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Asfa S, Toy HI, Arshinchi Bonab R, Chrousos GP, Pavlopoulou A, Geronikolou SA. Soft Tissue Ewing Sarcoma Cell Drug Resistance Revisited: A Systems Biology Approach. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:6288. [PMID: 37444135 PMCID: PMC10341845 DOI: 10.3390/ijerph20136288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 05/08/2023] [Accepted: 06/30/2023] [Indexed: 07/15/2023]
Abstract
Ewing sarcoma is a rare type of cancer that develops in the bones and soft tissues. Drug therapy represents an extensively used modality for the treatment of sarcomas. However, cancer cells tend to develop resistance to antineoplastic agents, thereby posing a major barrier in treatment effectiveness. Thus, there is a need to uncover the molecular mechanisms underlying chemoresistance in sarcomas and, hence, to enhance the anticancer treatment outcome. In this study, a differential gene expression analysis was conducted on high-throughput transcriptomic data of chemoresistant versus chemoresponsive Ewing sarcoma cells. By applying functional enrichment analysis and protein-protein interactions on the differentially expressed genes and their corresponding products, we uncovered genes with a hub role in drug resistance. Granted that non-coding RNA epigenetic regulators play a pivotal role in chemotherapy by targeting genes associated with drug response, we investigated the non-coding RNA molecules that potentially regulate the expression of the detected chemoresistance genes. Of particular importance, some chemoresistance-relevant genes were associated with the autonomic nervous system, suggesting the involvement of the latter in the drug response. The findings of this study could be taken into consideration in the clinical setting for the accurate assessment of drug response in sarcoma patients and the application of tailored therapeutic strategies.
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Affiliation(s)
- Seyedehsadaf Asfa
- Izmir Biomedicine and Genome Center (IBG), 35340 Izmir, Turkey; (S.A.); (H.I.T.); (R.A.B.)
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, 35340 Izmir, Turkey
| | - Halil Ibrahim Toy
- Izmir Biomedicine and Genome Center (IBG), 35340 Izmir, Turkey; (S.A.); (H.I.T.); (R.A.B.)
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, 35340 Izmir, Turkey
| | - Reza Arshinchi Bonab
- Izmir Biomedicine and Genome Center (IBG), 35340 Izmir, Turkey; (S.A.); (H.I.T.); (R.A.B.)
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, 35340 Izmir, Turkey
| | - George P. Chrousos
- Clinical, Translational and Experimental Surgery Research Centre, Biomedical Research Foundation Academy of Athens, Soranou Ephessiou 4, 11527 Athens, Greece;
- University Research Institute of Maternal and Child Health and Precision Medicine and UNESCO Chair on Adolescent Health Care, National and Kapodistrian University of Athens, Aghia Sophia Children’s Hospital, Levadeias 8, 11527 Athens, Greece
| | - Athanasia Pavlopoulou
- Izmir Biomedicine and Genome Center (IBG), 35340 Izmir, Turkey; (S.A.); (H.I.T.); (R.A.B.)
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, 35340 Izmir, Turkey
| | - Styliani A. Geronikolou
- Clinical, Translational and Experimental Surgery Research Centre, Biomedical Research Foundation Academy of Athens, Soranou Ephessiou 4, 11527 Athens, Greece;
- University Research Institute of Maternal and Child Health and Precision Medicine and UNESCO Chair on Adolescent Health Care, National and Kapodistrian University of Athens, Aghia Sophia Children’s Hospital, Levadeias 8, 11527 Athens, Greece
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2
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Keikha R, Hashemi-Shahri SM, Jebali A. The miRNA neuroinflammatory biomarkers in COVID-19 patients with different severity of illness. Neurologia 2023; 38:e41-e51. [PMID: 37344097 DOI: 10.1016/j.nrleng.2023.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 06/27/2021] [Indexed: 06/23/2023] Open
Abstract
INTRODUCTION The expression of specific miRNAs and their mRNA targets are changed in infectious disease. The aim of this study was to analyze the expression of pro-neuroinflammatory miRNAs, anti-neuroinflammatory miRNAs, and their mRNA targets in the serum of COVID-19 patients with different grades. METHODS COVID-19 patients with different grades were enrolled in this study and the expression of pro-neuroinflammatory miRNAs, anti-neuroinflammatory miRNAs, and their target mRNAs was analyzed by q-PCR. RESULTS The relative expression of anti- neuroinflammatory miRNAs (mir-21, mir-124, and mir-146a) was decreased and the relative expression of their target mRNAs (IL-12p53, Stat3, and TRAF6) was increased. Also, the relative expression of pro-neuroinflammatory miRNAs (mir-326, mir-155, and mir-27b) was increased and the relative expression of their target mRNA (PPARS, SOCS1, and CEBPA) was decreased in COVID-19 patients with increase of disease grade. A negative significant correlation was seen between mir-21 and IL-12p53 mRNA, mir-124 and Stat3 mRNA, mir-146a and TRAF6 mRNA, mir-27b and PPARS mRNA, mir-155 and SOCS1 mRNA, and between mir-326 and CEBPA mRNA in COVID-19 patients (P<0.05). CONCLUSIONS This study showed that the relative expression of anti- neuroinflammatory miRNAs was decreased and the relative expression of their targeted mRNAs was increased in COVID-19 patients from asymptomatic to critical illness. Also, this study showed that the relative expression of pro-neuroinflammatory miRNAs was increased and the relative expression of their targeted mRNA was decreased in COVID-19 patients from asymptomatic to critical illness.
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Affiliation(s)
- R Keikha
- Infectious Diseases and Tropical Medicine Research Center, Resistant Tuberculosis Institute, Zahedan University of Medical Sciences, Zahedan, Iran; Department of Pathology, Faculty of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | - S M Hashemi-Shahri
- Infectious Diseases and Tropical Medicine Research Center, Resistant Tuberculosis Institute, Zahedan University of Medical Sciences, Zahedan, Iran
| | - A Jebali
- Department of Medical Nanotechnology, Faculty of Advanced Sciences and Technology, Tehran Medical Science, Islamic Azad University, Tehran, Iran.
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3
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miRBind: A Deep Learning Method for miRNA Binding Classification. Genes (Basel) 2022; 13:genes13122323. [PMID: 36553590 PMCID: PMC9777820 DOI: 10.3390/genes13122323] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 11/30/2022] [Accepted: 12/08/2022] [Indexed: 12/15/2022] Open
Abstract
The binding of microRNAs (miRNAs) to their target sites is a complex process, mediated by the Argonaute (Ago) family of proteins. The prediction of miRNA:target site binding is an important first step for any miRNA target prediction algorithm. To date, the potential for miRNA:target site binding is evaluated using either co-folding free energy measures or heuristic approaches, based on the identification of binding 'seeds', i.e., continuous stretches of binding corresponding to specific parts of the miRNA. The limitations of both these families of methods have produced generations of miRNA target prediction algorithms that are primarily focused on 'canonical' seed targets, even though unbiased experimental methods have shown that only approximately half of in vivo miRNA targets are 'canonical'. Herein, we present miRBind, a deep learning method and web server that can be used to accurately predict the potential of miRNA:target site binding. We trained our method using seed-agnostic experimental data and show that our method outperforms both seed-based approaches and co-fold free energy approaches. The full code for the development of miRBind and a freely accessible web server are freely available.
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Nagar G, Mittal P, Gupta SRR, Pahuja M, Sanger M, Mishra R, Singh A, Singh IK. Multi-omics therapeutic perspective on ACVR1 gene: from genetic alterations to potential targeting. Brief Funct Genomics 2022; 22:123-142. [PMID: 36003055 DOI: 10.1093/bfgp/elac026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 07/04/2022] [Accepted: 07/20/2022] [Indexed: 11/13/2022] Open
Abstract
Activin A receptor type I (ACVR1), a transmembrane serine/threonine kinase, belongs to the transforming growth factor-β superfamily, which signals via phosphorylating the downstream effectors and SMAD transcription factors. Its central role in several biological processes and intracellular signaling is well known. Genetic variation in ACVR1 has been associated with a rare disease, fibrodysplasia ossificans progressive, and its somatic alteration is reported in rare cancer diffuse intrinsic pontine glioma. Furthermore, altered expression or variation of ACVR1 is associated with multiple pathologies such as polycystic ovary syndrome, congenital heart defects, diffuse idiopathic skeletal hyperostosis, posterior fossa ependymoma and other malignancies. Recent advancements have witnessed ACVR1 as a potential pharmacological target, and divergent promising approaches for its therapeutic targeting have been explored. This review highlights the structural and functional characteristics of receptor ACVR1, associated signaling pathways, genetic variants in several diseases and cancers, protein-protein interaction, gene expression, regulatory miRNA prediction and potential therapeutic targeting approaches. The comprehensive knowledge will offer new horizons and insights into future strategies harnessing its therapeutic potential.
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Keshavarz Alikhani H, Pourhamzeh M, Seydi H, Shokoohian B, Hossein-khannazer N, Jamshidi-adegani F, Al-Hashmi S, Hassan M, Vosough M. Regulatory Non-Coding RNAs in Familial Hypercholesterolemia, Theranostic Applications. Front Cell Dev Biol 2022; 10:894800. [PMID: 35813199 PMCID: PMC9260315 DOI: 10.3389/fcell.2022.894800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 06/01/2022] [Indexed: 11/13/2022] Open
Abstract
Familial hypercholesterolemia (FH) is a common monogenic disease which is associated with high serum levels of low-density lipoprotein cholesterol (LDL-C) and leads to atherosclerosis and cardiovascular disease (CVD). Early diagnosis and effective treatment strategy can significantly improve prognosis. Recently, non-coding RNAs (ncRNAs) have emerged as novel biomarkers for the diagnosis and innovative targets for therapeutics. Non-coding RNAs have essential roles in the regulation of LDL-C homeostasis, suggesting that manipulation and regulating ncRNAs could be a promising theranostic approach to ameliorate clinical complications of FH, particularly cardiovascular disease. In this review, we briefly discussed the mechanisms and pathophysiology of FH and novel therapeutic strategies for the treatment of FH. Moreover, the theranostic effects of different non-coding RNAs for the treatment and diagnosis of FH were highlighted. Finally, the advantages and disadvantages of ncRNA-based therapies vs. conventional therapies were discussed.
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Affiliation(s)
- Hani Keshavarz Alikhani
- Department of Regenerative Medicine, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Mahsa Pourhamzeh
- Department of Regenerative Medicine, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Homeyra Seydi
- Department of Regenerative Medicine, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Bahare Shokoohian
- Department of Regenerative Medicine, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Nikoo Hossein-khannazer
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Fatemeh Jamshidi-adegani
- Laboratory for Stem Cell and Regenerative Medicine, Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
| | - Sulaiman Al-Hashmi
- Laboratory for Stem Cell and Regenerative Medicine, Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
| | - Moustapha Hassan
- Experimental Cancer Medicine, Institution for Laboratory Medicine, Karolinska Institute, Stockholm, Sweden
| | - Massoud Vosough
- Department of Regenerative Medicine, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
- Experimental Cancer Medicine, Institution for Laboratory Medicine, Karolinska Institute, Stockholm, Sweden
- *Correspondence: Massoud Vosough,
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6
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Zaccagnini G, Greco S, Voellenkle C, Gaetano C, Martelli F. miR-210 hypoxamiR in Angiogenesis and Diabetes. Antioxid Redox Signal 2022; 36:685-706. [PMID: 34521246 DOI: 10.1089/ars.2021.0200] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Significance: microRNA-210 (miR-210) is the master hypoxia-inducible miRNA (hypoxamiR) since it has been found to be significantly upregulated under hypoxia in a wide range of cell types. Recent advances: Gene ontology analysis of its targets indicates that miR-210 modulates several aspects of cellular response to hypoxia. Due to its high pleiotropy, miR-210 not only plays a protective role by fine-tuning mitochondrial metabolism and inhibiting red-ox imbalance and apoptosis, but it can also promote cell proliferation, differentiation, and migration, substantially contributing to angiogenesis. Critical issues: As most miRNAs, modulating different gene pathways, also miR-210 can potentially lead to different and even opposite effects, depending on the physio-pathological contexts in which it acts. Future direction: The use of miRNAs as therapeutics is a fast growing field. This review aimed at highlighting the role of miR-210 in angiogenesis in the context of ischemic cardiovascular diseases and diabetes in order to clarify the molecular mechanisms underpinning miR-210 action. Particular attention will be dedicated to experimentally validated miR-210 direct targets involved in cellular processes related to angiogenesis and diabetes mellitus, such as mitochondrial metabolism, redox balance, apoptosis, migration, and adhesion. Antioxid. Redox Signal. 36, 685-706.
