autophagy, referring to an evolutionarily conserved, multi-step lysosomal degradation process, has been well-known to be initiated by Unc-51 like kinase 1 (ULK1) with some links to Parkinson's disease (PD). MicroRNAs (miRNAs), small and non-coding endogenous RNAs 22 ~ 24 nucleotides (nt) in length, have been demonstrated to play an essential role for modulating autophagy. Recently, the relationships between miRNAs and autophagy have been widely reported in PD; however, how microRNAs regulate autophagy still remains in its infancy. Thus, in this study, we computationally constructed the ULK1-regulated autophagic kinase subnetwork in PD and further identified ULK1 able to negatively regulate p70(S6K) in starvation-induced autophagy of neuroblastoma SH-SY5Y cells. Combination of in silico prediction and microarray analyses, we identified that miR-4487 and miR-595 could target ULK1 and experimentally verified they could negatively or positively regulate ULK1-mediated autophagy. In conclusion, these results may uncover the novel ULK1-p70(S6K) autophagic pathway, as well as miR-4487 and miR-595 as new ULK1 target miRNAs. Thus, these findings would provide a clue to explore ULK1 and its target miRNAs as potential biomarkers in the future PD therapy.
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Affiliation(s)
- Yi Chen
- Department of Gastrointestinal Surgery, State Key Laboratory of Biotherapy, Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Shuya Wang
- Department of Gastrointestinal Surgery, State Key Laboratory of Biotherapy, Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
- Northwestern University, Feinberg School of Medicine, 303 East Chicago Avenue, Chicago, Illinois 60611, USA
| | - Lan Zhang
- Department of Gastrointestinal Surgery, State Key Laboratory of Biotherapy, Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Tao Xie
- Department of Gastrointestinal Surgery, State Key Laboratory of Biotherapy, Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Sicheng Song
- Department of Gastrointestinal Surgery, State Key Laboratory of Biotherapy, Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Jian Huang
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Yonghui Zhang
- Department of Gastrointestinal Surgery, State Key Laboratory of Biotherapy, Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
- Collaborative Innovation Center for Biotherapy, Department of Pharmacology & Pharmaceutical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Liang Ouyang
- Department of Gastrointestinal Surgery, State Key Laboratory of Biotherapy, Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Bo Liu
- Department of Gastrointestinal Surgery, State Key Laboratory of Biotherapy, Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
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Forster SC, Tate MD, Hertzog PJ. MicroRNA as Type I Interferon-Regulated Transcripts and Modulators of the Innate Immune Response. Front Immunol 2015. [PMID: 26217335 PMCID: PMC4495342 DOI: 10.3389/fimmu.2015.00334] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Type I interferons (IFNs) are an important family of cytokines that regulate innate and adaptive immune responses to pathogens, in cancer and inflammatory diseases. While the regulation and role of protein-coding genes involved in these responses are well characterized, the role of non-coding microRNAs in the IFN responses is less developed. We review the emerging picture of microRNA regulation of the IFN response at the transcriptional and post-transcriptional level. This response forms an important regulatory loop; several microRNAs target transcripts encoding components at many steps of the type I IFN response, both production and action, at the receptor, signaling, transcription factor, and regulated gene level. Not only do IFNs regulate positive signaling molecules but also negative regulators such as SOCS1. In total, 36 microRNA are reported as IFN regulated. Given this apparent multipronged targeting of the IFN response by microRNAs and their well-characterized capacity to “buffer” responses in other situations, the prospects of improved sequencing and microRNA targeting technologies will facilitate the elucidation of the broader regulatory networks of microRNA in this important biological context, and their therapeutic and diagnostic potential.
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Affiliation(s)
- Samuel C Forster
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research , Clayton, VIC , Australia ; Department of Molecular and Translational Sciences, Monash University , Clayton, VIC , Australia ; Host-Microbiota Interactions Laboratory, Wellcome Trust Sanger Institute , Hinxton , UK
| | - Michelle D Tate
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research , Clayton, VIC , Australia ; Department of Molecular and Translational Sciences, Monash University , Clayton, VIC , Australia
| | - Paul J Hertzog
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research , Clayton, VIC , Australia ; Department of Molecular and Translational Sciences, Monash University , Clayton, VIC , Australia
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Eedunuri VK, Rajapakshe K, Fiskus W, Geng C, Chew SA, Foley C, Shah SS, Shou J, Mohamed JS, Coarfa C, O'Malley BW, Mitsiades N. miR-137 Targets p160 Steroid Receptor Coactivators SRC1, SRC2, and SRC3 and Inhibits Cell Proliferation. Mol Endocrinol 2015; 29:1170-83. [PMID: 26066330 DOI: 10.1210/me.2015-1080] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The p160 family of steroid receptor coactivators (SRCs) are pleiotropic transcription factor coactivators and "master regulators" of gene expression that promote cancer cell proliferation, survival, metabolism, migration, invasion, and metastasis. Cancers with high p160 SRC expression exhibit poor clinical outcomes and resistance to therapy, highlighting the SRCs as critical oncogenic drivers and, thus, therapeutic targets. microRNAs are important epigenetic regulators of protein expression. To examine the regulation of p160 SRCs by microRNAs, we used and combined 4 prediction algorithms to identify microRNAs that could target SRC1, SRC2, and SRC3 expression. For validation of these predictions, we assessed p160 SRC protein expression and cell viability after transfection of corresponding microRNA mimetics in breast cancer, uveal melanoma, and prostate cancer (PC) cell lines. Transfection of selected microRNA mimetics into breast cancer, uveal melanoma, and PC cells depleted SRC protein expression levels and exerted potent antiproliferative activity in these cell types. In particular, microRNA-137 (miR-137) depleted expression of SRC1, SRC2, and very potently, SRC3. The latter effect can be attributed to the presence of 3 miR-137 recognition sequences within the SRC3 3'-untranslated region. Using reverse phase protein array analysis, we identified a network of proteins, in addition to SRC3, that were modulated by miR-137 in PC cells. We also found that miR-137 and its host gene are epigenetically silenced in human cancer specimens and cell lines. These results support the development and testing of microRNA-based therapies (in particular based on restoring miR-137 levels) for targeting the oncogenic family of p160 SRCs in cancer.
