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Isaac R, Reis FCG, Ying W, Olefsky JM. Exosomes as mediators of intercellular crosstalk in metabolism. Cell Metab 2021; 33:1744-1762. [PMID: 34496230 PMCID: PMC8428804 DOI: 10.1016/j.cmet.2021.08.006] [Citation(s) in RCA: 284] [Impact Index Per Article: 94.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 07/07/2021] [Accepted: 08/11/2021] [Indexed: 02/08/2023]
Abstract
Exosomes are nanoparticles secreted by all cell types and are a large component of the broader class of nanoparticles termed extracellular vesicles (EVs). Once secreted, exosomes gain access to the interstitial space and ultimately the circulation, where they exert local paracrine or distal systemic effects. Because of this, exosomes are important components of an intercellular and intraorgan communication system capable of carrying biologic signals from one cell type or tissue to another. The exosomal cargo consists of proteins, lipids, miRNAs, and other RNA species, and many of the biologic effects of exosomes have been attributed to miRNAs. Exosomal miRNAs have also been used as disease biomarkers. The field of exosome biology and metabolism is rapidly expanding, with new discoveries and reports appearing on a regular basis, and it is possible that potential therapeutic approaches for the use of exosomes or miRNAs in metabolic diseases will be initiated in the near future.
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Affiliation(s)
- Roi Isaac
- Division of Endocrinology & Metabolism, Department of Medicine, University of California, San Diego, San Diego, CA, USA
| | - Felipe Castellani Gomes Reis
- Division of Endocrinology & Metabolism, Department of Medicine, University of California, San Diego, San Diego, CA, USA
| | - Wei Ying
- Division of Endocrinology & Metabolism, Department of Medicine, University of California, San Diego, San Diego, CA, USA
| | - Jerrold M Olefsky
- Division of Endocrinology & Metabolism, Department of Medicine, University of California, San Diego, San Diego, CA, USA.
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52
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Zhou H, Hussain SS, Shi BJ. One vector-based method to verify predicted plant miRNAs, target sequences, and function modes. Biotechnol Bioeng 2021; 118:3105-3116. [PMID: 34002369 DOI: 10.1002/bit.27821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 05/02/2021] [Accepted: 05/12/2021] [Indexed: 11/09/2022]
Abstract
Many microRNAs (miRNAs) have been predicted from small RNA sequencing data, but little was experimentally verified due to the lack of effective methods. Here, we developed a simple and reliable dual gene expression cassette vector-based method to verify predicted plant miRNAs. We cloned osa-miR528 as a known miRNA, hvu-miRX as a predicted miRNA and TaDREB3 open reading frame as a non-miRNA into the first gene expression cassette and fused their complementary or noncomplementary sequences as predicted target or nontarget sequences with the 3' untranslated region of green fluorescent protein (GFP) in the second one. When these constructs were bombarded into plant cells, only the construct containing both osa-miR528 or hvu-miRX and its complementary sequence did not generate green fluorescence. Stem-loop reverse-transcription polymerase chain reaction detected mature osa-miR528 or mature hvu-miRX in the cells, while northern analysis showed that GFP messenger RNA from the construct containing both osa-miR528 or hvu-miRX and its complementary sequence was degraded. Taken together, the results indicate that hvu-miRX is an authentic miRNA like osa-miR528, miRNA's complementary sequence is its target sequence, and both osa-miR528 and hvu-miRX silenced the GFP expression via a cleavage mode. Our method thus facilitates the verification of predicted plant miRNAs, target sequences, and function modes.
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Affiliation(s)
- Hui Zhou
- School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, South Australia, Australia
| | - Syed S Hussain
- School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, South Australia, Australia
| | - Bu-Jun Shi
- School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, South Australia, Australia
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53
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Tastsoglou S, Miliotis M, Kavakiotis I, Alexiou A, Gkotsi EC, Lambropoulou A, Lygnos V, Kotsira V, Maroulis V, Zisis D, Skoufos G, Hatzigeorgiou AG. PlasmiR: A Manual Collection of Circulating microRNAs of Prognostic and Diagnostic Value. Cancers (Basel) 2021; 13:cancers13153680. [PMID: 34359584 PMCID: PMC8345031 DOI: 10.3390/cancers13153680] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 07/11/2021] [Accepted: 07/19/2021] [Indexed: 11/16/2022] Open
Abstract
Only recently, microRNAs (miRNAs) were found to exist in traceable and distinctive amounts in the human circulatory system, bringing forth the intriguing possibility of using them as minimally invasive biomarkers. miRNAs are short non-coding RNAs that act as potent post-transcriptional regulators of gene expression. Extensive studies in cancer and other disease landscapes investigate the protective/pathogenic functions of dysregulated miRNAs, as well as their biomarker potential. A specialized resource amassing experimentally verified, circulating miRNA biomarkers does not exist. We queried the existing literature to identify articles assessing diagnostic/prognostic roles of miRNAs in blood, serum, or plasma samples. Articles were scrutinized in order to exclude instances lacking sufficient experimental documentation or employing no biomarker assessment methods. We incorporated information from more than 200 biomedical articles, annotating crucial meta-information including cohort sizes, inclusion-exclusion criteria, disease/healthy confirmation methods and quantification details. miRNAs and diseases were systematically characterized using reference resources. Our circulating miRNA biomarker collection is provided as an online database, plasmiR. It consists of 1021 entries regarding 251 miRNAs and 112 diseases. More than half of plasmiR's entries refer to cancerous and neoplastic conditions, 183 of them (32%) describing prognostic associations. plasmiR facilitates smart queries, emphasizing visualization and exploratory modes for all researchers.
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Affiliation(s)
- Spyros Tastsoglou
- Hellenic Pasteur Institute, 11521 Athens, Greece; (M.M.); (A.A.); (A.L.); (V.L.); (D.Z.); (G.S.)
