701
|
Bartoszewski R, Sikorski AF. Editorial focus: entering into the non-coding RNA era. Cell Mol Biol Lett 2018; 23:45. [PMID: 30250489 PMCID: PMC6145373 DOI: 10.1186/s11658-018-0111-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 09/12/2018] [Indexed: 12/11/2022] Open
Abstract
Recent developments in high-throughput genotyping technologies have revealed the existence of several new classes of RNA that do not encode proteins but serve other cellular roles. To date, these non-coding RNAs (ncRNAs) have been shown to modulate both gene expression and genome remodeling, thus contributing to the control of both normal and disease-related cellular processes. The attraction of this research topic can be seen in the increasing number of submissions on ncRNAs to molecular biology journals, including Cellular Molecular Biology Letters (CMBL). As researchers attempt to deepen the understanding of the role of ncRNAs in cell biology, it is worth discussing the broader importance of this research.
Collapse
Affiliation(s)
- Rafal Bartoszewski
- 1Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, Gdansk, Poland
| | - Aleksander F Sikorski
- 2Department of Cytobiochemistry, Faculty of Biotechnology, University of Wroclaw, Wroclaw, Poland
| |
Collapse
|
702
|
Li J, Sun H, Liu T, Kong J. MicroRNA-423 promotes proliferation, migration and invasion and induces chemoresistance of endometrial cancer cells. Exp Ther Med 2018; 16:4213-4224. [PMID: 30344696 DOI: 10.3892/etm.2018.6710] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 07/26/2018] [Indexed: 12/12/2022] Open
Abstract
Altered microRNA expression serves essential roles in tumorigenesis and progression in endometrial cancer. In the present study the effect of miR-423 on proliferation, chemosensitivity, migration and invasion of endometrial cancer cells was examined. A WST-1 assay was used to examine the proliferation of HEC-1B and Ishikawa endometrial cancer cells with either upregulation or downregulation of miR-423, with or without cisplatin treatment. The migration and invasion of HEC-1B and Ishikawa endometrial cancer cells were examined via Transwell migration and Matrigel invasion assays. Protein expression levels, including B cell lymphoma-2 (Bcl-2), Bcl-2 associated X protein, E- and N-cadherin, snail, vimentin, phosphatase and tensin homolog (PTEN) and protein kinase B (AKT) were examined by western blotting. A caspase-Glo3/7 assay was carried out to evaluate the effect of miR-423 on cisplatin-induced apoptosis in HEC-1B and Ishikawa endometrial cancer cells. Overexpression of miR-423 enhanced the proliferation, and increased migration and invasion in endometrial cancer cells. miR-423 also decreased the sensitivity of endometrial cancer cells following cisplatin treatment. miR-423 inhibited cisplatin-induced apoptosis in endometrial cancer cells by regulation of caspase 3/7 and Bcl-2 expression. Furthermore, the E-cadherin expression was significantly decreased, and the expression of N-cadherin, snail and Vimentin were increased in both HEC-1B cells and Ishikawa cells following overexpression of miR-423. Conversely, downregulation of miR-423 increased the expression of E-cadherin and decreased the expression of N-cadherin, snail and Vimentin. Further experiments demonstrated that the expression levels of PTEN and phosphorylated-AKT in HEC-1B and Ishikawa endometrial cancer cells was decreased and increased, respectively, following aberrant expression of miR-423. miR-423 displayed an important role in tumorigenesis and progression in endometrial cancer cells, and may therefore be used as a potential biomarker to predict chemotherapy response and prognosis in endometrial cancer.
Collapse
Affiliation(s)
- Jie Li
- Department of Geriatrics, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
| | - Huijie Sun
- Department of Geriatrics, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
| | - Ting Liu
- Department of Geriatrics, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
| | - Jian Kong
- Department of Geriatrics, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
| |
Collapse
|
703
|
Fadaka AO, Ojo BA, Adewale OB, Esho T, Pretorius A. Effect of dietary components on miRNA and colorectal carcinogenesis. Cancer Cell Int 2018; 18:130. [PMID: 30202241 PMCID: PMC6127951 DOI: 10.1186/s12935-018-0631-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 08/31/2018] [Indexed: 12/14/2022] Open
Abstract
Background Colorectal cancer (CRC) is one of the most common cancers diagnosed and among the commonest causes of cancer-related mortality globally. Despite the various available treatment options, millions of people still suffer from this illness and most of these treatment options have several limitations. Therefore, a less expensive, non-invasive or a treatment that requires the use of dietary products remains a focal point in this review. Main body Aberrant microRNA expression has been revealed to have a functional role in the initiation and progression of CRC. These has shown significant promise in the diagnosis and prognosis of CRC, owing to their unique expression profile associated with cancer types and malignancies. Moreover, microRNA therapeutics show a great promise in preclinical studies, and these encourage further development of their clinical use in CRC patients. Additionally, emerging studies show the chemo-preventive potential of dietary components in microRNA modulation using several CRC models. This review examines the dietary interplay between microRNAs and CRC incidence. Improving the understanding of the interactions between microRNAs and dietary components in the carcinogenesis of CRC will assist the study of CRC progression and finally, in developing personalized approaches for cancer prevention and therapy. Conclusion Although miRNA research is still at its infancy, it could serve as a promising predictive biomarkers and therapeutic targets for CRC. Given the ever-expanding number of miRNAs, understanding their functional aspects represents a promising option for further research.
Collapse
Affiliation(s)
- Adewale Oluwaseun Fadaka
- 1Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Cape Town, South Africa.,3Department of Biochemistry, Afe Babalola University, P.M.B. 5454, Ado-Ekiti, Ekiti State Nigeria
| | - Babajide A Ojo
- 2Department of Nutritional Science, Oklahoma State University, 301, Human Sciences, Stillwater, OK 74075 USA
| | - Olusola Bolaji Adewale
- 3Department of Biochemistry, Afe Babalola University, P.M.B. 5454, Ado-Ekiti, Ekiti State Nigeria
| | - Temitope Esho
- 4Institute of Biochemistry II, Medical Faculty, University of Cologne, Joseph-Stelzmann Str. 52, 50931 Cologne, Germany
| | - Ashley Pretorius
- Biotechnology Innovation Division, Aminotek PTY LTD, Suite 2C, Oude Westhof Village Square Bellville, 7530 South Africa
| |
Collapse
|
704
|
Reverse the down regulation of miR-92b-3p by hypoxia can suppress the proliferation of pulmonary artery smooth muscle cells by targeting USP28. Biochem Biophys Res Commun 2018; 503:3064-3077. [DOI: 10.1016/j.bbrc.2018.08.095] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Accepted: 08/13/2018] [Indexed: 11/22/2022]
|
705
|
Cabana-Domínguez J, Arenas C, Cormand B, Fernàndez-Castillo N. MiR-9, miR-153 and miR-124 are down-regulated by acute exposure to cocaine in a dopaminergic cell model and may contribute to cocaine dependence. Transl Psychiatry 2018; 8:173. [PMID: 30166527 PMCID: PMC6117282 DOI: 10.1038/s41398-018-0224-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 07/14/2018] [Indexed: 12/21/2022] Open
Abstract
Cocaine is one of the most used psychostimulant drugs worldwide. MicroRNAs are post-transcriptional regulators of gene expression that are highly expressed in brain, and several studies have shown that cocaine can alter their expression. In a previous study, we identified several protein-coding genes that are differentially expressed in a dopaminergic neuron-like model after an acute exposure to cocaine. Now, we used the prediction tool WebGestalt to identify miRNA molecules potentially involved in the regulation of these genes. Using the same cellular model, we found that seven of these miRNAs are down-regulated by cocaine: miR-124-3p, miR-124-5p, miR-137, miR-101-3p, miR-9-5p, miR-369-3p and miR-153-3p, the last three not previously related to cocaine. Furthermore, we found that three of the miRNA genes that are differentially expressed in our model (hsa-miR-9-1, hsa-miR-153-1 and hsa-miR-124-3) are nominally associated with cocaine dependence in a case-control study (2,085 cases and 4,293 controls). In summary, we highlighted novel miRNAs that may be involved in those cocaine-induced changes of gene expression that underlie addiction. Moreover, we identified genetic variants that contribute to cocaine dependence in three of these miRNA genes, supporting the idea that genes differentially expressed under cocaine may play an important role in the susceptibility to cocaine dependence.
Collapse
Affiliation(s)
- Judit Cabana-Domínguez
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Catalonia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Catalonia, Spain
- Institut de Recerca Sant Joan de Déu (IR-SJD), Esplugues de Llobregat, Catalonia, Spain
| | - Concepció Arenas
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Bru Cormand
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Catalonia, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain.
- Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Catalonia, Spain.
- Institut de Recerca Sant Joan de Déu (IR-SJD), Esplugues de Llobregat, Catalonia, Spain.
| | - Noèlia Fernàndez-Castillo
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Catalonia, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain.
- Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Catalonia, Spain.
- Institut de Recerca Sant Joan de Déu (IR-SJD), Esplugues de Llobregat, Catalonia, Spain.
| |
Collapse
|
706
|
von Brandenstein M, Bernhart SH, Pansky A, Richter C, Kohl T, Deckert M, Heidenreich A, Stadler PF, Montesinos-Rongen M, Fries JWU. Beyond the 3'UTR binding-microRNA-induced protein truncation via DNA binding. Oncotarget 2018; 9:32855-32867. [PMID: 30214689 PMCID: PMC6132356 DOI: 10.18632/oncotarget.26023] [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: 05/23/2018] [Accepted: 08/04/2018] [Indexed: 12/31/2022] Open
Abstract
Here, we present a miR mechanism which is active in the nucleus and is essential for the production of intron included, C-terminal truncated and biologically active proteins, like e.g. Vim3. We exemplified this mechanism by miRs, miR-15a and miR-498, which are overexpressed in clear cell renal carcinoma or oncocytoma. Both miRs directly interact with DNA in an intronic region, leading to transcriptional stop, and therefore repress the full length version of the pre-mRNA, resulting in intron included truncated proteins (Mxi-2 and Vim3). A computational survey shows that this miR:DNA interactions mechanism may be generally involved in regulating the human transcriptome, with putative interaction sites in intronic regions for over 1000 genes. In this work, an entirely new mechanism is revealed how miRs can repress full length protein translation, resulting in C-terminal truncated proteins.
Collapse
Affiliation(s)
| | - Stephan H Bernhart
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center of Bioinformatics, Leipzig University, Leipzig, Germany
| | - Andreas Pansky
- Department of Natural Sciences, University of Applied Sciences Bonn-Rhein-Sieg, Rheinbach, Germany
| | - Claudia Richter
- Institute of Pathology, University Hospital of Cologne, Cologne, Germany
| | - Tobias Kohl
- Department of Urology, University Hospital of Cologne, Cologne, Germany
| | - Martina Deckert
- Institute of Neuropathology, University Hospital of Cologne, Cologne, Germany
| | - Axel Heidenreich
- Department of Urology, University Hospital of Cologne, Cologne, Germany
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center of Bioinformatics, Leipzig University, Leipzig, Germany
| | | | - Jochen W U Fries
- Institute of Pathology, University Hospital of Cologne, Cologne, Germany
| |
Collapse
|
707
|
Karimi-Sales E, Jeddi S, Ebrahimi-Kalan A, Alipour MR. trans-Chalcone prevents insulin resistance and hepatic inflammation and also promotes hepatic cholesterol efflux in high-fat diet-fed rats: modulation of miR-34a-, miR-451-, and miR-33a-related pathways. Food Funct 2018; 9:4292-4298. [PMID: 30039136 DOI: 10.1039/c8fo00923f] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
Abstract
Insulin resistance and inflammation are strongly linked to non-alcoholic fatty liver disease (NAFLD) as a feature of the metabolic syndrome. Furthermore, the role of dysregulation of miR-34a, miR-451, and miR-33a in pathogenesis and progression of NAFLD has been identified. trans-Chalcone is a simple chalcone with anti-diabetic and anti-inflammatory activities. However, to the best of our knowledge, miRNA-dependent mechanisms of these protective effects under pathologic conditions are not understood. Thus, this study, for the first time, aimed to evaluate the effects of trans-Chalcone on miR-34a, miR-451, and miR-33a signaling pathways in the liver of high-fat (HF) emulsion-fed rats. To this aim, twenty-one rats were randomly and equally divided into three groups: control, which was gavaged with 10% tween 80; HF, which was gavaged with HF emulsion and 10% tween 80; and HF + trans-Chalcone (HF + TC), which was gavaged with HF emulsion and trans-Chalcone. Then, circulating levels of glucose and insulin were measured and used for the calculation of HOMA-IR. Hepatic expression levels of miR-34a, miR-451, miR-33a, SIRT1, and ABCA1 and also protein levels of ABCA1 and IL-8 were assayed. In this study, trans-chalcone increased hepatic cholesterol efflux and prevented insulin resistance and liver inflammation in HF emulsion-fed rats. These protective effects were modulated through the down-regulation of miR-34a and its associated elevation of SIRT1, the up-regulation of miR-451 which was associated with a reduction in IL-8, and the inhibition of miR-33a which was related to the elevation of ABCA1 in the liver of HF emulsion-fed rats. Therefore, trans-Chalcone exerts its beneficial effects by targeting hepatic miR-34a-, miR-451-, and miR-33a-related pathways.