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Affiliation(s)
- Germana Zaccagnini
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, San Donato Milanese, Italy
| | - Simona Greco
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, San Donato Milanese, Italy
| | - Christine Voellenkle
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, San Donato Milanese, Italy
| | - Carlo Gaetano
- Laboratorio di Epigenetica, Istituti Clinici Scientifici Maugeri IRCCS, Pavia, Italy
| | - Fabio Martelli
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, San Donato Milanese, Italy
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Ali A, Zeb I, Alouffi A, Zahid H, Almutairi MM, Ayed Alshammari F, Alrouji M, Termignoni C, Vaz IDS, Tanaka T. Host Immune Responses to Salivary Components - A Critical Facet of Tick-Host Interactions. Front Cell Infect Microbiol 2022; 12:809052. [PMID: 35372098 PMCID: PMC8966233 DOI: 10.3389/fcimb.2022.809052] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 02/04/2022] [Indexed: 12/15/2022] Open
Abstract
Tick sialome is comprised of a rich cocktail of bioactive molecules that function as a tool to disarm host immunity, assist blood-feeding, and play a vibrant role in pathogen transmission. The adaptation of the tick's blood-feeding behavior has lead to the evolution of bioactive molecules in its saliva to assist them to overwhelm hosts' defense mechanisms. During a blood meal, a tick secretes different salivary molecules including vasodilators, platelet aggregation inhibitors, anticoagulants, anti-inflammatory proteins, and inhibitors of complement activation; the salivary repertoire changes to meet various needs such as tick attachment, feeding, and modulation or impairment of the local dynamic and vigorous host responses. For instance, the tick's salivary immunomodulatory and cement proteins facilitate the tick's attachment to the host to enhance prolonged blood-feeding and to modulate the host's innate and adaptive immune responses. Recent advances implemented in the field of "omics" have substantially assisted our understanding of host immune modulation and immune inhibition against the molecular dynamics of tick salivary molecules in a crosstalk between the tick-host interface. A deep understanding of the tick salivary molecules, their substantial roles in multifactorial immunological cascades, variations in secretion, and host immune responses against these molecules is necessary to control these parasites. In this article, we reviewed updated knowledge about the molecular mechanisms underlying host responses to diverse elements in tick saliva throughout tick invasion, as well as host defense strategies. In conclusion, understanding the mechanisms involved in the complex interactions between the tick salivary components and host responses is essential to decipher the host defense mechanisms against the tick evasion strategies at tick-host interface which is promising in the development of effective anti-tick vaccines and drug therapeutics.
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Affiliation(s)
- Abid Ali
- Department of Zoology, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Ismail Zeb
- Department of Zoology, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Abdulaziz Alouffi
- King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Hafsa Zahid
- Department of Zoology, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Mashal M. Almutairi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Fahdah Ayed Alshammari
- College of Sciences and Literature Microbiology, Nothern Border University, Rafha, Saudi Arabia
| | - Mohammed Alrouji
- College of Applied Medical Sciences, Shaqra University, Shaqra, Saudi Arabia
| | - Carlos Termignoni
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Itabajara da Silva Vaz
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Tetsuya Tanaka
- Laboratory of Infectious Diseases, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima, Japan
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8
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Abstract
MicroRNAs (miRNAs) are small noncoding elements that play essential roles in the posttranscriptional regulation of biochemical processes. miRNAs recognize and target multiple mRNAs; therefore, investigating miRNA dysregulation is an indispensable strategy to understand pathological conditions and to design innovative drugs. Targeting miRNAs in diseases improve outcomes of several therapeutic strategies thus, this present study highlights miRNA targeting methods through experimental assays and bioinformatics tools. The first part of this review focuses on experimental miRNA targeting approaches for elucidating key biochemical pathways. A growing body of evidence about the miRNA world reveals the fact that it is not possible to uncover these molecules' structural and functional characteristics related to the biological processes with a deterministic approach. Instead, a systemic point of view is needed to truly understand the facts behind the natural complexity of interactions and regulations that miRNA regulations present. This task heavily depends both on computational and experimental capabilities. Fortunately, several miRNA bioinformatics tools catering to nonexperts are available as complementary wet-lab approaches. For this purpose, this work provides recent research and information about computational tools for miRNA targeting research.
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Affiliation(s)
- Hossein Ghanbarian
- Biotechnology Department & Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mehmet Taha Yıldız
- Division of Molecular Medicine, Hamidiye Institute of Health Sciences, University of Health Sciences-Turkey, Istanbul, Turkey
| | - Yusuf Tutar
- Division of Biochemistry, Department of Basic Pharmaceutical Sciences, Hamidiye Faculty of Pharmacy & Division of Molecular Medicine, Hamidiye Institute of Health Sciences, University of Health Sciences-Turkey, Istanbul, Turkey.
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9
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Cui J, Yuan Y, Shanmugam MK, Anbalagan D, Tan TZ, Sethi G, Kumar AP, Lim LHK. MicroRNA-196a promotes renal cancer cell migration and invasion by targeting BRAM1 to regulate SMAD and MAPK signaling pathways. Int J Biol Sci 2021; 17:4254-4270. [PMID: 34803496 PMCID: PMC8579441 DOI: 10.7150/ijbs.60805] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 09/16/2021] [Indexed: 12/23/2022] Open
Abstract
Rationale: MicroRNAs (miRNAs) are endogenous ~22nt RNAs that play critical regulatory roles in various biological and pathological processes, including various cancers. Their function in renal cancer has not been fully elucidated. It has been reported that miR-196a can act as oncogenes or as tumor suppressors depending on their target genes. However, the molecular target for miR-196a and the underlying mechanism in miR-196a promoted cell migration and invasion in renal cancer is still not clear. Methods: The expression, survival and correlation between miR-196a and BRAM1 were investigated using TCGA analysis and validated by RT-PCR and western blot. To visualize the effect of Bram1 on tumor metastasis in vivo, NOD-SCID gamma (NSG) mice were intravenously injected with RCC4 cells (106 cells/mouse) or RCC4 overexpressing Bram1. In addition, cell proliferation assays, migration and invasion assays were performed to examine the role of miR-196a in renal cells in vitro. Furthermore, immunoprecipitation was done to explore the binding targets of Bram1. Results: TCGA gene expression data from renal clear cell carcinoma patients showed a lower level of Bram1 expression in patients' specimens compared to adjacent normal tissues. Moreover, Kaplan‑Meier survival data clearly show that high expression of Bram1correlates to poor prognosis in renal carcinoma patients. Our mouse metastasis model confirmed that Bram1 overexpression resulted in an inhibition in tumor metastasis. Target-prediction analysis and dual-luciferase reporter assay demonstrated that Bram1 is a direct target of miR-196a in renal cells. Further, our in vitro functional assays revealed that miR-196a promotes renal cell proliferation, migration, and invasion. Rescue of Bram1 expression reversed miR-196a-induced cell migration. MiR-196a promotes renal cancer cell migration by directly targeting Bram1 and inhibits Smad1/5/8 phosphorylation and MAPK pathways through BMPR1A and EGFR. Conclusions: Our findings thus provide a new mechanism on the oncogenic role of miR-196a and the tumor-suppressive role of Bram1 in renal cancer cells. Dysregulated miR-196a and Bram1 represent potential prognostic biomarkers and may have therapeutic applications in renal cancer.
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Affiliation(s)
- Jianzhou Cui
- Department of Physiology , Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117456, Singapore.,NUS Immunology Programme, Life Sciences Institute, National University of Singapore, Singapore 117456, Singapore.,Immunology Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
| | - Yi Yuan
- Department of Physiology , Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117456, Singapore.,NUS Immunology Programme, Life Sciences Institute, National University of Singapore, Singapore 117456, Singapore.,NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117599, Singapore.,Cancer Science Institute of Singapore, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117559, Singapore
| | - Muthu K Shanmugam
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117559, Singapore
| | - Durkeshwari Anbalagan
- Department of Physiology , Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117456, Singapore.,NUS Immunology Programme, Life Sciences Institute, National University of Singapore, Singapore 117456, Singapore
| | - Tuan Zea Tan
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117599, Singapore.,Cancer Science Institute of Singapore, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117559, Singapore
| | - Gautam Sethi
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117559, Singapore
| | - Alan Prem Kumar
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117599, Singapore.,Cancer Science Institute of Singapore, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117559, Singapore.,Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117559, Singapore.,National University Cancer Institute, Singapore 119074, Singapore
| | - Lina H K Lim
- Department of Physiology , Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117456, Singapore.,NUS Immunology Programme, Life Sciences Institute, National University of Singapore, Singapore 117456, Singapore.,Immunology Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
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10
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Quillet A, Anouar Y, Lecroq T, Dubessy C. Prediction methods for microRNA targets in bilaterian animals: Toward a better understanding by biologists. Comput Struct Biotechnol J 2021; 19:5811-5825. [PMID: 34765096 PMCID: PMC8567327 DOI: 10.1016/j.csbj.2021.10.025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 09/20/2021] [Accepted: 10/15/2021] [Indexed: 12/13/2022] Open
Abstract
MicroRNAs (miRNAs) are small noncoding RNAs that regulate gene expression at the posttranscriptional level. Because of their wide network of interactions, miRNAs have become the focus of many studies over the past decade, particularly in animal species. To streamline the number of potential wet lab experiments, the use of miRNA target prediction tools is currently the first step undertaken. However, the predictions made may vary considerably depending on the tool used, which is mostly due to the complex and still not fully understood mechanism of action of miRNAs. The discrepancies complicate the choice of the tool for miRNA target prediction. To provide a comprehensive view of this issue, we highlight in this review the main characteristics of miRNA-target interactions in bilaterian animals, describe the prediction models currently used, and provide some insights for the evaluation of predictor performance.
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Affiliation(s)
- Aurélien Quillet
- Normandie Université, UNIROUEN, INSERM, Laboratoire Différenciation et Communication Neuronale et Neuroendocrine, 76000 Rouen, France
| | - Youssef Anouar
- Normandie Université, UNIROUEN, INSERM, Laboratoire Différenciation et Communication Neuronale et Neuroendocrine, 76000 Rouen, France
| | - Thierry Lecroq
- Normandie Université, UNIROUEN, UNIHAVRE, INSA Rouen, Laboratoire d'Informatique du Traitement de l'Information et des Systèmes, 76000 Rouen, France
| | - Christophe Dubessy
- Normandie Université, UNIROUEN, INSERM, Laboratoire Différenciation et Communication Neuronale et Neuroendocrine, 76000 Rouen, France.,Normandie Université, UNIROUEN, INSERM, PRIMACEN, 76000 Rouen, France
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11
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Khatun MS, Alam MA, Shoombuatong W, Mollah MNH, Kurata H, Hasan MM. Recent development of bioinformatics tools for microRNA target prediction. Curr Med Chem 2021; 29:865-880. [PMID: 34348604 DOI: 10.2174/0929867328666210804090224] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 06/10/2021] [Accepted: 06/15/2021] [Indexed: 11/22/2022]
Abstract
MicroRNAs (miRNAs) are central players that regulate the post-transcriptional processes of gene expression. Binding of miRNAs to target mRNAs can repress their translation by inducing the degradation or by inhibiting the translation of the target mRNAs. High-throughput experimental approaches for miRNA target identification are costly and time-consuming, depending on various factors. It is vitally important to develop the bioinformatics methods for accurately predicting miRNA targets. With the increase of RNA sequences in the post-genomic era, bioinformatics methods are being developed for miRNA studies specially for miRNA target prediction. This review summarizes the current development of state-of-the-art bioinformatics tools for miRNA target prediction, points out the progress and limitations of the available miRNA databases, and their working principles. Finally, we discuss the caveat and perspectives of the next-generation algorithms for the prediction of miRNA targets.
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Affiliation(s)
- Mst Shamima Khatun
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka 820-8502. Japan
| | - Md Ashad Alam
- Tulane Center for Biomedical Informatics and Genomics, Division of Biomedical Informatics and Genomics, John W. Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA 70112. United States
| | - Watshara Shoombuatong
- Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok 10700. Thailand
| | - Md Nurul Haque Mollah
- Laboratory of Bioinformatics, Department of Statistics, University of Rajshahi, Rajshahi, Bangladesh. 5Japan Society for the Promotion of Science, 5-3-1 Kojimachi, Chiyoda-ku, Tokyo 102-0083. Japan
| | - Hiroyuki Kurata
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka 820-8502. Japan
| | - Md Mehedi Hasan
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka 820-8502. Japan
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12
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Mittal P, Singh S, Sinha R, Shrivastava A, Singh A, Singh IK. Myeloid cell leukemia 1 (MCL-1): Structural characteristics and application in cancer therapy. Int J Biol Macromol 2021; 187:999-1018. [PMID: 34339789 DOI: 10.1016/j.ijbiomac.2021.07.166] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 07/24/2021] [Accepted: 07/26/2021] [Indexed: 12/20/2022]
Abstract
Apoptosis, a major hallmark of cancer cells, regulates cellular fate and homeostasis. BCL-2 (B-cell CLL/Lymphoma 2) protein family is popularly known to mediate the intrinsic mode of apoptosis, of which MCL-1 is a crucial member. Myeloid cell leukemia 1 (MCL-1) is an anti-apoptotic oncoprotein and one of the most investigated members of the BCL-2 family. It is commonly known to be genetically altered, aberrantly overexpressed, and primarily associated with drug resistance in various human cancers. Recent advancements in the development of selective MCL-1 inhibitors and evaluating their effectiveness in cancer treatment establish its popularity as a molecular target. The overall aim is the selective induction of apoptosis in cancer cells by using a single or combination of BCL-2 family inhibitors. Delineating the precise molecular mechanisms associated with MCL-1-mediated cancer progression will certainly improve the efficacy of clinical interventions aimed at MCL-1 and hence patient survival. This review is structured to highlight the structural characteristics of MCL-1, its specific interactions with NOXA, MCL-1-regulatory microRNAs, and at the same time focus on the emerging therapeutic strategies targeting our protein of interest (MCL-1), alone or in combination with other treatments.