- DIANA-Lab, Department of Computer Science and Biomedical Informatics, University of Thessaly, 35131 Lamia, Greece; (I.K.); (V.K.)
- Correspondence: (S.T.); (A.G.H.)
| | - Marios Miliotis
- Hellenic Pasteur Institute, 11521 Athens, Greece; (M.M.); (A.A.); (A.L.); (V.L.); (D.Z.); (G.S.)
- DIANA-Lab, Department of Computer Science and Biomedical Informatics, University of Thessaly, 35131 Lamia, Greece; (I.K.); (V.K.)
| | - Ioannis Kavakiotis
- DIANA-Lab, Department of Computer Science and Biomedical Informatics, University of Thessaly, 35131 Lamia, Greece; (I.K.); (V.K.)
| | - Athanasios Alexiou
- Hellenic Pasteur Institute, 11521 Athens, Greece; (M.M.); (A.A.); (A.L.); (V.L.); (D.Z.); (G.S.)
- DIANA-Lab, Department of Computer Science and Biomedical Informatics, University of Thessaly, 35131 Lamia, Greece; (I.K.); (V.K.)
| | - Eleni C. Gkotsi
- Department of Informatics and Telecommunications, Postgraduate Program: ‘Information Technologies in Medicine and Biology’, University of Athens, 15784 Athens, Greece; (E.C.G.); (V.M.)
| | - Anastasia Lambropoulou
- Hellenic Pasteur Institute, 11521 Athens, Greece; (M.M.); (A.A.); (A.L.); (V.L.); (D.Z.); (G.S.)
| | - Vasileios Lygnos
- Hellenic Pasteur Institute, 11521 Athens, Greece; (M.M.); (A.A.); (A.L.); (V.L.); (D.Z.); (G.S.)
| | - Vasiliki Kotsira
- DIANA-Lab, Department of Computer Science and Biomedical Informatics, University of Thessaly, 35131 Lamia, Greece; (I.K.); (V.K.)
| | - Vasileios Maroulis
- Department of Informatics and Telecommunications, Postgraduate Program: ‘Information Technologies in Medicine and Biology’, University of Athens, 15784 Athens, Greece; (E.C.G.); (V.M.)
| | - Dimitrios Zisis
- Hellenic Pasteur Institute, 11521 Athens, Greece; (M.M.); (A.A.); (A.L.); (V.L.); (D.Z.); (G.S.)
| | - Giorgos Skoufos
- Hellenic Pasteur Institute, 11521 Athens, Greece; (M.M.); (A.A.); (A.L.); (V.L.); (D.Z.); (G.S.)
- Department of Electrical and Computer Engineering, University of Thessaly, 38221 Volos, Greece
| | - Artemis G. Hatzigeorgiou
- Hellenic Pasteur Institute, 11521 Athens, Greece; (M.M.); (A.A.); (A.L.); (V.L.); (D.Z.); (G.S.)
- DIANA-Lab, Department of Computer Science and Biomedical Informatics, University of Thessaly, 35131 Lamia, Greece; (I.K.); (V.K.)
- Correspondence: (S.T.); (A.G.H.)
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54
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β-Cell pre-mir-21 induces dysfunction and loss of cellular identity by targeting transforming growth factor beta 2 (Tgfb2) and Smad family member 2 (Smad2) mRNAs. Mol Metab 2021; 53:101289. [PMID: 34246804 PMCID: PMC8361274 DOI: 10.1016/j.molmet.2021.101289] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 06/30/2021] [Accepted: 07/05/2021] [Indexed: 12/13/2022] Open
Abstract
OBJECTIVE β-cell microRNA-21 (miR-21) is increased by islet inflammatory stress but it decreases glucose-stimulated insulin secretion (GSIS). Thus, we sought to define the effects of miR-21 on β-cell function using in vitro and in vivo systems. METHODS We developed a tetracycline-on system of pre-miR-21 induction in clonal β-cells and human islets, along with transgenic zebrafish and mouse models of β-cell-specific pre-miR-21 overexpression. RESULTS β-cell miR-21 induction markedly reduced GSIS and led to reductions in transcription factors associated with β-cell identity and increased markers of dedifferentiation, which led us to hypothesize that miR-21 induces β-cell dysfunction by loss of cell identity. In silico analysis identified transforming growth factor-beta 2 (Tgfb2) and Smad family member 2 (Smad2) mRNAs as predicted miR-21 targets associated with the maintenance of β-cell identity. Tgfb2 and Smad2 were confirmed as direct miR-21 targets through RT-PCR, immunoblot, pulldown, and luciferase assays. In vivo zebrafish and mouse models exhibited glucose intolerance, decreased peak GSIS, decreased expression of β-cell identity markers, increased insulin and glucagon co-staining cells, and reduced Tgfb2 and Smad2 expression. CONCLUSIONS These findings implicate miR-21-mediated reduction of mRNAs specifying β-cell identity as a contributor to β-cell dysfunction by the loss of cellular differentiation.
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Abstract
Metastasis is a major contributor to cancer-associated deaths. It is characterized by a multistep process that occurs through the acquisition of molecular and phenotypic changes enabling cancer cells from a primary tumour to disseminate and colonize at distant organ sites. Over the past decade, the discovery and characterization of long noncoding RNAs (lncRNAs) have revealed the diversity of their regulatory roles, including key contributions throughout the metastatic cascade. Here, we review how lncRNAs promote metastasis by functioning in discrete pro-metastatic steps including the epithelial-mesenchymal transition, invasion and migration and organotrophic colonization, and by influencing the metastatic tumour microenvironment, often by interacting within ribonucleoprotein complexes or directly with other nucleic acid entities. We discuss well-characterized lncRNAs with in vivo phenotypes and highlight mechanistic commonalities such as convergence with the TGFβ-ZEB1/ZEB2 axis or the nuclear factor-κB pathway, in addition to lncRNAs with controversial mechanisms and the influence of methodologies on mechanistic interpretation. Furthermore, some lncRNAs can help identify tumours with increased metastatic risk and spur novel therapeutic strategies, with several lncRNAs having shown potential as novel targets for antisense oligonucleotide therapy in animal models. In addition to well-characterized examples of lncRNAs functioning in metastasis, we discuss controversies and ongoing challenges in lncRNA biology. Finally, we present areas for future study for this rapidly evolving field.