Collapse
Affiliation(s)
- Elham Karimi-Sales
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
| | | | | | | |
Collapse
|
708
|
Zubor P, Kubatka P, Dankova Z, Gondova A, Kajo K, Hatok J, Samec M, Jagelkova M, Krivus S, Holubekova V, Bujnak J, Laucekova Z, Zelinova K, Stastny I, Nachajova M, Danko J, Golubnitschaja O. miRNA in a multiomic context for diagnosis, treatment monitoring and personalized management of metastatic breast cancer. Future Oncol 2018; 14:1847-1867. [DOI: 10.2217/fon-2018-0061] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Metastatic breast cancer is characterized by aggressive spreading to distant organs. Despite huge multilevel research, there are still several important challenges that have to be clarified in the management of this disease. Therefore, recent investigations have implemented a modern, multiomic approach with the aim of identifying specific biomarkers for not only early detection but also to predict treatment responses and metastatic spread. Specific attention is paid to short miRNAs, which regulate gene expression at the post-transcriptional level. Aberrant miRNA expression could initiate cancer development, cell proliferation, invasion, migration, metastatic spread or drug resistance. An miRNA signature is, therefore, believed to be a promising biomarker and prediction tool that could be utilized in all phases of carcinogenesis. This article offers comprehensive information about miRNA profiles useful for diagnostic and treatment purposes that may sufficiently advance breast cancer management and improve individual outcomes in the near future.
Collapse
Affiliation(s)
- Pavol Zubor
- Department of Obstetrics & Gynecology, Jessenius Faculty of Medicine, Comenius University in Bratislava, Martin University Hospital, Martin, Slovak Republic
- Biomedical Center Martin, Division of Oncology, Jessenius Faculty of Medicine, Comenius University in Bratislava, Martin, Slovak Republic
| | - Peter Kubatka
- Biomedical Center Martin, Division of Oncology, Jessenius Faculty of Medicine, Comenius University in Bratislava, Martin, Slovak Republic
- Department of Medical Biology, Jessenius Faculty of Medicine, Comenius University in Bratislava, Martin, Slovak Republic
| | - Zuzana Dankova
- Biomedical Center Martin, Division of Oncology, Jessenius Faculty of Medicine, Comenius University in Bratislava, Martin, Slovak Republic
| | - Alexandra Gondova
- Department of Obstetrics & Gynecology, Jessenius Faculty of Medicine, Comenius University in Bratislava, Martin University Hospital, Martin, Slovak Republic
| | - Karol Kajo
- Department of Pathology, St Elizabeth Cancer Institute Hospital, Bratislava, Slovak Republic
- Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovak Republic
| | - Jozef Hatok
- Department of Medical Biochemistry, Jessenius Faculty of Medicine, Comenius University in Bratislava, Martin, Slovak Republic
| | - Marek Samec
- Department of Obstetrics & Gynecology, Jessenius Faculty of Medicine, Comenius University in Bratislava, Martin University Hospital, Martin, Slovak Republic
- Biomedical Center Martin, Division of Oncology, Jessenius Faculty of Medicine, Comenius University in Bratislava, Martin, Slovak Republic
| | - Marianna Jagelkova
- Department of Obstetrics & Gynecology, Jessenius Faculty of Medicine, Comenius University in Bratislava, Martin University Hospital, Martin, Slovak Republic
- Biomedical Center Martin, Division of Oncology, Jessenius Faculty of Medicine, Comenius University in Bratislava, Martin, Slovak Republic
| | - Stefan Krivus
- Department of Obstetrics & Gynecology, Jessenius Faculty of Medicine, Comenius University in Bratislava, Martin University Hospital, Martin, Slovak Republic
| | - Veronika Holubekova
- Biomedical Center Martin, Division of Oncology, Jessenius Faculty of Medicine, Comenius University in Bratislava, Martin, Slovak Republic
| | - Jan Bujnak
- Department of Obstetrics & Gynecology, Kukuras Michalovce Hospital, Michalovce, Slovak Republic
- Oncogynecology Unit, Penta Hospitals International, Svet Zdravia, Michalovce, Slovak Republic
| | - Zuzana Laucekova
- Department of Obstetrics & Gynecology, Jessenius Faculty of Medicine, Comenius University in Bratislava, Martin University Hospital, Martin, Slovak Republic
| | - Katarina Zelinova
- Department of Obstetrics & Gynecology, Jessenius Faculty of Medicine, Comenius University in Bratislava, Martin University Hospital, Martin, Slovak Republic
- Biomedical Center Martin, Division of Oncology, Jessenius Faculty of Medicine, Comenius University in Bratislava, Martin, Slovak Republic
| | - Igor Stastny
- Department of Obstetrics & Gynecology, Jessenius Faculty of Medicine, Comenius University in Bratislava, Martin University Hospital, Martin, Slovak Republic
- Biomedical Center Martin, Division of Oncology, Jessenius Faculty of Medicine, Comenius University in Bratislava, Martin, Slovak Republic
| | - Marcela Nachajova
- Department of Obstetrics & Gynecology, Jessenius Faculty of Medicine, Comenius University in Bratislava, Martin University Hospital, Martin, Slovak Republic
| | - Jan Danko
- Department of Obstetrics & Gynecology, Jessenius Faculty of Medicine, Comenius University in Bratislava, Martin University Hospital, Martin, Slovak Republic
| | - Olga Golubnitschaja
- Radiological Clinic, Rheinische Friedrich-Wilhelms-University of Bonn, Bonn, Germany
- Breast Cancer Research Center, Rheinische Friedrich-Wilhelms-University of Bonn, Bonn, Germany
- Center for Integrated Oncology, Cologne-Bonn, Rheinische Friedrich-Wilhelms-University of Bonn, Bonn, Germany
| |
Collapse
|
709
|
miR-145-loaded micelleplexes as a novel therapeutic strategy to inhibit proliferation and migration of osteosarcoma cells. Eur J Pharm Sci 2018; 123:28-42. [PMID: 30010029 DOI: 10.1016/j.ejps.2018.07.021] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 06/12/2018] [Accepted: 07/09/2018] [Indexed: 12/20/2022]
Abstract
Osteosarcoma (OS), the main primary malignancy of bone, is the second leading cause of cancer in children and young adults. Despite the advances in modern treatments, the 5-year survival rate is retained in 60-70%, since the conventional treatment options available are associated with relapse, chemoresistance, and development of metastases, which frequently lead to patients death. In this regard, there is an increasing need to search and develop novel and alternative therapeutic approaches. Concerning this, gene therapy appears as an innovative and promising treatment option. This therapeutic option aims to deliver genetic material, through nanosystems, to repress or replace the expression of mutated genes involved in important regulatory pathways. To attain this goal, gene therapy is decidedly dependent on the efficiency of utilized vectors, constituting such a very important parameter to take in consideration. In this work, the main goal was centered on the development and full characterization of an efficient micellar nanosystem, based on the chemical conjugation between the amphiphilic copolymer Pluronic® L64 and the cationic polymer polyethyleneimine (PEI), to deliver the therapeutic miRNA-145 into OS cells leading to inhibition of cell proliferation and migration, and ultimately inducing cell death, crafting a novel anticancer therapeutic approach to OS.
Collapse
|
710
|
Lopez S, Bermudez B, Montserrat-de la Paz S, Abia R, Muriana FJ. A microRNA expression signature of the postprandial state in response to a high-saturated-fat challenge. J Nutr Biochem 2018; 57:45-55. [DOI: 10.1016/j.jnutbio.2018.03.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 01/23/2018] [Accepted: 03/07/2018] [Indexed: 12/13/2022]
|
711
|
Fang M, Wang C, Zheng C, Luo J, Hou S, Liu K, Li X. Mir-29b promotes human aortic valve interstitial cell calcification via inhibiting TGF-β3 through activation of wnt3/β-catenin/Smad3 signaling. J Cell Biochem 2018; 119:5175-5185. [PMID: 29227539 PMCID: PMC6001435 DOI: 10.1002/jcb.26545] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 11/30/2017] [Indexed: 01/08/2023]
Abstract
Herein, we hypothesized that pro-osteogenic MicroRNAs (miRs) could play functional roles in the calcification of the aortic valve and aimed to explore the functional role of miR-29b in the osteoblastic differentiation of human aortic valve interstitial cells (hAVICs) and the underlying molecular mechanism. Osteoblastic differentiation of hAVICs isolated from human calcific aortic valve leaflets obtained intraoperatively was induced with an osteogenic medium. Alizarin red S staining was used to evaluate calcium deposition. The protein levels of osteogenic markers and other proteins were evaluated using western blotting and/or immunofluorescence while qRT-PCR was applied for miR and mRNA determination. Bioinformatics and luciferase reporter assay were used to identify the possible interaction between miR-29b and TGF-β3. Calcium deposition and the number of calcification nodules were pointedly and progressively increased in hAVICs during osteogenic differentiation. The levels of osteogenic and calcification markers were equally increased, thus confirming the mineralization of hAVICs. The expression of miR-29b was significantly increased during osteoblastic differentiation. Furthermore, the osteoblastic differentiation of hAVICs was significantly inhibited by the miR-29b inhibition. TGF-β3 was markedly downregulated while Smad3, Runx2, wnt3, and β-catenin were significantly upregulated during osteogenic induction at both the mRNA and protein levels. These effects were systematically induced by miR-29b overexpression while the inhibition of miR-29b showed the inverse trends. Moreover, TGF-β3 was a direct target of miR-29b. Inhibition of miR-29b hinders valvular calcification through the upregulation of the TGF-β3 via inhibition of wnt/β-catenin and RUNX2/Smad3 signaling pathways.
Collapse
Affiliation(s)
- Ming Fang
- Department of CardiologyHainan General HospitalHaikouHainanP.R. China
- Department of CardiologyShanghai Zhoupu HospitalShanghaiP.R. China
| | - Cheng‐Guang Wang
- Laboratory of System BiologyShanghai Advanced Research InstituteChinese Academy of SciencesShanghaiP.R. China
| | - Changzhu Zheng
- Department of CardiologyShanghai Zhoupu HospitalShanghaiP.R. China
| | - Jun Luo
- Department of CardiologyShanghai Zhoupu HospitalShanghaiP.R. China
| | - Shiqiang Hou
- Department of CardiologyShanghai Zhoupu HospitalShanghaiP.R. China
| | - Kangyong Liu
- Department of NeurologyShanghai Zhoupu HospitalShanghaiP.R. China
| | - Xinming Li
- Department of CardiologyShanghai Zhoupu HospitalShanghaiP.R. China
| |
Collapse
|
712
|
Pre-Analytical Handling Conditions and Small RNA Recovery from Urine for miRNA Profiling. J Mol Diagn 2018; 20:565-571. [PMID: 29936254 DOI: 10.1016/j.jmoldx.2018.04.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 03/19/2018] [Accepted: 04/30/2018] [Indexed: 12/24/2022] Open
Abstract
There are currently no standardized protocols for pre-analytical handling of urine to best preserve small RNA for miRNA profiling studies. miRNA is an attractive candidate as a potential biomarker because of the high level of stability in body fluids and its ability to be quantified on multiple high-throughput platforms. We present a comparison of small RNA recovery and stability in urine under alternate pre-analytical handling conditions and extend recommendations on what conditions optimize yield of miRNA from cell-free urine and urine extracellular vesicles (EVs). Using an affinity slurry for isolation of small RNA from urine, we found that urine samples held at room temperature (20°C) for up to 8 hours before processing yield the highest amounts of intact small RNAs from EVs. Some miRNA is lost from urine samples when held 2°C to 4°C and/or frozen before EV isolation, likely because of EV entrapment in uromodulin precipitates. However, we found that a simple 5-minute incubation of urine containing cold-induced precipitate at 37°C resolubilizes much of this precipitate and results in an increased recovery of EVs and miRNAs. Finally, small RNA integrity can be compromised when whole urine is held at 37°C for as little as 4 hours and is not conducive to efficient miRNA profiling.
