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Maharati A, Moghbeli M. Role of microRNA-505 during tumor progression and metastasis. Pathol Res Pract 2024; 258:155344. [PMID: 38744001 DOI: 10.1016/j.prp.2024.155344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 04/23/2024] [Accepted: 05/09/2024] [Indexed: 05/16/2024]
Abstract
Late diagnosis of cancer in advanced stages due to the lack of screening methods is considered as the main cause of poor prognosis and high mortality rate among these patients. Therefore, it is necessary to investigate the molecular tumor biology in order to introduce biomarkers that can be used in cancer screening programs and early diagnosis. MicroRNAs (miRNAs) have key roles in regulation of the cellular pathophysiological processes. Due to the high stability of miRNAs in body fluids, they are widely used as the non-invasive tumor markers. According to the numerous reports about miR-505 deregulation in a wide range of cancers, we investigated the role of miR-505 during tumor progression. It was shown that miR-505 mainly has the tumor suppressor functions through the regulation of signaling pathways, chromatin remodeling, and cellular metabolism. This review has an effective role in introducing miR-505 as a suitable marker for the early cancer diagnosis.
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Affiliation(s)
- Amirhosein Maharati
- Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Meysam Moghbeli
- Department of Medical Genetics and Molecular Medicine, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
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2
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Altalebi SAR, Haghi M, Hosseinpour Feizi MA. Expression study of microRNA cluster on chromosome 19 (C19MC) in tumor tissue and serum of breast cancer patient. Mol Biol Rep 2023; 50:9825-9831. [PMID: 37840066 DOI: 10.1007/s11033-023-08801-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Accepted: 09/05/2023] [Indexed: 10/17/2023]
Abstract
BACKGROUND Breast cancer (BC) is the most prevalent cancer among females worldwide. Numerous studies suggest that specific RNAs play a crucial role in carcinogenesis. The primate-specific microRNA gene cluster located on the 19q27.3 region of chromosome 19 (C19MC) could potentially regulate tumor cell proliferation, migration, and invasion. OBJECTIVE The objective of this study was to compare the expression of miRNAs from the C19MC cluster in breast cancer tumor and non-tumor samples, as well as in the serum of individuals affected by BC and healthy individuals. METHODS Peripheral blood was collected from 100 BC patients and 100 healthy individuals, and breast cancer samples including tumor and margin tissues were obtained. After RNA extraction, Real-time PCR was employed to investigate the expression of C19MC, specifically mir-515-1, mir-515-2, mir-516-A1, mir-516-A2, mir-516-B1, mir-516-B2, mir-517-A, mir-517-B, mir-517-C, and mir-518-A1, in the serum and tissue of BC patients and tumor margins. Statistical analyses and ROC curves were generated using GraphPad Prism software (v8.04), with a significance level set at p < 0.05. RESULTS Our findings demonstrate a strong correlation between high expression of all C19MC miRNAs mentioned, except for mir-517-B, mir-517-C and mir- 518 in BC. These miRNAs show potential as notable non-invasive tumor markers. CONCLUSION The data obtained from our study support the overall impact of C19MC miRNAs in BC detection and emphasize the potential role of several C19MC members in this process.
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Affiliation(s)
| | - Mehdi Haghi
- Department of Animal Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran.
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3
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Baciadonna L, Cornero FM, Clayton NS, Emery NJ. Mirror stimulation in Eurasian jays ( Garrulus glandarius). PeerJ 2023; 11:e14729. [PMID: 36819998 PMCID: PMC9938653 DOI: 10.7717/peerj.14729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 12/20/2022] [Indexed: 02/17/2023] Open
Abstract
Mirror exposure elicits a wide range of behavioral responses, some of which have been considered as part of possible evidence of mirror self-recognition (MSR). These responses can range from social behaviors, indicating that an animal considers its own reflection as a conspecific, to mirror-guided and self-directed actions. Evidence of MSR has been found categorically in only a few species, such as in magpies, chimpanzees, horses, and elephants. Evidence in corvids is currently debated due to inconsistent findings. In this study, we investigated the reaction of Eurasian jays when presenting them with three mirror-stimulation tasks. Based on the overall behavioral patterns across these three tasks, conclusions about birds' understanding of a reflective surface, and their perception of the reflection as either themselves or as a conspecific, appear premature. We highlight how the high neophobia of corvids and other methodological constraints might have hindered the likelihood to approach and explore a mirror, preventing the emergence of behaviors typically associated with MSR. Furthermore, we discuss how motivational factors, methodological constraints and species differences should be considered when interpreting behavioral responses to mirrors.
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Affiliation(s)
- Luigi Baciadonna
- Department of Psychology, University of Cambridge, Cambridge, United Kingdom,Biological and Experimental Psychology, School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom,Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | | | - Nicola S. Clayton
- Department of Psychology, University of Cambridge, Cambridge, United Kingdom
| | - Nathan J. Emery
- Biological and Experimental Psychology, School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
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4
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Lee SH, Ng CX, Wong SR, Chong PP. MiRNAs Overexpression and Their Role in Breast Cancer: Implications for Cancer Therapeutics. Curr Drug Targets 2023; 24:484-508. [PMID: 36999414 DOI: 10.2174/1389450124666230329123409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 12/20/2022] [Accepted: 01/30/2023] [Indexed: 04/01/2023]
Abstract
MicroRNAs have a plethora of roles in various biological processes in the cells and most human cancers have been shown to be associated with dysregulation of the expression of miRNA genes. MiRNA biogenesis involves two alternative pathways, the canonical pathway which requires the successful cooperation of various proteins forming the miRNA-inducing silencing complex (miRISC), and the non-canonical pathway, such as the mirtrons, simtrons, or agotrons pathway, which bypasses and deviates from specific steps in the canonical pathway. Mature miRNAs are secreted from cells and circulated in the body bound to argonaute 2 (AGO2) and miRISC or transported in vesicles. These miRNAs may regulate their downstream target genes via positive or negative regulation through different molecular mechanisms. This review focuses on the role and mechanisms of miRNAs in different stages of breast cancer progression, including breast cancer stem cell formation, breast cancer initiation, invasion, and metastasis as well as angiogenesis. The design, chemical modifications, and therapeutic applications of synthetic anti-sense miRNA oligonucleotides and RNA mimics are also discussed in detail. The strategies for systemic delivery and local targeted delivery of the antisense miRNAs encompass the use of polymeric and liposomal nanoparticles, inorganic nanoparticles, extracellular vesicles, as well as viral vectors and viruslike particles (VLPs). Although several miRNAs have been identified as good candidates for the design of antisense and other synthetic modified oligonucleotides in targeting breast cancer, further efforts are still needed to study the most optimal delivery method in order to drive the research beyond preclinical studies.
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Affiliation(s)
- Sau Har Lee
- School of Biosciences, Faculty of Health and Medical Sciences, Taylor's University, Subang Jaya, Selangor, Malaysia
- Centre for Drug Discovery and Molecular Pharmacology (CDDMP), Faculty of Health and Medical Sciences, Taylor's University, Subang Jaya, Selangor, Malaysia
| | - Chu Xin Ng
- School of Biosciences, Faculty of Health and Medical Sciences, Taylor's University, Subang Jaya, Selangor, Malaysia
| | - Sharon Rachel Wong
- School of Biosciences, Faculty of Health and Medical Sciences, Taylor's University, Subang Jaya, Selangor, Malaysia
| | - Pei Pei Chong
- School of Biosciences, Faculty of Health and Medical Sciences, Taylor's University, Subang Jaya, Selangor, Malaysia
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5
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Mir-326 potentiates radiosensitivity of cervical squamous cell carcinoma through downregulating SMO expression in the Hedgehog signaling pathway. Genes Genomics 2022; 44:981-991. [PMID: 35751784 DOI: 10.1007/s13258-022-01276-3] [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: 02/28/2022] [Accepted: 06/01/2022] [Indexed: 12/24/2022]
Abstract
BACKGROUND Radiotherapy resistance affects the therapeutic effect of cervical squamous cell carcinoma (CSCC). Smoothened (Smo) is an anticancer target of the Hedgehog (Hh) pathway and its mutation is related to drug resistance. OBJECTIVE To explore the roles of miR-326 and Smoothened (SMO) on radiation resistance in patients with cervical carcinoma. METHODS Expression of miR-326 and SMO in cervical cancer tissue and radioresistant cell lines were analyzed. The radiation response with the expression of miR-326 was evaluated in tissue and cells. Bioinformatics analysis and literature review were performed to explore the target of miR-326. The regulation of miR-326 to SMO mRNA was verified through the dual-luciferase reporter assay. RESULTS Patients with poor radiation response have lower miR-326 and higher SMO expression. Upregulation of miR-326 decreased SMO expression and its downstream proteins but does not affect the proliferation of CSCC cells. The upregulation of miR-326 increased radiation sensitivity of the CSCC cell through downregulating SMO and its downstream proteins in the Hedgehog (Hh) signaling pathway. CONCLUSIONS miR-326 may predict the treatment response to radiation, and upregulating miR-326 may improve the treatment response to radiation.
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6
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Kwon DG, Kim MK, Jeon YS, Nam YC, Park JS, Ryu DJ. State of the Art: The Immunomodulatory Role of MSCs for Osteoarthritis. Int J Mol Sci 2022; 23:1618. [PMID: 35163541 PMCID: PMC8835711 DOI: 10.3390/ijms23031618] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/21/2022] [Accepted: 01/27/2022] [Indexed: 01/15/2023] Open
Abstract
Osteoarthritis (OA) has generally been introduced as a degenerative disease; however, it has recently been understood as a low-grade chronic inflammatory process that could promote symptoms and accelerate the progression of OA. Current treatment strategies, including corticosteroid injections, have no impact on the OA disease progression. Mesenchymal stem cells (MSCs) based therapy seem to be in the spotlight as a disease-modifying treatment because this strategy provides enlarged anti-inflammatory and chondroprotective effects. Currently, bone marrow, adipose derived, synovium-derived, and Wharton's jelly-derived MSCs are the most widely used types of MSCs in the cartilage engineering. MSCs exert immunomodulatory, immunosuppressive, antiapoptotic, and chondrogenic effects mainly by paracrine effect. Because MSCs disappear from the tissue quickly after administration, recently, MSCs-derived exosomes received the focus for the next-generation treatment strategy for OA. MSCs-derived exosomes contain a variety of miRNAs. Exosomal miRNAs have a critical role in cartilage regeneration by immunomodulatory function such as promoting chondrocyte proliferation, matrix secretion, and subsiding inflammation. In the future, a personalized exosome can be packaged with ideal miRNA and proteins for chondrogenesis by enriching techniques. In addition, the target specific exosomes could be a gamechanger for OA. However, we should consider the off-target side effects due to multiple gene targets of miRNA.