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Affiliation(s)
- Vijay Kumar Eedunuri
- Adrienne Helis Malvin Medical Research Foundation (V.K.E.), New Orleans, Louisiana 70130; and Departments of Molecular and Cellular Biology (K.R., W.F., C.G., S.A.C., C.F., S.S.S., J.S., J.S.M., C.C., B.W.O., N.M.) and Department of Medicine (W.F., C.G., S.A.C., C.F., S.S.S., J.S., J.S.M., N.M.), Baylor College of Medicine, Houston, Texas 77030
| | - Kimal Rajapakshe
- Adrienne Helis Malvin Medical Research Foundation (V.K.E.), New Orleans, Louisiana 70130; and Departments of Molecular and Cellular Biology (K.R., W.F., C.G., S.A.C., C.F., S.S.S., J.S., J.S.M., C.C., B.W.O., N.M.) and Department of Medicine (W.F., C.G., S.A.C., C.F., S.S.S., J.S., J.S.M., N.M.), Baylor College of Medicine, Houston, Texas 77030
| | - Warren Fiskus
- Adrienne Helis Malvin Medical Research Foundation (V.K.E.), New Orleans, Louisiana 70130; and Departments of Molecular and Cellular Biology (K.R., W.F., C.G., S.A.C., C.F., S.S.S., J.S., J.S.M., C.C., B.W.O., N.M.) and Department of Medicine (W.F., C.G., S.A.C., C.F., S.S.S., J.S., J.S.M., N.M.), Baylor College of Medicine, Houston, Texas 77030
| | - Chuandong Geng
- Adrienne Helis Malvin Medical Research Foundation (V.K.E.), New Orleans, Louisiana 70130; and Departments of Molecular and Cellular Biology (K.R., W.F., C.G., S.A.C., C.F., S.S.S., J.S., J.S.M., C.C., B.W.O., N.M.) and Department of Medicine (W.F., C.G., S.A.C., C.F., S.S.S., J.S., J.S.M., N.M.), Baylor College of Medicine, Houston, Texas 77030
| | - Sue Anne Chew
- Adrienne Helis Malvin Medical Research Foundation (V.K.E.), New Orleans, Louisiana 70130; and Departments of Molecular and Cellular Biology (K.R., W.F., C.G., S.A.C., C.F., S.S.S., J.S., J.S.M., C.C., B.W.O., N.M.) and Department of Medicine (W.F., C.G., S.A.C., C.F., S.S.S., J.S., J.S.M., N.M.), Baylor College of Medicine, Houston, Texas 77030
| | - Christopher Foley
- Adrienne Helis Malvin Medical Research Foundation (V.K.E.), New Orleans, Louisiana 70130; and Departments of Molecular and Cellular Biology (K.R., W.F., C.G., S.A.C., C.F., S.S.S., J.S., J.S.M., C.C., B.W.O., N.M.) and Department of Medicine (W.F., C.G., S.A.C., C.F., S.S.S., J.S., J.S.M., N.M.), Baylor College of Medicine, Houston, Texas 77030
| | - Shrijal S Shah
- Adrienne Helis Malvin Medical Research Foundation (V.K.E.), New Orleans, Louisiana 70130; and Departments of Molecular and Cellular Biology (K.R., W.F., C.G., S.A.C., C.F., S.S.S., J.S., J.S.M., C.C., B.W.O., N.M.) and Department of Medicine (W.F., C.G., S.A.C., C.F., S.S.S., J.S., J.S.M., N.M.), Baylor College of Medicine, Houston, Texas 77030
| | - John Shou
- Adrienne Helis Malvin Medical Research Foundation (V.K.E.), New Orleans, Louisiana 70130; and Departments of Molecular and Cellular Biology (K.R., W.F., C.G., S.A.C., C.F., S.S.S., J.S., J.S.M., C.C., B.W.O., N.M.) and Department of Medicine (W.F., C.G., S.A.C., C.F., S.S.S., J.S., J.S.M., N.M.), Baylor College of Medicine, Houston, Texas 77030
| | - Junaith S Mohamed
- Adrienne Helis Malvin Medical Research Foundation (V.K.E.), New Orleans, Louisiana 70130; and Departments of Molecular and Cellular Biology (K.R., W.F., C.G., S.A.C., C.F., S.S.S., J.S., J.S.M., C.C., B.W.O., N.M.) and Department of Medicine (W.F., C.G., S.A.C., C.F., S.S.S., J.S., J.S.M., N.M.), Baylor College of Medicine, Houston, Texas 77030
| | - Cristian Coarfa
- Adrienne Helis Malvin Medical Research Foundation (V.K.E.), New Orleans, Louisiana 70130; and Departments of Molecular and Cellular Biology (K.R., W.F., C.G., S.A.C., C.F., S.S.S., J.S., J.S.M., C.C., B.W.O., N.M.) and Department of Medicine (W.F., C.G., S.A.C., C.F., S.S.S., J.S., J.S.M., N.M.), Baylor College of Medicine, Houston, Texas 77030
| | - Bert W O'Malley
- Adrienne Helis Malvin Medical Research Foundation (V.K.E.), New Orleans, Louisiana 70130; and Departments of Molecular and Cellular Biology (K.R., W.F., C.G., S.A.C., C.F., S.S.S., J.S., J.S.M., C.C., B.W.O., N.M.) and Department of Medicine (W.F., C.G., S.A.C., C.F., S.S.S., J.S., J.S.M., N.M.), Baylor College of Medicine, Houston, Texas 77030
| | - Nicholas Mitsiades
- Adrienne Helis Malvin Medical Research Foundation (V.K.E.), New Orleans, Louisiana 70130; and Departments of Molecular and Cellular Biology (K.R., W.F., C.G., S.A.C., C.F., S.S.S., J.S., J.S.M., C.C., B.W.O., N.M.) and Department of Medicine (W.F., C.G., S.A.C., C.F., S.S.S., J.S., J.S.M., N.M.), Baylor College of Medicine, Houston, Texas 77030
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Fuentes E, Palomo I, Alarcón M. Platelet miRNAs and cardiovascular diseases. Life Sci 2015; 133:29-44. [PMID: 26003375 DOI: 10.1016/j.lfs.2015.04.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Revised: 03/25/2015] [Accepted: 04/21/2015] [Indexed: 01/04/2023]
Abstract
Activated platelets play a critical role in the acute complications of atherosclerosis that cause life-threatening ischemic events at late stages of the disease. The miRNAs are a novel class of small, non-coding RNAs that play a significant role in both inflammatory and cardiovascular diseases. The miRNAs are known to be present in platelets and exert important regulatory functions. Here we systematically examine the genes that are regulated by platelet miRNAs (miRNA-223,miRNA-126,miRNA-21, miRNA-24 and miRNA-197) and the association with cardiovascular disease risks. Platelet-secreted miRNAs could be novel biomarkers associated with cardiovascular diseases.
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Affiliation(s)
- Eduardo Fuentes
- Department of Clinical Biochemistry and Immunohaematology, Faculty of Health Sciences, Interdisciplinary Excellence Research Program on Healthy Aging (PIEI-ES), Universidad de Talca, Talca, Chile; Centro de Estudios en Alimentos Procesados (CEAP), CONICYT-Regional, Gore Maule R09I2001, Chile
| | - Iván Palomo
- Department of Clinical Biochemistry and Immunohaematology, Faculty of Health Sciences, Interdisciplinary Excellence Research Program on Healthy Aging (PIEI-ES), Universidad de Talca, Talca, Chile; Centro de Estudios en Alimentos Procesados (CEAP), CONICYT-Regional, Gore Maule R09I2001, Chile.
| | - Marcelo Alarcón
- Department of Clinical Biochemistry and Immunohaematology, Faculty of Health Sciences, Interdisciplinary Excellence Research Program on Healthy Aging (PIEI-ES), Universidad de Talca, Talca, Chile; Centro de Estudios en Alimentos Procesados (CEAP), CONICYT-Regional, Gore Maule R09I2001, Chile.
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122
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Li Y, Zhang Z. Computational Biology in microRNA. WILEY INTERDISCIPLINARY REVIEWS-RNA 2015; 6:435-52. [DOI: 10.1002/wrna.1286] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Revised: 03/24/2015] [Accepted: 03/25/2015] [Indexed: 01/24/2023]
Affiliation(s)
- Yue Li
- Department of Computer Science; University of Toronto; Toronto Ontario Canada
- Donnelly Centre for Cellular and Biomolecular Research; University of Toronto; Toronto Ontario Canada
| | - Zhaolei Zhang
- Donnelly Centre for Cellular and Biomolecular Research; University of Toronto; Toronto Ontario Canada
- Department of Molecular Genetics; University of Toronto; Toronto Ontario Canada
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Nyayanit D, Gadgil CJ. Mathematical modeling of combinatorial regulation suggests that apparent positive regulation of targets by miRNA could be an artifact resulting from competition for mRNA. RNA (NEW YORK, N.Y.) 2015; 21:307-319. [PMID: 25576498 PMCID: PMC4338329 DOI: 10.1261/rna.046862.114] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Accepted: 11/10/2014] [Indexed: 06/04/2023]
Abstract
MicroRNAs bind to and regulate the abundance and activity of target messenger RNA through sequestration, enhanced degradation, and suppression of translation. Although miRNA have a predominantly negative effect on the target protein concentration, several reports have demonstrated a positive effect of miRNA, i.e., increase in target protein concentration on miRNA overexpression and decrease in target concentration on miRNA repression. miRNA-target pair-specific effects such as protection of mRNA degradation owing to miRNA binding can explain some of these effects. However, considering such pairs in isolation might be an oversimplification of the RNA biology, as it is known that one miRNA interacts with several targets, and conversely target mRNA are subject to regulation by several miRNAs. We formulate a mathematical model of this combinatorial regulation of targets by multiple miRNA. Through mathematical analysis and numerical simulations of this model, we show that miRNA that individually have a negative effect on their targets may exhibit an apparently positive net effect when the concentration of one miRNA is experimentally perturbed by repression/overexpression in such a multi-miRNA multitarget situation. We show that this apparent unexpected effect is due to competition and will not be observed when miRNA interact noncompetitively with the target mRNA. This result suggests that some of the observed unusual positive effects of miRNA may be due to the combinatorial complexity of the system rather than due to any inherently unusual positive effect of the miRNA on its target.