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Affiliation(s)
- Pooja Mittal
- Molecular Biology Research Lab, Department of Zoology, Deshbandhu College, University of Delhi, Kalkaji, New Delhi 110019, India
| | - Sujata Singh
- Molecular Biology Research Lab, Department of Zoology, Deshbandhu College, University of Delhi, Kalkaji, New Delhi 110019, India
| | - Rajesh Sinha
- Department of Dermatology, University of Alabama, Birmingham 35205, United States of America
| | - Anju Shrivastava
- Department of Zoology, University of Delhi, New Delhi, 110007, India
| | - Archana Singh
- Department of Botany, Hans Raj College, University of Delhi, New Delhi 110007, India.
| | - Indrakant Kumar Singh
- Molecular Biology Research Lab, Department of Zoology, Deshbandhu College, University of Delhi, Kalkaji, New Delhi 110019, India.
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13
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Keikha R, Jebali A. [The miRNA neuroinflammatory biomarkers in COVID-19 patients with different severity of illness]. Neurologia 2021:S0213-4853(21)00120-1. [PMID: 34305233 PMCID: PMC8282440 DOI: 10.1016/j.nrl.2021.06.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 06/27/2021] [Indexed: 11/03/2022] Open
Abstract
INTRODUCTION The expression of specific miRNAs and their mRNA targets are changed in infectious disease. The aim of this study was to analyze the expression of pro-neuroinflammatory miRNAs, anti- neuroinflammatory miRNAs, and their mRNA targets in the serum of COVID-19 patients with different grades. METHODS COVID-19 patients with different grades were enrolled in this study and the expression of pro-neuroinflammatory miRNAs, anti-neuroinflammatory miRNAs, and their target mRNAs was analyzed by q-PCR. RESULTS The relative expression of anti- neuroinflammatory miRNAs (mir-21, mir-124, and mir-146a) was decreased and the relative expression of their target mRNAs (IL-12p53, Stat3, and TRAF6) was increased. Also, the relative expression of pro-neuroinflammatory miRNAs (mir-326, mir-155, and mir-27b) was increased and the relative expression of their target mRNA (PPARS, SOCS1, and CEBPA) was decreased in COVID-19 patients with increase of disease grade. A negative significant correlation was seen between mir-21 and IL-12p53 mRNA, mir-124 and Stat3 mRNA, mir-146a and TRAF6 mRNA, mir-27b and PPARS mRNA, mir-155 and SOCS1 mRNA, and between mir-326 and CEBPA mRNA in COVID-19 patients (P<0.05). CONCLUSIONS This study showed that the relative expression of anti- neuroinflammatory miRNAs was decreased and the relative expression of their targeted mRNAs was increased in COVID-19 patients from asymptomatic to critical illness. Also, this study showed that the relative expression of pro-neuroinflammatory miRNAs was increased and the relative expression of their targeted mRNA was decreased in COVID-19 patients from asymptomatic to critical illness.
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Affiliation(s)
- Reza Keikha
- Infectious Diseases and Tropical Medicine Research Center, Resistant Tuberculosis Institute, Zahedan University of Medical Sciences, Zahedan, Iran.,Department of Pathology, Faculty of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Ali Jebali
- Department of Medical Nanotechnology, Faculty of Advanced Sciences and Technology, Tehran Medical Science, Islamic Azad University, Tehran, Iran
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14
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Jung JE, Lee JY, Park HR, Kang JW, Kim YH, Lee JH. MicroRNA-133 Targets Phosphodiesterase 1C in Drosophila and Human Oral Cancer Cells to Regulate Epithelial-Mesenchymal Transition. J Cancer 2021; 12:5296-5309. [PMID: 34335946 PMCID: PMC8317528 DOI: 10.7150/jca.56138] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 06/24/2021] [Indexed: 12/29/2022] Open
Abstract
Non-coding microRNAs (miRNAs) have been proposed to play diverse roles in cancer biology, including epithelial-mesenchymal transition (EMT) crucial for cancer progression. Previous comparative studies revealed distinct expression profiles of miRNAs relevant to tumorigenesis and progression of oral cancer. With putative targets of these miRNAs mostly validated in vitro, it remains unclear whether similar miRNA-target relationships exist in vivo. In this study, we employed a hybrid approach, utilizing both Drosophila melanogaster and human oral cancer cells, to validate projected miRNA-target relationships relevant to EMT. Notably, overexpression of dme-miR-133 resulted in significant tissue growth in Drosophila larval wing discs. The RT-PCR analysis successfully validated a subset of its putative targets, including Pde1c. Subsequent experiments performed in oral cancer cells confirmed conserved targeting of human PDE1C by hsa-miR-133. Furthermore, the elevated level of miR-133 and its targeting of PDE1C was positively correlated with enhanced migrative ability of oral cancer cells treated with LPS, along with the molecular signature of a facilitated EMT process induced by LPS and TGF-β. The analysis on the RNAseq data also revealed a negative correlation between the expression level of hsa-miR-133 and the survival of oral cancer patients. Taken together, our mammal-to-Drosophila-to-mammal approach successfully validates targeting of PDE1C by miR-133 both in vivo and in vitro, underlying the promoted EMT phenotypes and potentially influencing the prognosis of oral cancer patients. This hybrid approach will further aid to widen our scope in investigation of intractable human malignancies, including oral cancer.
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Affiliation(s)
- Ji Eun Jung
- Department of Life Science in Dentistry, School of Dentistry, Pusan National University, Yangsan 50612, Korea.,BK21 FOUR Project, School of Dentistry, Pusan National University, Yangsan 50612, Korea
| | - Joo Young Lee
- Dental and Life Science Institute, Pusan National University, Yangsan 50612, Korea
| | - Hae Ryoun Park
- Department of Life Science in Dentistry, School of Dentistry, Pusan National University, Yangsan 50612, Korea.,BK21 FOUR Project, School of Dentistry, Pusan National University, Yangsan 50612, Korea.,Dental and Life Science Institute, Pusan National University, Yangsan 50612, Korea.,Department of Oral Pathology, School of Dentistry, Pusan National University, Yangsan 50612, Korea
| | - Ji Wan Kang
- Interdisciplinary Program of Genomic Science, Pusan National University, Yangsan 50612, Korea
| | - Yun Hak Kim
- Department of Anatomy, Department of Biomedical Informatics, School of Medicine, Pusan National University, Yangsan 50612, Korea
| | - Ji Hye Lee
- Department of Life Science in Dentistry, School of Dentistry, Pusan National University, Yangsan 50612, Korea.,BK21 FOUR Project, School of Dentistry, Pusan National University, Yangsan 50612, Korea.,Dental and Life Science Institute, Pusan National University, Yangsan 50612, Korea.,Department of Oral Pathology, School of Dentistry, Pusan National University, Yangsan 50612, Korea
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15
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Arif KT, Okolicsanyi RK, Haupt LM, Griffiths LR. A combinatorial in silico approach for microRNA-target identification: Order out of chaos. Biochimie 2021; 187:121-130. [PMID: 34019954 DOI: 10.1016/j.biochi.2021.05.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 04/17/2021] [Accepted: 05/11/2021] [Indexed: 02/07/2023]
Abstract
Contemporary computational microRNA(miRNA)-target prediction tools have been playing a vital role in pursuing putative targets for a solitary miRNA or a group of miRNAs. These tools utilise a set of probabilistic algorithms, machine learning techniques and analyse experimentally validated miRNA targets to identify the potential miRNA-target pairs. Unfortunately, current tools generate a huge number of false-positive predictions. A standardized approach with a single tool or a combination of tools is still lacking. Moreover, sensitivity, specificity and overall efficiency of any single tool are yet to be satisfactory. Therefore, a systematic combination of selective online tools combining the factors regarding miRNA-target identification would be valuable as an miRNA-target prediction scheme. The focus of this study was to develop a theoretical framework by combining six available online tools to facilitate the current understanding of miRNA-target identification.
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Affiliation(s)
- Km Taufiqul Arif
- Queensland University of Technology (QUT), Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, 60 Musk Ave., Kelvin Grove, Queensland, 4059, Australia.
| | - Rachel K Okolicsanyi
- Queensland University of Technology (QUT), Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, 60 Musk Ave., Kelvin Grove, Queensland, 4059, Australia.
| | - Larisa M Haupt
- Queensland University of Technology (QUT), Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, 60 Musk Ave., Kelvin Grove, Queensland, 4059, Australia.
| | - Lyn R Griffiths
- Queensland University of Technology (QUT), Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, 60 Musk Ave., Kelvin Grove, Queensland, 4059, Australia.
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16
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Zheng Y, Yang Z, Jin C, Chen C, Wu N. hsa-miR-191-5p inhibits replication of human immunodeficiency virus type 1 by downregulating the expression of NUP50. Arch Virol 2021; 166:755-766. [PMID: 33420627 DOI: 10.1007/s00705-020-04899-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 10/13/2020] [Indexed: 01/24/2023]
Abstract
MicroRNAs (miRNAs) are important host molecules involved in human immunodeficiency virus type 1 (HIV-1) infection. Antiretroviral therapy (ART) can affect the miRNA expression profile, but differentially expressed miRNAs still remain to be identified. In this study, we used gene chips to analyze miRNA expression profiles in peripheral blood mononuclear cells from ART-naive HIV-1 patients and those receiving ART, as well as from uninfected individuals. We measured differences in miRNA expression by quantitative polymerase chain reaction (qPCR) in an expanded sample. We found significant differences in the expression of has-miR-191-5p among the three groups (P < 0.05). Furthermore, we showed that hsa-miR-191-5p has an inhibitory effect on HIV-1 replication in cell models in vitro. We identified CCR1 and NUP50 as target molecules of hsa-miR-191-5p and found that hsa-miR-191-5p inhibits the expression of CCR1 and NUP50. Knockdown of NUP50 resulted in significant inhibition of HIV-1 replication. In summary, our research shows that hsa-miR-191-5p expression is reduced in HIV-1-infected patients and acts an inhibitor of HIV-1 infection via a mechanism that may involve targeted repression of NUP50 expression.
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Affiliation(s)
- Yanghao Zheng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University, Hangzhou, 310003, China
| | | | - Changzhong Jin
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University, Hangzhou, 310003, China
| | - Chaoyu Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University, Hangzhou, 310003, China
| | - Nanping Wu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University, Hangzhou, 310003, China.
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17
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Viaut C, Weldon S, Münsterberg A. Fine-tuning of the PAX-SIX-EYA-DACH network by multiple microRNAs controls embryo myogenesis. Dev Biol 2021; 469:68-79. [PMID: 33080252 DOI: 10.1016/j.ydbio.2020.10.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 10/06/2020] [Accepted: 10/14/2020] [Indexed: 01/27/2023]
Abstract
MicroRNAs (miRNAs), short non-coding RNAs, which act post-transcriptionally to regulate gene expression, are of widespread significance during development and disease, including muscle disease. Advances in sequencing technology and bioinformatics led to the identification of a large number of miRNAs in vertebrates and other species, however, for many of these miRNAs specific roles have not yet been determined. LNA in situ hybridisation has revealed expression patterns of somite-enriched miRNAs, here we focus on characterising the functions of miR-128. We show that antagomiR-mediated knockdown (KD) of miR-128 in developing chick somites has a negative impact on skeletal myogenesis. Computational analysis identified the transcription factor EYA4 as a candidate target consistent with the observation that miR-128 and EYA4 display similar expression profiles. Luciferase assays confirmed that miR-128 interacts with the EYA4 3'UTR. In vivo experiments also suggest that EYA4 is regulated by miR-128. EYA4 is a member of the PAX-SIX-EYA-DACH (PSED) network of transcription factors. Therefore, we identified additional candidate miRNA binding sites in the 3'UTR of SIX1/4, EYA1/2/3 and DACH1. Using the miRanda algorithm, we found sites for miR-128, as well as for other myogenic miRNAs, miR-1a, miR-206 and miR-133a, some of these were experimentally confirmed as functional miRNA target sites. Our results reveal that miR-128 is involved in regulating skeletal myogenesis by directly targeting EYA4 with indirect effects on other PSED members, including SIX4 and PAX3. Hence, the inhibitory effect on myogenesis observed after miR-128 knockdown was rescued by concomitant knockdown of PAX3. Moreover, we show that the PSED network of transcription factors is co-regulated by multiple muscle-enriched microRNAs.