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Affiliation(s)
| | | | | | | | | | - Dong Jin Ryu
- Orthopedic Surgery, Inha University Hospital, 22332 Inhang-ro 27, Jung-gu, Incheon 22332, Korea; (D.G.K.); (M.K.K.); (Y.S.J.); (Y.C.N.); (J.S.P.)
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7
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Foo JB, Looi QH, How CW, Lee SH, Al-Masawa ME, Chong PP, Law JX. Mesenchymal Stem Cell-Derived Exosomes and MicroRNAs in Cartilage Regeneration: Biogenesis, Efficacy, miRNA Enrichment and Delivery. Pharmaceuticals (Basel) 2021; 14:1093. [PMID: 34832875 PMCID: PMC8618513 DOI: 10.3390/ph14111093] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 10/25/2021] [Accepted: 10/26/2021] [Indexed: 02/07/2023] Open
Abstract
Exosomes are the small extracellular vesicles secreted by cells for intercellular communication. Exosomes are rich in therapeutic cargos such as microRNA (miRNA), long non-coding RNA (lncRNA), small interfering RNA (siRNA), DNA, protein, and lipids. Recently, many studies have focused on miRNAs as a promising therapeutic factor to support cartilage regeneration. Exosomes are known to contain a substantial amount of a variety of miRNAs. miRNAs regulate the post-transcriptional gene expression by base-pairing with the target messenger RNA (mRNA), leading to gene silencing. Several exosomal miRNAs have been found to play a role in cartilage regeneration by promoting chondrocyte proliferation and matrix secretion, reducing scar tissue formation, and subsiding inflammation. The exosomal miRNA cargo can be modulated using techniques such as cell transfection and priming as well as post-secretion modifications to upregulate specific miRNAs to enhance the therapeutic effect. Exosomes are delivered to the joints through direct injection or via encapsulation within a scaffold for sustained release. To date, exosome therapy for cartilage injuries has yet to be optimized as the ideal cell source for exosomes, and the dose and method of delivery have yet to be identified. More importantly, a deeper understanding of the role of exosomal miRNAs in cartilage repair is paramount for the development of more effective exosome therapy.
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Affiliation(s)
- Jhi Biau Foo
- School of Pharmacy, Faculty of Health and Medical Sciences, Taylor’s University, Subang Jaya 47500, Malaysia;
- Centre for Drug Discovery and Molecular Pharmacology (CDDMP), Faculty of Health and Medical Sciences, Taylor’s University, Subang Jaya 47500, Malaysia;
| | - Qi Hao Looi
- My Cytohealth Sdn. Bhd., D353a, Menara Suezcap 1, KL Gateway, no. 2, Jalan Kerinchi, Gerbang Kerinchi Lestari, Kuala Lumpur 59200, Malaysia;
- National Orthopaedic Centre of Excellence in Research and Learning (NOCERAL), Department of Orthopaedic Surgery, Faculty of Medicine, University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Chee Wun How
- School of Pharmacy, Monash University Malaysia, Bandar Sunway 47500, Malaysia;
| | - Sau Har Lee
- Centre for Drug Discovery and Molecular Pharmacology (CDDMP), Faculty of Health and Medical Sciences, Taylor’s University, Subang Jaya 47500, Malaysia;
- Faculty of Health and Medical Sciences, School of Biosciences, Taylor’s University, Subang Jaya 47500, Malaysia;
| | - Maimonah Eissa Al-Masawa
- Centre for Tissue Engineering and Regenerative Medicine, Faculty of Medicine, Universiti Kebangsaan Malaysia Medical Centre, Jalan Yaacob Latif, Kuala Lumpur 56000, Malaysia;
| | - Pei Pei Chong
- Faculty of Health and Medical Sciences, School of Biosciences, Taylor’s University, Subang Jaya 47500, Malaysia;
| | - Jia Xian Law
- Centre for Tissue Engineering and Regenerative Medicine, Faculty of Medicine, Universiti Kebangsaan Malaysia Medical Centre, Jalan Yaacob Latif, Kuala Lumpur 56000, Malaysia;
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8
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Gao R, Ye H, Gao Q, Wang N, Zhou Y, Duan H. Inhibition of circular RNA_0000285 prevents cell proliferation and induces apoptosis in thyroid cancer by sponging microRNA-654-3p. Oncol Lett 2021; 22:673. [PMID: 34345298 PMCID: PMC8323011 DOI: 10.3892/ol.2021.12934] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 05/25/2021] [Indexed: 12/17/2022] Open
Abstract
Thyroid cancer is derived from follicular or thyroid cells and has become the most prevalent malignant tumor of endocrine organs, with increased morbidity and mortality. Circular RNAs (circRNAs) are used as prognostic and predictive markers for different types of cancer. However, the role of circRNA_0000285 in thyroid cancer and its potential molecular mechanism remain unclear. The present study aimed to investigate the roles and underlying molecular mechanism of circRNA_0000285 in thyroid cancer to identify novel treatments for this disease. The target binding site of circRNA_0000285 and microRNA-654-3p (miR-654-3p) were predicted and confirmed via the dual-luciferase reporter and RNA immunoprecipitation (RIP) assays. Thyroid cancer cell viability and apoptosis were determined via the MTT assay and flow cytometric analysis, respectively, whereas the expression levels of circRNA_0000285 and miR-654-3p were determined via reverse transcription-quantitative PCR analysis. In addition, the protein expression levels of the apoptosis-associated proteins, Bax and B-cell lymphoma 2 (Bcl-2), were detected via western blotting. The results of the dual-luciferase reporter and RIP assays demonstrated that miR-654-3p directly targeted circRNA_0000285. The expression levels of circRNA_0000285 and miR-654-3p in thyroid cancer cells (TPC-1 and FTC133) were upregulated and downregulated, respectively. Knockdown of circRNA_0000285 via small interfering (si)RNA inhibited circRNA_0000285 levels and increased miR-654-3p levels. In addition, miR-654-3p expression decreased following transfection with miR-654-3p inhibitor. Functional experiments demonstrated that circRNA_0000285-siRNA decreased thyroid cancer cell proliferation, promoted cell apoptosis, enhanced Bax expression and suppressed Bcl-2 expression. All these effects were reversed following transfection with miR-654-3p inhibitor. Taken together, the results of the present study suggest that circRNA_0000285 plays a vital role in thyroid cancer progression by regulating miR-654-3p, which provides a potential therapeutic target for this disease.
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Affiliation(s)
- Rongjun Gao
- Department of Thyroid Surgery, Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China
| | - Hui Ye
- Department of Thyroid Surgery, Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China
| | - Qingjun Gao
- Department of Thyroid Surgery, Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China
| | - Nanpeng Wang
- Department of Thyroid Surgery, Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China
| | - Yan Zhou
- Department of Thyroid Surgery, Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China
| | - Haisong Duan
- Department of Thyroid Surgery, Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China
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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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Adonin L, Drozdov A, Barlev NA. Sea Urchin as a Universal Model for Studies of Gene Networks. Front Genet 2021; 11:627259. [PMID: 33552139 PMCID: PMC7854572 DOI: 10.3389/fgene.2020.627259] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Accepted: 12/10/2020] [Indexed: 01/06/2023] Open
Abstract
The purple sea urchin Strongylocentrotus purpuratus has been used for over 150 years as a model organism in developmental biology. Using this model species, scientists have been able to describe, in detail, the mechanisms of cell cycle control and cell adhesion, fertilization, calcium signaling, cell differentiation, and death. Massive parallel sequencing of the sea urchin genome enabled the deciphering of the main components of gene regulatory networks during the activation of embryonic signaling pathways. This knowledge helped to extrapolate aberrations in somatic cells that may lead to diseases, including cancer in humans. Furthermore, since many, if not all, developmental signaling pathways were shown to be controlled by non-coding RNAs (ncRNAs), the sea urchin organism represents an attractive experimental model. In this review, we discuss the main discoveries in the genetics, genomics, and transcriptomics of sea urchins during embryogenesis with the main focus on the role of ncRNAs. This information may be useful for comparative studies between different organisms, and may help identify new regulatory networks controlled by ncRNAs.
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Affiliation(s)
- Leonid Adonin
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia.,Institute of Environmental and Agricultural Biology (X-BIO), Tyumen State University, Tyumen, Russia.,Orekhovich Institute of Biomedical Chemistry, Moscow, Russia
| | - Anatoliy Drozdov
- Zhirmunsky National Scientific Center of Marine Biology, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok, Russia
| | - Nickolai A Barlev
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia.,Orekhovich Institute of Biomedical Chemistry, Moscow, Russia.,Institute of Cytology, Russian Academy of Sciences, Saint-Petersburg, Russia
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11
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Riolo G, Cantara S, Marzocchi C, Ricci C. miRNA Targets: From Prediction Tools to Experimental Validation. Methods Protoc 2020; 4:1. [PMID: 33374478 PMCID: PMC7839038 DOI: 10.3390/mps4010001] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/17/2020] [Accepted: 12/22/2020] [Indexed: 12/12/2022] Open
Abstract
MicroRNAs (miRNAs) are post-transcriptional regulators of gene expression in both animals and plants. By pairing to microRNA responsive elements (mREs) on target mRNAs, miRNAs play gene-regulatory roles, producing remarkable changes in several physiological and pathological processes. Thus, the identification of miRNA-mRNA target interactions is fundamental for discovering the regulatory network governed by miRNAs. The best way to achieve this goal is usually by computational prediction followed by experimental validation of these miRNA-mRNA interactions. This review summarizes the key strategies for miRNA target identification. Several tools for computational analysis exist, each with different approaches to predict miRNA targets, and their number is constantly increasing. The major algorithms available for this aim, including Machine Learning methods, are discussed, to provide practical tips for familiarizing with their assumptions and understanding how to interpret the results. Then, all the experimental procedures for verifying the authenticity of the identified miRNA-mRNA target pairs are described, including High-Throughput technologies, in order to find the best approach for miRNA validation. For each strategy, strengths and weaknesses are discussed, to enable users to evaluate and select the right approach for their interests.