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Affiliation(s)
- Dimpal Nyayanit
- Chemical Engineering and Process Development Division, CSIR-National Chemical Laboratory, Pune 411008, India Academy of Scientific and Innovative Research, New Delhi 110001, India
| | - Chetan J Gadgil
- Chemical Engineering and Process Development Division, CSIR-National Chemical Laboratory, Pune 411008, India Academy of Scientific and Innovative Research, New Delhi 110001, India CSIR-Institute of Genomics and Integrative Biology, New Delhi 110020, India
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Kothandan R, Biswas S. Identifying microRNAs involved in cancer pathway using support vector machines. Comput Biol Chem 2015; 55:31-6. [PMID: 25677919 DOI: 10.1016/j.compbiolchem.2015.01.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Revised: 01/26/2015] [Accepted: 01/28/2015] [Indexed: 01/11/2023]
Abstract
Since Ambros' discovery of small non-protein coding RNAs in the early 1990s, the past two decades have seen an upsurge in the number of reports of predicted microRNAs (miR), which have been implicated in various functions. The correlation of miRs with cancer has spurred the usage of this class of non-coding RNAs in various cancer therapies, although most of them are at trial stages. However, the experimental identification of a miR to be associated with cancer is still an elaborate, time-consuming process. To aid this process of miR association, we undertook an in-silico study involving the identification of global signatures in experimentally validated microRNAs associated with cancer. Subsequently, a support vector machine based two-step binary classifier system has been trained and modeled from the features extracted from the above study. A total of 60 distinguishing features were selected and ranked to form the feature set for classification - 26 of these extracted from the miR sequence itself, and the remainder from the thermodynamics of folding and the hybridized miRNA-mRNA structure. The two step classifier model - miRSEQ and miRINT had reasonably good performance measures with fairly high values of Matthew's correlation coefficient (MCC) values ranging from 0.72 to 0.82 (availability: https://sites.google.com/site/sumitslab/tools).
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Affiliation(s)
- Ram Kothandan
- VISTA Lab, Department of Biological Sciences, BITS, Pilani - K K Birla Goa Campus, Zuarinagar, Goa 403726, India
| | - Sumit Biswas
- VISTA Lab, Department of Biological Sciences, BITS, Pilani - K K Birla Goa Campus, Zuarinagar, Goa 403726, India.
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Karathanou K, Theofilatos K, Kleftogiannis D, Alexakos C, Likothanassis S, Tsakalidis A, Mavroudi S. ncRNAclass: A Web Platform for Non-Coding RNA Feature Calculation and MicroRNAs and Targets Prediction. INT J ARTIF INTELL T 2015. [DOI: 10.1142/s0218213015400023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
According to the central dogma of Biology it was commonly accepted that most of the genetic information was transacted by proteins. Recent experimental techniques revealed that the majority of mammalian genomes and other complex organisms are in fact transcribed into non-coding RNAs. Typically, non-coding RNAs are small nucleotide sequences that are not transcribed into proteins and have a profound regulatory role. Present advances in computational biosciences linked their abnormal functionality to many diseases and re-stated the principles of basic therapeutic strategies. The effective identification of non-coding RNAs and their biological role emerges as a new and challenging bioinformatics problem. ncRNAclass ( http://biotools.ceid.upatras.gr/ncrnaclass/ ) is a web platform that allows for efficient computation of a set of features that can describe effectively the broad class of non-coding RNAs. Moreover, it enables the calculation of features that include information about the targeting behavior of miRNAs. The tool operates under a user-friendly interface and its pilot implementation incorporates prediction models for the well-known class of microRNAs and for prediction their mRNA targets. The prediction models are based on two novel evolutionary Machine Learning algorithms that achieve very high classification performance in comparison with existing methods. The platform is also equipped with a data warehouse, with manually curated sequences, that enables fast information retrieval and data mining utilities.
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Affiliation(s)
| | | | | | - Christos Alexakos
- Department of Computer Engineering and Informatics, University of Patras, Greece
| | - Spiros Likothanassis
- Department of Computer Engineering and Informatics, University of Patras, Greece
| | | | - Seferina Mavroudi
- Department of Computer Engineering and Informatics, University of Patras, Greece
- Department of Social Work, School of Sciences of Health and Care Technological Educational Institute of Patras, Greece
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127
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Abstract
MiRNAs regulate gene expression by binding predominantly to the 3' untranslated region (UTR) of target transcripts to prevent their translation and/or induce target degradation. In addition to the more than 1200 human miRNAs, human DNA tumor viruses such as Kaposi's sarcoma-associated herpesvirus (KSHV) and Epstein-Barr virus (EBV) encode miRNAs. Target predictions indicate that each miRNA targets hundreds of transcripts, many of which are regulated by multiple miRNAs. Thus, target identification is a big challenge for the field. Most methods used currently investigate single miRNA-target interactions and are not able to analyze complex miRNA-target networks. To overcome these challenges, cross-linking and immunoprecipitation (CLIP), a recently developed method to study direct RNA-protein interactions in living cells, has been successfully applied to miRNA target analysis. It utilizes Argonaute (Ago)-immunoprecipitation to isolate native Ago-miRNA-mRNA complexes. In four recent publications, two variants of the CLIP method (HITS-CLIP and PAR-CLIP) were utilized to determine the targetomes of human and viral miRNAs in cells infected with the gamma-herpesviruses KSHV and EBV, which are associated with a number of human cancers. Here, we briefly introduce herpesvirus-encoded miRNAs and then focus on how CLIP technology has largely impacted our understanding of viral miRNAs in viral biology and pathogenesis.
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Affiliation(s)
- Irina Haecker
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL, USA
| | - Rolf Renne
- Department of Molecular Genetics and Microbiology, Shands Cancer Center, Genetics Institute, University of Florida, Gainesville, FL, USA
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128
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Relationship between expression of onco-related miRNAs and the endoscopic appearance of colorectal tumors. Int J Mol Sci 2015; 16:1526-43. [PMID: 25584614 PMCID: PMC4307318 DOI: 10.3390/ijms16011526] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Accepted: 12/25/2014] [Indexed: 01/08/2023] Open
Abstract
Accumulating data indicates that certain microRNAs (miRNAs or miRs) are differently expressed in samples of tumors and paired non-tumorous samples taken from the same patients with colorectal tumors. We examined the expression of onco-related miRNAs in 131 sporadic exophytic adenomas or early cancers and in 52 sporadic flat elevated adenomas or early cancers to clarify the relationship between the expression of the miRNAs and the endoscopic morphological appearance of the colorectal tumors. The expression levels of miR-143, -145, and -34a were significantly reduced in most of the exophytic tumors compared with those in the flat elevated ones. In type 2 cancers, the miRNA expression profile was very similar to that of the exophytic tumors. The expression levels of miR-7 and -21 were significantly up-regulated in some flat elevated adenomas compared with those in exophytic adenomas. In contrast, in most of the miR-143 and -145 down-regulated cases of the adenoma-carcinoma sequence and in some of the de novo types of carcinoma, the up-regulation of oncogenic miR-7 and/or -21 contributed to the triggering mechanism leading to the carcinogenetic process. These findings indicated that the expression of onco-related miRNA was associated with the morphological appearance of colorectal tumors.