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Affiliation(s)
- Camille Viaut
- School of Biological Sciences, Cell and Developmental Biology, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Shannon Weldon
- School of Biological Sciences, Cell and Developmental Biology, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Andrea Münsterberg
- School of Biological Sciences, Cell and Developmental Biology, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
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18
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Selvaraj SR, Pipe SW. Not in the genotype: can unexplained hemophilia A result from "micro(RNA) management"? Transfusion 2020; 60:227-228. [PMID: 32022934 DOI: 10.1111/trf.15668] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 01/03/2020] [Indexed: 12/14/2022]
Affiliation(s)
- Sundar R Selvaraj
- Department of Pediatrics, University of Michigan, Ann Arbor, Michigan
| | - Steven W Pipe
- Department of Pediatrics, University of Michigan, Ann Arbor, Michigan.,Department of Pathology, University of Michigan, Ann Arbor, Michigan
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19
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Ninsuwon J, Waiyamitra P, Roongsitthichai A, Surachetpong W. Expressions of miR-155 and miR-181 and predictions of their structures and targets in pigs ( Sus scrofa). Vet World 2020; 13:1667-1673. [PMID: 33061243 PMCID: PMC7522940 DOI: 10.14202/vetworld.2020.1667-1673] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 06/30/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND AND AIM MicroRNAs (miRNAs) are responsible for gene expression control at the post-transcription level in many species. Several miRNAs are required in the regulation of immune responses, such as B-cell differentiation, T-cell receptor signaling pathway, CD4+ T cell selection, and so on. Studies on miRNAs have been extensively conducted in humans and mice; however, reports relevant to miRNAs, especially miR-155 and miR-181, in pigs are limited. Consequently, the present study aimed to investigate the structures, target genes, and expressions of miR-155 and miR-181 in various porcine cells and tissues. MATERIALS AND METHODS Five healthy male pigs from a porcine reproductive and respiratory syndrome virus-negative farm were studied. Before slaughter, blood samples were collected for peripheral blood mononuclear cell isolation. After slaughter, samples of spleen, lymph nodes, and forelimb muscles were collected. Both miR-155 and miR-181 were investigated for their structures with RNAfold web server, for their target genes from three online web servers, and for their expressions using polymerase chain reaction (PCR). RESULTS The structures of miR-155 and miR-181 contained hairpins with free energies of -35.27 and -35.29 kcal/mole, respectively. Target gene prediction revealed that miR-155 had perfect complementarity with Socs1 and Mapk3k14, while miR-181 had perfect complementarity with Ddx3x, Nfat5, Foxp1, and Mpp5. PCR showed that both miRNAs were detectable from all investigated cells and tissues. Moreover, the highest expression of both miRNAs was found from the lymph node of the pigs. CONCLUSION Both miR-155 and miR-181 might be involved with the regulation of porcine immune functions as both miRNAs were detected in several cells and tissues of the pigs. In addition, they had very high complementarities with the seed regions of several immune-related genes.
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Affiliation(s)
- Jirapat Ninsuwon
- Department of Veterinary Microbiology and Immunology, Faculty of Veterinary Medicine, Kasetsart University, Bangkok, Thailand
- Center for Advanced Studies for Agriculture and Food, Institute for Advanced Studies, Kasetsart University, Bangkok, Thailand
| | - Pitchaporn Waiyamitra
- Department of Veterinary Microbiology and Immunology, Faculty of Veterinary Medicine, Kasetsart University, Bangkok, Thailand
| | - Atthaporn Roongsitthichai
- Veterinary Clinic Research Unit, Faculty of Veterinary Sciences, Mahasarakham University, Maha Sarakham, Thailand
- Office of Academic Affairs, Faculty of Veterinary Sciences, Mahasarakham University, Maha Sarakham, Thailand
| | - Win Surachetpong
- Department of Veterinary Microbiology and Immunology, Faculty of Veterinary Medicine, Kasetsart University, Bangkok, Thailand
- Center for Advanced Studies for Agriculture and Food, Institute for Advanced Studies, Kasetsart University, Bangkok, Thailand
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20
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Cunningham SJ, Feng L, Allen TK, Reddy TE. Functional Genomics of Healthy and Pathological Fetal Membranes. Front Physiol 2020; 11:687. [PMID: 32655414 PMCID: PMC7325962 DOI: 10.3389/fphys.2020.00687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 05/27/2020] [Indexed: 11/23/2022] Open
Abstract
Premature preterm rupture of membranes (PPROM), rupture of fetal membranes before 37 weeks of gestation, is the leading identifiable cause of spontaneous preterm births. Often there is no obvious cause that is identified in a patient who presents with PPROM. Identifying the upstream molecular events that lead to fetal membrane weakening presents potentially actionable mechanisms which could lead to the identification of at-risk patients and to the development of new therapeutic interventions. Functional genomic studies have transformed understanding of the role of gene regulation in diverse cells and tissues involved health and disease. Here, we review the results of those studies in the context of fetal membranes. We will highlight relevant results from major coordinated functional genomics efforts and from targeted studies focused on individual cell or tissue models. Studies comparing gene expression and DNA methylation between healthy and pathological fetal membranes have found differential regulation between labor and quiescent tissue as well as in preterm births, preeclampsia, and recurrent pregnancy loss. Whole genome and exome sequencing studies have identified common and rare fetal variants associated with preterm births. However, few fetal membrane tissue studies have modeled the response to stimuli relevant to pregnancy. Fetal membranes are readily adaptable to cell culture and relevant cellular phenotypes are readily observable. For these reasons, this is now an unrealized opportunity for genomic studies isolating the effect of cell signaling cascades and mapping the fetal membrane responses that lead to PPROM and other pregnancy complications.
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Affiliation(s)
- Sarah J Cunningham
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC, United States.,University Program in Genetics and Genomics, Duke University, Durham, NC, United States.,Center for Genomic and Computational Biology, Duke University, Durham, NC, United States.,Center for Advanced Genomic Technologies, Duke University, Durham, NC, United States
| | - Liping Feng
- Department of Obstetrics and Gynecology, Duke University School of Medicine, Durham, NC, United States
| | - Terrence K Allen
- Department of Anesthesiology, Duke University Hospital, Durham, NC, United States
| | - Timothy E Reddy
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC, United States.,University Program in Genetics and Genomics, Duke University, Durham, NC, United States.,Center for Genomic and Computational Biology, Duke University, Durham, NC, United States.,Center for Advanced Genomic Technologies, Duke University, Durham, NC, United States
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21
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Polymorphism in the 3'-UTR of LIF but Not in the ATF6B Gene Associates with Schizophrenia Susceptibility: a Case-Control Study and In Silico Analyses. J Mol Neurosci 2020; 70:2093-2101. [PMID: 32504404 DOI: 10.1007/s12031-020-01616-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 05/26/2020] [Indexed: 12/17/2022]
Abstract
Schizophrenia (SCZ) is a multifactorial disorder caused by environmental and genetic factors. Studies have shown that various single-nucleotide polymorphisms (SNPs) in the binding sites of microRNAs contribute to the risk of developing SCZ. We aimed to investigate whether the variants located in the 3'-UTR region of LIF (rs929271T>G) and ATF6B (rs8283G>A) were associated with increased susceptibility to SCZ in a population from the south-east of Iran. In this case-control study, a total of 396 subjects were recruited. SNPs were genotyped via polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. Genotyping results showed that the G allele of rs929271 significantly increased the risk of SCZ (OR = 1.58 95%CI = 1.19-2.10, p = 0.001). As for rs929271, the GG genotype of co-dominant (OR = 2.54 95%CI = 1.39-4.64, p = 0.002) and recessive (OR = 2.91 95%CI = 1.77-4.80, p < 0.001) models were strongly linked to SCZ. No significant differences were observed between rs8283 polymorphism and predisposition to SCZ. In silico analyses predicted that rs929271 might alter the binding sites of microRNAs, which was believed to have an unclear role in the development of SCZ. Moreover, rs929271 polymorphism changed the LIF-mRNA folding structure. These findings provide fine pieces of evidence regarding the possible effects of LIF polymorphism in the development of SCZ and regulation of the LIF gene targeted by microRNAs.
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22
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Baskara-Yhuellou I, Tost J. The impact of microRNAs on alterations of gene regulatory networks in allergic diseases. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2020; 120:237-312. [PMID: 32085883 DOI: 10.1016/bs.apcsb.2019.11.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Allergic diseases including asthma are worldwide on the rise and contribute significantly to health expenditures. Allergic diseases are prototypic diseases with a strong gene by environment interaction component and epigenetic mechanisms might mediate the effects of the environment on the disease phenotype. MicroRNAs, small non-coding RNAs (miRNAs), regulate gene expression post-transcriptionally. Functional single-stranded miRNAs are generated in multiple steps of enzymatic processing from their precursors and mature miRNAs are included into the RNA-induced silencing complex (RISC). They imperfectly base-pair with the 3'UTR region of targeted genes leading to translational repression or mRNA decay. The cellular context and microenvironment as well the isoform of the mRNA control the dynamics and complexity of the regulatory circuits induced by miRNAs that regulate cell fate decisions and function. MiR-21, miR-146a/b and miR-155 are among the best understood miRNAs of the immune system and implicated in different diseases including allergic diseases. MiRNAs are implicated in the induction of the allergy reinforcing the Th2 phenotype (miR-19a, miR-24, miR-27), while other miRNAs promote regulatory T cells associated with allergen tolerance or unresponsiveness. In the current chapter we describe in detail the biogenesis and regulatory function of miRNAs and summarize current knowledge on miRNAs in allergic diseases and allergy relevant cell fate decisions focusing mainly on immune cells. Furthermore, we evoke the principles of regulatory loops and feedback mechanisms involving miRNAs on examples with relevance for allergic diseases. Finally, we show the potential of miRNAs and exosomes containing miRNAs present in several biological fluids that can be exploited with non-invasive procedures for diagnostic and potentially therapeutic purposes.
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Affiliation(s)
- Indoumady Baskara-Yhuellou
- Laboratory for Epigenetics & Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie François Jacob, Evry, France
| | - Jörg Tost
- Laboratory for Epigenetics & Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie François Jacob, Evry, France
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23
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Mulholland EJ, Green WP, Buckley NE, McCarthy HO. Exploring the Potential of MicroRNA Let-7c as a Therapeutic for Prostate Cancer. MOLECULAR THERAPY. NUCLEIC ACIDS 2019; 18:927-937. [PMID: 31760377 PMCID: PMC6883330 DOI: 10.1016/j.omtn.2019.09.031] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Revised: 09/02/2019] [Accepted: 09/08/2019] [Indexed: 01/20/2023]
Abstract
Prostate cancer (PCa) is one of the leading causes of mortality worldwide and often presents with aberrant microRNA (miRNA) expression. Identifying and understanding the unique expression profiles could aid in the detection and treatment of this disease. This review aims to identify miRNAs as potential therapeutic targets for PCa. Three bio-informatic searches were conducted to identify miRNAs that are reportedly implicated in the pathogenesis of PCa. Only hsa-Lethal-7 (let-7c), recognized for its role in PCa pathogenesis, was common to all three databases. Three further database searches were conducted to identify known targets of hsa-let-7c. Four targets were identified, HMGA2, c-Myc (MYC), TRAIL, and CASP3. An extensive review of the literature was undertaken to assess the role of hsa-let-7c in the progression of other malignancies and to evaluate its potential as a therapeutic target for PCa. The heterogeneous nature of cancer makes it logical to develop mechanisms by which the treatment of malignancies is tailored to an individual, harnessing specific knowledge of the underlying biology of the disease. Resetting cellular miRNA levels is an exciting prospect that will allow this ambition to be realized.
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Affiliation(s)
- Eoghan J Mulholland
- Gastrointestinal Stem Cell Biology Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - William P Green
- School of Pharmacy, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL, Northern Ireland
| | - Niamh E Buckley
- School of Pharmacy, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL, Northern Ireland
| | - Helen O McCarthy
- School of Pharmacy, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL, Northern Ireland.