Collapse
|
713
|
A stress-induced response complex (SIRC) shuttles miRNAs, siRNAs, and oligonucleotides to the nucleus. Proc Natl Acad Sci U S A 2018; 115:E5756-E5765. [PMID: 29866826 PMCID: PMC6016802 DOI: 10.1073/pnas.1721346115] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The deregulation of miRNA function is critical in the pathogenesis of cancer and other diseases. miRNAs and other noncoding RNAs (ncRNAs) tightly regulate gene expression, often in the cell nucleus. Heretofore, there has been no understanding that there exists a general shuttling mechanism that brings miRNAs, in addition to therapeutic oligonucleotides and siRNAs, from the cytoplasm into the nucleus. We have identified this shuttling mechanism, which occurs in response to cell stress. Nuclear imported miRNAs are functional, can potentially alter gene expression, and participate in cell stress response mechanisms. This shuttling mechanism can be augmented to target specific RNAs, including miRNA sponges, and long ncRNAs like Malat-1, which have been implicated in promoting tumor metastasis. Although some information is available for specific subsets of miRNAs and several factors have been shown to bind oligonucleotides (ONs), no general transport mechanism for these molecules has been identified to date. In this work, we demonstrate that the nuclear transport of ONs, siRNAs, and miRNAs responds to cellular stress. Furthermore, we have identified a stress-induced response complex (SIRC), which includes Ago-1 and Ago-2 in addition to the transcription and splicing regulators YB1, CTCF, FUS, Smad1, Smad3, and Smad4. The SIRC transports endogenous miRNAs, siRNAs, and ONs to the nucleus. We show that cellular stress can significantly increase ON- or siRNA-directed splicing switch events and endogenous miRNA targeting of nuclear RNAs.
Collapse
|
714
|
Ishibashi O, Akagi I, Ogawa Y, Inui T. MiR-141-3p is upregulated in esophageal squamous cell carcinoma and targets pleckstrin homology domain leucine-rich repeat protein phosphatase-2, a negative regulator of the PI3K/AKT pathway. Biochem Biophys Res Commun 2018; 501:507-513. [DOI: 10.1016/j.bbrc.2018.05.025] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 05/04/2018] [Indexed: 12/24/2022]
|
715
|
O’Doherty AM, O’Brien YM, Browne JA, Wingfield M, O’Shea LC. Expression of granulosa cell microRNAs, AVEN and ATRX are associated with human blastocyst development. Mol Reprod Dev 2018; 85:836-848. [DOI: 10.1002/mrd.22990] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 04/23/2018] [Indexed: 12/17/2022]
Affiliation(s)
- Alan M. O’Doherty
- School of Agriculture and Food Science, Veterinary Science Centre; University College Dublin; Dublin Ireland
| | - Yvonne M. O’Brien
- Merrion Fertility Clinic; National Maternity Hospital; Dublin Ireland
| | - John A. Browne
- School of Agriculture and Food Science, Veterinary Science Centre; University College Dublin; Dublin Ireland
| | - Mary Wingfield
- Merrion Fertility Clinic; National Maternity Hospital; Dublin Ireland
- School of Medicine, Health Sciences Centre, Conway Institute of Biomolecular and Biomedical Science; University College Dublin; Dublin Ireland
| | - Lynne C. O’Shea
- School of Medicine, Health Sciences Centre, Conway Institute of Biomolecular and Biomedical Science; University College Dublin; Dublin Ireland
| |
Collapse
|
716
|
Zedan AH, Hansen TF, Assenholt J, Pleckaitis M, Madsen JS, Osther PJS. microRNA expression in tumour tissue and plasma in patients with newly diagnosed metastatic prostate cancer. Tumour Biol 2018; 40:1010428318775864. [PMID: 29775158 DOI: 10.1177/1010428318775864] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Prostate cancer is the most common cancer among men in the western world. Clinical practice is continuously challenged by the pitfalls of the available diagnostic tools. microRNAs may represent promising biomarkers in many types of human cancers, including prostate cancer. The aim of this study was to investigate microRNA expression in tumour tissue and matched plasma in a cohort of patients with primary metastatic prostate cancer. The relative expression of 12 microRNAs was assessed in diagnostic needle biopsies from the prostate and matched plasma samples in two prospective cohorts (screening cohorts) comprising 21 patients with metastatic prostate cancer and 25 control patients. An independent validation cohort of plasma samples was collected prospectively from 149 newly diagnosed patients with local/locally advanced prostate cancer. Analyses were performed using real-time polymerase chain reaction. miRNA-93 showed a significant negative correlation between expression in tumour tissue and plasma in patients with metastatic prostate cancer. Furthermore, the plasma level of miRNA-93 significantly decreased after treatment in patients with local/locally advanced prostate cancer compared to baseline plasma level. The expression of six microRNAs (let-7b, miRNA-34a, -125b, -143, -145 and -221) was downregulated, and three microRNAs (miRNA-21, -25 and miRNA-93) were upregulated in tumour tissue compared to benign prostate tissue. In plasma, six microRNAs were upregulated (miRNA-21, -125b, -126, -141, -143 and -375), while let-7b was downregulated in patients with metastatic prostate cancer compared to the control cohort. In the metastatic prostate cancer cohort, the expression of four microRNAs (miRNA-125b, -126, -143 and -221), and miRNA-141 in tissue was associated with Gleason score and prostate-specific antigen, respectively. The expression of miRNA-93 in tumour tissue was correlated with matched plasma levels and showed a significant decrease in plasma level after intervention in local prostate cancer. Differential expression between tumour and benign prostate was detected for several microRNAs in both tissue and plasma.
Collapse
Affiliation(s)
- Ahmed Hussein Zedan
- 1 Urological Research Center, Department of Urology, Vejle Hospital, Vejle, Denmark.,2 Oncological Department, Vejle Hospital, Vejle, Denmark.,3 Institute of Regional Health Research, University of Southern Denmark, Odense, Denmark
| | - Torben Frøstrup Hansen
- 2 Oncological Department, Vejle Hospital, Vejle, Denmark.,3 Institute of Regional Health Research, University of Southern Denmark, Odense, Denmark
| | - Jannie Assenholt
- 4 Department of Biochemistry and Immunology, Vejle Hospital, Vejle, Denmark
| | | | - Jonna Skov Madsen
- 3 Institute of Regional Health Research, University of Southern Denmark, Odense, Denmark.,4 Department of Biochemistry and Immunology, Vejle Hospital, Vejle, Denmark
| | - Palle Jörn Sloth Osther
- 1 Urological Research Center, Department of Urology, Vejle Hospital, Vejle, Denmark.,3 Institute of Regional Health Research, University of Southern Denmark, Odense, Denmark
| |
Collapse
|
717
|
Bermisheva MA, Takhirova ZR, Gilyazova IR, Khusnutdinova EK. MicroRNA Biogenesis Pathway Gene Polymorphisms Are Associated with Breast Cancer Risk. RUSS J GENET+ 2018. [DOI: 10.1134/s1022795418040051] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
|
718
|
Robertson JC, Jorcyk CL, Oxford JT. DICER1 Syndrome: DICER1 Mutations in Rare Cancers. Cancers (Basel) 2018; 10:cancers10050143. [PMID: 29762508 PMCID: PMC5977116 DOI: 10.3390/cancers10050143] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 05/13/2018] [Accepted: 05/14/2018] [Indexed: 12/20/2022] Open
Abstract
DICER1 syndrome is a rare genetic disorder that predisposes individuals to multiple cancer types. Through mutations of the gene encoding the endoribonuclease, Dicer, DICER1 syndrome disrupts the biogenesis and processing of miRNAs with subsequent disruption in control of gene expression. Since the first description of DICER1 syndrome, case reports have documented novel germline mutations of the DICER1 gene in patients with cancers as well as second site mutations that alter the function of the Dicer protein expressed. Here, we present a review of mutations in the DICER1 gene, the respective protein sequence changes, and clinical manifestations of DICER1 syndrome. Directions for future research are discussed.
Collapse
Affiliation(s)
- Jake C Robertson
- Department of Biological Sciences, Boise State University, Boise, ID 83725-1515, USA.
| | - Cheryl L Jorcyk
- Department of Biological Sciences, Boise State University, Boise, ID 83725-1515, USA.
- Biomolecular Research Center, Boise State University, Boise, ID 83725-1511, USA.
| | - Julia Thom Oxford
- Department of Biological Sciences, Boise State University, Boise, ID 83725-1515, USA.
- Biomolecular Research Center, Boise State University, Boise, ID 83725-1511, USA.
| |
Collapse
|
719
|
Vaschetto LM. miRNA activation is an endogenous gene expression pathway. RNA Biol 2018; 15:826-828. [PMID: 29537927 PMCID: PMC6152443 DOI: 10.1080/15476286.2018.1451722] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 03/07/2018] [Indexed: 12/27/2022] Open
Abstract
Transfection of small non-coding RNAs (sncRNAs) molecules has become a routine technique widely used for silencing gene expression by triggering post-transcriptional and transcriptional RNA interference (RNAi) pathways. Moreover, in the past decade, small activating (saRNA) sequences targeting promoter regions were also reported, thereby a RNA-based gene activation (RNAa) mechanism has been proposed. In this regard, Turner and colleagues recently discovered an endogenous microRNA (miRNA) which binds its promoter in order to upregulate its own expression. Interestingly, several miRNA-induced RNA activation (miRNAa) phenomena have since then been identified. My objective here is to introduce the reader into the emergent miRNAa research field, as well as bring together important discoveries about this unexplored transcriptional activation pathway.
Collapse
Affiliation(s)
- Luis M. Vaschetto
- Instituto de Diversidad y Ecología Animal, Consejo Nacional de Investigaciones Científicas y Técnicas (IDEA, CONICET), Av. Vélez Sarsfield 299, X5000JJC Córdoba, Argentina
- Cátedra de Diversidad Animal I, Facultad de Ciencias Exactas, Físicas y Naturales, Universidad Nacional de Córdoba, (FCEFyN, UNC), Av. Vélez Sarsfield 299, X5000JJC Córdoba, Argentina
| |
Collapse
|
720
|
Hayder H, O'Brien J, Nadeem U, Peng C. MicroRNAs: crucial regulators of placental development. Reproduction 2018; 155:R259-R271. [PMID: 29615475 DOI: 10.1530/rep-17-0603] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 04/03/2018] [Indexed: 12/25/2022]
Abstract
MicroRNAs (miRNAs) are small non-coding single-stranded RNAs that are integral to a wide range of cellular processes mainly through the regulation of translation and mRNA stability of their target genes. The placenta is a transient organ that exists throughout gestation in mammals, facilitating nutrient and gas exchange and waste removal between the mother and the fetus. miRNAs are expressed in the placenta, and many studies have shown that miRNAs play an important role in regulating trophoblast differentiation, migration, invasion, proliferation, apoptosis, vasculogenesis/angiogenesis and cellular metabolism. In this review, we provide a brief overview of canonical and non-canonical pathways of miRNA biogenesis and mechanisms of miRNA actions. We highlight the current knowledge of the role of miRNAs in placental development. Finally, we point out several limitations of the current research and suggest future directions.