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129
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Papadopoulos EI, Fragoulis EG, Scorilas A. Human l-DOPA decarboxylase mRNA is a target of miR-145: A prediction to validation workflow. Gene 2015; 554:174-80. [DOI: 10.1016/j.gene.2014.10.043] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Revised: 10/16/2014] [Accepted: 10/25/2014] [Indexed: 12/23/2022]
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Oulas A, Karathanasis N, Louloupi A, Pavlopoulos GA, Poirazi P, Kalantidis K, Iliopoulos I. Prediction of miRNA targets. Methods Mol Biol 2015; 1269:207-29. [PMID: 25577381 DOI: 10.1007/978-1-4939-2291-8_13] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Computational methods for miRNA target prediction are currently undergoing extensive review and evaluation. There is still a great need for improvement of these tools and bioinformatics approaches are looking towards high-throughput experiments in order to validate predictions. The combination of large-scale techniques with computational tools will not only provide greater credence to computational predictions but also lead to the better understanding of specific biological questions. Current miRNA target prediction tools utilize probabilistic learning algorithms, machine learning methods and even empirical biologically defined rules in order to build models based on experimentally verified miRNA targets. Large-scale protein downregulation assays and next-generation sequencing (NGS) are now being used to validate methodologies and compare the performance of existing tools. Tools that exhibit greater correlation between computational predictions and protein downregulation or RNA downregulation are considered the state of the art. Moreover, efficiency in prediction of miRNA targets that are concurrently verified experimentally provides additional validity to computational predictions and further highlights the competitive advantage of specific tools and their efficacy in extracting biologically significant results. In this review paper, we discuss the computational methods for miRNA target prediction and provide a detailed comparison of methodologies and features utilized by each specific tool. Moreover, we provide an overview of current state-of-the-art high-throughput methods used in miRNA target prediction.
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Affiliation(s)
- Anastasis Oulas
- Institute of Marine Biology, Biotechnology and Aquaculture-HCMR, Heraklion, Crete, Greece
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131
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Alexander MS, Kunkel LM. Skeletal Muscle MicroRNAs: Their Diagnostic and Therapeutic Potential in Human Muscle Diseases. J Neuromuscul Dis 2015; 2:1-11. [PMID: 27547731 PMCID: PMC4988517 DOI: 10.3233/jnd-140058] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
MicroRNAs (miRNAs) are small 21-24 nucleotide RNAs that are capable of regulating multiple signaling pathways across multiple tissues. MicroRNAs are dynamically regulated and change in expression levels during periods of early development, tissue regeneration, cancer, and various other disease states. Recently, microRNAs have been isolated from whole serum and muscle biopsies to identify unique diagnostic signatures for specific neuromuscular disease states. Functional studies of microRNAs in cell lines and animal models of neuromuscular diseases have elucidated their importance in contributing to neuromuscular disease progression and pathologies. The ability of microRNAs to alter the expression of an entire signaling pathway opens up their unique ability to be used as potential therapeutic entry points for the treatment of disease. Here, we will review the recent findings of key microRNAs and their dysregulation in various neuromuscular diseases. Additionally, we will highlight the current strategies being used to regulate the expression of key microRNAs as they have become important players in the clinical treatment of some of the neuromuscular diseases.
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Affiliation(s)
- Matthew S Alexander
- Division of Genetics and Genomics at Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics and Genetics at Harvard Medical School, Boston, MA, USA; The Stem Cell Program at Boston Children's Hospital, Boston, MA, USA
| | - Louis M Kunkel
- Division of Genetics and Genomics at Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics and Genetics at Harvard Medical School, Boston, MA, USA; The Stem Cell Program at Boston Children's Hospital, Boston, MA, USA; The Manton Center for Orphan Disease Research at Boston Children's Hospital, Boston, MA, USA; Harvard Stem Cell Institute, Cambridge, MA, USA
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132
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Yip DKS, Pang IK, Yip KY. Systematic exploration of autonomous modules in noisy microRNA-target networks for testing the generality of the ceRNA hypothesis. BMC Genomics 2014; 15:1178. [PMID: 25539629 PMCID: PMC4367885 DOI: 10.1186/1471-2164-15-1178] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 12/11/2014] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND In the competing endogenous RNA (ceRNA) hypothesis, different transcripts communicate through a competition for their common targeting microRNAs (miRNAs). Individual examples have clearly shown the functional importance of ceRNA in gene regulation and cancer biology. It remains unclear to what extent gene expression levels are regulated by ceRNA in general. One major hurdle to studying this problem is the intertwined connections in miRNA-target networks, which makes it difficult to isolate the effects of individual miRNAs. RESULTS Here we propose computational methods for decomposing a complex miRNA-target network into largely autonomous modules called microRNA-target biclusters (MTBs). Each MTB contains a relatively small number of densely connected miRNAs and mRNAs with few connections to other miRNAs and mRNAs. Each MTB can thus be individually analyzed with minimal crosstalk with other MTBs. Our approach differs from previous methods for finding modules in miRNA-target networks by not making any pre-assumptions about expression patterns, thereby providing objective information for testing the ceRNA hypothesis. We show that the expression levels of miRNAs and mRNAs in an MTB are significantly more anti-correlated than random miRNA-mRNA pairs and other validated and predicted miRNA-target pairs, demonstrating the biological relevance of MTBs. We further show that there is widespread correlation of expression between mRNAs in same MTBs under a wide variety of parameter settings, and the correlation remains even when co-regulatory effects are controlled for, which suggests potential widespread expression buffering between these mRNAs, which is consistent with the ceRNA hypothesis. Lastly, we also propose a potential use of MTBs in functional annotation of miRNAs. CONCLUSIONS MTBs can be used to help identify autonomous miRNA-target modules for testing the generality of the ceRNA hypothesis experimentally. The identified modules can also be used to test other properties of miRNA-target networks in general.
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Affiliation(s)
- Danny Kit-Sang Yip
- />Department of Computer Science and Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Iris K Pang
- />School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Kevin Y Yip
- />Department of Computer Science and Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
- />Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
- />CUHK-BGI Innovation Institute of Trans-omics, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
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133
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Liu Z, Borlak J, Tong W. Deciphering miRNA transcription factor feed-forward loops to identify drug repurposing candidates for cystic fibrosis. Genome Med 2014; 6:94. [PMID: 25484921 PMCID: PMC4256829 DOI: 10.1186/s13073-014-0094-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 10/23/2014] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Cystic fibrosis (CF) is a fatal genetic disorder caused by mutations in the CF transmembrane conductance regulator (CFTR) gene that primarily affects the lungs and the digestive system, and the current drug treatment is mainly able to alleviate symptoms. To improve disease management for CF, we considered the repurposing of approved drugs and hypothesized that specific microRNA (miRNA) transcription factors (TF) gene networks can be used to generate feed-forward loops (FFLs), thus providing treatment opportunities on the basis of disease specific FFLs. METHODS Comprehensive database searches revealed significantly enriched TFs and miRNAs in CF and CFTR gene networks. The target genes were validated using ChIPBase and by employing a consensus approach of diverse algorithms to predict miRNA gene targets. STRING analysis confirmed protein-protein interactions (PPIs) among network partners and motif searches defined composite FFLs. Using information extracted from SM2miR and Pharmaco-miR, an in silico drug repurposing pipeline was established based on the regulation of miRNA/TFs in CF/CFTR networks. RESULTS In human airway epithelium, a total of 15 composite FFLs were constructed based on CFTR specific miRNA/TF gene networks. Importantly, nine of them were confirmed in patient samples and CF epithelial cells lines, and STRING PPI analysis provided evidence that the targets interacted with each other. Functional analysis revealed that ubiquitin-mediated proteolysis and protein processing in the endoplasmic reticulum dominate the composite FFLs, whose major functions are folding, sorting, and degradation. Given that the mutated CFTR gene disrupts the function of the chloride channel, the constructed FFLs address mechanistic aspects of the disease and, among 48 repurposing drug candidates, 26 were confirmed with literature reports and/or existing clinical trials relevant to the treatment of CF patients. CONCLUSION The construction of FFLs identified promising drug repurposing candidates for CF and the developed strategy may be applied to other diseases as well.