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Affiliation(s)
- S John Liu
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, USA
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA, USA
| | - Ha X Dang
- Department of Internal Medicine, Washington University in St Louis, St Louis, MO, USA
- Siteman Cancer Center, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Daniel A Lim
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA, USA
- San Francisco Veterans Affairs Medical Center, San Francisco, CA, USA
| | - Felix Y Feng
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
| | - Christopher A Maher
- Department of Internal Medicine, Washington University in St Louis, St Louis, MO, USA.
- Siteman Cancer Center, Washington University in St Louis, St Louis, MO, USA.
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA.
- Department of Biomedical Engineering, Washington University in St Louis, St Louis, MO, USA.
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56
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Mortazavi SS, Bahmanpour Z, Daneshmandpour Y, Roudbari F, Sheervalilou R, Kazeminasab S, Emamalizadeh B. An updated overview and classification of bioinformatics tools for MicroRNA analysis, which one to choose? Comput Biol Med 2021; 134:104544. [PMID: 34119921 DOI: 10.1016/j.compbiomed.2021.104544] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 05/30/2021] [Accepted: 05/30/2021] [Indexed: 12/16/2022]
Abstract
The term 'MicroRNA' (miRNA) refers to a class of small endogenous non-coding RNAs (ncRNAs) regenerated from hairpin transcripts. Recent studies reveal miRNAs' regulatory involvement in essential biological processes through translational repression or mRNA degradation. Recently, there is a growing body of literature focusing on the importance of miRNAs and their functions. In this respect, several databases have been developed to manage the dispersed data produced. Therefore, it is necessary to know the parameters and characteristics of each database to benefit their data. Besides, selecting the correct database is of great importance to scientists who do not have enough experience in this field. A comprehensive classification along with an explanation of the information contained in each database leads to facilitating access to these resources. In this regard, we have classified relevant databases into several categories, including miRNA sequencing and annotation, validated/predicted miRNA targets, disease-related miRNA, SNP in miRNA sequence or target site, miRNA-related pathways, or gene ontology, and mRNA-miRNA interactions. Hence, this review introduces available miRNA databases and presents a convenient overview to inform researchers of different backgrounds to find suitable miRNA-related bioinformatics web tools and relevant information rapidly.
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Affiliation(s)
| | - Zahra Bahmanpour
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Yousef Daneshmandpour
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | | | - Somayeh Kazeminasab
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran; Research Vice-Chancellor, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Babak Emamalizadeh
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
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57
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Lamberti MJ, Nigro A, Casolaro V, Rumie Vittar NB, Dal Col J. Damage-Associated Molecular Patterns Modulation by microRNA: Relevance on Immunogenic Cell Death and Cancer Treatment Outcome. Cancers (Basel) 2021; 13:cancers13112566. [PMID: 34073766 PMCID: PMC8197279 DOI: 10.3390/cancers13112566] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 05/14/2021] [Accepted: 05/18/2021] [Indexed: 02/06/2023] Open
Abstract
Simple Summary Inside the cell, damage-associated molecular pattern molecules (DAMPs) play several physiological functions, but when they are released or translocated to the extracellular space, they gain additional immunogenic roles. Thus, DAMPs are considered key hallmarks of immunogenic cell death (ICD) in cancer, a functionally unique regulated form of stress-mediated cell death that activates the immune system response against tumor cells. Several epigenetic modulators of DAMPs have been reported. In this review, we aimed to provide an overview of the effects of microRNAs (miRNAs) on the expression of DAMPs and the putative link between miRNA, DAMPs, and cell death, focused on ICD. Overall, we propose that miRNAs, by targeting DAMPs, play critical roles in the regulation of both cell death and immune-associated mechanisms in cancer, while evidence of their potential involvement in ICD is limited. Finally, we discuss emerging data regarding the impact of miRNAs’ modulation on cancer treatment outcome. Abstract Immunogenic cell death (ICD) in cancer is a functionally unique regulated form of stress-mediated cell death that activates both the innate and adaptive immune response against tumor cells. ICD makes dying cancer cells immunogenic by improving both antigenicity and adjuvanticity. The latter relies on the spatiotemporally coordinated release or exposure of danger signals (DAMPs) that drive robust antigen-presenting cell activation. The expression of DAMPs is often constitutive in tumor cells, but it is the initiating stressor, called ICD-inducer, which finally triggers the intracellular response that determines the kinetics and intensity of their release. However, the contribution of cell-autonomous features, such as the epigenetic background, to the development of ICD has not been addressed in sufficient depth. In this context, it has been revealed that several microRNAs (miRNAs), besides acting as tumor promoters or suppressors, can control the ICD-associated exposure of some DAMPs and their basal expression in cancer. Here, we provide a general overview of the dysregulation of cancer-associated miRNAs whose targets are DAMPs, through which new molecular mediators that underlie the immunogenicity of ICD were identified. The current status of miRNA-targeted therapeutics combined with ICD inducers is discussed. A solid comprehension of these processes will provide a framework to evaluate miRNA targets for cancer immunotherapy.
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Affiliation(s)
- María Julia Lamberti
- INBIAS, CONICET-UNRC, Río Cuarto, Córdoba 5800, Argentina;
- Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, Baronissi, 84081 Salerno, Italy; (A.N.); (V.C.)