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24
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Zhang J, Liu L, Li J, Le TD. LncmiRSRN: identification and analysis of long non-coding RNA related miRNA sponge regulatory network in human cancer. Bioinformatics 2019; 34:4232-4240. [PMID: 29955818 DOI: 10.1093/bioinformatics/bty525] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 06/27/2018] [Indexed: 02/07/2023] Open
Abstract
Motivation MicroRNAs (miRNAs) are small non-coding RNAs with the length of ∼22 nucleotides. miRNAs are involved in many biological processes including cancers. Recent studies show that long non-coding RNAs (lncRNAs) are emerging as miRNA sponges, playing important roles in cancer physiology and development. Despite accumulating appreciation of the importance of lncRNAs, the study of their complex functions is still in its preliminary stage. Based on the hypothesis of competing endogenous RNAs (ceRNAs), several computational methods have been proposed for investigating the competitive relationships between lncRNAs and miRNA target messenger RNAs (mRNAs). However, when the mRNAs are released from the control of miRNAs, it remains largely unknown as to how the sponge lncRNAs influence the expression levels of the endogenous miRNA targets. Results We propose a novel method to construct lncRNA related miRNA sponge regulatory networks (LncmiRSRNs) by integrating matched lncRNA and mRNA expression profiles with clinical information and putative miRNA-target interactions. Using the method, we have constructed the LncmiRSRNs for four human cancers (glioblastoma multiforme, lung cancer, ovarian cancer and prostate cancer). Based on the networks, we discover that after being released from miRNA control, the target mRNAs are normally up-regulated by the sponge lncRNAs, and only a fraction of sponge lncRNA-mRNA regulatory relationships and hub lncRNAs are shared by the four cancers. Moreover, most sponge lncRNA-mRNA regulatory relationships show a rewired mode between different cancers, and a minority of sponge lncRNA-mRNA regulatory relationships conserved (appearing) in different cancers may act as a common pivot across cancers. Besides, differential and conserved hub lncRNAs may act as potential cancer drivers to influence the cancerous state in cancers. Functional enrichment and survival analysis indicate that the identified differential and conserved LncmiRSRN network modules work as functional units in biological processes, and can distinguish metastasis risks of cancers. Our analysis demonstrates the potential of integrating expression profiles, clinical information and miRNA-target interactions for investigating lncRNA regulatory mechanism. Availability and implementation LncmiRSRN is freely available (https://github.com/zhangjunpeng411/LncmiRSRN). Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Junpeng Zhang
- School of Engineering, Dali University, Dali, Yunnan, China
| | - Lin Liu
- School of Information Technology and Mathematical Sciences, University of South Australia, Mawson Lakes, SA, Australia
| | - Jiuyong Li
- School of Information Technology and Mathematical Sciences, University of South Australia, Mawson Lakes, SA, Australia
| | - Thuc Duy Le
- School of Information Technology and Mathematical Sciences, University of South Australia, Mawson Lakes, SA, Australia
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Razmara E, Bitaraf A, Yousefi H, Nguyen TH, Garshasbi M, Cho WCS, Babashah S. Non-Coding RNAs in Cartilage Development: An Updated Review. Int J Mol Sci 2019; 20:E4475. [PMID: 31514268 PMCID: PMC6769748 DOI: 10.3390/ijms20184475] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 09/02/2019] [Accepted: 09/02/2019] [Indexed: 02/06/2023] Open
Abstract
In the development of the skeleton, the long bones are arising from the process of endochondral ossification (EO) in which cartilage is replaced by bone. This complex process is regulated by various factors including genetic, epigenetic, and environmental elements. It is recognized that DNA methylation, higher-order chromatin structure, and post-translational modifications of histones regulate the EO. With emerging understanding, non-coding RNAs (ncRNAs) have been identified as another mode of EO regulation, which is consist of microRNAs (miRNAs or miRs) and long non-coding RNAs (lncRNAs). There is expanding experimental evidence to unlock the role of ncRNAs in the differentiation of cartilage cells, as well as the pathogenesis of several skeletal disorders including osteoarthritis. Cutting-edge technologies such as epigenome-wide association studies have been employed to reveal disease-specific patterns regarding ncRNAs. This opens a new avenue of our understanding of skeletal cell biology, and may also identify potential epigenetic-based biomarkers. In this review, we provide an updated overview of recent advances in the role of ncRNAs especially focus on miRNA and lncRNA in the development of bone from cartilage, as well as their roles in skeletal pathophysiology.
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Affiliation(s)
- Ehsan Razmara
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran P.O. Box 14115-111, Iran
| | - Amirreza Bitaraf
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran P.O. Box 14115-111, Iran
| | - Hassan Yousefi
- Department of Biochemistry and Molecular Biology, LSUHSC School of Medicine, New Orleans, LA 70112, USA
| | - Tina H Nguyen
- Department of Biochemistry and Molecular Biology, LSUHSC School of Medicine, New Orleans, LA 70112, USA
| | - Masoud Garshasbi
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran P.O. Box 14115-111, Iran
| | | | - Sadegh Babashah
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran P.O. Box 14115-111, Iran.
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26
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Shanmugapriya, Othman N, Sasidharan S. Prediction of genes and protein-protein interaction networking for miR-221-5p using bioinformatics analysis. GENE REPORTS 2019. [DOI: 10.1016/j.genrep.2019.100426] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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27
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Kim S, Trudo SP, Gallaher DD. Apiaceous and Cruciferous Vegetables Fed During the Post-Initiation Stage Reduce Colon Cancer Risk Markers in Rats. J Nutr 2019; 149:249-257. [PMID: 30649390 DOI: 10.1093/jn/nxy257] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 07/20/2018] [Accepted: 09/13/2018] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Vegetable consumption reduces colon cancer risk when fed in the initiation stage of carcinogenesis; however, the effect of vegetable consumption during the post-initiation stage has rarely been examined. OBJECTIVE We investigated the chemopreventive effects of feeding apiaceous and cruciferous vegetables on colon cancer risk in the post-initiation stage. METHODS Thirty male Wistar rats (∼5 wk, 92 g) were subcutaneously injected with 1,2-dimethylhydrazine 1 time/wk for 2 wk. One week after the last dose, rats were randomly assigned to 3 groups: the basal diet, an apiaceous vegetable-containing diet (API; 21% fresh wt/wt), or a cruciferous vegetable-containing diet (CRU; 21% fresh wt/wt). All diets contained ∼20% protein, 7% fat, and 63% digestible carbohydrate. Experimental diets were fed for 10 wk, after which colons were harvested. RESULTS CRU reduced aberrant crypt foci (ACF) number compared to the basal group (P = 0.014) and API (P = 0.013), whereas API decreased the proportion of dysplastic ACF relative to the basal group (P < 0.05). Both CRU and API reduced doublecortin-like kinase 1-positive marker expression relative to basal by 57.9% (P = 0.009) and 51.4% (P < 0.02). The numbers of CD44-positive ACF did not differ between the groups. We identified 14 differentially expressed microRNAs (miRNAs). Of these, expression of 6 miRNAs were greater or tended to be greater (P ≤ 0.10) in one or both vegetable-containing groups compared to the basal group. Bioinformatic analysis of these expression changes in miRNA predicted a change in WNT/β-catenin signaling, indicating downregulation of β-catenin in the vegetable-fed groups. Consistent with this bioinformatics analysis, β-catenin-accumulated ACF were decreased in CRU (93.1%, P = 0.012), but not in API (54.4%, P = 0.125), compared to the basal group. CONCLUSION Both apiaceous and cruciferous vegetables, fed post-initiation, reduce colonic preneoplastic lesions as well as cancer stem cell marker expression in rats, possibly by suppressing oncogenic signaling through changes in miRNA expression.
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Affiliation(s)
- Sangyub Kim
- Department of Food Science and Nutrition, University of Minnesota, St. Paul, MN
| | - Sabrina P Trudo
- Department of Food Science and Nutrition, University of Minnesota, St. Paul, MN.,School of Human Environmental Sciences, University of Arkansas, Fayetteville, AR
| | - Daniel D Gallaher
- Department of Food Science and Nutrition, University of Minnesota, St. Paul, MN
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Dong Q, Yuan G, Liu M, Xie Q, Hu J, Wang M, Liu S, Ma X, Pan Y. Downregulation of microRNA-374a predicts poor prognosis in human glioma. Exp Ther Med 2019; 17:2077-2084. [PMID: 30867694 DOI: 10.3892/etm.2019.7190] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Accepted: 12/03/2018] [Indexed: 12/13/2022] Open
Abstract
Certain microRNAs (miRNAs/miRs) may be used as prognostic biomarkers in various types of cancer. The purpose of the present study was to identify miRNAs that were abnormally expressed in glioma of different grades, and to evaluate their clinical implications in patients with glioma. The differentially expressed miRNAs were evaluated from the expression profiles of six glioma tissues (three low-grade and three high-grade gliomas) determined using a microarray platform. Reverse transcription-quantitative polymerase chain reaction analysis was used to further verify the aberrant expression of the candidate miRNA in a set of 42 patients and 5 healthy controls. The miRNA target genes were predicted and the protein-protein interaction network was generated; furthermore, functional enrichment analysis of the target genes in Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways was performed. Kaplan-Meier curves and Log-rank analysis, as well as multivariate Cox regression analysis were performed to assess the association of the candidate miRNA with patient survival. A total of 15 differentially expressed miRNAs, including 13 downregulated and 2 upregulated miRNAs, were identified by comparison of low-grade and high-grade glioma tissues. The miR-374a expression of high-grade gliomas was significantly lower than that of low-grade gliomas (fold change, -4.43; P=0.027). The expression levels of miR-374a gradually decreased with the increase of the pathological grade of glioma. Pearson's Chi-square test was used to determine the association of miR-374a expression with several clinicopathological factors. Furthermore, low expression of miR-374a was determined to be an independent prognostic marker and that it was significantly associated with overall survival (P=0.0213). GO and KEGG pathway analysis revealed that the target genes of miR-374a may be involved in the regulation of the RNA polymerase II promoter and mTOR signaling pathway. The four hub genes (CCND1, SP1, CDK4, CDK6) were also identified by PPI network analysis. In conclusion, the present study indicated that miR-374a may be used as a promising prognostic biomarker for the screening of high-risk populations and for the assessment of the prognosis of patients with glioma.
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Affiliation(s)
- Qiang Dong
- Department of Neurosurgery, The Second Hospital of Lanzhou University, Lanzhou, Gansu 730030, P.R. China
| | - Guoqiang Yuan
- Institute of Neurology, The Second Hospital of Lanzhou University, Lanzhou, Gansu 730030, P.R. China
| | - Min Liu
- Department of Pharmacy, Hebei North University, Zhangjiakou, Hebei 075000, P.R. China
| | - Qiqi Xie
- Department of Orthopaedics, The Second Hospital of Lanzhou University, Lanzhou, Gansu 730030, P.R. China
| | - Jianhong Hu
- Department of Neurosurgery, The Second Hospital of Lanzhou University, Lanzhou, Gansu 730030, P.R. China
| | - Maolin Wang
- Department of Neurosurgery, The Second Hospital of Lanzhou University, Lanzhou, Gansu 730030, P.R. China
| | - Shangyu Liu
- Department of Neurosurgery, The Second Hospital of Lanzhou University, Lanzhou, Gansu 730030, P.R. China
| | - Xiaojun Ma
- Department of Neurosurgery, The Second Hospital of Lanzhou University, Lanzhou, Gansu 730030, P.R. China
| | - Yawen Pan
- Department of Neurosurgery, The Second Hospital of Lanzhou University, Lanzhou, Gansu 730030, P.R. China.,Institute of Neurology, The Second Hospital of Lanzhou University, Lanzhou, Gansu 730030, P.R. China
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Nirvani M, Khuu C, Tulek A, Utheim TP, Sand LP, Snead ML, Sehic A. Transcriptomic analysis of MicroRNA expression in enamel-producing cells. Gene 2018; 688:193-203. [PMID: 30529249 DOI: 10.1016/j.gene.2018.11.089] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 10/29/2018] [Accepted: 11/23/2018] [Indexed: 01/23/2023]
Abstract
There is little evidence for the involvement of microRNAs (miRNAs) in the regulation of circadian rhythms during enamel development. Few studies have used ameloblast-like cell line LS8 to study the circadian rhythm of gene activities related to enamel formation. However, the transcriptomic analysis of miRNA expression in LS8 cells has not been established yet. In this study, we analyze the oscillations of miRNAs in LS8 cells during one-day cycle of 24 h by next generation deep sequencing. After removal of low quality reads, contaminants, and ligation products, we obtained a high number of clean reads in all 12 samples from four different time points. The length distribution analysis indicated that 77.5% of clean reads were between 21 and 24 nucleotides (nt), of which 35.81% reads exhibited a length of 22 nt. In total, we identified 1471 miRNAs in LS8 cells throughout all four time-points. 1330 (90.41%) miRNAs were identified as known miRNA sequences, whereas 139 (9.59%) were unannotated and classified as novel miRNA sequences. The differential expression analysis showed that 191 known miRNAs exhibited significantly (P-value < 0.01) different levels of expression across three time-points investigated (T6, T12, and T18) compared to T0. Verification of sequencing data using qRT-PCR on six selected miRNAs suggested good correlation between the two methods. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed significant enrichment of predicted target genes of differentially expressed miRNAs. The present study shows that miRNAs are highly expressed in LS8 cells and that a significant number of them oscillate during one-day cycle of 24 h. This is the first transcriptomic analysis of miRNAs in ameloblast-like cell line LS8 that can be potentially used to further characterize the epigenetic regulation of miRNAs during enamel formation.
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Affiliation(s)
- Minou Nirvani
- Department of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway.
| | - Cuong Khuu
- Department of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - Amela Tulek
- Department of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - Tor Paaske Utheim
- Department of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway; Department of Medical Biochemistry, Oslo University Hospital, Oslo, Norway; Department of Maxillofacial Surgery, Oslo University Hospital, Oslo, Norway
| | - Lars Peter Sand
- Department of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - Malcolm L Snead
- Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry, University of Southern California, Los Angeles, CA, USA
| | - Amer Sehic
- Department of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway; Department of Maxillofacial Surgery, Oslo University Hospital, Oslo, Norway
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30
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Lee SY, Shin SY, Yoon YJ, Park YR. A Filtering Method for Identification of Significant Target mRNAs of Coexpressed and Differentially Expressed MicroRNA Clusters. JOURNAL OF HEALTHCARE ENGINEERING 2018; 2018:4932904. [PMID: 30298100 PMCID: PMC6157198 DOI: 10.1155/2018/4932904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 02/08/2018] [Accepted: 07/16/2018] [Indexed: 11/17/2022]
Abstract
MicroRNA (miRNA) binding is primarily based on sequence, but structure-specific binding is also possible. Various prediction algorithms have been developed for predicting miRNA target genes; the results, however, have relatively high levels of false positives, and the degree of overlap between predicted targets from different methods is poor or null. We devised a new method for identifying significant miRNA target genes from an extensive list of predicted miRNA target gene relationships using hypergeometric distributions. We evaluated our method in statistical and semantic aspects using a common miRNA cluster from six solid tumors. Our method provides statistically and semantically significant miRNA target genes. Complementing target prediction algorithms with our proposed method may have a significant synergistic effect in finding and evaluating functional annotation and enrichment analysis for miRNA.