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Affiliation(s)
- Zhichao Liu
- />Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079 USA
| | - Jürgen Borlak
- />Centre for Pharmacology and Toxicology, Hannover Medical School, Carl-Neuberg-Straße 1, 30625 Hannover, Germany
| | - Weida Tong
- />Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079 USA
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134
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Fan X, Kurgan L. Comprehensive overview and assessment of computational prediction of microRNA targets in animals. Brief Bioinform 2014; 16:780-94. [DOI: 10.1093/bib/bbu044] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Indexed: 12/26/2022] Open
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135
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Zhang Y, Guo X, Xiong L, Yu L, Li Z, Guo Q, Li Z, Li B, Lin N. Comprehensive analysis of microRNA-regulated protein interaction network reveals the tumor suppressive role of microRNA-149 in human hepatocellular carcinoma via targeting AKT-mTOR pathway. Mol Cancer 2014; 13:253. [PMID: 25424347 PMCID: PMC4255446 DOI: 10.1186/1476-4598-13-253] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2014] [Accepted: 11/19/2014] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Our previous study identified AKT1, AKT2 and AKT3 as unfavorable prognostic factors for patients with hepatocellular carcinoma (HCC). However, limited data are available on their exact mechanisms in HCC. Since microRNAs (miRNAs) are implicated in various human cancers including HCC, we aimed to screen miRNAs targeting AKTs and investigate their underlying mechanisms in HCC by integrating bioinformatics prediction, network analysis, functional assay and clinical validation. METHODS Five online programs of miRNA target prediction and RNAhybrid which calculate the minimum free energy (MFE) of the duplex miRNA:mRNA were used to screen optimized miRNA-AKT interactions. Then, miRNA-regulated protein interaction network was constructed and 5 topological features ('Degree', 'Node-betweenness', 'Edge-betweenness', 'Closeness' and 'Modularity') were analyzed to link candidate miRNA-AKT interactions to oncogenesis and cancer hallmarks. Further systematic experiments were performed to validate the prediction results. RESULTS Six optimized miRNA-AKT interactions (miR-149-AKT1, miR-302d-AKT1, miR-184-AKT2, miR-708-AKT2, miR-122-AKT3 and miR-124-AKT3) were obtained by combining the miRNA target prediction and MFE calculation. Then, 103 validated targets for the 6 candidate miRNAs were collected from miRTarBase. According to the enrichment analysis on GO items and KEGG pathways, these validated targets were significantly enriched in many known oncogenic pathways for HCC. In addition, miRNA-regulated protein interaction network were divided into 5 functional modules. Importantly, AKT1 and its interaction with mTOR respectively had the highest node-betweenness and edge-betweenness, implying their bottleneck roles in the network. Further experiments confirmed that miRNA-149 directly targeted AKT1 in HCC by a miRNA luciferase reporter approach. Then, re-expression of miR-149 significantly inhibited HCC cell proliferation and tumorigenicity by regulating AKT1/mTOR pathway. Notably, miR-149 down-regulation in clinical HCC tissues was correlated with tumor aggressiveness and poor prognosis of patients. CONCLUSION This comprehensive analysis identified a list of miRNAs targeting AKTs and revealed their critical roles in HCC malignant progression. Especially, miR-149 may function as a tumor suppressive miRNA and play an important role in inhibiting the HCC tumorigenesis by modulating the AKT/mTOR pathway. Our clinical evidence also highlight the prognostic potential of miR-149 in HCC. The newly identified miR-149/AKT/mTOR axis might be a promising therapeutic target in the prevention and treatment of HCC.
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Affiliation(s)
| | | | | | | | | | | | | | - Boan Li
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
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136
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A Common Polymorphism Within MSLN Affects miR-611 Binding Site and Soluble Mesothelin Levels in Healthy People. J Thorac Oncol 2014; 9:1662-8. [DOI: 10.1097/jto.0000000000000322] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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137
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Filshtein TJ, Mackenzie CO, Dale MD, Dela-Cruz PS, Ernst DM, Frankenberger EA, He C, Heath KL, Jones AS, Jones DK, King ER, Maher MB, Mitchell TJ, Morgan RR, Sirobhushanam S, Halkyard SD, Tiwari KB, Rubin DA, Borchert GM, Larson ED. OrbId: Origin-based identification of microRNA targets. Mob Genet Elements 2014; 2:184-192. [PMID: 23087843 PMCID: PMC3469430 DOI: 10.4161/mge.21617] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
MicroRNAs coordinate networks of mRNAs, but predicting specific sites of interactions is complicated by the very few bases of complementarity needed for regulation. Although efforts to characterize the specific requirements for microRNA (miR) regulation have made some advances, no general model of target recognition has been widely accepted. In this work, we describe an entirely novel approach to miR target identification. The genomic events responsible for the creation of individual miR loci have now been described with many miRs now known to have been initially formed from transposable element (TE) sequences. In light of this, we propose that limiting miR target searches to transcripts containing a miR's progenitor TE can facilitate accurate target identification. In this report we outline the methodology behind OrbId (Origin-based identification of microRNA targets). In stark contrast to the principal miR target algorithms (which rely heavily on target site conservation across species and are therefore most effective at predicting targets for older miRs), we find OrbId is particularly efficacious at predicting the mRNA targets of miRs formed more recently in evolutionary time. After defining the TE origins of > 200 human miRs, OrbId successfully generated likely target sets for 191 predominately primate-specific human miR loci. While only a handful of the loci examined were well enough conserved to have been previously evaluated by existing algorithms, we find ~80% of the targets for the oldest miR (miR-28) in our analysis contained within the principal Diana and TargetScan prediction sets. More importantly, four of the 15 OrbId miR-28 putative targets have been previously verified experimentally. In light of OrbId proving best-suited for predicting targets for more recently formed miRs, we suggest OrbId makes a logical complement to existing, conservation based, miR target algorithms.
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Affiliation(s)
- Teresa J Filshtein
- School of Biological Sciences; Illinois State University; Normal, IL USA
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mRNA destabilization is the dominant effect of mammalian microRNAs by the time substantial repression ensues. Mol Cell 2014; 56:104-15. [PMID: 25263593 DOI: 10.1016/j.molcel.2014.08.028] [Citation(s) in RCA: 358] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Revised: 08/21/2014] [Accepted: 08/22/2014] [Indexed: 01/01/2023]
Abstract
MicroRNAs (miRNAs) regulate target mRNAs through a combination of translational repression and mRNA destabilization, with mRNA destabilization dominating at steady state in the few contexts examined globally. Here, we extend the global steady-state measurements to additional mammalian contexts and find that regardless of the miRNA, cell type, growth condition, or translational state, mRNA destabilization explains most (66%->90%) miRNA-mediated repression. We also determine the relative dynamics of translational repression and mRNA destabilization for endogenous mRNAs as a miRNA is induced. Although translational repression occurs rapidly, its effect is relatively weak, such that by the time consequential repression ensues, the effect of mRNA destabilization dominates. These results imply that consequential miRNA-mediated repression is largely irreversible and provide other insights into the nature of miRNA-mediated regulation. They also simplify future studies, dramatically extending the known contexts and time points for which monitoring mRNA changes captures most of the direct miRNA effects.