- Correspondence: (M.J.L.); (J.D.C.)
| | - Annunziata Nigro
- Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, Baronissi, 84081 Salerno, Italy; (A.N.); (V.C.)
| | - Vincenzo Casolaro
- Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, Baronissi, 84081 Salerno, Italy; (A.N.); (V.C.)
| | | | - Jessica Dal Col
- Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, Baronissi, 84081 Salerno, Italy; (A.N.); (V.C.)
- Correspondence: (M.J.L.); (J.D.C.)
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Zhang H, Shen YW, Zhang LJ, Chen JJ, Bian HT, Gu WJ, Zhang H, Chen HZ, Zhang WD, Luan X. Targeting Endothelial Cell-Specific Molecule 1 Protein in Cancer: A Promising Therapeutic Approach. Front Oncol 2021; 11:687120. [PMID: 34109132 PMCID: PMC8181400 DOI: 10.3389/fonc.2021.687120] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 05/10/2021] [Indexed: 12/21/2022] Open
Abstract
Despite the dramatic advances in cancer research in the past few years, effective therapeutic strategies are urgently needed. Endothelial cell-specific molecule 1 (ESM-1), a soluble dermatan sulfate proteoglycan, also known as endocan, serves as a diagnostic and prognostic indicator due to its aberrant expression under pathological conditions, including cancer, sepsis, kidney diseases, and cardiovascular disease. Significantly, ESM-1 can promote cancer progression and metastasis through the regulation of tumor cell proliferation, migration, invasion, and drug resistant. In addition, ESM-1 is involved in the tumor microenvironment, containing inflammation, angiogenesis, and lymph angiogenesis. This article reviews the molecular and biological characteristics of ESM-1 in cancer, the underlying mechanisms, the currently clinical and pre-clinical applications, and potential therapeutic strategies. Herein, we propose that ESM-1 is a new therapeutic target for cancer therapy.
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Affiliation(s)
- He Zhang
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,School of Pharmacy, Fudan University, Shanghai, China
| | - Yi-Wen Shen
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Li-Jun Zhang
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Jin-Jiao Chen
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,School of Pharmacy, Fudan University, Shanghai, China
| | - Hui-Ting Bian
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,School of Pharmacy, Fudan University, Shanghai, China
| | - Wen-Jie Gu
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Hong Zhang
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Hong-Zhuan Chen
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Wei-Dong Zhang
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,School of Pharmacy, Second Military Medical University, Shanghai, China
| | - Xin Luan
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
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59
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Gut microbiota-microRNA interactions in ankylosing spondylitis. Autoimmun Rev 2021; 20:102827. [PMID: 33864943 DOI: 10.1016/j.autrev.2021.102827] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 02/17/2021] [Indexed: 12/20/2022]
Abstract
Ankylosing spondylitis (AS) is a chronic autoimmune inflammatory disability that is part of the rheumatic disease group of spondyloarthropathies. AS commonly influences the joints of the axial skeleton. The contributions to AS pathogenesis of genetic susceptibility (particularly HLA-B27 and ERAP-1) and epigenetic modifications, like non-coding RNAs, as well as environmental factors, have been investigated over the last few years. But the fundamental etiology of AS remains elusive to date. The evidence summarized here indicates that in the immunopathogenesis of AS, microRNAs and the gut microbiome perform critical functions. We discuss significant advances in the immunological mechanisms underlying AS and address potential cross-talk between the gut microbiome and host microRNAs. This critical interaction implicates a co-evolutionary symbiotic link between host immunity and the gut microbiome.
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60
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Zubáňová V, Červinková Z, Kučera O, Palička V. The Connection between MicroRNAs from Visceral Adipose Tissue and Non-Alcoholic Fatty Liver Disease. ACTA MEDICA (HRADEC KRÁLOVÉ) 2021; 64:1-7. [PMID: 33855952 DOI: 10.14712/18059694.2021.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Non-Alcoholic Fatty Liver Disease (NAFLD) is one of the most important causes of liver disease worldwide leading the foreground cause of liver transplantation. Recently miRNAs, small non-coding molecules were identified as an important player in the negative translational regulation of many protein-coding genes involved in hepatic metabolism. Visceral adipose tissue was found to take part in lipid and glucose metabolism and to release many inflammatory mediators that may contribute to progression of NAFLD from simple steatosis to Non-Alcoholic SteatoHepatitis. Since visceral adipose tissue enlargement and dysregulated levels of miRNAs were observed in patients with NAFLD, the aim of this paper is to reflect the current knowledge of the role of miRNAs released from visceral adipose tissue and NAFLD.
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Affiliation(s)
- Veronika Zubáňová
- Department of Clinical Biochemistry and Diagnostics, Charles University, Faculty of Medicine in Hradec Králové and University Hospital Hradec Králové, Czech Republic.
| | - Zuzana Červinková
- Department of Physiology, Charles University, Faculty of Medicine in Hradec Králové, Czech Republic
| | - Otto Kučera
- Department of Physiology, Charles University, Faculty of Medicine in Hradec Králové, Czech Republic
| | - Vladimír Palička
- Department of Clinical Biochemistry and Diagnostics, Charles University, Faculty of Medicine in Hradec Králové and University Hospital Hradec Králové, Czech Republic
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61
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Gollavilli PN, Parma B, Siddiqui A, Yang H, Ramesh V, Napoli F, Schwab A, Natesan R, Mielenz D, Asangani IA, Brabletz T, Pilarsky C, Ceppi P. The role of miR-200b/c in balancing EMT and proliferation revealed by an activity reporter. Oncogene 2021; 40:2309-2322. [PMID: 33654197 PMCID: PMC7994202 DOI: 10.1038/s41388-021-01708-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 02/08/2021] [Accepted: 02/09/2021] [Indexed: 12/16/2022]
Abstract
Since their discovery, microRNAs (miRNAs) have been widely studied in almost every aspect of biology and medicine, leading to the identification of important gene regulation circuits and cellular mechanisms. However, investigations are generally focused on the analysis of their downstream targets and biological functions in overexpression and knockdown approaches, while miRNAs endogenous levels and activity remain poorly understood. Here, we used the cellular plasticity-regulating process of epithelial-to-mesenchymal transition (EMT) as a model to show the efficacy of a fluorescent sensor to separate cells with distinct EMT signatures, based on miR-200b/c activity. The system was further combined with a CRISPR-Cas9 screening platform to unbiasedly identify miR-200b/c upstream regulating genes. The sensor allows to infer miRNAs fundamental biological properties, as profiling of sorted cells indicated miR-200b/c as a molecular switch between EMT differentiation and proliferation, and suggested a role for metabolic enzymes in miR-200/EMT regulation. Analysis of miRNAs endogenous levels and activity for in vitro and in vivo applications could lead to a better understanding of their biological role in physiology and disease.