Collapse
Affiliation(s)
- Heyam Hayder
- Department of BiologyYork University, Toronto, Ontario, Canada
| | - Jacob O'Brien
- Department of BiologyYork University, Toronto, Ontario, Canada
| | - Uzma Nadeem
- Department of BiologyYork University, Toronto, Ontario, Canada
| | - Chun Peng
- Department of BiologyYork University, Toronto, Ontario, Canada
| |
Collapse
|
721
|
Ultimo S, Zauli G, Martelli AM, Vitale M, McCubrey JA, Capitani S, Neri LM. Influence of physical exercise on microRNAs in skeletal muscle regeneration, aging and diseases. Oncotarget 2018; 9:17220-17237. [PMID: 29682218 PMCID: PMC5908319 DOI: 10.18632/oncotarget.24991] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 03/06/2018] [Indexed: 12/21/2022] Open
Abstract
Skeletal muscle is a dynamic tissue with remarkable plasticity and its growth and regeneration are highly organized, with the activation of specific transcription factors, proliferative pathways and cytokines. The decline of skeletal muscle tissue with age, is one of the most important causes of functional loss of independence in older adults. Maintaining skeletal muscle function throughout the lifespan is a prerequisite for good health and independent living. Physical activity represents one of the most effective preventive agents for muscle decay in aging. Several studies have underlined the importance of microRNAs (miRNAs) in the control of myogenesis and of skeletal muscle regeneration and function. In this review, we reported an overview and recent advances about the role of miRNAs expressed in the skeletal muscle, miRNAs regulation by exercise in skeletal muscle, the consequences of different physical exercise training modalities in the skeletal muscle miRNA profile, their regulation under pathological conditions and the role of miRNAs in age-related muscle wasting. Specific miRNAs appear to be involved in response to different types of exercise and therefore to play an important role in muscle fiber identity and myofiber gene expression in adults and elder population. Understanding the roles and regulation of skeletal muscle miRNAs during muscle regeneration may result in new therapeutic approaches in aging or diseases with impaired muscle function or re-growth.
Collapse
Affiliation(s)
- Simona Ultimo
- Department of Morphology, Surgery and Experimental Medicine, University of Ferrara, Ferrara, Italy
| | - Giorgio Zauli
- Department of Morphology, Surgery and Experimental Medicine, University of Ferrara, Ferrara, Italy
| | - Alberto M Martelli
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Marco Vitale
- Department of Medicine and Surgery, University of Parma, Parma, Italy.,CoreLab, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy
| | - James A McCubrey
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, USA
| | - Silvano Capitani
- Department of Morphology, Surgery and Experimental Medicine, University of Ferrara, Ferrara, Italy
| | - Luca M Neri
- Department of Morphology, Surgery and Experimental Medicine, University of Ferrara, Ferrara, Italy
| |
Collapse
|
722
|
In silico identification of microRNAs predicted to regulate N-myristoyltransferase and Methionine Aminopeptidase 2 functions in cancer and infectious diseases. PLoS One 2018; 13:e0194612. [PMID: 29579063 PMCID: PMC5868815 DOI: 10.1371/journal.pone.0194612] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2017] [Accepted: 03/06/2018] [Indexed: 01/16/2023] Open
Abstract
Protein myristoylation is a key protein modification carried out by N-Myristoyltransferase (NMT) after Methionine aminopeptidase 2 (MetAP2) removes methionine from the amino-terminus of the target protein. Protein myristoylation by NMT augments several signaling pathways involved in a myriad of cellular processes, including developmental pathways and pathways that when dysregulated lead to cancer or immune dysfunction. The emerging evidence pointing to NMT-mediated myristoylation as a major cellular regulator underscores the importance of understanding the framework of this type of signaling event. Various studies have investigated the role that myristoylation plays in signaling dysfunction by examining differential gene or protein expression between normal and diseased states, such as cancers or following HIV-1 infection, however no study exists that addresses the role of microRNAs (miRNAs) in the regulation of myristoylation. By performing a large scale bioinformatics and functional analysis of the miRNAs that target key genes involved in myristoylation (NMT1, NMT2, MetAP2), we have narrowed down a list of promising candidates for further analysis. Our condensed panel of miRNAs identifies 35 miRNAs linked to cancer, 21 miRNAs linked to developmental and immune signaling pathways, and 14 miRNAs linked to infectious disease (primarily HIV). The miRNAs panel that was analyzed revealed several NMT-targeting mRNAs (messenger RNA) that are implicated in diseases associated with NMT signaling alteration, providing a link between the realms of miRNA and myristoylation signaling. These findings verify miRNA as an additional facet of myristoylation signaling that must be considered to gain a full perspective. This study provides the groundwork for future studies concerning NMT-transcript-binding miRNAs, and will potentially lead to the development of new diagnostic/prognostic biomarkers and therapeutic targets for several important diseases.
Collapse
|
723
|
Simonato M. Epilepsy an Update on Disease Mechanisms: The Potential Role of MicroRNAs. Front Neurol 2018; 9:176. [PMID: 29615968 PMCID: PMC5868323 DOI: 10.3389/fneur.2018.00176] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Accepted: 03/07/2018] [Indexed: 01/25/2023] Open
Abstract
So far, research on epilepsy mechanisms has been designed mainly using animal models and tracking down molecular mechanisms underlying seizures in that model. While this approach is clearly valuable, it can be questioned if it is the best possible. One attractive alternative approach may stem from the consideration of epilepsy as a complex disease of a very complex organ, the brain. This short review summarizes data from analyses of the alterations in expression of microRNAs and their target messenger RNAs in a specific brain subregion, the dentate gyrus of the hippocampus, in three experimental models of lesional epilepsy. The findings are discussed within the conceptual framework of complex systems.
Collapse
Affiliation(s)
- Michele Simonato
- Department of Medical Sciences, University of Ferrara, Ferrara, Italy.,School of Medicine, University Vita-Salute San Raffaele, Milan, Italy
| |
Collapse
|
724
|
Gruszka R, Zakrzewska M. The Oncogenic Relevance of miR-17-92 Cluster and Its Paralogous miR-106b-25 and miR-106a-363 Clusters in Brain Tumors. Int J Mol Sci 2018; 19:ijms19030879. [PMID: 29547527 PMCID: PMC5877740 DOI: 10.3390/ijms19030879] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 03/13/2018] [Accepted: 03/14/2018] [Indexed: 12/25/2022] Open
Abstract
The fundamental function of ribonucleic acids is to transfer genetic information from DNA to protein during translation process, however, this is not the only way connecting active RNA sequences with essential biological processes. Up until now, many RNA subclasses of different size, structure, and biological function were identified. Among them, there are non-coding single-stranded microRNAs (miRNAs). This subclass comprises RNAs of 19–25 nucleotides in length that modulate the activity of well-defined coding RNAs and play a crucial role in many physiological and pathological processes. miRNA genes are located both in exons, introns, and also within non-translated regions. Several miRNAs that are transcribed from the adjacent miRNA genes are called cluster. One of the largest ones is miR-17-92 cluster known as OncomiR-1 due to its strong link to oncogenesis. Six miRNAs from the OncomiR-1 have been shown to play important roles in various physiological cellular processes but also through inhibition of cell death in many cancer-relevant processes. Due to the origin and similarity of the sequence, miR-17-92 cluster and paralogs, miR-106b-25 and miR-106a-363 clusters were defined. Here we discuss the oncogenic function of those miRNA subgroups found in many types of cancers, including brain tumors.
Collapse
Affiliation(s)
- Renata Gruszka
- Department of Molecular Pathology and Neuropathology, Medical University of Lodz, Pomorska 251, 92-213 Lodz, Poland.
| | - Magdalena Zakrzewska
- Department of Molecular Pathology and Neuropathology, Medical University of Lodz, Pomorska 251, 92-213 Lodz, Poland.
| |
Collapse
|
725
|
Romero-Barrios N, Legascue MF, Benhamed M, Ariel F, Crespi M. Splicing regulation by long noncoding RNAs. Nucleic Acids Res 2018; 46:2169-2184. [PMID: 29425321 PMCID: PMC5861421 DOI: 10.1093/nar/gky095] [Citation(s) in RCA: 186] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 01/05/2018] [Accepted: 02/01/2018] [Indexed: 12/13/2022] Open
Abstract
Massive high-throughput sequencing techniques allowed the identification of thousands of noncoding RNAs (ncRNAs) and a plethora of different mRNA processing events occurring in higher organisms. Long ncRNAs can act directly as long transcripts or can be processed into active small si/miRNAs. They can modulate mRNA cleavage, translational repression or the epigenetic landscape of their target genes. Recently, certain long ncRNAs have been shown to play a crucial role in the regulation of alternative splicing in response to several stimuli or during disease. In this review, we focus on recent discoveries linking gene regulation by alternative splicing and its modulation by long and small ncRNAs.
Collapse
Affiliation(s)
- Natali Romero-Barrios
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Universities Paris-Sud, Evry and Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment 630, 91405 Orsay, France
| | - Maria Florencia Legascue
- Instituto de Agrobiotecnología del Litoral, CONICET, Universidad Nacional del Litoral, Colectora Ruta Nacional 168 km 0, 3000 Santa Fe, Argentina
| | - Moussa Benhamed
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Universities Paris-Sud, Evry and Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment 630, 91405 Orsay, France
| | - Federico Ariel
- Instituto de Agrobiotecnología del Litoral, CONICET, Universidad Nacional del Litoral, Colectora Ruta Nacional 168 km 0, 3000 Santa Fe, Argentina
| | - Martin Crespi
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Universities Paris-Sud, Evry and Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment 630, 91405 Orsay, France
| |
Collapse
|
726
|
Islam W, Qasim M, Noman A, Adnan M, Tayyab M, Farooq TH, Wei H, Wang L. Plant microRNAs: Front line players against invading pathogens. Microb Pathog 2018. [PMID: 29524548 DOI: 10.1016/j.micpath.2018.03.008] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Plants are attacked by a large number of pathogens. To defend against these pathogens, plants activate or repress a vast array of genes. For genetic expression and reprogramming, host endogenous small RNAs (sRNAs) are the key factors. Among these sRNAs, microRNAs (miRNAs) mediate gene regulation through RNA silencing at the post-transcriptional level and play an essential role in the defense responses to biotic and abiotic stress. In the recent years, high-throughput sequencing has enabled the researchers to uncover the role of plant miRNAs during pathogen invasion. So here we have reviewed the recent research findings illustrating the plant miRNAs active involvement in various defense processes during fungal, bacterial, viral and nematode infections. However, rapid validation of direct targets of miRNAs is the dire need of time, which can be very helpful in improving the plant resistance against various pathogenic diseases.
Collapse
Affiliation(s)
- Waqar Islam
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Govt. of Punjab, Agriculture Department, Lahore, Pakistan.
| | - Muhammad Qasim
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, 350002, China
| | - Ali Noman
- College of Crop Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Department of Botany, Govt. College University, Faisalabad, Pakistan
| | - Muhammad Adnan
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Muhammad Tayyab
- College of Crop Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Taimoor Hassan Farooq
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Huang Wei
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Liande Wang
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, 350002, China.
| |
Collapse
|
727
|
Ye Q, Tian GP, Cheng HP, Zhang X, Ou X, Yu XH, Tan RQ, Yang FY, Gong D, Huang C, Pan YJ, Zhang J, Chen LY, Zhao ZW, Xie W, Li L, Zhang M, Xia XD, Zheng XL, Tang CK. MicroRNA-134 Promotes the Development of Atherosclerosis Via the ANGPTL4/LPL Pathway in Apolipoprotein E Knockout Mice. J Atheroscler Thromb 2018; 25:244-253. [PMID: 28867683 PMCID: PMC5868510 DOI: 10.5551/jat.40212] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
AIMS Atherosclerosis is the most common cause of cardiovascular disease, such as myocardial infarction and stroke. Previous study revealed that microRNA (miR)-134 promotes lipid accumulation and proinflammatory cytokine secretion through angiopoietin-like 4 (ANGPTL4)/lipid lipoprotein (LPL) signaling in THP-1 macrophages. METHODS ApoE KO male mice on a C57BL/6 background were fed a high-fat/high-cholesterol Western diet, from 8 to 16 weeks of age. Mice were divided into four groups, and received a tail vein injection of miR-134 agomir, miR-134 antagomir, or one of the corresponding controls, respectively, once every 2 weeks after starting the Western diet. After 8 weeks we measured aortic atherosclerosis, LPL Activity, mRNA and protein levels of ANGPTL4 and LPL, LPL/ low-density lipoprotein receptor related protein 1 Complex Formation, proinflammatory cytokine secretion and lipid levels. RESULTS Despite this finding, the influence of miR-134 on atherosclerosis in vivo remains to be determined. Using the well-characterized mouse atherosclerosis model of apolipoprotein E knockout, we found that systemic delivery of miR-134 agomir markedly enhanced the atherosclerotic lesion size, together with a significant increase in proinflammatory cytokine secretion and peritoneal macrophages lipid contents. Moreover, overexpression of miR-134 decreased ANGPTL4 expression but increased LPL expression and activity in both aortic tissues and peritoneal macrophages, which was accompanied by increased formation of LPL/low-density lipoprotein receptor-related protein 1 complexes in peritoneal macrophages. However, an opposite effect was observed in response to miR-134 antagomir. CONCLUSIONS These findings suggest that miR-134 accelerates atherogenesis by promoting lipid accumulation and proinflammatory cytokine secretion via the ANGPTL4/LPL pathway. Therefore, targeting miR-134 may offer a promising strategy for the prevention and treatment of atherosclerotic cardiovascular disease.