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139
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Genome-wide discovery of novel and conserved microRNAs in white shrimp (Litopenaeus vannamei). Mol Biol Rep 2014; 42:61-9. [PMID: 25227525 DOI: 10.1007/s11033-014-3740-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Accepted: 09/11/2014] [Indexed: 12/27/2022]
Abstract
Of late years, a large amount of conserved and species-specific microRNAs (miRNAs) have been performed on identification from species which are economically important but lack a full genome sequence. In this study, Solexa deep sequencing and cross-species miRNA microarray were used to detect miRNAs in white shrimp. We identified 239 conserved miRNAs, 14 miRNA* sequences and 20 novel miRNAs by bioinformatics analysis from 7,561,406 high-quality reads representing 325,370 distinct sequences. The all 20 novel miRNAs were species-specific in white shrimp and not homologous in other species. Using the conserved miRNAs from the miRBase database as a query set to search for homologs from shrimp expressed sequence tags (ESTs), 32 conserved computationally predicted miRNAs were discovered in shrimp. In addition, using microarray analysis in the shrimp fed with Panax ginseng polysaccharide complex, 151 conserved miRNAs were identified, 18 of which were significant up-expression, while 49 miRNAs were significant down-expression. In particular, qRT-PCR analysis was also performed for nine miRNAs in three shrimp tissues such as muscle, gill and hepatopancreas. Results showed that these miRNAs expression are tissue specific. Combining results of the three methods, we detected 20 novel and 394 conserved miRNAs. Verification with quantitative reverse transcription (qRT-PCR) and Northern blot showed a high confidentiality of data. The study provides the first comprehensive specific miRNA profile of white shrimp, which includes useful information for future investigations into the function of miRNAs in regulation of shrimp development and immunology.
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140
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The malignancy suppression role of miR-23a by targeting the BCR/ABL oncogene in chromic myeloid leukemia. Cancer Gene Ther 2014; 21:397-404. [PMID: 25213664 DOI: 10.1038/cgt.2014.44] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Accepted: 07/25/2014] [Indexed: 12/22/2022]
Abstract
The aim of this study was to investigate the role and mechanism of miR-23a in the regulation of BCR/ABL and to provide a new prognostic biomarker for chronic myeloid leukemia (CML). The expression levels of miR-23a and BCR/ABL were assessed in 42 newly diagnosed CML patients, 37 CML patients in first complete remission and 25 healthy controls. Quantitative real-time PCR, western blot analysis and colony formation assay were used to evaluate changes induced by overexpression or inhibition of miR-23a or BCR/ABL. MiR-23a mimic or negative control mimic was transfected into a CML cell line (K562) and two lung cancer cell lines (H157 and SKMES1) using Lipofectamine 2000, and the cells were used for real-time reverse transcription-PCR (RT-PCR) and western blot analysis. We found that the downregulation of miR-23a expression was a frequent event in both leukemia cell lines and primary leukemic cells from patients with de novo CML. The microarray results showed that most of the CML patients expressed high levels of BCR/ABL and low levels of miR-23a. Real-time RT-PCR and western blot analysis showed that the BCR/ABL levels in miR-23a-transfected cells were lower than those in the control groups. Ectopic expression of miR-23a in K562 cells led to cellular senescence. Moreover, when K562 cells were treated with 5-aza-2'-deoxycytidine, a DNA methylation inhibitor, BCR/ABL expression was upregulated, which indicates epigenetic silencing of miR-23a in leukemic cells. BCR/ABL and miR-23a expressions were inversely related to CML, and BCR/ABL expression was regulated by miR-23a in leukemic cells. The epigenetic silencing of miR-23a led to derepression of BCR/ABL expression, and consequently contributes to CML development and progression.
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141
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Abstract
SIGNIFICANCE Chronic hypoxia can drive maladaptive responses in numerous organ systems, leading to a multitude of chronic mammalian diseases. Oxygen homeostasis is intimately linked with mitochondrial metabolism, and dysfunction in these systems can combine to form the backbone of hypoxic-ischemic injury in multiple tissue beds. Increased appreciation of the crucial roles of hypoxia-associated miRNA (hypoxamirs) in metabolism adds a new dimension to our understanding of the regulation of hypoxia-induced disease. RECENT ADVANCES Myriad factors related to glycolysis (e.g., aldolase A and hexokinase II), tricarboxylic acid cycle function (e.g., glutaminase and iron-sulfur cluster assembly protein 1/2), and apoptosis (e.g., p53) have been recently implicated as targets of hypoxamirs. In addition, several hypoxamirs have been implicated in the regulation of the master transcription factor of hypoxia, hypoxia-inducible factor-1α, clarifying how the cellular program of hypoxia is sustained and resolved. CRITICAL ISSUES Central to the discussion of metabolic change in hypoxia is the Warburg effect, a shift toward anaerobic metabolism that persists after normal oxygen levels have been restored. Many newly discovered targets of hypoxia-driven microRNA converge on pathways known to be involved in this pathological phenomenon and the apoptosis-resistant phenotype associated with it. FUTURE DIRECTIONS The often synergistic functions of miRNA may make them ideal therapeutic targets. The use of antisense inhibitors is currently being considered in diseases in which hypoxia and metabolic dysregulation predominate. In addition, exploration of pleiotripic miRNA functions will likely continue to offer unique insights into the mechanistic relationships of their downstream target pathways and associated hypoxic phenotypes.
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Affiliation(s)
- Katherine A Cottrill
- Division of Cardiovascular Medicine, Department of Medicine, Harvard Medical School, Brigham and Women's Hospital , Boston, Massachusetts
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142
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Hébrant A, Floor S, Saiselet M, Antoniou A, Desbuleux A, Snyers B, La C, de Saint Aubain N, Leteurtre E, Andry G, Maenhaut C. miRNA expression in anaplastic thyroid carcinomas. PLoS One 2014; 9:e103871. [PMID: 25153510 PMCID: PMC4143225 DOI: 10.1371/journal.pone.0103871] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2012] [Accepted: 07/08/2014] [Indexed: 12/13/2022] Open
Abstract
Anaplastic thyroid carcinoma (ATC) is the most lethal form of thyroid neoplasia and represents an end stage of thyroid tumor progression. No effective treatment exists so far. In this study, we analyzed the miRNA expression profiles of 11 ATC by microarrays and their relationship with the mRNA expression profiles of the same 11 ATC samples. ATC show distinct miRNA expression profiles compared to other less aggressive thyroid tumor types. ATC show 18 commonly deregulated miRNA compared to normal thyroid tissue (17 downregulated and 1 upregulated miRNA). First, the analysis of a combined approach of the mRNA gene expression and of the bioinformatically predicted mRNA targets of the deregulated miRNA suggested a role for these regulations in the epithelial to mesenchymal transition (EMT) process in ATC. Second, the direct interaction between one of the upregulated mRNA target, the LOX gene which is an EMT key player, and a downregulated miRNA, the miR-29a, was experimentally validated by a luciferase assay in HEK cell. Third, we confirmed that the ATC tissue is composed of about 50% of tumor associated macrophages (TAM) and suggested, by taking into account our data and published data, their most likely direct or paracrine intercommunication between them and the thyroid tumor cells, amplifying the tumor aggressiveness. Finally, we demonstrated by in situ hybridization a specific thyrocyte localization of 3 of the deregulated miRNA: let-7g, miR-29a and miR-30e and we pointed out the importance of identifying the cell type localization before drawing any conclusion on the physiopathological role of a given gene.