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Affiliation(s)
- Paradesi Naidu Gollavilli
- Interdisciplinary Center for Clinical Research (IZKF), Friedrich-Alexander University of Erlangen-Nuremberg (FAU), Erlangen, Germany
| | - Beatrice Parma
- Interdisciplinary Center for Clinical Research (IZKF), Friedrich-Alexander University of Erlangen-Nuremberg (FAU), Erlangen, Germany
| | - Aarif Siddiqui
- Interdisciplinary Center for Clinical Research (IZKF), Friedrich-Alexander University of Erlangen-Nuremberg (FAU), Erlangen, Germany.,Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Hai Yang
- Department of Surgery, Friedrich-Alexander University of Erlangen- Nuremberg (FAU) and University Hospital of Erlangen, Erlangen, Germany
| | - Vignesh Ramesh
- Interdisciplinary Center for Clinical Research (IZKF), Friedrich-Alexander University of Erlangen-Nuremberg (FAU), Erlangen, Germany
| | - Francesca Napoli
- Interdisciplinary Center for Clinical Research (IZKF), Friedrich-Alexander University of Erlangen-Nuremberg (FAU), Erlangen, Germany.,Department of Oncology at San Luigi Hospital, University of Turin, Turin, Italy
| | - Annemarie Schwab
- Interdisciplinary Center for Clinical Research (IZKF), Friedrich-Alexander University of Erlangen-Nuremberg (FAU), Erlangen, Germany
| | - Ramakrishnan Natesan
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
| | - Dirk Mielenz
- Department of Molecular Immunology, Friedrich-Alexander University of Erlangen-Nuremberg, Erlangen, Germany
| | - Irfan Ahmed Asangani
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
| | - Thomas Brabletz
- Department of Experimental Medicine-I, Friedrich-Alexander University of Erlangen-Nuremberg, Erlangen, Germany
| | - Christian Pilarsky
- Department of Surgery, Friedrich-Alexander University of Erlangen- Nuremberg (FAU) and University Hospital of Erlangen, Erlangen, Germany
| | - Paolo Ceppi
- Interdisciplinary Center for Clinical Research (IZKF), Friedrich-Alexander University of Erlangen-Nuremberg (FAU), Erlangen, Germany. .,Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark.
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Bohra A, Gandham P, Rathore A, Thakur V, Saxena RK, Naik SJS, Varshney RK, Singh NP. Identification of microRNAs and their gene targets in cytoplasmic male sterile and fertile maintainer lines of pigeonpea. PLANTA 2021; 253:59. [PMID: 33538916 DOI: 10.1007/s00425-021-03568-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 01/04/2021] [Indexed: 06/12/2023]
Abstract
Comparative analysis of genome-wide miRNAs and their gene targets between cytoplasmic male sterile (CMS) and fertile lines of pigeonpea suggests a possible role of miRNA-regulated pathways in reproductive development. Exploitation of hybrid vigor using CMS technology has delivered nearly 50% yield gain in pigeonpea. Among various sterility-inducing cytoplasms (A1-A9) reported so far in pigeonpea, A2 and A4 are the two major sources that facilitate hybrid seed production. Recent evidence suggests involvement of micro RNA in vast array of biological processes including plant reproductive development. In pigeonpea, information about the miRNAs is insufficient. In view of this, we sequenced six small RNA libraries of CMS line UPAS 120A and isogenic fertile line UPAS 120B using Illumina technology. Results revealed 316 miRNAs including 248 known and 68 novel types. A total of 637 gene targets were predicted for known miRNAs, while 324 genes were associated with novel miRNAs. Degradome analysis revealed 77 gene targets of predicted miRNAs, which included a variety of transcription factors playing key roles in plant reproduction such as F-box family proteins, apetala 2, auxin response factors, ethylene-responsive factors, homeodomain-leucine zipper proteins etc. Differential expression of both known and novel miRNAs implied roles for both conserved as well as species-specific players. We also obtained several miRNA families such as miR156, miR159, miR167 that are known to influence crucial aspects of plant fertility. Gene ontology and pathway level analyses of the target genes showed their possible implications for crucial events during male reproductive development such as tapetal degeneration, pollen wall formation, retrograde signaling etc. To the best of our knowledge, present study is first to combine deep sequencing of small RNA and degradome for elucidating the role of miRNAs in flower and male reproductive development in pigeonpea.
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Affiliation(s)
- Abhishek Bohra
- ICAR-Indian Institute of Pulses Research (IIPR), Kanpur, India.
| | - Prasad Gandham
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Abhishek Rathore
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Vivek Thakur
- Hyderabad Central University (HCU), Hyderabad, India
| | - Rachit K Saxena
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | | | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
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63
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Nazarov PV, Kreis S. Integrative approaches for analysis of mRNA and microRNA high-throughput data. Comput Struct Biotechnol J 2021; 19:1154-1162. [PMID: 33680358 PMCID: PMC7895676 DOI: 10.1016/j.csbj.2021.01.029] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 01/19/2021] [Accepted: 01/20/2021] [Indexed: 12/11/2022] Open
Abstract
Review on tools and databases linking miRNA and its mRNA targetome. Databases show little overlap in miRNA targetome predictions suggesting strong contextual effects. Deconvolution and deep learning approaches are promising new approaches to improve miRNA targetome predictions.