Collapse
Affiliation(s)
- Qiong Ye
- Institute of Cardiovascular Research, Key Laboratory for Atherosclerology of Hunan Province, Medical Research Center, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hunan, China
- Department of Cardiovascular Medicine, The Second Affiliated Hospital of University of South China, Hunan, China
- Department of Ultrasound, Huadu District People's Hospital of Guangzhou, Guangdong, China
| | - Guo-Ping Tian
- Department of Cardiovascular Medicine, The Second Affiliated Hospital of University of South China, Hunan, China
| | - Hai-Peng Cheng
- Institute of Cardiovascular Research, Key Laboratory for Atherosclerology of Hunan Province, Medical Research Center, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hunan, China
| | - Xin Zhang
- Institute of Cardiovascular Research, Key Laboratory for Atherosclerology of Hunan Province, Medical Research Center, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hunan, China
| | - Xiang Ou
- Department of Endocrinology, The First Hospital of Changsha, Changsha, China
| | - Xiao-Hua Yu
- Institute of Cardiovascular Research, Key Laboratory for Atherosclerology of Hunan Province, Medical Research Center, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hunan, China
| | - Ru-Qi Tan
- Department of Cardiovascular Medicine, The Second Affiliated Hospital of University of South China, Hunan, China
| | - Feng-Yun Yang
- Department of Cardiovascular Medicine, The Second Affiliated Hospital of University of South China, Hunan, China
| | - Duo Gong
- Institute of Cardiovascular Research, Key Laboratory for Atherosclerology of Hunan Province, Medical Research Center, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hunan, China
| | - Chong Huang
- Institute of Cardiovascular Research, Key Laboratory for Atherosclerology of Hunan Province, Medical Research Center, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hunan, China
| | - Yan-Jun Pan
- Department of Cardiovascular Medicine, The Second Affiliated Hospital of University of South China, Hunan, China
| | - Jie Zhang
- Department of Spinal Surgery, The Second Affiliated Hospital of University of South China, Hunan, China
| | - Ling-Yan Chen
- Institute of Cardiovascular Research, Key Laboratory for Atherosclerology of Hunan Province, Medical Research Center, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hunan, China
| | - Zhen-Wang Zhao
- Institute of Cardiovascular Research, Key Laboratory for Atherosclerology of Hunan Province, Medical Research Center, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hunan, China
| | - Wei Xie
- Institute of Cardiovascular Research, Key Laboratory for Atherosclerology of Hunan Province, Medical Research Center, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hunan, China
| | - Liang Li
- Institute of Cardiovascular Research, Key Laboratory for Atherosclerology of Hunan Province, Medical Research Center, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hunan, China
| | - Min Zhang
- Institute of Cardiovascular Research, Key Laboratory for Atherosclerology of Hunan Province, Medical Research Center, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hunan, China
| | - Xiao-Dan Xia
- Institute of Cardiovascular Research, Key Laboratory for Atherosclerology of Hunan Province, Medical Research Center, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hunan, China
| | - Xi-Long Zheng
- Department of Biochemistry and Molecular Biology, Libin Cardiovascular Institute of Alberta, Cumming School of Medicine, University of Calgary, Health Sciences Center, 3330 Hospital Dr NW, Calgary, Alberta, Canada
| | - Chao-Ke Tang
- Institute of Cardiovascular Research, Key Laboratory for Atherosclerology of Hunan Province, Medical Research Center, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hunan, China
- Address for correspondence: Chao-Ke Tang, Institute of Cardiovascular Research, University of South China, Hengyang, Hunan 421001, China E-mail:
| |
Collapse
|
728
|
Irimie AI, Zimta AA, Ciocan C, Mehterov N, Dudea D, Braicu C, Berindan-Neagoe I. The Unforeseen Non-Coding RNAs in Head and Neck Cancer. Genes (Basel) 2018; 9:genes9030134. [PMID: 29494516 PMCID: PMC5867855 DOI: 10.3390/genes9030134] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 02/21/2018] [Accepted: 02/22/2018] [Indexed: 12/18/2022] Open
Abstract
Previously ignored non-coding RNAs (ncRNAs) have become the subject of many studies. However, there is an imbalance in the amount of consideration that ncRNAs are receiving. Some transcripts such as microRNAs (miRNAs) or small interfering RNAs (siRNAs) have gained much attention, but it is necessary to investigate other “pieces of the RNA puzzle”. These can offer a more complete view over normal and pathological cell behavior. The other ncRNA species are less studied, either due to their recent discovery, such as stable intronic sequence RNA (sisRNA), YRNA, miRNA-offset RNAs (moRNA), telomerase RNA component (TERC), natural antisense transcript (NAT), transcribed ultraconserved regions (T-UCR), and pseudogene transcript, or because they are still largely seen as non-coding transcripts with no relevance to pathogenesis. Moreover, some are still considered housekeeping RNAs, for instance small nucleolar RNAs (snoRNAs) and TERC. Our review summarizes the biogenesis, mechanism of action and potential role of less known ncRNAs in head and neck cancer, with a particular focus on the installment and progress for this particular cancer type.
Collapse
Affiliation(s)
- Alexandra Iulia Irimie
- Department of Prosthetic Dentistry and Dental Materials, Division Dental Propaedeutic, Aesthetic, "IuliuHatieganu" University of Medicine and Pharmacy, Cluj-Napoca, 23 Marinescu Street, 40015 Cluj-Napoca, Romania.
| | - Alina-Andreea Zimta
- MEDFUTURE-Research Center for Advanced Medicine, University of Medicine and Pharmacy Iuliu-Hatieganu, 23 Marinescu Street, 40015 Cluj-Napoca, Romania.
| | - Cristina Ciocan
- MEDFUTURE-Research Center for Advanced Medicine, University of Medicine and Pharmacy Iuliu-Hatieganu, 23 Marinescu Street, 40015 Cluj-Napoca, Romania.
| | - Nikolay Mehterov
- Department of Medical Biology, Medical University Plovdiv, BulVasilAprilov 15-А, Plovdiv 4002, Bulgaria.
- Technological Center for Emergency Medicine, BulVasilAprilov 15-А, Plovdiv 4002, Bulgaria.
| | - Diana Dudea
- Department of Prosthetic Dentistry and Dental Materials, Division Dental Propaedeutic, Aesthetic, "IuliuHatieganu" University of Medicine and Pharmacy, Cluj-Napoca, 23 Marinescu Street, 40015 Cluj-Napoca, Romania.
| | - Cornelia Braicu
- Research Center for Functional Genomics and Translational Medicine, "IuliuHatieganu" University of Medicine and Pharmacy, 23 Marinescu Street, 40015 Cluj-Napoca, Romania.
| | - Ioana Berindan-Neagoe
- MEDFUTURE-Research Center for Advanced Medicine, University of Medicine and Pharmacy Iuliu-Hatieganu, 23 Marinescu Street, 40015 Cluj-Napoca, Romania.
- Research Center for Functional Genomics and Translational Medicine, "IuliuHatieganu" University of Medicine and Pharmacy, 23 Marinescu Street, 40015 Cluj-Napoca, Romania.
- Department of Functional Genomics and Experimental Pathology, The Oncology Institute "Prof. Dr. Ion Chiricuta", Republicii 34 Street, 400015 Cluj-Napoca, Romania.
| |
Collapse
|
729
|
Di Mauro V, Barandalla-Sobrados M, Catalucci D. The noncoding-RNA landscape in cardiovascular health and disease. Noncoding RNA Res 2018; 3:12-19. [PMID: 30159435 PMCID: PMC6084835 DOI: 10.1016/j.ncrna.2018.02.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 12/27/2017] [Accepted: 02/08/2018] [Indexed: 12/22/2022] Open
Abstract
The cardiovascular system plays a pivotal role in regulating and maintaining homeostasis in the human body. Therefore any alteration in regulatory networks that orchestrate heart development as well as adaptation to physiological and environmental stress might result in pathological conditions, which represent the leading cause of death worldwide [1]. The latest advances in genome-wide techniques challenged the "protein-central dogma" with the discovery of the so-called non-coding RNAs (ncRNAs). Despite their lack of protein coding potential, ncRNAs have been largely demonstrated to regulate the majority of biological processes and have also been largely implicated in cardiovascular disorders. This review will first discuss the important mechanistic aspects of some of the classes of ncRNAs such as biogenesis, mechanism of action, as well as their involvement in cardiac diseases. The ncRNA potential uses as therapeutic molecules, with a specific focus on the latest technologies for their in vivo delivery as drug targets, will be described.
Collapse
Affiliation(s)
- Vittoria Di Mauro
- National Research Council, Institute of Genetics and Biomedical Research, Milan Unit, Milan, Italy
- Humanitas Clinical and Research Center, Rozzano, Milan, Italy
| | - Maria Barandalla-Sobrados
- National Research Council, Institute of Genetics and Biomedical Research, Milan Unit, Milan, Italy
- Humanitas Clinical and Research Center, Rozzano, Milan, Italy
| | - Daniele Catalucci
- National Research Council, Institute of Genetics and Biomedical Research, Milan Unit, Milan, Italy
- Humanitas Clinical and Research Center, Rozzano, Milan, Italy
| |
Collapse
|
730
|
Liu H, Lei C, He Q, Pan Z, Xiao D, Tao Y. Nuclear functions of mammalian MicroRNAs in gene regulation, immunity and cancer. Mol Cancer 2018; 17:64. [PMID: 29471827 PMCID: PMC5822656 DOI: 10.1186/s12943-018-0765-5] [Citation(s) in RCA: 226] [Impact Index Per Article: 37.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 01/12/2018] [Indexed: 12/19/2022] Open
Abstract
MicroRNAs (miRNAs) are endogenous non-coding RNAs that contain approximately 22 nucleotides. They serve as key regulators in various biological processes and their dysregulation is implicated in many diseases including cancer and autoimmune disorders. It has been well established that the maturation of miRNAs occurs in the cytoplasm and miRNAs exert post-transcriptional gene silencing (PTGS) via RNA-induced silencing complex (RISC) pathway in the cytoplasm. However, numerous studies reaffirm the existence of mature miRNA in the nucleus, and nucleus-cytoplasm transport mechanism has also been illustrated. Moreover, active regulatory functions of nuclear miRNAs were found including PTGS, transcriptional gene silencing (TGS), and transcriptional gene activation (TGA), in which miRNAs bind nascent RNA transcripts, gene promoter regions or enhancer regions and exert further effects via epigenetic pathways. Based on existing interaction rules, some miRNA binding sites prediction software tools are developed, which are evaluated in this article. In addition, we attempt to explore and review the nuclear functions of miRNA in immunity, tumorigenesis and invasiveness of tumor. As a non-canonical aspect of miRNA action, nuclear miRNAs supplement miRNA regulatory networks and could be applied in miRNA based therapies.