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Affiliation(s)
- Aline Hébrant
- Institute of Interdisciplinary Research (IRIBHM), School of Medicine, Université libre de Bruxelles, Campus Erasme, Brussels, Belgium
| | - Sébastien Floor
- Institute of Interdisciplinary Research (IRIBHM), School of Medicine, Université libre de Bruxelles, Campus Erasme, Brussels, Belgium
| | - Manuel Saiselet
- Institute of Interdisciplinary Research (IRIBHM), School of Medicine, Université libre de Bruxelles, Campus Erasme, Brussels, Belgium
| | - Aline Antoniou
- Institute of Interdisciplinary Research (IRIBHM), School of Medicine, Université libre de Bruxelles, Campus Erasme, Brussels, Belgium
| | - Alice Desbuleux
- Institute of Interdisciplinary Research (IRIBHM), School of Medicine, Université libre de Bruxelles, Campus Erasme, Brussels, Belgium
| | - Bérengère Snyers
- Institute of Interdisciplinary Research (IRIBHM), School of Medicine, Université libre de Bruxelles, Campus Erasme, Brussels, Belgium
| | - Caroline La
- Institute of Interdisciplinary Research (IRIBHM), School of Medicine, Université libre de Bruxelles, Campus Erasme, Brussels, Belgium
| | | | - Emmanuelle Leteurtre
- Université de Lille 2, Faculté de Médecine, Lille, France
- CHRU de Lille, Institut de Pathologie, Lille, France
| | - Guy Andry
- Institut Jules Bordet, Bruxelles, Belgium
| | - Carine Maenhaut
- Institute of Interdisciplinary Research (IRIBHM), School of Medicine, Université libre de Bruxelles, Campus Erasme, Brussels, Belgium
- WELBIO, School of Medicine, Université libre de Bruxelles, Campus Erasme, Brussels, Belgium
- * E-mail:
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143
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Ekimler S, Sahin K. Computational Methods for MicroRNA Target Prediction. Genes (Basel) 2014; 5:671-83. [PMID: 25153283 PMCID: PMC4198924 DOI: 10.3390/genes5030671] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Revised: 08/06/2014] [Accepted: 08/14/2014] [Indexed: 12/14/2022] Open
Abstract
MicroRNAs (miRNAs) have been identified as one of the most important molecules that regulate gene expression in various organisms. miRNAs are short, 21–23 nucleotide-long, single stranded RNA molecules that bind to 3' untranslated regions (3' UTRs) of their target mRNAs. In general, they silence the expression of their target genes via degradation of the mRNA or by translational repression. The expression of miRNAs, on the other hand, also varies in different tissues based on their functions. It is significantly important to predict the targets of miRNAs by computational approaches to understand their effects on the regulation of gene expression. Various computational methods have been generated for miRNA target prediction but the resulting lists of candidate target genes from different algorithms often do not overlap. It is crucial to adjust the bioinformatics tools for more accurate predictions as it is equally important to validate the predicted target genes experimentally.
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Affiliation(s)
- Semih Ekimler
- Molecular Biology and Genetics Department, Faculty of Science, Istanbul University, Vezneciler Fatih, 34134 Istanbul, Turkey.
| | - Kaniye Sahin
- Molecular Biology and Genetics Department, Faculty of Science, Istanbul University, Vezneciler Fatih, 34134 Istanbul, Turkey.
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144
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Amer M, Elhefnawi M, El-Ahwany E, Awad AF, Gawad NA, Zada S, Tawab FMA. Hsa-miR-195 targets PCMT1 in hepatocellular carcinoma that increases tumor life span. Tumour Biol 2014; 35:11301-9. [PMID: 25119594 DOI: 10.1007/s13277-014-2445-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 08/04/2014] [Indexed: 02/06/2023] Open
Abstract
MicroRNAs are small 19-25 nucleotides which have been shown to play important roles in the regulation of gene expression in many organisms. Downregulation or accumulation of miRNAs implies either tumor suppression or oncogenic activation. In this study, differentially expressed hsa-miR-195 in hepatocellular carcinoma (HCC) was identified and analyzed. The prediction was done using a consensus approach of tools. The validation steps were done at two different levels in silico and in vitro. FGF7, GHR, PCMT1, CITED2, PEX5, PEX13, NOVA1, AXIN2, and TSPYL2 were detected with high significant (P < 0.005). These genes are involved in important pathways in cancer like MAPK signaling pathway, Jak-STAT signaling pathways, regulation of actin cytoskeleton, angiogenesis, Wnt signaling pathway, and TGF-beta signaling pathway. In vitro target validation was done for protein-L-isoaspartate (D-aspartate) O-methyltransferase (PCMT1). The co-transfection of pmirGLO-PCMT1 and pEGP-miR-195 showed highly significant results. Firefly luciferase was detected using Lumiscensor and t test analysis was done. Firefly luciferase expression was significantly decreased (P < 0.001) in comparison to the control. The low expression of firefly luciferase validates the method of target prediction that we used in this work by working on PCMT1 as a target for miR-195. Furthermore, the rest of the predicted genes are suspected to be real targets for hsa-miR-195. These target genes control almost all the hallmarks of liver cancer which can be used as therapeutic targets in cancer treatment.
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Affiliation(s)
- Marwa Amer
- Biotechnology Department, Faculty of Biotechnology, Misr University for Science and Technology, Giza, Egypt,
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145
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Yang Y, Boss IW, McIntyre LM, Renne R. A systems biology approach identified different regulatory networks targeted by KSHV miR-K12-11 in B cells and endothelial cells. BMC Genomics 2014; 15:668. [PMID: 25106478 PMCID: PMC4147158 DOI: 10.1186/1471-2164-15-668] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Accepted: 08/01/2014] [Indexed: 01/01/2023] Open
Abstract
Background Kaposi’s sarcoma associated herpes virus (KSHV) is associated with tumors of endothelial and lymphoid origin. During latent infection, KSHV expresses miR-K12-11, an ortholog of the human tumor gene hsa-miR-155. Both gene products are microRNAs (miRNAs), which are important post-transcriptional regulators that contribute to tissue specific gene expression. Advances in target identification technologies and molecular interaction databases have allowed a systems biology approach to unravel the gene regulatory networks (GRNs) triggered by miR-K12-11 in endothelial and lymphoid cells. Understanding the tissue specific function of miR-K12-11 will help to elucidate underlying mechanisms of KSHV pathogenesis. Results Ectopic expression of miR-K12-11 differentially affected gene expression in BJAB cells of lymphoid origin and TIVE cells of endothelial origin. Direct miRNA targeting accounted for a small fraction of the observed transcriptome changes: only 29 genes were identified as putative direct targets of miR-K12-11 in both cell types. However, a number of commonly affected biological pathways, such as carbohydrate metabolism and interferon response related signaling, were revealed by gene ontology analysis. Integration of transcriptome profiling, bioinformatic algorithms, and databases of protein-protein interactome from the ENCODE project identified different nodes of GRNs utilized by miR-K12-11 in a tissue-specific fashion. These effector genes, including cancer associated transcription factors and signaling proteins, amplified the regulatory potential of a single miRNA, from a small set of putative direct targets to a larger set of genes. Conclusions This is the first comparative analysis of miRNA-K12-11’s effects in endothelial and B cells, from tissues infected with KSHV in vivo. MiR-K12-11 was able to broadly modulate gene expression in both cell types. Using a systems biology approach, we inferred that miR-K12-11 establishes its GRN by both repressing master TFs and influencing signaling pathways, to counter the host anti-viral response and to promote proliferation and survival of infected cells. The targeted GRNs are more reproducible and informative than target gene identification, and our approach can be applied to other regulatory factors of interest. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-668) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | - Lauren M McIntyre
- Department of Molecular Genetics and Microbiology, University of Florida, 2033 Mowry Road, Gainesville, FL 32610, USA.