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Affiliation(s)
| | | | | | - Claudia Ricci
- Department of Medical, Surgical and Neurological Sciences, University of Siena, 53100 Siena, Italy; (G.R.); (S.C.); (C.M.)
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12
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Regulatory Mechanisms of Epigenetic miRNA Relationships in Human Cancer and Potential as Therapeutic Targets. Cancers (Basel) 2020; 12:cancers12102922. [PMID: 33050637 PMCID: PMC7600069 DOI: 10.3390/cancers12102922] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 10/03/2020] [Accepted: 10/07/2020] [Indexed: 12/15/2022] Open
Abstract
Simple Summary By the virtue of targeting multiple genes, a microRNA (miRNA) can infer variable consequences on tumorigenesis by appearing as both a tumour suppressor and oncogene. miRNAs can regulate gene expression by modulating genome-wide epigenetic status of genes that are involved in various cancers. These miRNAs perform direct inhibition of key mediators of the epigenetic machinery, such as DNA methyltransferases (DNMTs) and histone deacetylases (HDACs) genes. Along with miRNAs gene expression, similar to other protein-coding genes, miRNAs are also controlled by epigenetic mechanisms. Overall, this reciprocal interaction between the miRNAs and the epigenetic architecture is significantly implicated in the aberrant expression of miRNAs detected in various human cancers. Comprehensive knowledge of the miRNA-epigenetic dynamics in cancer is essential for the discovery of novel anticancer therapeutics. Abstract Initiation and progression of cancer are under both genetic and epigenetic regulation. Epigenetic modifications including alterations in DNA methylation, RNA and histone modifications can lead to microRNA (miRNA) gene dysregulation and malignant cellular transformation and are hereditary and reversible. miRNAs are small non-coding RNAs which regulate the expression of specific target genes through degradation or inhibition of translation of the target mRNA. miRNAs can target epigenetic modifier enzymes involved in epigenetic modulation, establishing a trilateral regulatory “epi–miR–epi” feedback circuit. The intricate association between miRNAs and the epigenetic architecture is an important feature through which to monitor gene expression profiles in cancer. This review summarises the involvement of epigenetically regulated miRNAs and miRNA-mediated epigenetic modulations in various cancers. In addition, the application of bioinformatics tools to study these networks and the use of therapeutic miRNAs for the treatment of cancer are also reviewed. A comprehensive interpretation of these mechanisms and the interwoven bond between miRNAs and epigenetics is crucial for understanding how the human epigenome is maintained, how aberrant miRNA expression can contribute to tumorigenesis and how knowledge of these factors can be translated into diagnostic and therapeutic tool development.
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Maucher D, Schmidt B, Kuhlmann K, Schumann J. Polyunsaturated Fatty Acids of Both the Omega-3 and the Omega-6 Family Abrogate the Cytokine-Induced Upregulation of miR-29a-3p by Endothelial Cells. Molecules 2020; 25:molecules25194466. [PMID: 33003296 PMCID: PMC7583866 DOI: 10.3390/molecules25194466] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 09/17/2020] [Accepted: 09/27/2020] [Indexed: 11/16/2022] Open
Abstract
Cellular processes fundamentally depend on protein expression control. At this, protein expression is regulated on the transcriptional and the post-transcriptional level. PUFAs are already known to affect gene transcription. The present study was conducted to answer the question whether PUFAs are also able to impact on the miRNA-mediated post-transcriptional fine-tuning of mRNA copy numbers. To this end, cellular miRNA profiles were screened by means of next-generation sequencing and NanoString analysis to compare PUFA-enriched to unsupplemented endothelial cells exposed to an inflammatory milieu. Validation took place by droplet digital PCR, allowing for an absolute quantification of RNA copy numbers. The analyses revealed that the stimulation-induced upregulation of miR-29a-3p is blocked by PUFA enrichment of endothelial cells. What is more, mRNA copy numbers of miR-29a-3p targets, namely the coagulation factors PAI-1, TF, and vWF, as well as the proinflammatory cytokines IL-1β, IL-6, and IL-8, were reduced in PUFA-enriched endothelial cells compared to unsupplemented cells, counteracting the stimulatory effect of an inflammatory environment. These data hint toward a new mechanism of action by which PUFAs modulate the functionality of endothelial cells. Apparently, the inflammation-modulating properties of PUFAs are also mediated at the post-transcriptional level.
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Affiliation(s)
| | | | | | - Julia Schumann
- Correspondence: ; Tel.: +49-345-5571776; Fax: +49-345-5571781
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14
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Placental miRNAs in feto-maternal communication mediated by extracellular vesicles. Placenta 2020; 102:27-33. [PMID: 33218575 DOI: 10.1016/j.placenta.2020.07.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 07/02/2020] [Accepted: 07/06/2020] [Indexed: 02/07/2023]
Abstract
A complex network composed of at least 1900 microRNA (miRNA) species orchestrates the development and function of the human placenta. These molecules regulate genes and pathways operating major functional processes in trophoblast cells such as proliferation, invasion, differentiation, and metabolism. Nevertheless, the cellular localization and role of most placental miRNAs remain to be determined. The existence of eutherian- (C14MC) and primate-specific miRNA clusters (C19MC), together with human placenta-specific miRNAs, indicate the relevance of these molecules in evolution and diversification of the placenta, including the acquisition of its unique features in humans. They may be related also to diseases that are exclusively present in primates, such as preeclampsia. Changes in the miRNA expression profile have been reported in several placental pathologies. Which miRNAs are involved in the pathomechanism of these diseases or act to maintain placental homeostasis is uncertain. Placenta-derived miRNAs are packed into extracellular vesicles (EVs) and distributed through the maternal circulation to distant organs, where they contribute to adaptations required during pregnancy. Similarly, the placenta also receives molecular information from other tissues to adapt fetoplacental metabolic demands to the maternal energetic supply. These processes can be impaired in pathologic conditions. Therefore, the collection of circulating placental miRNAs constitutes potentially a minimally-invasive approach to assess the fetoplacental status and to diagnose pregnancy diseases. Future therapies may include manipulation of miRNA levels for prevention and treatment of placental complications to protect maternal health and fetal development.
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15
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Tan BWQ, Sim WL, Cheong JK, Kuan WS, Tran T, Lim HF. MicroRNAs in chronic airway diseases: Clinical correlation and translational applications. Pharmacol Res 2020; 160:105045. [PMID: 32590100 DOI: 10.1016/j.phrs.2020.105045] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 06/18/2020] [Accepted: 06/19/2020] [Indexed: 12/19/2022]
Abstract
MicroRNAs (miRNAs) are short single-stranded RNAs that have pivotal roles in disease pathophysiology through transcriptional and translational modulation of important genes. It has been implicated in the development of many diseases, such as stroke, cardiovascular conditions, cancers and inflammatory airway diseases. There is recent evidence that miRNAs play important roles in the pathogenesis of asthma and chronic obstructive pulmonary disease (COPD), and could help to distinguish between T2-low (non-eosinophilic, steroid-insensitive) versus T2-high (eosinophilic, steroid-sensitive) disease endotypes. As these are the two most prevalent chronic respiratory diseases globally, with rising disease burden, miRNA research might lead to the development of new diagnostic and therapeutic targets. Research involving miRNAs in airway disease is challenging because: (i) asthma and COPD are heterogeneous inflammatory airway diseases; there are overlapping but distinct inter- and intra-disease differences in the immunological pathophysiology, (ii) there exists more than 2000 known miRNAs and a single miRNA can regulate multiple targets, (iii) differential effects of miRNAs could be present in different cellular subtypes and tissues, and (iv) dysregulated miRNA expression might be a direct consequence of an indirect effect of airway disease onset or progression. As miRNAs are actively secreted in fluids and remain relatively stable, they have the potential for biomarker development and therapeutic targets. In this review, we summarize the preclinical data on potential miRNA biomarkers that mediate different pathophysiological mechanisms in airway disease. We discuss the framework for biomarker development using miRNA and highlight the need for careful patient characterization and endotyping in the screening and validation cohorts, profiling both airway and blood samples to determine the biological fluids of choice in different disease states or severity, and adopting an untargeted approach. Collaboration between the various stakeholders - pharmaceutical companies, laboratory professionals and clinician-scientists is crucial to reduce the difficulties and cost required to bring miRNA research into the translational stage for airway diseases.
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Affiliation(s)
- Bryce W Q Tan
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Wei Liang Sim
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Jit Kong Cheong
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Win Sen Kuan
- Department of Emergency Medicine, National University Hospital, National University Health System, Singapore
| | - Thai Tran
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Hui Fang Lim
- Division of Respiratory & Critical Care Medicine, Department of Medicine, National University Hospital, National University Health System, Singapore; Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.
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16
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DiPaola JD, Yindee M, Plotnik JM. Investigating the use of sensory information to detect and track prey by the Sunda pangolin (Manis javanica) with conservation in mind. Sci Rep 2020; 10:9787. [PMID: 32555311 PMCID: PMC7300028 DOI: 10.1038/s41598-020-65898-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 05/11/2020] [Indexed: 11/16/2022] Open
Abstract
Pangolins are of conservation concern as one of the most heavily poached, yet least understood mammals. The Sunda pangolin (Manis javanica) in particular is a critically endangered species. Here, we investigate the behaviour of these pangolins, for the first time, using a battery of cognitive tasks based on a manipulation of available sensory information. In an object-choice task in which only one of two containers was baited with food, the pangolins were able to find the food with olfactory information alone (N = 2), but not with visual or acoustic information alone (N = 1). The single subject tested on all three domains was further tested on how he used smell to find food by providing him with an opportunity to find it from a controlled distance or by using scent trails as a guide. The results suggest that our subject may have the capacity to exploit scent trails left by prey which can be tracked to a final source, though we found no evidence to suggest that he had the ability to initiate hunts based on distant prey odors. Despite the small sample size, this is the first controlled experiment to investigate pangolin foraging behaviour and cognition, which may have implications for the future protection of pangolin habitat based on the location of prey species.