Collapse
Affiliation(s)
- Hongyu Liu
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, 410008, China
- Key Laboratory of Carcinogenesis, Ministry of Education, Cancer Research Institute, School of Basic Medicine, Central South University, 110 Xiangya Road, Changsha, Hunan, 410078, China
| | - Cheng Lei
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, 410008, China
- Key Laboratory of Carcinogenesis, Ministry of Education, Cancer Research Institute, School of Basic Medicine, Central South University, 110 Xiangya Road, Changsha, Hunan, 410078, China
| | - Qin He
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, 410008, China
- Key Laboratory of Carcinogenesis, Ministry of Education, Cancer Research Institute, School of Basic Medicine, Central South University, 110 Xiangya Road, Changsha, Hunan, 410078, China
| | - Zou Pan
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, 410008, China
- Key Laboratory of Carcinogenesis, Ministry of Education, Cancer Research Institute, School of Basic Medicine, Central South University, 110 Xiangya Road, Changsha, Hunan, 410078, China
| | - Desheng Xiao
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, 410078, China
| | - Yongguang Tao
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, 410008, China.
- Key Laboratory of Carcinogenesis, Ministry of Education, Cancer Research Institute, School of Basic Medicine, Central South University, 110 Xiangya Road, Changsha, Hunan, 410078, China.
- Department of Thoracic Surgery, Second Xiangya Hospital, Central South University, Changsha, China.
| |
Collapse
|
731
|
Ferhan AR, Jackman JA, Park JH, Cho NJ, Kim DH. Nanoplasmonic sensors for detecting circulating cancer biomarkers. Adv Drug Deliv Rev 2018; 125:48-77. [PMID: 29247763 DOI: 10.1016/j.addr.2017.12.004] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 09/29/2017] [Accepted: 12/08/2017] [Indexed: 12/20/2022]
Abstract
The detection of cancer biomarkers represents an important aspect of cancer diagnosis and prognosis. Recently, the concept of liquid biopsy has been introduced whereby diagnosis and prognosis are performed by means of analyzing biological fluids obtained from patients to detect and quantify circulating cancer biomarkers. Unlike conventional biopsy whereby primary tumor cells are analyzed, liquid biopsy enables the detection of a wide variety of circulating cancer biomarkers, including microRNA (miRNA), circulating tumor DNA (ctDNA), proteins, exosomes and circulating tumor cells (CTCs). Among the various techniques that have been developed to detect circulating cancer biomarkers, nanoplasmonic sensors represent a promising measurement approach due to high sensitivity and specificity as well as ease of instrumentation and operation. In this review, we discuss the relevance and applicability of three different categories of nanoplasmonic sensing techniques, namely surface plasmon resonance (SPR), localized surface plasmon resonance (LSPR) and surface-enhanced Raman scattering (SERS), for the detection of different classes of circulating cancer biomarkers.
Collapse
Affiliation(s)
- Abdul Rahim Ferhan
- School of Materials Science and Engineering, Nanyang Technological University, Singapore, 639798, Singapore
| | - Joshua A Jackman
- School of Materials Science and Engineering, Nanyang Technological University, Singapore, 639798, Singapore
| | - Jae Hyeon Park
- School of Materials Science and Engineering, Nanyang Technological University, Singapore, 639798, Singapore
| | - Nam-Joon Cho
- School of Materials Science and Engineering, Nanyang Technological University, Singapore, 639798, Singapore.
| | - Dong-Hwan Kim
- School of Chemical Engineering, Sungkyunkwan University, 16419, Republic of Korea.
| |
Collapse
|
732
|
Mondal T, Bag I, SNCVL P, Garikapati KR, Bhadra U, Pal Bhadra M. Two way controls of apoptotic regulators consign DmArgonaute-1 a better clasp on it. PLoS One 2018; 13:e0190548. [PMID: 29385168 PMCID: PMC5791970 DOI: 10.1371/journal.pone.0190548] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 12/16/2017] [Indexed: 02/02/2023] Open
Abstract
Argonaute family proteins are well conserved among all organisms. Its role in mitotic cell cycle progression and apoptotic cell elimination is poorly understood. Earlier we have established the contribution of Ago-1 in cell cycle control related to G2/M cyclin in Drosophila. Here we have extended our study in understanding the relationship of Ago-1 in regulating apoptosis during Drosophila development. Apoptosis play a critical role in controlling organ shape and size during development of multi cellular organism. Multifarious regulatory pathways control apoptosis during development among which highly conserved JNK (c-Jun N-terminal kinase) pathway play a crucial role. Here we have over expressed Ago-1 in Drosophila eye and brain by employing UAS (upstream activation sequence)-GAL4 system under the expression of eye and brain specific driver. Over expression of Ago-1 resulted in reduced number of ommatidia in the eye and produced smaller size brain in adult and larval Drosophila. A drastic reversal of the phenotype towards normal was observed upon introduction of a single copy of the dominant negative mutation of basket (bsk, Drosophila homolog of JNK) indicating an active and physical involvement of the bsk with Ago-1 in inducing developmental apoptotic process. Further study showed that Ago-1 stimulates phosphorylation of JNK through transforming growth factor-β activated kinase 1- hemipterous (Tak1-hep) axis of JNK pathway. JNK phosphorylation results in up regulation of pro-apoptotic genes head involution defective (hid), grim & reaper (rpr) and induces activation of Drosophila caspases (cysteinyl aspartate proteinases);DRONC (Death regulator Nedd2-like caspase), ICE (alternatively Drice, Death related ICE-like caspase) and DCP1 (Death caspase-1) by inhibiting apoptotic inhibitor protein DIAP1 (Death-associated inhibitor of apoptosis 1). Further, Ago-1 also inhibits miR-14 expression to trigger apoptosis. Our findings propose that Ago-1 acts as a key regulator in controlling cell death, tumor regression and stress response in metazoan providing a constructive bridge between RNAi machinery and cell death.
Collapse
Affiliation(s)
- Tanmoy Mondal
- Department of Chemical Biology, CSIR-Indian Institute of Chemical Technology, Tarnaka, Hyderabad, Telangana State, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-IICT Campus, Hyderabad, India
| | - Indira Bag
- Department of Chemical Biology, CSIR-Indian Institute of Chemical Technology, Tarnaka, Hyderabad, Telangana State, India
| | - Pushpavalli SNCVL
- Department of Chemical Biology, CSIR-Indian Institute of Chemical Technology, Tarnaka, Hyderabad, Telangana State, India
| | - Koteswara Rao Garikapati
- Department of Chemical Biology, CSIR-Indian Institute of Chemical Technology, Tarnaka, Hyderabad, Telangana State, India
| | - Utpal Bhadra
- Gene Silencing and Functional Genomics Group, CSIR-Centre For Cellular and Molecular Biology, Uppal Road, Hyderabad, Telangana State, India
| | - Manika Pal Bhadra
- Department of Chemical Biology, CSIR-Indian Institute of Chemical Technology, Tarnaka, Hyderabad, Telangana State, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-IICT Campus, Hyderabad, India
- * E-mail: ,
| |
Collapse
|
733
|
Calkins SS, Elledge NC, Mueller KE, Marek SM, Couger MB, Elshahed MS, Youssef NH. Development of an RNA interference (RNAi) gene knockdown protocol in the anaerobic gut fungus Pecoramyces ruminantium strain C1A. PeerJ 2018; 6:e4276. [PMID: 29404209 PMCID: PMC5796279 DOI: 10.7717/peerj.4276] [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: 08/18/2017] [Accepted: 12/29/2017] [Indexed: 12/25/2022] Open
Abstract
Members of the anaerobic gut fungi (AGF) reside in rumen, hindgut, and feces of ruminant and non-ruminant herbivorous mammals and reptilian herbivores. No protocols for gene insertion, deletion, silencing, or mutation are currently available for the AGF, rendering gene-targeted molecular biological manipulations unfeasible. Here, we developed and optimized an RNA interference (RNAi)-based protocol for targeted gene silencing in the anaerobic gut fungus Pecoramyces ruminantium strain C1A. Analysis of the C1A genome identified genes encoding enzymes required for RNA silencing in fungi (Dicer, Argonaute, Neurospora crassa QDE-3 homolog DNA helicase, Argonaute-interacting protein, and Neurospora crassa QIP homolog exonuclease); and the competency of C1A germinating spores for RNA uptake was confirmed using fluorescently labeled small interfering RNAs (siRNA). Addition of chemically-synthesized siRNAs targeting D-lactate dehydrogenase (ldhD) gene to C1A germinating spores resulted in marked target gene silencing; as evident by significantly lower ldhD transcriptional levels, a marked reduction in the D-LDH specific enzymatic activity in intracellular protein extracts, and a reduction in D-lactate levels accumulating in the culture supernatant. Comparative transcriptomic analysis of untreated versus siRNA-treated cultures identified a few off-target siRNA-mediated gene silencing effects. As well, significant differential up-regulation of the gene encoding NAD-dependent 2-hydroxyacid dehydrogenase (Pfam00389) in siRNA-treated C1A cultures was observed, which could possibly compensate for loss of D-LDH as an electron sink mechanism in C1A. The results demonstrate the feasibility of RNAi in anaerobic fungi, and opens the door for gene silencing-based studies in this fungal clade.
Collapse
Affiliation(s)
- Shelby S Calkins
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Nicole C Elledge
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA.,Current affiliation: University of Texas A&M Corpus Christi, Department of Life Sciences, Marine Biology Program, USA
| | - Katherine E Mueller
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Stephen M Marek
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK, USA
| | - M B Couger
- High Performance Computing Center, Oklahoma State University, Stillwater, OK, USA
| | - Mostafa S Elshahed
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Noha H Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| |
Collapse
|
734
|
Abstract
Mitochondria are cytosolic organelles essential for generating energy and maintaining cell homeostasis. Despite their critical function, the handful of proteins expressed by the mitochondrial genome is insufficient to maintain mitochondrial structure or activity. Accordingly, mitochondrial metabolism is fully dependent on factors encoded by the nuclear DNA, including many proteins synthesized in the cytosol and imported into mitochondria via established mechanisms. However, there is growing evidence that mammalian mitochondria can also import cytosolic noncoding RNA via poorly understood processes. Here, we summarize our knowledge of mitochondrial RNA, discuss recent progress in understanding the molecular mechanisms and functional impact of RNA import into mitochondria, and identify rising challenges and opportunities in this rapidly evolving field.
Collapse
Affiliation(s)
- Kyoung Mi Kim
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, Maryland 21224, USA
| | - Ji Heon Noh
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, Maryland 21224, USA
| | - Kotb Abdelmohsen
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, Maryland 21224, USA
| | - Myriam Gorospe
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, Maryland 21224, USA
| |
Collapse
|
735
|
Lee H, Tak H, Park SJ, Jo YK, Cho DH, Lee EK. microRNA-200a-3p enhances mitochondrial elongation by targeting mitochondrial fission factor. BMB Rep 2018; 50:214-219. [PMID: 28148392 PMCID: PMC5437966 DOI: 10.5483/bmbrep.2017.50.4.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Indexed: 12/31/2022] Open
Abstract
Mitochondria play pivotal roles in the ATP production, apoptosis and generation of reactive oxygen species. Although dynamic regulation of mitochondria morphology is a critical step to maintain cellular homeostasis, the regulatory mechanisms are not yet fully elucidated. In this study, we identified miR-200a-3p as a novel regulator of mitochondrial dynamics by targeting mitochondrial fission factor (MFF). We demonstrated that the ectopic expression of miR-200a-3p enhanced mitochondrial elongation, mitochondrial ATP synthesis, mitochondrial membrane potential and oxygen consumption rate. These results indicate that miR-200a-3p positively regulates mitochondrial elongation by downregulating MFF expression.