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Affiliation(s)
- Su Yeon Lee
- Bioinformatics Team, Samsung SDS, Seoul, Republic of Korea
| | - Soo-Yong Shin
- Department of Digital Health, SAIHST, Sungkyunkwan University, Seoul, Republic of Korea
| | - Young Jo Yoon
- Office of Clinical Research Information, Asan Medical Center, Seoul, Republic of Korea
| | - Yu Rang Park
- Department of Biomedical Systems Informatics, Yonsei University College of Medicine, Seoul, Republic of Korea
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31
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Monsanto-Hearne V, Johnson KN. miRNAs in Insects Infected by Animal and Plant Viruses. Viruses 2018; 10:E354. [PMID: 29970868 PMCID: PMC6071220 DOI: 10.3390/v10070354] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 06/29/2018] [Accepted: 06/29/2018] [Indexed: 12/13/2022] Open
Abstract
Viruses vectored by insects cause severe medical and agricultural burdens. The process of virus infection of insects regulates and is regulated by a complex interplay of biomolecules including the small, non-coding microRNAs (miRNAs). Considered an anomaly upon its discovery only around 25 years ago, miRNAs as a class have challenged the molecular central dogma which essentially typifies RNAs as just intermediaries in the flow of information from DNA to protein. miRNAs are now known to be common modulators or fine-tuners of gene expression. While recent years has seen an increased emphasis on understanding the role of miRNAs in host-virus associations, existing literature on the interaction between insects and their arthropod-borne viruses (arboviruses) is largely restricted to miRNA abundance profiling. Here we analyse the commonalities and contrasts between miRNA abundance profiles with different host-arbovirus combinations and outline a suggested pipeline and criteria for functional analysis of the contribution of miRNAs to the insect vector-virus interaction. Finally, we discuss the potential use of the model organism, Drosophila melanogaster, in complementing research on the role of miRNAs in insect vector-virus interaction.
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Affiliation(s)
- Verna Monsanto-Hearne
- School of Biological Sciences, The University of Queensland, Brisbane 4072, Australia.
| | - Karyn N Johnson
- School of Biological Sciences, The University of Queensland, Brisbane 4072, Australia.
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Sulforaphane promotes apoptosis, and inhibits proliferation and self-renewal of nasopharyngeal cancer cells by targeting STAT signal through miRNA-124-3p. Biomed Pharmacother 2018; 103:473-481. [DOI: 10.1016/j.biopha.2018.03.121] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Revised: 03/19/2018] [Accepted: 03/20/2018] [Indexed: 12/22/2022] Open
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Hao P, Waxman DJ. Functional Roles of Sex-Biased, Growth Hormone-Regulated MicroRNAs miR-1948 and miR-802 in Young Adult Mouse Liver. Endocrinology 2018; 159:1377-1392. [PMID: 29346554 PMCID: PMC5839735 DOI: 10.1210/en.2017-03109] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 01/10/2018] [Indexed: 02/07/2023]
Abstract
Sex-specific temporal patterns of pituitary growth hormone (GH) secretion determine the sex-biased transcription of hundreds of genes in the liver and impart important sex differences in liver physiology, metabolism, and disease. Sex differences in hepatic gene expression vary widely, ranging from less than twofold to >1000-fold in the mouse. Here, we use small RNA sequencing to discover 24 sex-biased mouse liver microRNAs (miRNAs), and then investigate the roles of two of these miRNAs in GH-regulated liver sex differences. Studies in prepubertal and young adult mice, and in mice in which pituitary hormones are ablated or where sex-specific hepatic GH signaling is dysregulated, demonstrated that the male-biased miR-1948 and the female-biased miR-802 are both regulated by sex-specific pituitary GH secretory patterns, acquire sex specificity at puberty, and are dependent on the GH-activated transcription factor STAT5 for their sex-specific expression. Both miRNAs are within genomic regions characterized by sex-biased chromatin accessibility. miR-1948, an uncharacterized miRNA, has essential features for correct Drosha/Dicer processing, generates a bona fide mature miRNA with strong strand bias for the 5p arm, and is bound by Argonaute in liver tissue, as is miR-802. In vivo studies using inhibitory locked nucleic acid sequences revealed that miR-1948-5p preferentially represses female-biased messenger RNAs (mRNAs) and induces male-biased mRNAs in male liver; conversely, miR-802-5p preferentially represses male-biased mRNAs and increases levels of female-biased mRNAs in female liver. Cytochrome P450 mRNAs were strongly enriched as targets of both miRNAs. Thus, miR-1948-5p and miR-802-5p are functional components of the GH regulatory network that shapes sex-differential gene expression in mouse liver.
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Affiliation(s)
- Pengying Hao
- Department of Biology and Bioinformatics Program, Boston University, Boston, Massachusetts 02215
| | - David J. Waxman
- Department of Biology and Bioinformatics Program, Boston University, Boston, Massachusetts 02215
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34
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Mishra A, Bohra A. Non-coding RNAs and plant male sterility: current knowledge and future prospects. PLANT CELL REPORTS 2018; 37:177-191. [PMID: 29332167 DOI: 10.1007/s00299-018-2248-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2017] [Accepted: 01/02/2018] [Indexed: 06/07/2023]
Abstract
Latest outcomes assign functional role to non-coding (nc) RNA molecules in regulatory networks that confer male sterility to plants. Male sterility in plants offers great opportunity for improving crop performance through application of hybrid technology. In this respect, cytoplasmic male sterility (CMS) and sterility induced by photoperiod (PGMS)/temperature (TGMS) have greatly facilitated development of high-yielding hybrids in crops. Participation of non-coding (nc) RNA molecules in plant reproductive development is increasingly becoming evident. Recent breakthroughs in rice definitively associate ncRNAs with PGMS and TGMS. In case of CMS, the exact mechanism through which the mitochondrial ORFs exert influence on the development of male gametophyte remains obscure in several crops. High-throughput sequencing has enabled genome-wide discovery and validation of these regulatory molecules and their target genes, describing their potential roles performed in relation to CMS. Discovery of ncRNA localized in plant mtDNA with its possible implication in CMS induction is intriguing in this respect. Still, conclusive evidences linking ncRNA with CMS phenotypes are currently unavailable, demanding complementing genetic approaches like transgenics to substantiate the preliminary findings. Here, we review the recent literature on the contribution of ncRNAs in conferring male sterility to plants, with an emphasis on microRNAs. Also, we present a perspective on improved understanding about ncRNA-mediated regulatory pathways that control male sterility in plants. A refined understanding of plant male sterility would strengthen crop hybrid industry to deliver hybrids with improved performance.
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Affiliation(s)
- Ankita Mishra
- ICAR-Indian Institute of Pulses Research (IIPR), Kanpur, 208024, India
| | - Abhishek Bohra
- ICAR-Indian Institute of Pulses Research (IIPR), Kanpur, 208024, India.
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Abstract
A variety of molecular techniques can be used in order to unravel the molecular composition of cells. In particular, the microarray technology has been used to identify novel biomarkers that may be useful in the diagnosis, prognosis, or treatment of cancer. The microarray technology is ideal for biomarker discovery as it allows for the screening of a large number of molecules at once. In this review, we focus on microRNAs (miRNAs) which are key molecules in cells and regulate gene expression post-transcriptionally. miRNAs are small, single-stranded RNA molecules that bind to complementary mRNAs. Binding of miRNAs to mRNAs leads either to degradation, or translational inhibition of the target mRNA. Roughly one third of all the mRNAs are postulated to be regulated by miRNAs. miRNAs are known to be deregulated in different types of cancer, including breast cancer, and it has been demonstrated that deregulation of several miRNAs can be used as biological markers in cancer. miRNA expression can for example discriminate between normal, benign and malignant breast tissue, and between different breast cancer subtypes.In the post-genomic era, an important task of molecular biology is to understand gene regulation in the context of biological networks. Because miRNAs have such a pronounced role in cells, it is pivotal to understand the mechanisms that underlie their control, and to identify how miRNAs influence cancer development and progression.
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Affiliation(s)
- Andliena Tahiri
- Department of Clinical Molecular Biology (EpiGen), Division of Medicine, Akershus University Hospital, Lørenskog, Norway
| | - Miriam R Aure
- Department of Cancer Genetics, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Ullernchausseen 70, 0379, Oslo, Norway
| | - Vessela N Kristensen
- Department of Clinical Molecular Biology (EpiGen), Division of Medicine, Akershus University Hospital, Lørenskog, Norway.
- Department of Cancer Genetics, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Ullernchausseen 70, 0379, Oslo, Norway.
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Felli C, Baldassarre A, Masotti A. Intestinal and Circulating MicroRNAs in Coeliac Disease. Int J Mol Sci 2017; 18:ijms18091907. [PMID: 28878141 PMCID: PMC5618556 DOI: 10.3390/ijms18091907] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 08/23/2017] [Accepted: 08/24/2017] [Indexed: 12/11/2022] Open
Abstract
MicroRNAs (miRNAs) are short non-coding RNAs that regulate gene expression at the post-transcriptional level and play a key role in the pathogenesis of autoimmune and gastrointestinal diseases. Previous studies have revealed that miRNAs are dysregulated in intestinal biopsies of patients affected by coeliac disease (CD). Combined bioinformatics analyses of miRNA expression profiles and mRNA target genes as classified by Gene Ontology, are powerful tools to investigate the functional role of miRNAs in coeliac disease. However, little is still known about the function of circulating miRNAs, their expression level compared to tissue miRNAs, and whether the mechanisms of post-transcriptional regulation are the same of tissue miRNAs. In any case, if we assume that a cell-cell communication process has to occur, and that circulating miRNAs are delivered to recipient cells, we can derive useful information by performing target predictions. Interestingly, all of the mRNA targets of dysregulated miRNAs reported in the literature (i.e., miR-31-5p, miR-192, miR-194, miR-449a and miR-638) belong to several important biological processes, such as Wnt signaling, cell proliferation and differentiation, and adherens junction pathways. Although we think that these predictions have to be necessarily confirmed by “wet-lab” data, the miRNAs dysregulated during the development of CD could be potentially involved in the pathogenesis of coeliac disease and their correlation with circulating miRNAs offers new possibilities to use them as disease biomarkers.
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Affiliation(s)
- Cristina Felli
- Research Laboratories, Bambino Gesù Children's Hospital-IRCCS, V.le di San Paolo 15, 00146 Rome, Italy.
| | - Antonella Baldassarre
- Research Laboratories, Bambino Gesù Children's Hospital-IRCCS, V.le di San Paolo 15, 00146 Rome, Italy.
| | - Andrea Masotti
- Research Laboratories, Bambino Gesù Children's Hospital-IRCCS, V.le di San Paolo 15, 00146 Rome, Italy.
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Monsanto-Hearne V, Asad S, Asgari S, Johnson KN. Drosophila microRNA modulates viral replication by targeting a homologue of mammalian cJun. J Gen Virol 2017; 98:1904-1912. [DOI: 10.1099/jgv.0.000831] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Affiliation(s)
- Verna Monsanto-Hearne
- School of Biological Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Sultan Asad
- School of Biological Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Sassan Asgari
- School of Biological Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Karyn N. Johnson
- School of Biological Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
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Liang B, Wang X, Song X, Bai R, Yang H, Yang Z, Xiao C, Bian Y. MicroRNA-20a/b regulates cholesterol efflux through post-transcriptional repression of ATP-binding cassette transporter A1. Biochim Biophys Acta Mol Cell Biol Lipids 2017; 1862:929-938. [PMID: 28602962 DOI: 10.1016/j.bbalip.2017.06.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 05/27/2017] [Accepted: 06/07/2017] [Indexed: 12/16/2022]
Abstract
ATP-binding cassette transporter A1 (ABCA1) plays a crucial role in reverse cholesterol transport and exhibits anti-atherosclerosis effects. Some microRNAs (miRs) regulate ABCA1 expression, and recent studies have shown that miR-20a/b might play a critical role in atherosclerotic diseases. Here, we attempted to clarify the potential contribution of miR-20a/b in post-transcriptional regulation of ABCA1, cholesterol efflux, and atherosclerosis. We performed bioinformatics analysis and found that miR-20a/b was highly conserved and directly bound to ABCA1 mRNA with low binding free energy. Luciferase-reporter assay also confirmed that miR-20a/b significantly reduced luciferase activity associated with the ABCA1 3' untranslated region reporter construct. Additionally, miR-20a/b decreased ABCA1 expression, which, in turn, decreased cholesterol efflux and increased cholesterol content in THP-1 and RAW 264.7 macrophage-derived foam cells. In contrast, miR-20a/b inhibitors increased ABCA1 expression and cholesterol efflux, decreased cholesterol content, and inhibited foam-cell formation. Consistent with our in vitro results, miR-20a/b-treated ApoE-/- mice showed decreased ABCA1expression in the liver and reductions of reverse cholesterol transport in vivo. Furthermore, miR-20a/b regulated the formation of nascent high-density lipoprotein and promoted atherosclerotic development, whereas miR-20a/b knockdown attenuated atherosclerotic formation. miR-20 is a new miRNA capable of targeting ABCA1 and regulating ABCA1 expression. Therefore, miR-20 inhibition constitutes a new strategy for ABCA1-based treatment of atherosclerosis.