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Affiliation(s)
- Joshua D DiPaola
- Animal Behavior and Conservation Program, Department of Psychology, Hunter College, City University of New York, 695 Park Avenue, Room 611N, New York, NY, 10065, USA
| | - Marnoch Yindee
- Livestock and Wildlife Hospital, Faculty of Veterinary Science, Mahidol University, 199 Moo 9, Highway No. 323, Sai Yok, Kanchanaburi, 71150, Thailand.,Akkharatchakumari Veterinary College, Walailak University, 222 Thaiburi, Thasala, Nakhon Si Thammarat, 80161, Thailand
| | - Joshua M Plotnik
- Animal Behavior and Conservation Program, Department of Psychology, Hunter College, City University of New York, 695 Park Avenue, Room 611N, New York, NY, 10065, USA. .,Psychology Program, The Graduate Center, City University of New York, 365 Fifth Avenue, New York, NY, 10016, USA.
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17
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Fernandez GJ, Ferreira JH, Vechetti IJ, de Moraes LN, Cury SS, Freire PP, Gutiérrez J, Ferretti R, Dal-Pai-Silva M, Rogatto SR, Carvalho RF. MicroRNA-mRNA Co-sequencing Identifies Transcriptional and Post-transcriptional Regulatory Networks Underlying Muscle Wasting in Cancer Cachexia. Front Genet 2020; 11:541. [PMID: 32547603 PMCID: PMC7272700 DOI: 10.3389/fgene.2020.00541] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 05/05/2020] [Indexed: 12/23/2022] Open
Abstract
Cancer cachexia is a metabolic syndrome with alterations in gene regulatory networks that consequently lead to skeletal muscle wasting. Integrating microRNAs-mRNAs omics profiles offers an opportunity to understand transcriptional and post-transcriptional regulatory networks underlying muscle wasting. Here, we used RNA sequencing to simultaneously integrate and explore microRNAs and mRNAs expression profiles in the tibialis anterior (TA) muscles of the Lewis Lung Carcinoma (LLC) model of cancer cachexia. We found 1,008 mRNAs and 18 microRNAs differentially expressed in cachectic mice compared with controls. Although our transcriptomic analysis demonstrated a high heterogeneity in mRNA profiles of cachectic mice, we identified a reduced number of differentially expressed genes that were uniformly regulated within cachectic muscles. This set of uniformly regulated genes is associated with the extracellular matrix (ECM), proteolysis, and inflammatory response. We also used transcriptomic data to perform enrichment analysis of transcriptional factor binding sites in promoter sequences, which revealed activation of the atrophy-related transcription factors NF-κB, Stat3, AP-1, and FoxO. Furthermore, the integration of mRNA and microRNA expression profiles identified post-transcriptional regulation by microRNAs of genes involved in ECM organization, cell migration, transcription factors binding, ion transport, and the FoxO signaling pathway. Our integrative analysis of microRNA-mRNA co-profiles comprehensively characterized regulatory relationships of molecular pathways and revealed microRNAs targeting ECM-associated genes in cancer cachexia.
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Affiliation(s)
- Geysson Javier Fernandez
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University, Botucatu, Brazil.,Faculty of Medicine, University of Antioquia, Medellín, Colombia
| | - Juarez Henrique Ferreira
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University, Botucatu, Brazil
| | - Ivan José Vechetti
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University, Botucatu, Brazil
| | - Leonardo Nazario de Moraes
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University, Botucatu, Brazil
| | - Sarah Santiloni Cury
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University, Botucatu, Brazil
| | - Paula Paccielli Freire
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University, Botucatu, Brazil
| | - Jayson Gutiérrez
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Renato Ferretti
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University, Botucatu, Brazil
| | - Maeli Dal-Pai-Silva
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University, Botucatu, Brazil
| | - Silvia Regina Rogatto
- Department of Clinical Genetics, University Hospital of Southern Denmark, Vejle, Institute of Regional Health Research, University of Southern Denmark, Odense, Denmark
| | - Robson Francisco Carvalho
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University, Botucatu, Brazil
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18
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Circular RNA hsa_circ_0000467 Promotes the Development of Gastric Cancer by Competitively Binding to MicroRNA miR-326-3p. BIOMED RESEARCH INTERNATIONAL 2020; 2020:4030826. [PMID: 32090087 PMCID: PMC7026707 DOI: 10.1155/2020/4030826] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 12/14/2019] [Accepted: 01/02/2020] [Indexed: 12/13/2022]
Abstract
Circular RNAs are a class of endogenous noncoding RNAs that play an important role in gene regulation. These RNAs are involved in the development and progression of various cancers, but their roles in gastric cancer have not yet been thoroughly elucidated. This study showed that hsa_circ_0000467 expression was higher in gastric cancer tissues than in corresponding adjacent tissues (P < 0.050) and that hsa_circ_0000467 expression levels were correlated with gastric cancer histological grade (P < 0.050). In addition, hsa_circ_0000467 was remarkably upregulated in gastric cancer cell lines (P < 0.001). Cell function experiments indicated that hsa_circ_0000467 downregulation decreased the proliferation and invasion ability of BGC-823 and SGC-7901 cells and the number of cells entering the G2/M phase. A direct binding interaction was detected between hsa_circ_0000467 and miR-326-3p by dual-luciferase reporter assays. In addition, the results showed that inhibition of miR-326-3p reversed the decreases in the proliferation and invasion of BGC-823 and SGC-7901 cells caused by hsa_circ_0000647 downregulation. Inhibition of miR-326-3p also decreased the number of cells entering the G2/M phase and the expression of cyclin D1. In conclusion, hsa_circ_0000467 plays a regulatory role in the development and progression of gastric cancer by regulating miR-326-3p, and this circRNA may be a potential diagnostic marker and therapeutic target of gastric cancer.
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19
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Dutta RK, Chinnapaiyan S, Unwalla H. Aberrant MicroRNAomics in Pulmonary Complications: Implications in Lung Health and Diseases. MOLECULAR THERAPY. NUCLEIC ACIDS 2019; 18:413-431. [PMID: 31655261 PMCID: PMC6831837 DOI: 10.1016/j.omtn.2019.09.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Revised: 09/09/2019] [Accepted: 09/11/2019] [Indexed: 02/07/2023]
Abstract
Over the last few decades, evolutionarily conserved molecular networks have emerged as important regulators in the expression and function of eukaryotic genomes. Recently, miRNAs (miRNAs), a large family of small, non-coding regulatory RNAs were identified in these networks as regulators of endogenous genes by exerting post-transcriptional gene regulation activity in a broad range of eukaryotic species. Dysregulation of miRNA expression correlates with aberrant gene expression and can play an essential role in human health and disease. In the context of the lung, miRNAs have been implicated in organogenesis programming, such as proliferation, differentiation, and morphogenesis. Gain- or loss-of-function studies revealed their pivotal roles as regulators of disease development, potential therapeutic candidates/targets, and clinical biomarkers. An altered microRNAome has been attributed to several pulmonary diseases, such as asthma, chronic pulmonary obstructive disease, cystic fibrosis, lung cancer, and idiopathic pulmonary fibrosis. Considering the relevant roles and functions of miRNAs under physiological and pathological conditions, they may lead to the invention of new diagnostic and therapeutic tools. This review will focus on recent advances in understanding the role of miRNAs in lung development, lung health, and diseases, while also exploring the progress and prospects of their application as therapeutic leads or as biomarkers.
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Affiliation(s)
- Rajib Kumar Dutta
- Department of Immunology and Nano-medicine, Institute of Neuroimmune Pharmacology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA
| | - Srinivasan Chinnapaiyan
- Department of Immunology and Nano-medicine, Institute of Neuroimmune Pharmacology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA
| | - Hoshang Unwalla
- Department of Immunology and Nano-medicine, Institute of Neuroimmune Pharmacology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA.
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20
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Hu C, Liang X, Fang S, Xu L, Gong M, Wang Y, Bi Y, Hong S, He Y. ATRA induces the differentiation of hepatic progenitor cells by upregulating microRNA-200a. In Vitro Cell Dev Biol Anim 2019; 55:713-722. [PMID: 31515718 DOI: 10.1007/s11626-019-00390-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Accepted: 07/21/2019] [Indexed: 02/07/2023]
Abstract
Hepatic progenitor cells (HPCs) are potential seed cells for hepatocyte transplantation treatment of liver diseases. ATRA can induce the differentiation and mature function of hepatic progenitor cells, but the mechanism is still poorly understood. Here, by using microRNA array to analyze the expression profiles of microRNA (miR), we found that miR-200 family molecules in HPCs were upregulated after ATRA treatment, especially miR-200a-3p, 200c-3p, and 141-3p. ATRA induction could downregulate the expression of hepatic stem markers Oct4 and AFP, and improve the expression of hepatic markers ALB, CK18, and TAT, and the activity of ALB-GLuc, as well as indocyanine green uptake and glycogen storage function of HPCs. These above effects of ATRA on HPC differentiation were almost inhibited by blocking of miR-200a-3p, but not miR-200c-3p and 141-3p using antagomir. Cell autophagy is associated with ATRA regulation in HPCs, compared with control group, the expression of LC3 and Beclin1 increased in ATRA-treated HPCs, and orange and red fluorescent spot, which represents autophagy flow, also enhanced after ATRA treatment. However, ATRA-induced cell autophagy level was inhibited in antagomir-200a-3p+ATRA-treated cells. Therefore, the present study indicates that antagomir-200a-3p is related to ATRA-induced hepatic differentiation of HPCs through regulating cell autophagy, supporting the possible use of ATRA as a key inducer in HPC-based therapy of liver diseases.