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146
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Argonaute CLIP-Seq reveals miRNA targetome diversity across tissue types. Sci Rep 2014; 4:5947. [PMID: 25103560 PMCID: PMC4894423 DOI: 10.1038/srep05947] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 07/09/2014] [Indexed: 01/08/2023] Open
Abstract
To date, analyses of individual targets have provided evidence of a miRNA targetome that extends beyond the boundaries of messenger RNAs (mRNAs) and can involve non-Watson-Crick base pairing in the miRNA seed region. Here we report our findings from analyzing 34 Argonaute HITS-CLIP datasets from several human and mouse cell types. Investigation of the architectural (i.e. bulge vs. contiguous pairs) and sequence (Watson-Crick vs. G:U pairs) preferences for human and mouse miRNAs revealed that many heteroduplexes are “non-canonical” i.e. their seed region comprises G:U and bulge combinations. The genomic distribution of miRNA targets differed distinctly across cell types but remained congruent across biological replicates of the same cell type. For some cell types intergenic and intronic targets were more frequent whereas in other cell types mRNA targets prevailed. The findings suggest an expanded model of miRNA targeting that is more frequent than the standard model currently in use. Lastly, our analyses of data from different cell types and laboratories revealed consistent Ago-loaded miRNA profiles across replicates whereas, unexpectedly, the Ago-loaded targets exhibited a much more dynamic behavior across biological replicates.
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147
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Cipollini M, Landi S, Gemignani F. MicroRNA binding site polymorphisms as biomarkers in cancer management and research. Pharmgenomics Pers Med 2014; 7:173-91. [PMID: 25114582 PMCID: PMC4126202 DOI: 10.2147/pgpm.s61693] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
MicroRNAs (miRNAs) are important regulators of eukaryotic gene expression. They have been implicated in a broad range of biological processes, and miRNA-related genetic alterations probably underlie several human diseases. Single nucleotide polymorphisms of transcripts may modulate the posttranscriptional regulation of gene expression by miRNAs and explain interindividual variability in cancer risk and in chemotherapy response. On the basis of recent association studies published in the literature, the present review mainly summarizes the potential role of miRNAs as molecular biomarkers for disease susceptibility, diagnosis, prognosis, and drug-response prediction in tumors. Many clues suggest a role for polymorphisms within the 3' untranslated regions of KRAS rs61764370, SET8 rs16917496, and MDM4 rs4245739 as SNPs in miRNA binding sites highly promising in the biology of human cancer. However, more studies are needed to better characterize the composite spectrum of genetic determinants for future use of markers in risk prediction and clinical management of diseases, heading toward personalized medicine.
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Affiliation(s)
| | - Stefano Landi
- Department of Biology, University of Pisa, Pisa, Italy
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148
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Huang J, Dang J, Borchert GM, Eilbeck K, Zhang H, Xiong M, Jiang W, Wu H, Blake JA, Natale DA, Tan M. OMIT: dynamic, semi-automated ontology development for the microRNA domain. PLoS One 2014; 9:e100855. [PMID: 25025130 PMCID: PMC4099014 DOI: 10.1371/journal.pone.0100855] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Accepted: 05/30/2014] [Indexed: 01/11/2023] Open
Abstract
As a special class of short non-coding RNAs, microRNAs (a.k.a. miRNAs or miRs) have been reported to perform important roles in various biological processes by regulating respective target genes. However, significant barriers exist during biologists' conventional miR knowledge discovery. Emerging semantic technologies, which are based upon domain ontologies, can render critical assistance to this problem. Our previous research has investigated the construction of a miR ontology, named Ontology for MIcroRNA Target Prediction (OMIT), the very first of its kind that formally encodes miR domain knowledge. Although it is unavoidable to have a manual component contributed by domain experts when building ontologies, many challenges have been identified for a completely manual development process. The most significant issue is that a manual development process is very labor-intensive and thus extremely expensive. Therefore, we propose in this paper an innovative ontology development methodology. Our contributions can be summarized as: (i) We have continued the development and critical improvement of OMIT, solidly based on our previous research outcomes. (ii) We have explored effective and efficient algorithms with which the ontology development can be seamlessly combined with machine intelligence and be accomplished in a semi-automated manner, thus significantly reducing large amounts of human efforts. A set of experiments have been conducted to thoroughly evaluate our proposed methodology.
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Affiliation(s)
- Jingshan Huang
- School of Computing, University of South Alabama, Mobile, Alabama, United States of America
| | - Jiangbo Dang
- Corporate Technology, Siemens Corporation, Princeton, New Jersey, United States of America
| | - Glen M. Borchert
- Department of Biology, University of South Alabama, Mobile, Alabama, United States of America
| | - Karen Eilbeck
- School of Medicine, University of Utah, Salt Lake City, Utah, United States of America
| | - He Zhang
- School of Computing, University of South Alabama, Mobile, Alabama, United States of America
| | - Min Xiong
- School of Computing, University of South Alabama, Mobile, Alabama, United States of America
| | - Weijian Jiang
- School of Computing, University of South Alabama, Mobile, Alabama, United States of America
| | - Hao Wu
- School of Computing, University of South Alabama, Mobile, Alabama, United States of America
| | - Judith A. Blake
- The Jackson Laboratory, Bar Harbor, Maine, United States of America
| | - Darren A. Natale
- Georgetown University Medical Center, Washington, DC, United States of America
| | - Ming Tan
- Mitchell Cancer Institute, University of South Alabama, Mobile, Alabama, United States of America
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149
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Autophagy and microRNA dysregulation in liver diseases. Arch Pharm Res 2014; 37:1097-116. [PMID: 25015129 DOI: 10.1007/s12272-014-0439-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 06/29/2014] [Indexed: 02/07/2023]
Abstract
Autophagy is a catabolic process through which organelles and cellular components are sequestered into autophagosomes and degraded via fusion with lysosomes. Autophagy plays a role in many physiological processes, including stress responses, energy homeostasis, elimination of cellular organelles, and tissue remodeling. In addition, autophagy capacity changes in various disease states. A series of studies have shown that autophagy is strictly controlled to maintain homeostatic balance of energy metabolism and cellular organelle and protein turnover. These studies have also shown that this process is post-transcriptionally controlled by small noncoding microRNAs that regulate gene expression through complementary base pairing with mRNAs. Conversely, autophagy regulates the expression of microRNAs. Therefore, dysregulation of the link between autophagy and microRNA expression exacerbates the pathogenesis of various diseases. In this review, we summarize the roles of autophagy and microRNA dysregulation in the course of liver diseases, with the aim of understanding how microRNAs modify key autophagic effector molecules, and we discuss how this dysregulation affects both physiological and pathological conditions. This article may advance our understanding of the cellular and molecular bases of liver disease progression and promote the development of strategies for pharmacological intervention.
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150
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Altered expression of miR-202 in cerebellum of multiple-system atrophy. Mol Neurobiol 2014; 51:180-6. [PMID: 24981430 DOI: 10.1007/s12035-014-8788-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Accepted: 06/09/2014] [Indexed: 10/25/2022]
Abstract
Cerebellar degeneration is a devastating manifestation of cerebellar-type multiple-system atrophy (MSA), a rapidly progressive neurodegenerative disease, and the exact pathogenesis is unknown. Here, we examined the expression of micro-RNAs (miRNAs), which are short noncoding RNAs, in the cerebellum of MSA and the key target genes. miRNA microarray found 11 miRNAs with significantly different expression in MSA cerebellum compared to cerebellum from age-, sex-, and postmortem interval-matched controls. miR-202 was the most upregulated in the MSA samples. In silico analysis, followed by target gene luciferase assay, in vitro transfection, and Western blotting in human samples showed that miR-202 downregulates Oct1 (Pou2f1), a transcription factor expressed in cerebellar Purkinje cells. Transfection of Neuro-2a cells with miR-202 enhanced oxidative stress-induced cell death, and an antagomir to miR-202 inhibited this effect of miR-202. This study provides novel insight into the role of miRNA in cerebellar degeneration and suggests that miR-202 is a key miRNA mediating the pathogenesis of MSA.
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