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Affiliation(s)
- Bin Liang
- Department of Cardiology, The Second Hospital of Shanxi Medical University, 382 Wuyi Road, Taiyuan, China; Key Laboratory of Cardiovascular Medicine and Clinical Pharmacology of Shanxi Province, 382 Wuyi Road, Taiyuan, China
| | - Xin Wang
- Department of Rheumatology, The Second Hospital of Shanxi Medical University, 382 Wuyi Road, Taiyuan, China
| | - Xiaosu Song
- Department of Cardiology, The Second Hospital of Shanxi Medical University, 382 Wuyi Road, Taiyuan, China; Key Laboratory of Cardiovascular Medicine and Clinical Pharmacology of Shanxi Province, 382 Wuyi Road, Taiyuan, China
| | - Rui Bai
- Department of Cardiology, The Second Hospital of Shanxi Medical University, 382 Wuyi Road, Taiyuan, China; Key Laboratory of Cardiovascular Medicine and Clinical Pharmacology of Shanxi Province, 382 Wuyi Road, Taiyuan, China
| | - Huiyu Yang
- Department of Cardiology, The Second Hospital of Shanxi Medical University, 382 Wuyi Road, Taiyuan, China; Key Laboratory of Cardiovascular Medicine and Clinical Pharmacology of Shanxi Province, 382 Wuyi Road, Taiyuan, China
| | - Zhiming Yang
- Department of Cardiology, The Second Hospital of Shanxi Medical University, 382 Wuyi Road, Taiyuan, China; Key Laboratory of Cardiovascular Medicine and Clinical Pharmacology of Shanxi Province, 382 Wuyi Road, Taiyuan, China
| | - Chuanshi Xiao
- Key Laboratory of Cardiovascular Medicine and Clinical Pharmacology of Shanxi Province, 382 Wuyi Road, Taiyuan, China; Department of Cardiology, The First Hospital of Shanxi Medical University, 85 Jiefang South Road, Taiyuan, China
| | - Yunfei Bian
- Department of Cardiology, The Second Hospital of Shanxi Medical University, 382 Wuyi Road, Taiyuan, China; Key Laboratory of Cardiovascular Medicine and Clinical Pharmacology of Shanxi Province, 382 Wuyi Road, Taiyuan, China.
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Cora' D, Re A, Caselle M, Bussolino F. MicroRNA-mediated regulatory circuits: outlook and perspectives. Phys Biol 2017; 14:045001. [PMID: 28586314 DOI: 10.1088/1478-3975/aa6f21] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
MicroRNAs have been found to be necessary for regulating genes implicated in almost all signaling pathways, and consequently their dysfunction influences many diseases, including cancer. Understanding of the complexity of the microRNA-mediated regulatory network has grown in terms of size, connectivity and dynamics with the development of computational and, more recently, experimental high-throughput approaches for microRNA target identification. Newly developed studies on recurrent microRNA-mediated circuits in regulatory networks, also known as network motifs, have substantially contributed to addressing this complexity, and therefore to helping understand the ways by which microRNAs achieve their regulatory role. This review provides a summarizing view of the state-of-the-art, and perspectives of research efforts on microRNA-mediated regulatory motifs. In this review, we discuss the topological properties characterizing different types of circuits, and the regulatory features theoretically enabled by such properties, with a special emphasis on examples of circuits typifying their biological significance in experimentally validated contexts. Finally, we will consider possible future developments, in particular regarding microRNA-mediated circuits involving long non-coding RNAs and epigenetic regulators.
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Affiliation(s)
- Davide Cora'
- Department of Oncology, University of Torino, Str. Prov. 142 Km 3.95, I-10060 Candiolo, Italy. Candiolo Cancer Institute-FPO, IRCCS, Str. Prov. 142 Km 3.95, I-10060 Candiolo, Italy. Center for Molecular Systems Biology, University of Torino, Regione Gonzole 10, I-10043 Orbassano, Italy. Current address: Department of Translational Medicine, Piemonte Orientale University 'Amedeo Avogadro', Via Solaroli 17, I-28100 Novara, Italy
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Singh NK. miRNAs target databases: developmental methods and target identification techniques with functional annotations. Cell Mol Life Sci 2017; 74:2239-2261. [PMID: 28204845 PMCID: PMC11107700 DOI: 10.1007/s00018-017-2469-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 01/09/2017] [Accepted: 01/18/2017] [Indexed: 12/13/2022]
Abstract
PURPOSE microRNA (miRNA) regulates diverse biological mechanisms and metabolisms in plants and animals. Thus, the discoveries of miRNA has revolutionized the life sciences and medical research.The miRNA represses and cleaves the targeted mRNA by binding perfect or near perfect or imperfect complementary base pairs by RNA-induced silencing complex (RISC) formation during biogenesis process. One miRNA interacts with one or more mRNA genes and vice versa, hence takes part in causing various diseases. In this paper, the different microRNA target databases and their functional annotations developed by various researchers have been reviewed. The concurrent research review aims at comprehending the significance of miRNA and presenting the existing status of annotated miRNA target resources built by researchers henceforth discovering the knowledge for diagnosis and prognosis. METHODS AND RESULTS This review discusses the applications and developmental methodologies for constructing target database as well as the utility of user interface design. An integrated architecture is drawn and a graphically comparative study of present status of miRNA targets in diverse diseases and various biological processes is performed. These databases comprise of information such as miRNA target-associated disease, transcription factor binding sites (TFBSs) in miRNA genomic locations, polymorphism in miRNA target, A-to-I edited target, Gene Ontology (GO), genome annotations, KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways, target expression analysis, TF-miRNA and miRNA-mRNA interaction networks, drugs-targets interactions, etc. CONCLUSION miRNA target databases contain diverse experimentally and computationally predicted target through various algorithms. The comparison of various miRNA target database has been performed on various parameters. The computationally predicted target databases suffer from false positive information as there is no common theory for prediction of miRNA targets. The review conclusion emphasizes the need of more intelligent computational improvement for the miRNA target identification, their functional annotations and datasbase development.
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Affiliation(s)
- Nagendra Kumar Singh
- Department of Biological Science and Engineering, Maulana Azad National Institute of Technology, Bhopal, 462003, India.
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Nirvani M, Khuu C, Utheim TP, Hollingen HS, Amundsen SF, Sand LP, Sehic A. Circadian rhythms and gene expression during mouse molar tooth development. Acta Odontol Scand 2017; 75:144-153. [PMID: 28030993 DOI: 10.1080/00016357.2016.1271999] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
OBJECTIVES Incremental markings in dental enamel suggest that the circadian clock may influence the molecular underpinnings orchestrating enamel formation. The aim of this study was to investigate whether the genes and microRNAs (miRNAs) oscillate in a circadian pattern during tooth and enamel development. MATERIAL AND METHODS Comparative gene and miRNA expression profiling of the first mandibular molar tooth germ isolated at different time-points during the light and night period was performed using microarrays and validated using real-time RT-PCR. Bioinformatic analysis was carried out using Ingenuity Pathway Analysis (IPA), and TargetScan software was used in order to identify computationally predicted miRNA-mRNA target relationships. RESULTS In total, 439 genes and 32 miRNAs exhibited significantly different (p < 0.05) levels of expression in the light phase compared with the night phase tooth germs. Genes involved in enamel formation, i.e. Amelx, Ambn, Amtn, and Odam, oscillated in a circadian pattern. Furthermore, the circadian clock genes, in particular Clock and Bmal1, oscillated in mouse molar tooth germ during 24-h intervals. The expression of Clock and Bmal1 was inversely correlated with the expression of miR-182 and miR-141, respectively. CONCLUSIONS MiRNAs, including miR-182 and miR-141, are involved in the control of peripheral circadian rhythms in the developing tooth by regulating the expression of genes coding for circadian transcription factors such as CLOCK and BMAL1. Regulation of circadian rhythms may be important for enamel phenotype, and the morphology of dental enamel may vary between individuals due to differences in circadian profiles.
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Affiliation(s)
- Minou Nirvani
- Department of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - Cuong Khuu
- Department of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - Tor Paaske Utheim
- Department of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
- Department of Medical Biochemistry, Oslo University Hospital, Oslo, Norway
- Department of Ophthalmology, Drammen Hospital, Vestre Viken Hospital Trust, Drammen, Norway
- Faculty of Health Sciences, University College of South East Norway, Kongsberg, Norway
| | | | - Simon Furre Amundsen
- Department of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - Lars Peter Sand
- Department of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - Amer Sehic
- Department of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
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Nosirov B, Billaud J, Vandenbon A, Diez D, Wijaya E, Ishii KJ, Teraguchi S, Standley DM. Mapping circulating serum miRNAs to their immune-related target mRNAs. Adv Appl Bioinform Chem 2017; 10:1-9. [PMID: 28203094 PMCID: PMC5295801 DOI: 10.2147/aabc.s121598] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Purpose Evidence suggests that circulating serum microRNAs (miRNAs) might preferentially target immune-related mRNAs. If this were the case, we hypothesized that immune-related mRNAs would have more predicted serum miRNA binding sites than other mRNAs and, reciprocally, that serum miRNAs would have more immune-related mRNA targets than non-serum miRNAs. Materials and methods We developed a consensus target predictor using the random forest framework and calculated the number of predicted miRNA–mRNA interactions in various subsets of miRNAs (serum, non-serum) and mRNAs (immune related, nonimmune related). Results Immune-related mRNAs were predicted to be targeted by serum miRNA more than other mRNAs. Moreover, serum miRNAs were predicted to target many more immune-related mRNA targets than non-serum miRNAs; however, these two biases in immune-related mRNAs and serum miRNAs appear to be completely independent. Conclusion Immune-related mRNAs have more miRNA binding sites in general, not just for serum miRNAs; likewise, serum miRNAs target many more mRNAs than non-serum miRNAs overall, regardless of whether they are immune related or not. Nevertheless, these two independent phenomena result in a significantly larger number of predicted serum miRNA–immune mRNA interactions than would be expected by chance.
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Affiliation(s)
| | | | | | | | | | - Ken J Ishii
- Laboratory of Vaccine Science, WPI Immunology Frontier Research Center, Osaka University, Suita; Laboratory of Adjuvant Innovation, National Institute of Biomedical Innovation, Osaka
| | | | - Daron M Standley
- Systems Immunology Lab; Lab of Integrated Biological Information, Institute for Virus Research Kyoto University, Kyoto, Japan
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Filella X, Foj L. miRNAs as novel biomarkers in the management of prostate cancer. ACTA ACUST UNITED AC 2017; 55:715-736. [DOI: 10.1515/cclm-2015-1073] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 11/29/2015] [Indexed: 12/15/2022]
Abstract
AbstractmicroRNAs (miRNAs) are small non-coding RNAs that control gene expression posttranscriptionally and are part of the giant non codifying genoma. Cumulating data suggest that miRNAs are promising potential biomarkers for many diseases, including cancer. Prostate cancer (PCa) detection is currently based in the serum prostate-specific antigen biomarker and digital rectal examination. However, these methods are limited by a low predictive value and the adverse consequences associated with overdiagnosis and overtreatment. New biomarkers that could be used for PCa detection and prognosis are still needed. Recent studies have demonstrated that aberrant expressions of microRNAs are associated with the underlying mechanisms of PCa. This review attempts to extensively summarize the current knowledge of miRNA expression patterns, as well as their targets and involvement in PCa pathogenesis. We focused our review in the value of circulating and urine miRNAs as biomarkers in PCa patients, highlighting the existing discrepancies between different studies, probably associated with the important methodological issues related to their quantitation and normalization. The majority of studies have been performed in serum or plasma, but urine obtained after prostate massage appears as a new way to explore the usefulness of miRNAs. Large screening studies to select a miRNA profile have been completed, but bioinformatics tools appear as a new approach to select miRNAs that are relevant in PCa development. Promising preliminary results were published concerning miR-141, miR-375 and miR-21, but larger and prospective studies using standardized methodology are necessary to define the value of miRNAs in the detection and prognosis of PCa.
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Identification and Target Prediction of MicroRNAs in Ulmus pumila L. Seedling Roots under Salt Stress by High-Throughput Sequencing. FORESTS 2016. [DOI: 10.3390/f7120318] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Xu Y, Chen Y, Li D, Liu Q, Xuan Z, Li WH. TargetLink, a new method for identifying the endogenous target set of a specific microRNA in intact living cells. RNA Biol 2016; 14:259-274. [PMID: 27982722 DOI: 10.1080/15476286.2016.1270006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
MicroRNAs are small non-coding RNAs acting as posttranscriptional repressors of gene expression. Identifying mRNA targets of a given miRNA remains an outstanding challenge in the field. We have developed a new experimental approach, TargetLink, that applied locked nucleic acid (LNA) as the affinity probe to enrich target genes of a specific microRNA in intact cells. TargetLink also consists a rigorous and systematic data analysis pipeline to identify target genes by comparing LNA-enriched sequences between experimental and control samples. Using miR-21 as a test microRNA, we identified 12 target genes of miR-21 in a human colorectal cancer cell by this approach. The majority of the identified targets interacted with miR-21 via imperfect seed pairing. Target validation confirmed that miR-21 repressed the expression of the identified targets. The cellular abundance of the identified miR-21 target transcripts varied over a wide range, with some targets expressed at a rather low level, confirming that both abundant and rare transcripts are susceptible to regulation by microRNAs, and that TargetLink is an efficient approach for identifying the target set of a specific microRNA in intact cells. C20orf111, one of the novel targets identified by TargetLink, was found to reside in the nuclear speckle and to be reliably repressed by miR-21 through the interaction at its coding sequence.