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Affiliation(s)
- Chaoqun Hu
- Stem Cell Biology and Therapy Laboratory, Department of Pediatric Surgery, Ministry of Education Key Laboratory of Child Development and Disorders, The Children's Hospital of Chongqing Medical University, Building 5, Room 501, 136 Zhongshan Er Road, Chongqing, 400014, People's Republic of China
| | - Xiaohua Liang
- Stem Cell Biology and Therapy Laboratory, Department of Pediatric Surgery, Ministry of Education Key Laboratory of Child Development and Disorders, The Children's Hospital of Chongqing Medical University, Building 5, Room 501, 136 Zhongshan Er Road, Chongqing, 400014, People's Republic of China
| | - Shuyu Fang
- Stem Cell Biology and Therapy Laboratory, Department of Pediatric Surgery, Ministry of Education Key Laboratory of Child Development and Disorders, The Children's Hospital of Chongqing Medical University, Building 5, Room 501, 136 Zhongshan Er Road, Chongqing, 400014, People's Republic of China
| | - Lei Xu
- Department of Microbiology, Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Mengjia Gong
- Stem Cell Biology and Therapy Laboratory, Department of Pediatric Surgery, Ministry of Education Key Laboratory of Child Development and Disorders, The Children's Hospital of Chongqing Medical University, Building 5, Room 501, 136 Zhongshan Er Road, Chongqing, 400014, People's Republic of China
| | - Yi Wang
- Stem Cell Biology and Therapy Laboratory, Department of Pediatric Surgery, Ministry of Education Key Laboratory of Child Development and Disorders, The Children's Hospital of Chongqing Medical University, Building 5, Room 501, 136 Zhongshan Er Road, Chongqing, 400014, People's Republic of China
| | - Yang Bi
- Stem Cell Biology and Therapy Laboratory, Department of Pediatric Surgery, Ministry of Education Key Laboratory of Child Development and Disorders, The Children's Hospital of Chongqing Medical University, Building 5, Room 501, 136 Zhongshan Er Road, Chongqing, 400014, People's Republic of China
| | - Siqi Hong
- Stem Cell Biology and Therapy Laboratory, Department of Pediatric Surgery, Ministry of Education Key Laboratory of Child Development and Disorders, The Children's Hospital of Chongqing Medical University, Building 5, Room 501, 136 Zhongshan Er Road, Chongqing, 400014, People's Republic of China.
| | - Yun He
- Stem Cell Biology and Therapy Laboratory, Department of Pediatric Surgery, Ministry of Education Key Laboratory of Child Development and Disorders, The Children's Hospital of Chongqing Medical University, Building 5, Room 501, 136 Zhongshan Er Road, Chongqing, 400014, People's Republic of China.
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21
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Neller KCM, Klenov A, Hudak KA. Prediction and Characterization of miRNA/Target Pairs in Non-Model Plants Using RNA-seq. ACTA ACUST UNITED AC 2019; 4:e20090. [PMID: 31083771 PMCID: PMC9285518 DOI: 10.1002/cppb.20090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Plant microRNAs (miRNAs) are ∼20- to 24-nucleotide small RNAs that post-transcriptionally regulate gene expression of mRNA targets. Here, we present a workflow to characterize the miRNA transcriptome of a non-model plant, focusing on miRNAs and targets that are differentially expressed under one experimental treatment. We cover RNA-seq experimental design to create paired small RNA and mRNA libraries and perform quality control of raw data, de novo mRNA transcriptome assembly and annotation, miRNA prediction, differential expression, target identification, and functional enrichment analysis. Additionally, we include validation of differential expression and miRNA-induced target cleavage using qRT-PCR and modified RNA ligase-mediated 5' rapid amplification of cDNA ends, respectively. Our procedure relies on freely available software and web resources. It is intended for users that lack programming skills but can navigate a command-line interface. To enable an understanding of formatting requirements and anticipated results, we provide sample RNA-seq data and key input/output files for each stage. © 2019 The Authors. This is an open access article under the terms of the Creative Commons Attribution-NonCommercial License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes.
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Affiliation(s)
- Kira C M Neller
- Department of Biology, York University, Toronto, Ontario, Canada
| | - Alexander Klenov
- Department of Biology, York University, Toronto, Ontario, Canada
| | - Katalin A Hudak
- Department of Biology, York University, Toronto, Ontario, Canada
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22
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Zhu H, Xiao X, Chai Y, Li D, Yan X, Tang H. MiRNA-29a modulates visceral hyperalgesia in irritable bowel syndrome by targeting HTR7. Biochem Biophys Res Commun 2019; 511:671-678. [DOI: 10.1016/j.bbrc.2019.02.126] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 02/23/2019] [Indexed: 02/06/2023]
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23
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Shu S, Liu X, Xu M, Gao X, Chen S, Zhang L, Li R. MicroRNA-320a acts as a tumor suppressor in endometrial carcinoma by targeting IGF-1R. Int J Mol Med 2019; 43:1505-1512. [PMID: 30628637 DOI: 10.3892/ijmm.2019.4051] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 12/27/2018] [Indexed: 11/06/2022] Open
Abstract
Dysregulation of microRNAs (miRs) is implicated in the carcinogenesis of various types of malignant tumor by manipulating cell growth and apoptosis. Abnormal expression of miR‑320a is involved in tumorigenesis of many types of cancer. The potential association of miR‑320a and the possible regulatory mechanisms in endometrial carcinoma is rarely elucidated. In the present study, it was demonstrated that miR‑320a expression was decreased in endometrial carcinoma tissues and cell lines. The present results also indicated that overexpression of miR‑320a suppressed cell proliferation through inducing G2/M phrase arrest and apoptosis. Insulin‑like growth factor receptror‑1 (IGF‑1R) was verified to be the potential target of miR‑320a by computational analysis and luciferase reporter assays. In addition, overexpression of miR‑320a reduced endogenous IGF‑1R expression in cells. Furthermore, it was demonstrated that upregulation of miR‑320a inhibited phosphorylated (p)‑protein kinase B and p‑mechanistic target of rapamycin activation and promoted B cell lymphoma‑2‑associated death promoter expression. Reintroduction of IGF‑1R into miR‑320a‑overexpressed cells antagonized the impact of miR‑320a on its downstream protein, which demonstrated that the tumor suppressive role of miR‑320a in endometrial carcinoma is exerted by the signal pathway mediated by IGF‑1R. It was therefore concluded that miR‑320a served an anti‑tumor role on endometrial carcinoma through the regulation of IGF‑1R, and miR‑320a may be used as the target for the gene therapy of endometrial carcinoma.
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Affiliation(s)
- Shanrong Shu
- Department of Gynecology and Obstetrics, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong 510630, P.R. China
| | - Xiaoping Liu
- Department of Hematology, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou, Guangdong 510630, P.R. China
| | - Ming Xu
- Department of Medical Ultrasound, Institute of Diagnostic and Interventional Ultrasound, The First Affiliated Hospital of Sun Yat‑Sen University, Guangzhou, Guangdong 510080, P.R. China
| | - Xuesong Gao
- Department of Gynecology and Obstetrics, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong 510630, P.R. China
| | - Shu Chen
- Department of Gynecology and Obstetrics, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong 510630, P.R. China
| | - Lai Zhang
- Department of Clinical Medicine, Medical College of Jinan University, Guangzhou, Guangdong 510630, P.R. China
| | - Ruiman Li
- Department of Gynecology and Obstetrics, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong 510630, P.R. China
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Zhou Y, Xia Z, Cheng Z, Xu G, Yang X, Liu S, Zhu Y. Inducible microRNA-590-5p inhibits host antiviral response by targeting the soluble interleukin-6 (IL6) receptor. J Biol Chem 2018; 293:18168-18179. [PMID: 30291142 DOI: 10.1074/jbc.ra118.005057] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 09/21/2018] [Indexed: 01/09/2023] Open
Abstract
MicroRNA (miR)-590-5p has been identified as an important regulator of some signaling pathways such as cell proliferation and tumorigenesis. However, little is known about its role during viral infection. Here, we report that miR-590-5p was significantly induced by various viruses and effectively potentiated virus replication in different viral infection systems. Furthermore, miR-590-5p substantially attenuated the virus-induced expression of type I and type III interferons (IFNs) and inflammatory cytokines, resulting in impaired downstream antiviral signaling. Interleukin-6 receptor (IL6R) was identified as a target of miR-590-5p. Interestingly, the role of miR-590-5p in virus-triggered signaling was abolished in IL6R knockout cells, and this could be rescued by restoring the expression of the soluble IL6R (sIL6R) but not the membrane-bound IL6R (mIL6R), suggesting that sIL6R is indispensable for miR-590-5p in modulating the host antiviral response. Furthermore, miR-590-5p down-regulated endogenous sIL6R and mIL6R expression through a translational repression mechanism. These findings thus uncover a previously uncharacterized role and the underlying mechanism of miR-590-5p in the innate immune response to viral infection.
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Affiliation(s)
- Yaqin Zhou
- From the State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China
| | - Zhangchuan Xia
- From the State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China
| | - Zhikui Cheng
- From the State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China
| | - Gang Xu
- From the State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China
| | - Xiaodan Yang
- From the State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China
| | - Shi Liu
- From the State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China
| | - Ying Zhu
- From the State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China.
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miR-214-Dependent Increase of PHLPP2 Levels Mediates the Impairment of Insulin-Stimulated Akt Activation in Mouse Aortic Endothelial Cells Exposed to Methylglyoxal. Int J Mol Sci 2018; 19:ijms19020522. [PMID: 29425121 PMCID: PMC5855744 DOI: 10.3390/ijms19020522] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 02/06/2018] [Accepted: 02/06/2018] [Indexed: 01/08/2023] Open
Abstract
Evidence has been provided linking microRNAs (miRNAs) and diabetic complications, by the regulation of molecular pathways, including insulin-signaling, involved in the pathophysiology of vascular dysfunction. Methylglyoxal (MGO) accumulates in diabetes and is associated with cardiovascular complications. This study aims to analyze the contribution of miRNAs in the MGO-induced damaging effect on insulin responsiveness in mouse aortic endothelial cells (MAECs). miRNA modulation was performed by transfection of specific miRNA mimics and inhibitors in MAECs, treated or not with MGO. miRNA-target protein levels were evaluated by Western blot. PH domain leucine-rich repeat protein phosphatase 2 (PHLPP2) regulation by miR-214 was tested by luciferase assays and by the use of a target protector specific for miR-214 on PHLPP2-3′UTR. This study reveals a 4-fold increase of PHLPP2 in MGO-treated MAECs. PHLPP2 levels inversely correlate with miR-214 modulation. Moreover, miR-214 overexpression is able to reduce PHLPP2 levels in MGO-treated MAECs. Interestingly, a direct regulation of PHLPP2 is proved to be dependent by miR-214. Finally, the inhibition of miR-214 impairs the insulin-dependent Akt activation, while its overexpression rescues the insulin effect on Akt activation in MGO-treated MAECs. In conclusion, this study shows that PHLPP2 is a target of miR-214 in MAECs, and identifies miR-214 downregulation as a contributing factor to MGO-induced endothelial insulin-resistance.