Advanced sequencing technologies such as RNASeq provide the means for production of massive amounts of data, including transcriptome-wide expression levels of coding RNAs (mRNAs) and non-coding RNAs such as miRNAs, lncRNAs, piRNAs and many other RNA species. In silico analysis of datasets, representing only one RNA species is well established and a variety of tools and pipelines are available. However, attaining a more systematic view of how different players come together to regulate the expression of a gene or a group of genes requires a more intricate approach to data analysis. To fully understand complex transcriptional networks, datasets representing different RNA species need to be integrated. In this review, we will focus on miRNAs as key post-transcriptional regulators summarizing current computational approaches for miRNA:target gene prediction as well as new data-driven methods to tackle the problem of comprehensively and accurately dissecting miRNome-targetome interactions.
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Key Words
- CCA, canonical correlation analysis
- CDS, coding sequence
- CLASH, cross-linking, ligation and sequencing of hybrids
- CLIP, cross-linking immunoprecipitation
- CNN, convolutional neural network
- Data integration
- GO, gene ontology
- ICA, independent component analysis
- Matrix factorization
- NGS, next-generation sequencing
- NMF, non-negative matrix factorization
- PCA, principal component analysis
- RNASeq, high-throughput RNA sequencing
- TDMD, target RNA-directed miRNA degradation
- TF, transcription factors
- Target prediction
- Transcriptomics
- circRNA, circular RNA
- lncRNA, long non-coding RNA
- mRNA, messenger RNA
- miRNA, microRNA
- microRNA
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Affiliation(s)
- Petr V Nazarov
- Multiomics Data Science Research Group, Department of Oncology & Quantitative Biology Unit, Luxembourg Institute of Health (LIH), Strassen L-1445, Luxembourg
| | - Stephanie Kreis
- Signal Transduction Group, Department of Life Sciences and Medicine, University of Luxembourg, Belvaux L-4367, Luxembourg
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64
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Li D, Yuan Q, Xiong L, Li A, Xia Y. The miR-4739/DLX3 Axis Modulates Bone Marrow-Derived Mesenchymal Stem Cell (BMSC) Osteogenesis Affecting Osteoporosis Progression. Front Endocrinol (Lausanne) 2021; 12:703167. [PMID: 34925225 PMCID: PMC8678599 DOI: 10.3389/fendo.2021.703167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 11/08/2021] [Indexed: 11/23/2022] Open
Abstract
Osteoporosis is a complex multifactorial disorder linked to various risk factors and medical conditions. Bone marrow-derived mesenchymal stem cell (BMSC) dysfunction potentially plays a critical role in osteoporosis pathogenesis. Herein, the study identified that miR-4739 was upregulated in BMSC cultures harvested from osteoporotic subjects. BMSCs were isolated from normal and osteoporotic bone marrow tissues and identified for their osteogenic differentiation potential. In osteoporotic BMSCs, miR-4739 overexpression significantly inhibited cell viability, osteoblast differentiation, mineralized nodule formation, and heterotopic bone formation, whereas miR-4739 inhibition exerted opposite effects. Through direct binding, miR-4739 inhibited distal-less homeobox 3 (DLX3) expression. In osteoporotic BMSCs, DLX3 knockdown also inhibited BMSC viability and osteogenic differentiation. Moreover, DLX3 knockdown partially attenuated the effects of miR-4739 inhibition upon BMSCs. Altogether, the miR-4739/DLX3 axis modulates the capacity of BMSCs to differentiate into osteoblasts, which potentially plays a role in osteoporosis pathogenesis. The in vivo and clinical functions of the miR-4739/DLX3 axis require further investigation.
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Affiliation(s)
- Ding Li
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, China
- *Correspondence: Ding Li,
| | - Qi Yuan
- Department of Hepatopathy, The Hunan Provincial People’s Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, China
| | - Liang Xiong
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Aoyu Li
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Yu Xia
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, China
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65
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Riolo G, Cantara S, Marzocchi C, Ricci C. miRNA Targets: From Prediction Tools to Experimental Validation. Methods Protoc 2020; 4:1. [PMID: 33374478 PMCID: PMC7839038 DOI: 10.3390/mps4010001] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/17/2020] [Accepted: 12/22/2020] [Indexed: 12/12/2022] Open
Abstract
MicroRNAs (miRNAs) are post-transcriptional regulators of gene expression in both animals and plants. By pairing to microRNA responsive elements (mREs) on target mRNAs, miRNAs play gene-regulatory roles, producing remarkable changes in several physiological and pathological processes. Thus, the identification of miRNA-mRNA target interactions is fundamental for discovering the regulatory network governed by miRNAs. The best way to achieve this goal is usually by computational prediction followed by experimental validation of these miRNA-mRNA interactions. This review summarizes the key strategies for miRNA target identification. Several tools for computational analysis exist, each with different approaches to predict miRNA targets, and their number is constantly increasing. The major algorithms available for this aim, including Machine Learning methods, are discussed, to provide practical tips for familiarizing with their assumptions and understanding how to interpret the results. Then, all the experimental procedures for verifying the authenticity of the identified miRNA-mRNA target pairs are described, including High-Throughput technologies, in order to find the best approach for miRNA validation. For each strategy, strengths and weaknesses are discussed, to enable users to evaluate and select the right approach for their interests.
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Affiliation(s)
| | | | | | - Claudia Ricci
- Department of Medical, Surgical and Neurological Sciences, University of Siena, 53100 Siena, Italy; (G.R.); (S.C.); (C.M.)