Collapse
Affiliation(s)
- Heejin Lee
- Department of Biochemistry, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
| | - Hyosun Tak
- Department of Biochemistry, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
| | - So Jung Park
- Department of Gerontology, Graduate School of East-West Medical Science, Kyung Hee University, Yongin 17014, Korea
| | - Yoon Kyung Jo
- Department of Gerontology, Graduate School of East-West Medical Science, Kyung Hee University, Yongin 17014, Korea
| | - Dong Hyung Cho
- Department of Gerontology, Graduate School of East-West Medical Science, Kyung Hee University, Yongin 17014, Korea
| | - Eun Kyung Lee
- Department of Biochemistry, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
| |
Collapse
|
736
|
Mostoufi-Afshar S, Tabatabaei M, Ghahramani Seno MM. Mycobacterium avium subsp. paratuberculosis induces differential cytosine methylation at miR-21 transcription start site region. IRANIAN JOURNAL OF VETERINARY RESEARCH 2018; 19:262-269. [PMID: 30774666 PMCID: PMC6361596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 08/06/2018] [Accepted: 08/28/2018] [Indexed: 06/09/2023]
Abstract
Mycobacterium avium subspecies paratuberculosis (MAP), as an obligate intracellular bacterium, causes paratuberculosis (Johne's disease) in ruminants. Plus, MAP has consistently been isolated from Crohn's disease (CD) lesions in humans; a notion implying possible direct causative effect for MAP in CD development. Infections caused by MAP are refractory to treatment and in many cases the treatment does not easily resolve the infection. Studying the molecular mechanisms of host-pathogen interaction is helpful in identifying possible drug targets. In this line, it has already been shown that in macrophages infected with various bacteria, including mycobacteria, micro RNA 21 (miR-21) is upregulated, a change that results in diminished macrophages clearance ability and favours pathogens survival within the cells. However, the molecular mechanism(s) by which the intracellular bacteria induce miR-21 expression is not known. In order to verify possible effects from epigenetic changes induced by intracellular bacteria, we studied the cytosine methylation changes at the transcription start regions of miR-21 in THP-1 macrophages infected with MAP. For this purpose, genomic DNA was extracted from infected cells and the methylation status at the region of interest was evaluated by bisulfite conversion method. Our work showed that MAP directs de-methylation of the cystosines at CpG di-nucleotides in this region, while non-CpG cytosines of this region did not show significant changes. Interestingly, the CpG cytosines that were differentially methylated in the infected macrophages occur at the binding sites of the transcription factors already known to regulate miR-21 expression.
Collapse
Affiliation(s)
- S. Mostoufi-Afshar
- Graduated from School of Veterinary Medicine, Shiraz University, Shiraz, Iran
| | - M. Tabatabaei
- Department of Pathobiology, School of Veterinary Medicine, Shiraz University, Shiraz, Iran
| | - M. M. Ghahramani Seno
- Department of Basic Sciences, and Division of Biotechnology, Department of Pathobiology, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran
| |
Collapse
|
737
|
Meta-Analysis of MicroRNAs Dysregulated in the Hippocampal Dentate Gyrus of Animal Models of Epilepsy. eNeuro 2017; 4:eN-NWR-0152-17. [PMID: 29291240 PMCID: PMC5745610 DOI: 10.1523/eneuro.0152-17.2017] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 11/21/2017] [Accepted: 11/22/2017] [Indexed: 12/12/2022] Open
Abstract
The identification of mechanisms transforming normal to seizure-generating tissue after brain injury is key to developing new antiepileptogenic treatments. MicroRNAs (miRNAs) may act as regulators and potential treatment targets for epileptogenesis. Here, we undertook a meta-analysis of changes in miRNA expression in the hippocampal dentate gyrus (DG) following an epileptogenic insult in three epilepsy models. We identified 26 miRNAs significantly differentially expressed during epileptogenesis, and five differentially expressed in chronic epilepsy. Of these, 13 were not identified in any of the individual studies. To assess the role of these miRNAs, we predicted their mRNA targets and then filtered the list to include only target genes expressed in DG and negatively correlated with miRNA expression. Functional enrichment analysis of mRNA targets of miRNAs dysregulated during epileptogenesis suggested a role for molecular processes related to inflammation and synaptic function. Our results identify new miRNAs associated with epileptogenesis from existing data, highlighting the utility of meta-analysis in maximizing value from preclinical data.
Collapse
|
738
|
A logic-based dynamic modeling approach to explicate the evolution of the central dogma of molecular biology. PLoS One 2017; 12:e0189922. [PMID: 29267315 PMCID: PMC5739447 DOI: 10.1371/journal.pone.0189922] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2017] [Accepted: 12/05/2017] [Indexed: 01/23/2023] Open
Abstract
It is nearly half a century past the age of the introduction of the Central Dogma (CD) of molecular biology. This biological axiom has been developed and currently appears to be all the more complex. In this study, we modified CD by adding further species to the CD information flow and mathematically expressed CD within a dynamic framework by using Boolean network based on its present-day and 1965 editions. We show that the enhancement of the Dogma not only now entails a higher level of complexity, but it also shows a higher level of robustness, thus far more consistent with the nature of biological systems. Using this mathematical modeling approach, we put forward a logic-based expression of our conceptual view of molecular biology. Finally, we show that such biological concepts can be converted into dynamic mathematical models using a logic-based approach and thus may be useful as a framework for improving static conceptual models in biology.
Collapse
|
739
|
Avital G, França GS, Yanai I. Bimodal Evolutionary Developmental miRNA Program in Animal Embryogenesis. Mol Biol Evol 2017; 35:646-654. [PMID: 29237075 DOI: 10.1093/molbev/msx316] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
miRNAs play essential roles in the mechanics of gene regulation, however, on an organismal-scale, the processes in which they are deployed are not well understood. Here, we adopt an evolutionary developmental approach to study miRNA function by examining their expression throughout embryogenesis in both Caenorhabditis elegans and Drosophila melanogaster. We find that, in both species, miRNA transcriptomic shifts in a punctuated fashion during the mid-developmental transition, specifying two dominant modes of early and late expression profiles. Strikingly, late-expressed miRNAs are enriched for phylogenetic conservation and function by fine-tuning the expression of their targets, implicating a role in the canalization of cell types during differentiation. In contrast, early expressed miRNAs are inversely expressed with their targets suggesting strong target-inhibition. Taken together, our work exposes a bimodal role for miRNA function during animal development, involving late-expressed physiological roles and early expressed repressive roles.
Collapse
Affiliation(s)
- Gal Avital
- Department of Biology, Technion-Israel Institute of Technology, Haifa, Israel.,Department of Biochemistry and Molecular Pharmacology, Institute for Computational Medicine, New York University School of Medicine, New York, NY
| | - Gustavo S França
- Department of Biochemistry and Molecular Pharmacology, Institute for Computational Medicine, New York University School of Medicine, New York, NY
| | - Itai Yanai
- Department of Biochemistry and Molecular Pharmacology, Institute for Computational Medicine, New York University School of Medicine, New York, NY
| |
Collapse
|
740
|
Chen Y, Wang J, Yang S, Utturkar S, Crodian J, Cummings S, Thimmapuram J, San Miguel P, Kuang S, Gribskov M, Plaut K, Casey T. Effect of high-fat diet on secreted milk transcriptome in midlactation mice. Physiol Genomics 2017; 49:747-762. [PMID: 29093195 DOI: 10.1152/physiolgenomics.00080.2017] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
High-fat diet (HFD) during lactation alters milk composition and is associated with development of metabolic diseases in the offspring. We hypothesized that HFD affects milk microRNA (miRNA) and mRNA content, which potentially impact offspring development. Our objective was to determine the effect of maternal HFD on secreted milk transcriptome. To meet this objective, 4 wk old female ICR mice were divided into two treatments: control diet containing 10% kcal fat and HFD containing 60% kcal fat. After 4 wk on CD or HFD, mice were bred while continuously fed the same diets. On postnatal day 2 (P2), litters were normalized to 10 pups, and half the pups in each litter were cross-fostered between treatments. Milk was collected from dams on P10 and P12. Total RNA was isolated from milk fat fraction of P10 samples and used for mRNA-Seq and small RNA-Seq. P12 milk was used to determine macronutrient composition. After 4 wk of prepregnancy feeding HFD mice weighed significantly more than did the control mice. Lactose and fat concentration were significantly ( P < 0.05) higher in milk of HFD dams. Pup weight was significantly greater ( P < 0.05) in groups suckled by HFD vs. control dams. There were 25 miRNA and over 1,500 mRNA differentially expressed (DE) in milk of HFD vs. control dams. DE mRNA and target genes of DE miRNA enriched categories that were primarily related to multicellular organismal development. Maternal HFD impacts mRNA and miRNA content of milk, if bioactive nucleic acids are absorbed by neonate differences may affect development.
Collapse
Affiliation(s)
- Y. Chen
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana
| | - J. Wang
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana
| | - S. Yang
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana
| | - S. Utturkar
- Bioinformatics Core, Purdue University, West Lafayette, Indiana
| | - J. Crodian
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana
| | - S. Cummings
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana
| | - J. Thimmapuram
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana
| | - P. San Miguel
- Genomics Core at Purdue University, West Lafayette, Indiana
| | - S. Kuang
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana
| | - M. Gribskov
- Bioinformatics Core, Purdue University, West Lafayette, Indiana
| | - K. Plaut
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana
| | - T. Casey
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana
| |
Collapse
|
741
|
Transcription start site-associated small RNAs in the PTEN gene. Proc Natl Acad Sci U S A 2017; 114:E10510-E10511. [PMID: 29138324 DOI: 10.1073/pnas.1718027114] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
|
742
|
Bortolomeazzi M, Gaffo E, Bortoluzzi S. A survey of software tools for microRNA discovery and characterization using RNA-seq. Brief Bioinform 2017; 20:918-930. [DOI: 10.1093/bib/bbx148] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 10/12/2017] [Indexed: 01/08/2023] Open
Affiliation(s)
| | - Enrico Gaffo
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | | |
Collapse
|
743
|
Hassanlou M, Soltani BM, Mowla SJ. Expression and Function of hsa-miR-6165 in Human Cell Lines and During the NT2 Cell Neural Differentiation Process. J Mol Neurosci 2017; 63:254-266. [PMID: 28956260 DOI: 10.1007/s12031-017-0954-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 07/20/2017] [Indexed: 12/31/2022]
Abstract
MicroRNAs are small non-coding RNAs that posttranscriptionally regulate mRNA expression. hsa-miR-6165 which was previously discovered in our group is located in the forth intron of p75NTR gene and its function is still under investigation. As P75NTR has diverse cellular functions, some of the complexity of its function could be attributed to the internally located microRNA. Our analysis revealed that treatment of HCT116 cells with 5-azacytidine promoted differential expression of hsa-miR-6165 from its host gene which is consistent with the bioinformatic prediction of an independent promoter for hsa-miR-6165. In addition, hsa-miR-6165 promoter is capable of driving GFP reporter gene in HeLa cells. The putative target gene expression level which was detected using RT-qPCR is inversely proportional to the expression level of hsa-miR-6165 during NT2 cell neural differentiation. Furthermore, hsa-miR-6165 overexpression resulted in significant downregulation of ABLIM-1, PVRL1, and PDK1 target genes, while it attenuates NT2 neural differentiation. Hsa-miR-6165 overexpression in SW480 cells also resulted in significant downregulation of PKD1, DAGLA, and PLXNA2 putative target genes, while it increases the sub-G1 cell population of SW480 and HEK293T cells as detected by flow cytometry. Overall, in this study, we report an independent promoter for hsa-miR-6165 which is active in HeLa cells. Additionally, hsa-miR-6165 targets ABLIM-1, PVRL1, PKD1, PLXNA2, and PDK1 genes, and unlike in HEK293T and SW480 cells, hsa-miR-6165 overexpression does not affect HeLa cells while its downregulation reduces sub-G1 cell population. Our results validate that hsa-miR-6165 affects the cell cycle progression and could increase apoptosis in human cell lines.
Collapse
Affiliation(s)
- Maryam Hassanlou
- Molecular Genetics Department, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Bahram Mohammad Soltani
- Molecular Genetics Department, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
| | - Seyed Javad Mowla
- Molecular Genetics Department, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
| |
Collapse
|
744
|
Iacomino G, Siani A. Role of microRNAs in obesity and obesity-related diseases. GENES AND NUTRITION 2017; 12:23. [PMID: 28974990 PMCID: PMC5613467 DOI: 10.1186/s12263-017-0577-z] [Citation(s) in RCA: 134] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 09/12/2017] [Indexed: 12/15/2022]
Abstract
In recent years, the link between regulatory microRNAs (miRNAs) and diseases has been the object of intensive research. miRNAs have emerged as key mediators of metabolic processes, playing crucial roles in maintaining/altering physiological processes, including energy balance and metabolic homeostasis. Altered miRNAs expression has been reported in association with obesity, both in animal and human studies. Dysregulation of miRNAs may affect the status and functions of different tissues and organs, including the adipose tissue, pancreas, liver, and muscle, possibly contributing to metabolic abnormalities associated with obesity and obesity-related diseases. More recently, the discovery of circulating miRNAs easily detectable in plasma and other body fluids has emphasized their potential as both endocrine signaling molecules and disease indicators. In this review, the status of current research on the role of miRNAs in obesity and related metabolic abnormalities is summarized and discussed.