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Ma X, Shi W, Peng L, Qin X, Hui Y. MiR-96 enhances cellular proliferation and tumorigenicity of human cervical carcinoma cells through PTPN9. Saudi J Biol Sci 2018; 25:863-867. [PMID: 30108433 PMCID: PMC6087804 DOI: 10.1016/j.sjbs.2017.10.020] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 10/11/2017] [Accepted: 10/11/2017] [Indexed: 01/05/2023] Open
Abstract
Up to date, the cervical cancer remains to be one of the leading gynecological malignancies worldwide. MicroRNAs (miRNAs) play critical roles in the process of tumor initiation and progression. However, miR-96 has rarely been investigated in human cervical carcinoma. We aimed to investigate the biological function and underlying molecular mechanism of miR-96 in human cervical carcinoma. MiR-96 levels were determined by qRT-PCR. Protein tyrosine phosphatase, non-receptor type 9 (PTPN9) mRNA and protein levels were investigated by qRT-PCR and western blotting. The cellular proliferation in cervical cells was monitored by CyQuant assay. Soft agar assay was employed to determine the tumorigenicity. 3' UTR luciferase assay was used to validate the target gene of miR-96. SPSS was used to analyze statistical significance in different treatment. MiR-96 was dramatically upregulated in human cervical tumor tissues. Overexpression of miR-96 was found to significantly promote the cellular proliferation and tumorigenicity of cervical cells. Furthermore, we showed that PTPN9 was a direct target gene of miR-96 and had opposite effect to those of miR-96 on cervical cells. MiR-96 may promote the cellular proliferation and tumorigenicity of cervical cells by silencing PTPN9. Our study highlights an importantly regulatory role of miR-96 and suggests that an appropriate manipulation of miR-96 may be a new treatment of human cervical carcinoma in the future.
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Affiliation(s)
- Xiaoping Ma
- Department of Gynecology and Obstetrics, The Affiliated Liaocheng People's Hospital of Shandong University, Liaocheng 252000, Shandong Province, PR China
| | - Wentian Shi
- Department of Gynecology and Obstetrics, The Affiliated Liaocheng People's Hospital of Shandong University, Liaocheng 252000, Shandong Province, PR China
| | - Lina Peng
- Department of Gynecology and Obstetrics, The Affiliated Liaocheng People's Hospital of Shandong University, Liaocheng 252000, Shandong Province, PR China
| | - Xuying Qin
- Department of Gynecology and Obstetrics, The Affiliated Liaocheng People's Hospital of Shandong University, Liaocheng 252000, Shandong Province, PR China
| | - Yuzuo Hui
- Department of Neurosurgery, The Affiliated Liaocheng People's Hospital of Shandong University, Liaocheng 252000, Shandong Province, PR China
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Abstract
The advent of RNA interference (RNAi) technology has profoundly impacted molecular biology research and medicine but has also advanced the field of skin care. Both effector molecules of RNAi, short-interfering RNA molecules and microRNAs (miRNAs), have been explored for their relative impact and utility for treating a variety of skin conditions. These post-transcriptional RNA regulatory molecules down-modulate protein expression through targeting of the 3' untranslated regions of messenger RNAs, leading to their degradation or repression through sequestration. As researchers hunt for genetic linkages to skin diseases, miRNA regulators have emerged as key players in the biology of keratinocytes, fibroblasts, melanocytes, and other cells of the skin. Herein, we attempt to coalesce the current efforts to combat various skin disorders and diseases through the development of miRNA-based technologies.
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Affiliation(s)
- Paul Lawrence
- Biocogent, LLC, 25 Health Sciences Drive, Stony Brook, NY 11790 USA
| | - Joseph Ceccoli
- Biocogent, LLC, 25 Health Sciences Drive, Stony Brook, NY 11790 USA
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Ma C, Xu B, Husaiyin S, Wang L, Wusainahong K, Ma J, Zhu K, Niyazi M. MicroRNA-505 predicts prognosis and acts as tumor inhibitor in cervical carcinoma with inverse association with FZD4. Biomed Pharmacother 2017; 92:586-594. [DOI: 10.1016/j.biopha.2017.04.028] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 04/02/2017] [Accepted: 04/10/2017] [Indexed: 12/20/2022] Open
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Li H, Sheng Y, Zhang Y, Gao N, Deng X, Sheng X. MicroRNA-138 is a potential biomarker and tumor suppressor in human cervical carcinoma by reversely correlated with TCF3 gene. Gynecol Oncol 2017; 145:569-576. [DOI: 10.1016/j.ygyno.2017.01.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2016] [Revised: 01/16/2017] [Accepted: 01/17/2017] [Indexed: 11/16/2022]
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Gou Q, Wu K, Zhou JK, Xie Y, Liu L, Peng Y. Profiling and bioinformatic analysis of circular RNA expression regulated by c-Myc. Oncotarget 2017; 8:71587-71596. [PMID: 29069731 PMCID: PMC5641074 DOI: 10.18632/oncotarget.17788] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 03/26/2017] [Indexed: 02/05/2023] Open
Abstract
The c-Myc transcription factor is involved in cell proliferation, cell cycle and apoptosis by activating or repressing transcription of multiple genes. Circular RNAs (circRNAs) are widely expressed non-coding RNAs participating in the regulation of gene expression. Using a high-throughput microarray assay, we showed that Myc regulates the expression of certain circRNAs. A total of 309 up- and 252 down-regulated circRNAs were identified. Among them, randomly selected 8 circRNAs were confirmed by real-time PCR. Subsequently, Myc-binding sites were found to generally exist in the promoter regions of differentially expressed circRNAs. Based on miRNA sponge mechanism, we constructed circRNAs/miRNAs network regulated by Myc, suggesting that circRNAs may widely regulate protein expression through miRNA sponge mechanism. Lastly, we took advantage of Gene Ontology and KEGG analyses to point out that Myc-regulated circRNAs could impact cell proliferation through affecting Ras signaling pathway and pathways in cancer. Our study for the first time demonstrated that Myc transcription factor regulates the expression of circRNAs, adding a novel component of the Myc tumorigenic program and opening a window to investigate the function of certain circRNAs in tumorigenesis.
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Affiliation(s)
- Qiheng Gou
- Department of Thoracic Surgery and Lab of Non-Coding RNAs in Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China
| | - Ke Wu
- Department of Thoracic Surgery and Lab of Non-Coding RNAs in Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China
| | - Jian-Kang Zhou
- Department of Thoracic Surgery and Lab of Non-Coding RNAs in Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China
| | - Yuxin Xie
- Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Lunxu Liu
- Department of Thoracic Surgery and Lab of Non-Coding RNAs in Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China
| | - Yong Peng
- Department of Thoracic Surgery and Lab of Non-Coding RNAs in Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China
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Stenfeldt C, Arzt J, Smoliga G, LaRocco M, Gutkoska J, Lawrence P. Proof-of-concept study: profile of circulating microRNAs in Bovine serum harvested during acute and persistent FMDV infection. Virol J 2017; 14:71. [PMID: 28388926 PMCID: PMC5384155 DOI: 10.1186/s12985-017-0743-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2017] [Accepted: 03/29/2017] [Indexed: 02/07/2023] Open
Abstract
Background Changes in the levels of circulating microRNAs (miRNAs) in the serum of humans and animals have been detected as a result of infection with a variety of viruses. However, to date, such a miRNA profiling study has not been conducted for foot-and-mouth disease virus (FMDV) infection. Methods The relative abundance of 169 miRNAs was measured in bovine serum collected at three different phases of FMDV infection in a proof-of-concept study using miRNA PCR array plates. Results Alterations in specific miRNA levels were detected in serum during acute, persistent, and convalescent phases of FMDV infection. Subclinical FMDV persistence produced a circulating miRNA profile distinct from cattle that had cleared infection. bta-miR-17-5p was highest expressed during acute infection, whereas bta-miR-31 was the highest during FMDV persistence. Interestingly, miR-1281was significantly down-regulated during both acute and persistent infection. Cattle that cleared infection resembled the baseline profile, adding support to applying serum miRNA profiling for identification of sub-clinically infected FMDV carriers. Significantly regulated miRNAs during acute or persistent infection were associated with cellular proliferation, apoptosis, modulation of the immune response, and lipid metabolism. Conclusions These findings suggest a role for non-coding regulatory RNAs in FMDV infection of cattle. Future studies will delineate the individual contributions of the reported miRNAs to FMDV replication, determine if this miRNA signature is applicable across all FMDV serotypes, and may facilitate development of novel diagnostic applications. Electronic supplementary material The online version of this article (doi:10.1186/s12985-017-0743-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Carolina Stenfeldt
- Plum Island Animal Disease Center, USDA/ARS/NAA/FADRU, P.O. Box 848, Greenport, NY, 11944-0848, USA
| | - Jonathan Arzt
- Plum Island Animal Disease Center, USDA/ARS/NAA/FADRU, P.O. Box 848, Greenport, NY, 11944-0848, USA
| | - George Smoliga
- Plum Island Animal Disease Center, USDA/ARS/NAA/FADRU, P.O. Box 848, Greenport, NY, 11944-0848, USA
| | - Michael LaRocco
- Plum Island Animal Disease Center, USDA/ARS/NAA/FADRU, P.O. Box 848, Greenport, NY, 11944-0848, USA
| | - Joseph Gutkoska
- Plum Island Animal Disease Center, USDA/ARS/NAA/FADRU, P.O. Box 848, Greenport, NY, 11944-0848, USA
| | - Paul Lawrence
- Plum Island Animal Disease Center, USDA/ARS/NAA/FADRU, P.O. Box 848, Greenport, NY, 11944-0848, USA.