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66
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Shaker F, Nikravesh A, Arezumand R, Aghaee-Bakhtiari SH. Web-based tools for miRNA studies analysis. Comput Biol Med 2020; 127:104060. [DOI: 10.1016/j.compbiomed.2020.104060] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 10/12/2020] [Accepted: 10/12/2020] [Indexed: 02/07/2023]
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67
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The Importance of AGO 1 and 4 in Post-Transcriptional Gene Regulatory Function of tRF5-GluCTC, an Respiratory Syncytial Virus-Induced tRNA-Derived RNA Fragment. Int J Mol Sci 2020; 21:ijms21228766. [PMID: 33233493 PMCID: PMC7699471 DOI: 10.3390/ijms21228766] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 11/16/2020] [Accepted: 11/17/2020] [Indexed: 12/18/2022] Open
Abstract
Respiratory syncytial virus (RSV) is the most common cause of lower respiratory tract infection in infants, the elderly, and immune-compromised patients. It is also a significant contributor to upper respiratory tract infection in the pediatric population. However, its disease mechanisms are still largely unknown. We have recently shown that a tRNA-derived RNA fragment (tRF) from the 5′-end of mature tRNA encoding GluCTC (tRF5-GluCTC), a recently discovered non-coding RNA, is functionally important for RSV replication and host gene regulation at the post-transcriptional level. However, how tRF5-GluCTC carries out the gene regulation is not fully known. In this study, we found that tRF5-GluCTC has impaired gene trans-silencing function in cells deficient of AGO1 or 4, while AGO2 and 3 seem not involved in tRF5-GluCTC-mediated gene regulation. By pulling down individual AGO protein, we discovered that tRF5-GluCTC is detectable only in the AGO4 complex, confirming the essential role of AGO4 in gene regulation and also suggesting that AGO1 contributes to the gene trans-silencing activity of tRF5-GluCTC in an atypical way. We also found that the P protein of RSV is associated with both AGO1 and 4 and AGO4 deficiency leads to reduced infectious viral particles. In summary, this study demonstrates the importance of AGO1 and 4 in mediating the gene trans-silencing function of tRF5-GluCTC.
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68
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Boscher E, Hernandez-Rapp J, Petry S, Keraudren R, Rainone S, Loiselle A, Goupil C, Turgeon A, St-Amour I, Planel E, Hébert SS. Advances and Challenges in Understanding MicroRNA Function in Tauopathies: A Case Study of miR-132/212. Front Neurol 2020; 11:578720. [PMID: 33117266 PMCID: PMC7553085 DOI: 10.3389/fneur.2020.578720] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 09/01/2020] [Indexed: 01/08/2023] Open
Abstract
In the past decade, several groups have reported that microRNAs (miRNAs) can participate in the regulation of tau protein at different levels, including its expression, alternative splicing, phosphorylation, and aggregation. These observations are significant, since the abnormal regulation and deposition of tau is associated with nearly 30 neurodegenerative disorders. Interestingly, miRNA profiles go awry in tauopathies such as Alzheimer's disease, progressive supranuclear palsy, and frontotemporal dementia. Understanding the role and impact of miRNAs on tau biology could therefore provide important insights into disease risk, diagnostics, and perhaps therapeutics. In this Perspective article, we discuss recent advances in miRNA research related to tau. While proof-of-principle studies hold promise, physiological validation remains limited. To help fill this gap, we describe herein a pure tauopathy mouse model deficient for the miR-132/212 cluster. This miRNA family is strongly downregulated in human tauopathies and shown to regulate tau in vitro and in vivo. No significant differences in survival, motor deficits or body weight were observed in PS19 mice lacking miR-132/212. Age-specific effects were seen on tau expression and phosphorylation but not aggregation. Moreover, various miR-132/212 targets previously implicated in tau modulation were unaffected (GSK-3β, Foxo3a, Mapk1, p300) or, unexpectedly, reduced (Mapk3, Foxo1, p300, Calpain 2) in miR-132/212-deficient PS19 mice. These observations highlight the challenges of miRNA research in living models, and current limitations of transgenic tau mouse models lacking functional miRNA binding sites. Based on these findings, we finally recommend different strategies to better understand the role of miRNAs in tau physiology and pathology.