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Affiliation(s)
- Yan Xu
- a Department of Cell Biology and of Biochemistry , University of Texas Southwestern Medical Center , Dallas , TX , USA
| | - Yan Chen
- a Department of Cell Biology and of Biochemistry , University of Texas Southwestern Medical Center , Dallas , TX , USA
| | - Daliang Li
- a Department of Cell Biology and of Biochemistry , University of Texas Southwestern Medical Center , Dallas , TX , USA
| | - Qing Liu
- a Department of Cell Biology and of Biochemistry , University of Texas Southwestern Medical Center , Dallas , TX , USA
| | - Zhenyu Xuan
- b Department of Biological Sciences , Center for Systems Biology, The University of Texas at Dallas , Richardson , TX , USA
| | - Wen-Hong Li
- a Department of Cell Biology and of Biochemistry , University of Texas Southwestern Medical Center , Dallas , TX , USA
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Jiang J, Gao Q, Wang T, Lin H, Zhan Q, Chu Z, Huang R, Zhou X, Liang X, Guo W. MicroRNA expression profiles of granulocytic myeloid‑derived suppressor cells from mice bearing Lewis lung carcinoma. Mol Med Rep 2016; 14:4567-4574. [PMID: 27748875 PMCID: PMC5102002 DOI: 10.3892/mmr.2016.5845] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 09/22/2016] [Indexed: 01/01/2023] Open
Abstract
Myeloid-derived suppressor cells (MDSCs) are a group of heterogeneous myeloid cells that can suppress antitumor immunity. MDSCs are divided into granulocytic (G-MDSCs) and monocytic subsets. In the present study, the microRNA profiles of the G-MDSCs were determined and the differential expression of microRNAs between G-MDSCs from tumor-bearing mice and tumor-free mice was examined. The number of G-MDSCs in spleens of Lewis lung carcinoma (LLC)-bearing mice was ~6-fold higher than in spleens of normal mice (13.54±1.74% vs. 2.14±1.44%; P<0.01) and G-MDSCs account for about 72.9% of all MDSCs. The microRNA (miRNA) profiles of the G-MDSCs from spleen of LLC-bearing mice were obtained using a microRNA microarray and compared with their counterparts from spleens of tumor-free mice. A total of 43 miRNAs with >1.3-fold increased or decreased change were differentially expressed between the experimental and control group mice. The levels of nine of these differentially expressed miRNAs, miRNA-468 (miR-486), miR-192, miR-128, miR-125a, miR-149, miR-27a, miR-125b, miR-350 and miR-328, were also analyzed by RT-qPCR to validate the microarray data. The concordance rate between the results tested by the two methods was 88.9%. Bioinformatics analyses revealed that these miRNAs may act on various target genes, including Adar, Pik3r1, Rybp and Rabgap1, to regulate the survival, differentiation and the function of tumor-induced granulocytic MDSCs. The results revealed microRNAs and potential targets that may be vital for regulating survival, differentiation and function of G-MDSCs induced by LLC. Further investigation should be performed to clarify the roles of these microRNAs in regulating LLC-induced granulocytic MDSCs and the target genes that mediate their functions.
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Affiliation(s)
- Jingwei Jiang
- Department of Oncology, Huashan Hospital, Fudan University, Shanghai 200040, P.R. China
| | - Qingmin Gao
- Department of Oncology, Huashan Hospital, Fudan University, Shanghai 200040, P.R. China
| | - Tian Wang
- Department of Oncology, Huashan Hospital, Fudan University, Shanghai 200040, P.R. China
| | - Hao Lin
- Department of Oncology, Huashan Hospital, Fudan University, Shanghai 200040, P.R. China
| | - Qiong Zhan
- Department of Oncology, Huashan Hospital, Fudan University, Shanghai 200040, P.R. China
| | - Zhaohui Chu
- Department of Oncology, Huashan Hospital, Fudan University, Shanghai 200040, P.R. China
| | - Ruofan Huang
- Department of Oncology, Huashan Hospital, Fudan University, Shanghai 200040, P.R. China
| | - Xinli Zhou
- Department of Oncology, Huashan Hospital, Fudan University, Shanghai 200040, P.R. China
| | - Xiaohua Liang
- Department of Oncology, Huashan Hospital, Fudan University, Shanghai 200040, P.R. China
| | - Weijian Guo
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P.R. China
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Moriya N, Kataoka H, Nishikawa JI, Kugawa F. Identification of Candidate Target Cyp Genes for microRNAs Whose Expression Is Altered by PCN and TCPOBOP, Representative Ligands of PXR and CAR. Biol Pharm Bull 2016; 39:1381-6. [PMID: 27237601 DOI: 10.1248/bpb.b16-00279] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that are involved in mRNA post-transcriptional regulation. The deregulation of miRNAs affects the expression of drug-metabolizing enzymes, drug transporters, and nuclear receptors, all of which are important in regulating drug metabolism. miRNA expression can be altered by several endogenous or exogenous agents, such as steroid hormones, carcinogens, and therapeutic drugs. However, it is unclear whether hepatic miRNA expression is regulated by nuclear receptors, such as pregnane X receptor (PXR) and constitutive androstane receptor (CAR), which are indispensable for the expression of the CYPs. Here we investigated the effects of the mouse PXR and CAR ligands pregnenolone-16α-carbonitrile (PCN) and 1,4-bis[(3,5-dichloropyridin-2-yl)oxy]benzene (TCPOBOP) on hepatic miRNA expression in mice. We found that the expression of 9 miRNAs was increased (>2-fold) and of 4 miRNAs was decreased (>50%) in response to PCN, while TCPOBOP treatment led to the up-regulation of 8 miRNAs and down-regulation of 6 miRNAs. Using several miRNA target prediction algorithms, we found that the predicted target genes included several lesser known Cyp genes (Cyp1a1, Cyp1b1, Cyp2b10, Cyp2c38, Cyp2u1, Cyp4a12a/b, Cyp4v3, Cyp17a1, Cyp39a1, and Cyp51). We analyzed the expression of these genes in response to PCN and TCPOBOP and found changes in their mRNA levels, some of which were negatively correlated with the expression of their corresponding miRNAs, suggesting that miRNAs may play a role in regulating Cyp enzyme expression. Further studies will be required to fully elucidate the miRNA regulatory mechanisms that contribute to modulating CYP expression.
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Affiliation(s)
- Nozomu Moriya
- Department of Biopharmaceutics, Hyogo University of Health Sciences
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Rahat MA, Preis M. Role of microRNA in regulation of myeloma-related angiogenesis and survival. World J Hematol 2016; 5:51-60. [DOI: 10.5315/wjh.v5.i2.51] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 11/19/2015] [Accepted: 01/22/2016] [Indexed: 02/05/2023] Open
Abstract
Multiple myeloma (MM) is a malignant disease caused by clonal proliferation of plasma cells that result in monoclonal gammopathy and severe end organ damage. Despite the uniform clinical signs, the disease is very diverse in terms of the nature and sequence of the underlying molecular events. Multiple cellular processes are involved in helping the malignant cells to remain viable and maintain proliferative properties in the hypoxic microenvironment of the bone marrow. Specifically, the process of angiogenesis, triggered by the interactions between the malignant MM cells and the stroma cells around them, was found to be critical for MM progression. In this review we highlight the current understanding about the epigenetic regulation of the proliferation and apoptosis of MM cells and its dependency on angiogenesis in the bone marrow that is carried out by different microRNAs.
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Huntley RP, Sitnikov D, Orlic-Milacic M, Balakrishnan R, D'Eustachio P, Gillespie ME, Howe D, Kalea AZ, Maegdefessel L, Osumi-Sutherland D, Petri V, Smith JR, Van Auken K, Wood V, Zampetaki A, Mayr M, Lovering RC. Guidelines for the functional annotation of microRNAs using the Gene Ontology. RNA (NEW YORK, N.Y.) 2016; 22:667-76. [PMID: 26917558 PMCID: PMC4836642 DOI: 10.1261/rna.055301.115] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 01/19/2016] [Indexed: 05/07/2023]
Abstract
MicroRNA regulation of developmental and cellular processes is a relatively new field of study, and the available research data have not been organized to enable its inclusion in pathway and network analysis tools. The association of gene products with terms from the Gene Ontology is an effective method to analyze functional data, but until recently there has been no substantial effort dedicated to applying Gene Ontology terms to microRNAs. Consequently, when performing functional analysis of microRNA data sets, researchers have had to rely instead on the functional annotations associated with the genes encoding microRNA targets. In consultation with experts in the field of microRNA research, we have created comprehensive recommendations for the Gene Ontology curation of microRNAs. This curation manual will enable provision of a high-quality, reliable set of functional annotations for the advancement of microRNA research. Here we describe the key aspects of the work, including development of the Gene Ontology to represent this data, standards for describing the data, and guidelines to support curators making these annotations. The full microRNA curation guidelines are available on the GO Consortium wiki (http://wiki.geneontology.org/index.php/MicroRNA_GO_annotation_manual).
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Affiliation(s)
- Rachael P Huntley
- Centre for Cardiovascular Genetics, Institute of Cardiovascular Science, University College London, London WC1E 6JF, United Kingdom
| | | | | | - Rama Balakrishnan
- Department of Genetics, Stanford University, MC-5477 Stanford, California 94305, USA
| | - Peter D'Eustachio
- Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, New York 10016, USA
| | - Marc E Gillespie
- College of Pharmacy and Health Sciences, St. John's University, Queens, New York 11439, USA
| | - Doug Howe
- Zebrafish Model Organism Database, 5291 University of Oregon Eugene, Oregon 97403-5291, USA
| | - Anastasia Z Kalea
- Centre for Cardiovascular Genetics, Institute of Cardiovascular Science, University College London, London WC1E 6JF, United Kingdom
| | - Lars Maegdefessel
- Karolinska Institute, Department of Medicine, Center for Molecular Medicine (CMM) L8:03, Stockholm 17176, Sweden
| | - David Osumi-Sutherland
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton CB10 1SD, Cambridge, UK
| | - Victoria Petri
- Human and Molecular Genetics Center, Medical College of Wisconsin Department of Physiology, Medical College of Wisconsin Department of Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
| | - Jennifer R Smith
- Human and Molecular Genetics Center, Medical College of Wisconsin Department of Physiology, Medical College of Wisconsin Department of Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
| | - Kimberly Van Auken
- Division of Biology, California Institute of Technology, Pasadena, California 91125, USA
| | - Valerie Wood
- Cambridge Systems Biology and Department of Biochemistry, University of Cambridge, Sanger Building, Cambridge CB2 1GA, United Kingdom
| | - Anna Zampetaki
- King's British Heart Foundation Centre, King's College London, London SE5 9NU, United Kingdom
| | - Manuel Mayr
- King's British Heart Foundation Centre, King's College London, London SE5 9NU, United Kingdom
| | - Ruth C Lovering
- Centre for Cardiovascular Genetics, Institute of Cardiovascular Science, University College London, London WC1E 6JF, United Kingdom
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Liu X, Li J, Qin F, Dai S. miR-152 as a tumor suppressor microRNA: Target recognition and regulation in cancer. Oncol Lett 2016; 11:3911-3916. [PMID: 27313716 DOI: 10.3892/ol.2016.4509] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2015] [Accepted: 03/01/2016] [Indexed: 11/05/2022] Open
Abstract
MicroRNAs (miRNAs or miRs) are endogenous translation repressors of protein-coding genes that act by binding to the 3'-untranslated region of their target genes, and may contribute to tumorigenesis by functioning as oncogenes or tumor suppressor genes. miR-152, a member of the miR-148/152 family, is aberrantly expressed in various diseases, including various types of cancer. A growing body of evidence has demonstrated that miR-152 may act as a tumor suppressor gene by regulating its target genes, which are associated with cell proliferation, migration and invasion in human cancer. In the present review, the gene structure and functions of miR-152 are discussed, and in particular, its regulatory mechanism, experimentally validated targets and tumor suppressor role in cancer, are highlighted.
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Affiliation(s)
- Xuexiang Liu
- Department of Laboratory Science, The Fourth Hospital Affiliated to Guangxi Medical University, Liuzhou, Guangxi 545005, P.R. China
| | - Jinwan Li
- Department of Laboratory Science, The Fourth Hospital Affiliated to Guangxi Medical University, Liuzhou, Guangxi 545005, P.R. China
| | - Fengxian Qin
- Department of Laboratory Science, The Fourth Hospital Affiliated to Guangxi Medical University, Liuzhou, Guangxi 545005, P.R. China
| | - Shengming Dai
- Department of Laboratory Science, The Fourth Hospital Affiliated to Guangxi Medical University, Liuzhou, Guangxi 545005, P.R. China
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