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Nguyen PNN, Huang CJ, Sugii S, Cheong SK, Choo KB. Selective activation of miRNAs of the primate-specific chromosome 19 miRNA cluster (C19MC) in cancer and stem cells and possible contribution to regulation of apoptosis. J Biomed Sci 2017; 24:20. [PMID: 28270145 PMCID: PMC5341377 DOI: 10.1186/s12929-017-0326-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 02/22/2017] [Indexed: 12/16/2022] Open
Abstract
Background The human chromosome 19 miRNA cluster (C19MC) of 43 genes is a primate-specific miRNA cluster that may have biological significance in the genetic complexity of the primate. Despite previous reports on individual C19MC miRNA expression in cancer and stem cells, systematic studies on C19MC miRNA expression and biological functions are lacking. Results Cluster-wide C19MC miRNA expression profiling by microarray analysis showed wholesome C19MC activation in embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs). However, in multipotent adipose-derived mesenchymal stem cells (MSCs) and a unipotent human white pre-adipocyte cell line, only selected C19MC miRNAs were expressed. MiRNA copy number analysis also showed selective C19MC expression in cancer cells with expression patterns highly similar to those in MSCs, suggesting similar miRNA regulatory mechanisms in these cells. Selective miRNA expression also suggests complex transcriptional mechanism(s) regulating C19MC expression under specific cellular and pathological conditions. Bioinformatics analysis showed that sixteen of the C19MC miRNAs share the same “AAGUGC” seed sequence with members of the miR-302/-372 family, which are known cellular reprogramming factors. In particular, C19MC-AAGUGC-miRNAs with the nucleotides 2-7 canonical seed position as in miR-302/-372 miRNAs, may play similar roles as miR-302/-372 in induced pluripotency. A biased 3p-arm selection of the C19MC-AAGUGC-miRNAs was observed indicating that targets of the 3p species of these miRNAs may be biologically significant in regulating stemness. Furthermore, bioinformatics analysis of the putative targets of the C19MC-AAGUGC-miRNAs predicted significant involvement of signaling pathways in reprogramming, many of which contribute to promoting apoptosis by indirect activation of the pro-apoptotic proteins BAK/BAX via suppression of genes of the cell survival pathways, or by enhancing caspase-8 activation through targeting inhibitors of TRAIL-inducing apoptosis. Conclusions This work demonstrated selective C19MC expression in MSCs and cancer cells, and, through miRNA profiling and bioinformatics analysis, predicted C19MC modulation of apoptosis in induced pluripotency and tumorigenesis. Electronic supplementary material The online version of this article (doi:10.1186/s12929-017-0326-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Phan Nguyen Nhi Nguyen
- Centre for Stem Cell Research, Universiti Tunku Abdul Rahman, 43000, Kajang, Selangor, Malaysia.,Postgraduate Program, Universiti Tunku Abdul Rahman, 43000, Kajang, Selangor, Malaysia
| | - Chiu-Jung Huang
- Centre for Stem Cell Research, Universiti Tunku Abdul Rahman, 43000, Kajang, Selangor, Malaysia.,Department of Animal Science & Graduate Institute of Biotechnology, Chinese Culture University, Taipei, Taiwan
| | - Shigeki Sugii
- Singapore BioImaging Consortium, A*Star, Singapore, Singapore.,Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Soon Keng Cheong
- Centre for Stem Cell Research, Universiti Tunku Abdul Rahman, 43000, Kajang, Selangor, Malaysia.,Department of Preclinical Sciences, Faculty of Medicine and Health Sciences, Universiti Tunku Abdul Rahman, 43000, Kajang, Selangor, Malaysia
| | - Kong Bung Choo
- Centre for Stem Cell Research, Universiti Tunku Abdul Rahman, 43000, Kajang, Selangor, Malaysia. .,Department of Preclinical Sciences, Faculty of Medicine and Health Sciences, Center for Stem Cell Research, Universiti Tunku Abdul Rahman, Sungai Long campus, Bandar Sungai Long, Cheras, 43000, Kajang, Selangor Darul Ehsan, Malaysia.
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Endogenous microRNA-424 predicts clinical outcome and its inhibition acts as cancer suppressor in human non-small cell lung cancer. Biomed Pharmacother 2017; 89:208-214. [PMID: 28231541 DOI: 10.1016/j.biopha.2017.01.163] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 01/27/2017] [Accepted: 01/29/2017] [Indexed: 01/15/2023] Open
Abstract
PURPOSE We examined the expression, clinical correlation and functional mechanisms of endogenous microRNA-424 (miR-424) in human non-small cell lung cancer (NSCLC). METHODS Expression pattern of endogenous miR-424 was examined by qRT-PCR in clinical samples obtained from 233 NSCLC patients. Correlations between differential miR-424 expression level (low vs. high) and NSCLC patients' clinicopathological parameters or survival were statistically examined. In in vitro NSCLC H596 and SW900 cells, miR-424 was either upregulated or downregulation by lentiviral transduction. Their effects on cancer cell viability, proliferation, and cell-cycle transition were also examined. RESULTS MiR-424 expression was not different between NSCLC tumors and healthy lung tissues. However, it is much upregulated in NSCLC tumors associated with patients at advanced clinical stages. Statistical analyses demonstrated that high endogenous miR-424 expression in NSCLC tumors was significantly correlated with patients' advanced clinical stages, aggressive tumor metastasis, and short survival. In addition, Cox regression model predicted that endogenous miR-424 might be an independent prognostic marker in NSCLC. In in vitro NSCLC cell lines, miR-424 downregulation had a significant suppressing effect on cancer proliferation and G1 to S phase cell-cycle transition. On the other hand, miR-424 upregulation had no effect on NSCLC in vitro. CONCLUSION High endogenous miR-424 expression in tumors may predict poor prognosis of patients with NSCLC. Inhibiting endogenous miR-424 may also serve an effective cancer suppressor in NSCLC.
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Gutkoska J, LaRocco M, Ramirez-Medina E, de Los Santos T, Lawrence P. Host microRNA-203a Is antagonistic to the progression of foot-and-mouth disease virus infection. Virology 2017; 504:52-62. [PMID: 28152384 DOI: 10.1016/j.virol.2017.01.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 01/22/2017] [Accepted: 01/23/2017] [Indexed: 12/11/2022]
Abstract
Sam68 was previously shown to be a critical host factor for foot-and-mouth disease virus (FMDV) replication. MicroRNA (miR) miR-203a is reportedly a negative regulator of Sam68 expression both in vitro and in vivo. Here, transfection of miR-203a-3p and miR-203a-5p mimics separately and in combination in a porcine cell line followed by FMDV infection resulted in diminished viral protein synthesis and a 4 and 6log reduction in virus titers relative to negative controls, respectively. Unexpectedly, Sam68 expression was increased by miR-203a-5p transfection, but not miR-203a-3p. miR-203a-5p also down-regulated Survivin expression, which was predicted to play a role in FMDV infection. Moreover, miR-203a-5p but not miR-203a-3p affected a reduction in FMDV viral RNA. These effects were not replicated with a related Picornavirus, suggesting FMDV specificity. Importantly, miR-203a-3p and miR-203a-5p impaired FMDV infection across multiple FMDV serotypes. We concluded that miR-203a-3p and miR-203a-5p represent attractive potential naturally occurring bio-therapeutics against FMDV.
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Affiliation(s)
- Joseph Gutkoska
- Plum Island Animal Disease Center Foreign Animal Disease Research Unit (FADRU) Agricultural Research Service (ARS), United States Department of Agriculture (USDA), 40550 Route 25, Orient Point, NY 11957, United States
| | - Michael LaRocco
- Plum Island Animal Disease Center Foreign Animal Disease Research Unit (FADRU) Agricultural Research Service (ARS), United States Department of Agriculture (USDA), 40550 Route 25, Orient Point, NY 11957, United States
| | - Elizabeth Ramirez-Medina
- Plum Island Animal Disease Center Foreign Animal Disease Research Unit (FADRU) Agricultural Research Service (ARS), United States Department of Agriculture (USDA), 40550 Route 25, Orient Point, NY 11957, United States
| | - Teresa de Los Santos
- Plum Island Animal Disease Center Foreign Animal Disease Research Unit (FADRU) Agricultural Research Service (ARS), United States Department of Agriculture (USDA), 40550 Route 25, Orient Point, NY 11957, United States
| | - Paul Lawrence
- Plum Island Animal Disease Center Foreign Animal Disease Research Unit (FADRU) Agricultural Research Service (ARS), United States Department of Agriculture (USDA), 40550 Route 25, Orient Point, NY 11957, United States.
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Humphries B, Wang Z, Yang C. The role of microRNAs in metal carcinogen-induced cell malignant transformation and tumorigenesis. Food Chem Toxicol 2016; 98:58-65. [PMID: 26903202 PMCID: PMC4992468 DOI: 10.1016/j.fct.2016.02.012] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 02/13/2016] [Indexed: 02/07/2023]
Abstract
MicroRNAs (miRNAs), an important component of epigenetic mechanisms of carcinogenesis, have been shown to play crucial roles in cancer initiation, metastasis, prognosis and responses to drug treatment and may serve as biomarkers for early diagnosis of cancer and tools for cancer therapy. Metal carcinogens, such as arsenic, cadmium, hexavalent chromium and nickel, are well-established human carcinogens causing various cancers upon long term exposure. However, the mechanism of metal carcinogenesis has not been well understood, which limits our capability to effectively diagnose and treat human cancers resulting from chronic metal carcinogen exposure. Over recent years, the role of miRNAs in metal carcinogenesis has been actively explored and a growing body of evidence indicates the critical involvement of miRNAs in metal carcinogenesis. This review aims to discuss recent studies showing that miRNAs play important roles in metal carcinogen-induced cell malignant transformation and tumorigenesis. Some thoughts for future further studies in this field are also presented.