Collapse
Affiliation(s)
- Giuseppe Iacomino
- Institute of Food Sciences, CNR, Via Roma, 64, 83100 Avellino, Italy
| | - Alfonso Siani
- Institute of Food Sciences, CNR, Via Roma, 64, 83100 Avellino, Italy
| |
Collapse
|
745
|
A Concise Review of MicroRNA Exploring the Insights of MicroRNA Regulations in Bacterial, Viral and Metabolic Diseases. Mol Biotechnol 2017; 59:518-529. [DOI: 10.1007/s12033-017-0034-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
|
746
|
Marie-Claire C, Jourdaine C, Lépine JP, Bellivier F, Bloch V, Vorspan F. Pharmacoepigenomics of opiates and methadone maintenance treatment: current data and perspectives. Pharmacogenomics 2017; 18:1359-1372. [DOI: 10.2217/pgs-2017-0040] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Current treatments of opioid addiction include primarily maintenance medications such as methadone. Chronic exposure to opiate and/or long-lasting maintenance treatment induce modulations of gene expression in brain and peripheral tissues. There is increasing evidence that epigenetic modifications underlie these modulations. This review summarizes published results on opioid-induced epigenetic changes in animal models and in patients. The epigenetic modifications observed with other drugs of abuse often used by opiate abusers are also outlined. Specific methadone maintenance treatment induced epigenetic modifications at different treatment stages may be combined with the ones resulting from patients’ substance use history. Therefore, research comparing groups of addicts with similar history and substances use disorders but contrasting for well-characterized treatment phenotypes should be encouraged.
Collapse
Affiliation(s)
- Cynthia Marie-Claire
- Variabilité de réponse aux psychotropes, INSERMU1144/Faculté de Pharmacie de Paris/Université Paris Descartes/Université ParisDiderot/Université Sorbonne Paris Cité, Paris, France
| | - Clément Jourdaine
- AP-HP, GH Saint-Louis – Lariboisière – F. Widal, Pôle de Psychiatrie et de Médecine Addictologique, 75475 Paris cedex 10, France
| | - Jean-Pierre Lépine
- AP-HP, GH Saint-Louis – Lariboisière – F. Widal, Pôle de Psychiatrie et de Médecine Addictologique, 75475 Paris cedex 10, France
| | - Frank Bellivier
- Variabilité de réponse aux psychotropes, INSERMU1144/Faculté de Pharmacie de Paris/Université Paris Descartes/Université ParisDiderot/Université Sorbonne Paris Cité, Paris, France
- AP-HP, GH Saint-Louis – Lariboisière – F. Widal, Pôle de Psychiatrie et de Médecine Addictologique, 75475 Paris cedex 10, France
| | - Vanessa Bloch
- Variabilité de réponse aux psychotropes, INSERMU1144/Faculté de Pharmacie de Paris/Université Paris Descartes/Université ParisDiderot/Université Sorbonne Paris Cité, Paris, France
| | - Florence Vorspan
- Variabilité de réponse aux psychotropes, INSERMU1144/Faculté de Pharmacie de Paris/Université Paris Descartes/Université ParisDiderot/Université Sorbonne Paris Cité, Paris, France
- AP-HP, GH Saint-Louis – Lariboisière – F. Widal, Pôle de Psychiatrie et de Médecine Addictologique, 75475 Paris cedex 10, France
| |
Collapse
|
747
|
Kiripolsky J, McCabe LG, Kramer JM. Innate immunity in Sjögren's syndrome. Clin Immunol 2017; 182:4-13. [PMID: 28396235 PMCID: PMC6025757 DOI: 10.1016/j.clim.2017.04.003] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 04/04/2017] [Accepted: 04/05/2017] [Indexed: 12/18/2022]
Abstract
Sjögren's syndrome (SS) is an autoimmune disease of exocrine tissue that primarily affects women. Although patients typically experience xerostomia and xerophthalmia, numerous systemic disease manifestations are seen. Innate immune hyperactivity is integral to many autoimmune diseases, including SS. Results from SS mouse models suggest that innate immune dysregulation drives disease and this is a seminal event in SS pathogenesis. Findings in SS patients corroborate those in mouse models, as innate immune cells and pathways are dysregulated both in exocrine tissue and in peripheral blood. We will review the role of the innate immune system in SS pathogenesis. We will discuss the etiology of SS with an emphasis on innate immune dysfunction. Moreover, we will review the innate cells that mediate inflammation in SS, the pathways implicated in disease, and the potential mechanisms governing their dysregulation. Finally, we will discuss emerging therapeutic approaches to target dysregulated innate immune signaling in SS.
Collapse
Affiliation(s)
- Jeremy Kiripolsky
- Department of Oral Biology, School of Dental Medicine, State University of New York at Buffalo, Buffalo, NY 14214, United States
| | - Liam G McCabe
- Department of Oral Biology, School of Dental Medicine, State University of New York at Buffalo, Buffalo, NY 14214, United States
| | - Jill M Kramer
- Department of Oral Biology, School of Dental Medicine, State University of New York at Buffalo, Buffalo, NY 14214, United States; Department of Oral Diagnostic Sciences, School of Dental Medicine, State University of New York at Buffalo, Buffalo, NY 14214, United States.
| |
Collapse
|
748
|
McMillan KJ, Murray TK, Bengoa-Vergniory N, Cordero-Llana O, Cooper J, Buckley A, Wade-Martins R, Uney JB, O'Neill MJ, Wong LF, Caldwell MA. Loss of MicroRNA-7 Regulation Leads to α-Synuclein Accumulation and Dopaminergic Neuronal Loss In Vivo. Mol Ther 2017; 25:2404-2414. [PMID: 28927576 DOI: 10.1016/j.ymthe.2017.08.017] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 06/13/2017] [Accepted: 08/24/2017] [Indexed: 12/15/2022] Open
Abstract
Abnormal alpha-synuclein (α-synuclein) expression and aggregation is a key characteristic of Parkinson's disease (PD). However, the exact mechanism(s) linking α-synuclein to the other central feature of PD, dopaminergic neuron loss, remains unclear. Therefore, improved cell and in vivo models are needed to investigate the role of α-synuclein in dopaminergic neuron loss. MicroRNA-7 (miR-7) regulates α-synuclein expression by binding to the 3' UTR of the Synuclein Alpha Non A4 Component of Amyloid Precursor (SNCA) gene and inhibiting its translation. We show that miR-7 is decreased in the substantia nigra of patients with PD and, therefore, may play an essential role in the regulation of α-synuclein expression. Furthermore, we have found that lentiviral-mediated expression of miR-7 complementary binding sites to stably induce a loss of miR-7 function results in an increase in α-synuclein expression in vitro and in vivo. We have also shown that depletion of miR-7 using a miR-decoy produces a loss of nigral dopaminergic neurons accompanied by a reduction of striatal dopamine content. These data suggest that miR-7 has an important role in the regulation of α-synuclein and dopamine physiology and may provide a new paradigm to study the pathology of PD.
Collapse
Affiliation(s)
- Kirsty J McMillan
- Regenerative Medicine Laboratory, School of Clinical Sciences, Bristol BS1 8TH, UK
| | - Tracey K Murray
- Eli Lilly & Co. Ltd., Erl Wood Manor, Windlesham, Surrey GU20 6PH, UK
| | - Nora Bengoa-Vergniory
- Department of Physiology, Anatomy and Genetics, Oxford Parkinson's Disease Center, Oxford OX1 3QX, UK
| | - Oscar Cordero-Llana
- Regenerative Medicine Laboratory, School of Clinical Sciences, Bristol BS1 8TH, UK
| | - Jane Cooper
- Eli Lilly & Co. Ltd., Erl Wood Manor, Windlesham, Surrey GU20 6PH, UK
| | - Amy Buckley
- Trinity College Institute for Neuroscience, Trinity College Dublin, Dublin 2, Ireland
| | - Richard Wade-Martins
- Department of Physiology, Anatomy and Genetics, Oxford Parkinson's Disease Center, Oxford OX1 3QX, UK
| | - James B Uney
- Regenerative Medicine Laboratory, School of Clinical Sciences, Bristol BS1 8TH, UK
| | - Michael J O'Neill
- Eli Lilly & Co. Ltd., Erl Wood Manor, Windlesham, Surrey GU20 6PH, UK
| | - Liang F Wong
- Regenerative Medicine Laboratory, School of Clinical Sciences, Bristol BS1 8TH, UK
| | - Maeve A Caldwell
- Trinity College Institute for Neuroscience, Trinity College Dublin, Dublin 2, Ireland.
| |
Collapse
|
749
|
An alternative microRNA-mediated post-transcriptional regulation of GADD45A by p53 in human non-small-cell lung cancer cells. Sci Rep 2017; 7:7153. [PMID: 28769054 PMCID: PMC5541050 DOI: 10.1038/s41598-017-07332-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 06/28/2017] [Indexed: 01/30/2023] Open
Abstract
GADD45A (growth arrest and DNA damage inducible alpha), a stress response gene induced by genotoxic and nongenotoxic stresses, is implicated in various key processes, including the control of cell cycle checkpoints and DNA repair. The expression of GADD45A is directly regulated by numerous transcription factors, with p53 being the most representative. Moreover, post-transcriptional regulation also plays a role in GADD45A expression. However, little is known about the regulatory effects of microRNAs (miRNAs) on GADD45A expression. As a potential tumour suppressor, miR-138 has pleiotropic biological functions in various cancers. We have previously reported p53-mediated activation of miR-138 in human non-small-cell lung cancer (NSCLC) cells. In this study, we found that miR-138 specifically targeted AGO2, which affects the stability and maturation of miR-130b. Decreased expression of miR-130b promoted the expression of GADD45A and resulted in the G2/M phase arrest and proliferation inhibition in human NSCLC cells. Our results suggested that p53 could alternatively upregulate GADD45A in human NSCLC cells through a post-transcriptional pathway in which miR-138 is involved.
Collapse
|
750
|
Induction of alpha-methylacyl-CoA racemase by miR-138 via up-regulation of β-catenin in prostate cancer cells. J Cancer Res Clin Oncol 2017; 143:2201-2210. [PMID: 28741117 DOI: 10.1007/s00432-017-2484-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 07/19/2017] [Indexed: 10/19/2022]
Abstract
PURPOSE Alpha-methylacyl-CoA racemase (AMACR) is highly overexpressed in prostate cancer (PCa) and its transcriptional regulators include various transcription factors and CTNNB1/β-catenin. Our previous findings suggested a post-transcriptional regulation by the tumor-suppressive microRNA miR-138 in PCa. Thus, the aim of this study was to demonstrate the direct interaction of miR-138 with the 3'-UTR of AMACR. Furthermore, the influence of miR-138 on the expression of AMACR and selected AMACR regulators was investigated in PCa cells. METHODS Using DU-145, PC-3, and LNCaP PCa cells, the effect of exogenous miR-138 on AMACR and selected AMACR regulators was determined by quantitative PCR and Western blot. Luciferase reporter assays were used to verify target and promoter interaction. RESULTS Using a luciferase reporter assay a direct interaction of miR-138 with the AMACR-3'-UTR was confirmed. Surprisingly, AMACR expression was up-regulated by up to 125% by exogenous miR-138 in PCa cells. The lack of any miR-138 binding sites within the AMACR promoter suggested an indirect mechanism of up-regulation. Therefore, the effect of miR-138 on selected AMACR regulators including CTNNB1/β-catenin, RELA, SMAD4, SP1, and TCF4 was evaluated. MiR-138 solely evoked an up-regulation of CTNNB1 mRNA expression and β-catenin protein levels by up to 75%. Further in silico analysis revealed a binding site for miR-138 within the CTNNB1 promoter. MiR-138 could enhance the activity of the CTNNB1 promoter, which in turn could contribute to the observed AMACR up-regulation. CONCLUSIONS The present findings suggest that miR-138 can indirectly up-regulate AMACR via transcriptional induction of CTNNB1, at least in vitro in PCa cells.
Collapse
|