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Affiliation(s)
- Brock Humphries
- Department of Physiology, Michigan State University, East Lansing, MI 48824, USA; Cellular and Molecular Biology Graduate Program, Michigan State University, East Lansing, MI 48824, USA
| | - Zhishan Wang
- Department of Physiology, Michigan State University, East Lansing, MI 48824, USA
| | - Chengfeng Yang
- Department of Physiology, Michigan State University, East Lansing, MI 48824, USA; Cellular and Molecular Biology Graduate Program, Michigan State University, East Lansing, MI 48824, USA; Institute for Integrative Toxicology, Michigan State University, East Lansing, MI 48824, USA.
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36
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Yang H, Zhang L, An J, Zhang Q, Liu C, He B, Hao DJ. MicroRNA-Mediated Reprogramming of Somatic Cells into Neural Stem Cells or Neurons. Mol Neurobiol 2016; 54:1587-1600. [DOI: 10.1007/s12035-016-0115-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 09/09/2016] [Indexed: 12/21/2022]
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The microRNA-200 family: small molecules with novel roles in cancer development, progression and therapy. Oncotarget 2016; 6:6472-98. [PMID: 25762624 PMCID: PMC4466628 DOI: 10.18632/oncotarget.3052] [Citation(s) in RCA: 265] [Impact Index Per Article: 33.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 01/06/2015] [Indexed: 12/11/2022] Open
Abstract
MicroRNAs (miRNAs) are a large family of small non-coding RNAs that negatively regulate protein-coding gene expression post-transcriptionally via base pairing between the 5′ seed region of a miRNA and the 3′ untranslated region (3′UTR) of a messenger RNA (mRNA). Recent evidence has supported the critical role that miRNAs play in many diseases including cancer. The miR-200 family consisting of 5 members (miR-200a, -200b, -200c, -141, -429) is an emerging miRNA family that has been shown to play crucial roles in cancer initiation and metastasis, and potentially be important for the diagnosis and treatment of cancer. While miR-200s were found to be critically involved in the metastatic colonization to the lungs in mouse mammary xenograft tumor models, a large number of studies demonstrated their strong suppressive effects on cell transformation, cancer cell proliferation, migration, invasion, tumor growth and metastasis. This review aims to discuss research findings about the role of the miR-200 family in cancer initiation, each step of cancer metastatic cascade, cancer diagnosis and treatment. A comprehensive summary of currently validated miR-200 targets is also presented. It is concluded that miR-200 family may serve as novel targets for the therapy of multiple types of cancer.
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Ammonia-induced miRNA expression changes in cultured rat astrocytes. Sci Rep 2016; 6:18493. [PMID: 26755400 PMCID: PMC4709596 DOI: 10.1038/srep18493] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Accepted: 11/19/2015] [Indexed: 12/20/2022] Open
Abstract
Hepatic encephalopathy is a neuropsychiatric syndrome evolving from cerebral osmotic disturbances and oxidative/nitrosative stress. Ammonia, the main toxin of hepatic encephalopathy, triggers astrocyte senescence in an oxidative stress-dependent way. As miRNAs are critically involved in cell cycle regulation and their expression may be regulated by oxidative stress, we analysed, whether astrocyte senescence is a consequence of ammonia-induced miRNA expression changes. Using a combined miRNA and gene microarray approach, 43 miRNA species which were downregulated and 142 genes which were upregulated by NH4Cl (5 mmol/l, 48 h) in cultured rat astrocytes were found. Ammonia-induced miRNA and gene expression changes were validated by qPCR and 43 potential miRNA target genes, including HO-1, were identified by matching upregulated mRNA species with predicted targets of miRNA species downregulated by ammonia. Inhibition of HO-1 targeting miRNAs which were downregulated by NH4Cl strongly upregulated HO-1 mRNA and protein levels and inhibited astrocyte proliferation in a HO-1-dependent way. Preventing ammonia-induced upregulation of HO-1 by taurine (5 mmol/l) as well as blocking HO-1 activity by tin-protoporphyrine IX fully prevented ammonia-induced proliferation inhibition and senescence. The data suggest that ammonia induces astrocyte senescence through NADPH oxidase-dependent downregulation of HO-1 targeting miRNAs and concomitant upregulation of HO-1 at both mRNA and protein level.
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Davis GM, Haas MA, Pocock R. MicroRNAs: Not "Fine-Tuners" but Key Regulators of Neuronal Development and Function. Front Neurol 2015; 6:245. [PMID: 26635721 PMCID: PMC4656843 DOI: 10.3389/fneur.2015.00245] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 11/09/2015] [Indexed: 12/21/2022] Open
Abstract
MicroRNAs (miRNAs) are a class of short non-coding RNAs that operate as prominent post-transcriptional regulators of eukaryotic gene expression. miRNAs are abundantly expressed in the brain of most animals and exert diverse roles. The anatomical and functional complexity of the brain requires the precise coordination of multilayered gene regulatory networks. The flexibility, speed, and reversibility of miRNA function provide precise temporal and spatial gene regulatory capabilities that are crucial for the correct functioning of the brain. Studies have shown that the underlying molecular mechanisms controlled by miRNAs in the nervous systems of invertebrate and vertebrate models are remarkably conserved in humans. We endeavor to provide insight into the roles of miRNAs in the nervous systems of these model organisms and discuss how such information may be used to inform regarding diseases of the human brain.
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Affiliation(s)
- Gregory M. Davis
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Department of Anatomy and Developmental Biology, Monash University, Melbourne, VIC, Australia
| | - Matilda A. Haas
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Department of Anatomy and Developmental Biology, Monash University, Melbourne, VIC, Australia
| | - Roger Pocock
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Department of Anatomy and Developmental Biology, Monash University, Melbourne, VIC, Australia
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Jelbert SA, Taylor AH, Gray RD. Investigating animal cognition with the Aesop's Fable paradigm: Current understanding and future directions. Commun Integr Biol 2015; 8:e1035846. [PMID: 26478777 PMCID: PMC4594378 DOI: 10.1080/19420889.2015.1035846] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Revised: 03/25/2015] [Accepted: 03/26/2015] [Indexed: 11/16/2022] Open
Abstract
The Aesop's Fable paradigm – in which subjects drop stones into tubes of water to obtain floating out-of-reach rewards – has been used to assess causal understanding in rooks, crows, jays and human children. To date, the performance of corvids suggests that they can recognize the functional properties of a variety of objects including size, weight and solidity, and they seem to be more capable of learning from causal information than arbitrary information. However, 2 alternative explanations for their performance have yet to be ruled out. The perceptual-motor feedback hypothesis suggests that subjects may attend solely to the movement of the reward, repeating actions which bring the reward closer, while the object-bias hypothesis suggests that subjects could pass certain tasks by preferring to handle objects that resemble natural stones. Here we review our current understanding of performance on the Aesop's Fable tasks, and suggest that studies controlling for feedback and object preferences will help us determine exactly what animals understand about the cause and effect of water displacement.
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Affiliation(s)
- Sarah A Jelbert
- School of Psychology; University of Auckland ; Auckland, New Zealand
| | - Alex H Taylor
- School of Psychology; University of Auckland ; Auckland, New Zealand
| | - Russell D Gray
- School of Psychology; University of Auckland ; Auckland, New Zealand
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Khalaj M, Tavakkoli M, Stranahan AW, Park CY. Pathogenic microRNA's in myeloid malignancies. Front Genet 2014; 5:361. [PMID: 25477897 PMCID: PMC4237136 DOI: 10.3389/fgene.2014.00361] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 09/27/2014] [Indexed: 12/21/2022] Open
Abstract
Recent studies have significantly improved our understanding of the role microRNAs (miRNAs) play in regulating normal hematopoiesis. miRNAs are critical for maintaining hematopoietic stem cell function and the development of mature progeny. Thus, perhaps it is not surprising that miRNAs serve as oncogenes and tumor suppressors in hematologic malignancies arising from hematopoietic stem and progenitor cells, such as the myeloid disorders. A number of studies have extensively documented the widespread dysregulation of miRNA expression in human acute myeloid leukemia (AML), inspiring numerous explorations of the functional role of miRNAs in myeloid leukemogenesis. While these investigations have confirmed that a large number of miRNAs exhibit altered expression in AML, only a small fraction has been confirmed as functional mediators of AML development or maintenance. Herein, we summarize the miRNAs for which strong experimental evidence supports their functional roles in AML pathogenesis. We also discuss the implications of these studies on the development of miRNA-directed therapies in AML.
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Affiliation(s)
- Mona Khalaj
- Weill Graduate School of Medical Sciences, Cornell University NY, USA ; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center NY, USA
| | - Montreh Tavakkoli
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center NY, USA
| | - Alec W Stranahan
- Weill Graduate School of Medical Sciences, Cornell University NY, USA ; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center NY, USA
| | - Christopher Y Park
- Weill Graduate School of Medical Sciences, Cornell University NY, USA ; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center NY, USA ; Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center NY, USA
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Mechanisms of miRNA-Mediated Gene Regulation from Common Downregulation to mRNA-Specific Upregulation. Int J Genomics 2014; 2014:970607. [PMID: 25180174 PMCID: PMC4142390 DOI: 10.1155/2014/970607] [Citation(s) in RCA: 351] [Impact Index Per Article: 35.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Revised: 07/09/2014] [Accepted: 07/17/2014] [Indexed: 12/12/2022] Open
Abstract
Discovered in 1993, micoRNAs (miRNAs) are now recognized as one of the major regulatory gene families in eukaryotes. To date, 24521 microRNAs have been discovered and there are certainly more to come. It was primarily acknowledged that miRNAs result in gene expression repression at both the level of mRNA stability by conducting mRNA degradation and the level of translation (at initiation and after initiation) by inhibiting protein translation or degrading the polypeptides through binding complementarily to 3′UTR of the target mRNAs. Nevertheless, some studies revealed that miRNAs have the capability of activating gene expression directly or indirectly in respond to different cell types and conditions and in the presence of distinct cofactors. This reversibility in their posttranslational gene regulatory natures enables the bearing cells to rapidly response to different cell conditions and consequently block unnecessary energy wastage or maintain the cell state. This paper provides an overview of the current understandings of the miRNA characteristics including their genes and biogenesis, as well as their mediated downregulation. We also review up-to-date knowledge of miRNA-mediated gene upregulation through highlighting some notable examples and discuss the emerging concepts of their associations with other posttranscriptional gene regulation processes.
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