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Affiliation(s)
- Emmanuelle Boscher
- Axe Neurosciences, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC, Canada.,Département de Psychiatrie et Neurosciences, Université Laval, Québec, QC, Canada
| | - Julia Hernandez-Rapp
- Axe Neurosciences, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC, Canada.,Département de Psychiatrie et Neurosciences, Université Laval, Québec, QC, Canada
| | - Serena Petry
- Axe Neurosciences, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC, Canada.,Département de Psychiatrie et Neurosciences, Université Laval, Québec, QC, Canada
| | - Remi Keraudren
- Axe Neurosciences, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC, Canada.,Département de Psychiatrie et Neurosciences, Université Laval, Québec, QC, Canada
| | - Sara Rainone
- Axe Neurosciences, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC, Canada.,Département de Psychiatrie et Neurosciences, Université Laval, Québec, QC, Canada
| | - Andréanne Loiselle
- Axe Neurosciences, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC, Canada.,Département de Psychiatrie et Neurosciences, Université Laval, Québec, QC, Canada
| | - Claudia Goupil
- Axe Neurosciences, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC, Canada.,Département de Psychiatrie et Neurosciences, Université Laval, Québec, QC, Canada
| | - Andréanne Turgeon
- Axe Neurosciences, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC, Canada.,Département de Psychiatrie et Neurosciences, Université Laval, Québec, QC, Canada
| | - Isabelle St-Amour
- Axe Neurosciences, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC, Canada.,Département de Psychiatrie et Neurosciences, Université Laval, Québec, QC, Canada
| | - Emmanuel Planel
- Axe Neurosciences, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC, Canada.,Département de Psychiatrie et Neurosciences, Université Laval, Québec, QC, Canada
| | - Sébastien S Hébert
- Axe Neurosciences, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC, Canada.,Département de Psychiatrie et Neurosciences, Université Laval, Québec, QC, Canada
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69
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Liu B, Sun Y, Tang M, Liang C, Huang CP, Niu Y, Wang Z, Chang C. The miR-361-3p increases enzalutamide (Enz) sensitivity via targeting the ARv7 and MKNK2 to better suppress the Enz-resistant prostate cancer. Cell Death Dis 2020; 11:807. [PMID: 32978369 PMCID: PMC7519644 DOI: 10.1038/s41419-020-02932-w] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 08/07/2020] [Accepted: 08/13/2020] [Indexed: 12/14/2022]
Abstract
The androgen receptor splicing variant 7 (ARv7) that lacks the ligand-binding domain is increasingly considered as a key player leading to enzalutamide (Enz) resistance in patients with prostate cancer (PCa). However, the detailed mechanisms of how ARv7 expression is regulated and whether it also needs other factors to induce maximal Enz resistance remain unclear. Here, we identified a microRNA, miR-361-3p, whose expression is lower in patients with recurrent PCa, could function via binding to the 3'UTR of ARv7, but not the wild type of AR, to suppress its expression to increase the Enz sensitivity. Importantly, we found that miR-361-3p could also bind to the 3'UTR of MAP kinase-interacting serine/threonine kinase 2 (MKNK2) to suppress its expression to further increase the Enz sensitivity. In turn, the increased Enz can then function via a feedback mechanism through altering the HIF-2α/VEGFA signaling to suppress the expression of miR-361-3p under hypoxia conditions. Preclinical studies using an in vivo mouse model with orthotopically xenografted CWR22Rv1 cells demonstrated that combining the Enz with the small molecule miR-361-3p would result in better suppression of the Enz-resistant PCa tumor progression. Together, these preclinical studies demonstrate that miR-361-3p can function via suppressing the expression of ARv7 and MKNK2 to maximally increase the Enz sensitivity, and targeting these newly identified Enz/miR-361-3p/ARv7 and/or Enz/miR-361-3p/MKNK2 signals with small molecules may help in the development of novel therapies to better suppress the CRPC in patients that already have developed the Enz resistance.
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Affiliation(s)
- Bianjiang Liu
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- George Whipple Lab for Cancer Research, Departments of Pathology, Urology and Radiation Oncology, and The Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, NY, USA
| | - Yin Sun
- George Whipple Lab for Cancer Research, Departments of Pathology, Urology and Radiation Oncology, and The Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, NY, USA
| | - Min Tang
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- George Whipple Lab for Cancer Research, Departments of Pathology, Urology and Radiation Oncology, and The Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, NY, USA
| | - Chao Liang
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Chi-Ping Huang
- Sex Hormone Research Center and Department of Urology, China Medical University/Hospital, Taichung, Taiwan
| | - Yuanjie Niu
- George Whipple Lab for Cancer Research, Departments of Pathology, Urology and Radiation Oncology, and The Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, NY, USA
| | - Zengjun Wang
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.
| | - Chawnshang Chang
- George Whipple Lab for Cancer Research, Departments of Pathology, Urology and Radiation Oncology, and The Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, NY, USA.
- Sex Hormone Research Center and Department of Urology, China Medical University/Hospital, Taichung, Taiwan.
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70
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Frei T, Cella F, Tedeschi F, Gutiérrez J, Stan GB, Khammash M, Siciliano V. Characterization and mitigation of gene expression burden in mammalian cells. Nat Commun 2020; 11:4641. [PMID: 32934213 PMCID: PMC7492461 DOI: 10.1038/s41467-020-18392-x] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 08/18/2020] [Indexed: 12/19/2022] Open
Abstract
Despite recent advances in circuit engineering, the design of genetic networks in mammalian cells is still painstakingly slow and fraught with inexplicable failures. Here, we demonstrate that transiently expressed genes in mammalian cells compete for limited transcriptional and translational resources. This competition results in the coupling of otherwise independent exogenous and endogenous genes, creating a divergence between intended and actual function. Guided by a resource-aware mathematical model, we identify and engineer natural and synthetic miRNA-based incoherent feedforward loop (iFFL) circuits that mitigate gene expression burden. The implementation of these circuits features the use of endogenous miRNAs as elementary components of the engineered iFFL device, a versatile hybrid design that allows burden mitigation to be achieved across different cell-lines with minimal resource requirements. This study establishes the foundations for context-aware prediction and improvement of in vivo synthetic circuit performance, paving the way towards more rational synthetic construct design in mammalian cells.
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Affiliation(s)
- Timothy Frei
- Department of Biosystems Science and Engineering (D-BSSE), ETH Zürich, Mattenstrasse 26, Basel, 4058, Switzerland
| | - Federica Cella
- Istituto Italiano di Tecnologia-IIT, Largo Barsanti e Matteucci, Naples, 80125, Italy
- University of Genoa, Genoa, 16132, Italy
| | - Fabiana Tedeschi
- Istituto Italiano di Tecnologia-IIT, Largo Barsanti e Matteucci, Naples, 80125, Italy
| | - Joaquín Gutiérrez
- Department of Biosystems Science and Engineering (D-BSSE), ETH Zürich, Mattenstrasse 26, Basel, 4058, Switzerland
| | - Guy-Bart Stan
- Department of Bioengineering and Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK
| | - Mustafa Khammash
- Department of Biosystems Science and Engineering (D-BSSE), ETH Zürich, Mattenstrasse 26, Basel, 4058, Switzerland.
| | - Velia Siciliano
- Istituto Italiano di Tecnologia-IIT, Largo Barsanti e Matteucci, Naples, 80125, Italy.
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71
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Chehade M, Bullock M, Glover A, Hutvagner G, Sidhu S. Key MicroRNA's and Their Targetome in Adrenocortical Cancer. Cancers (Basel) 2020; 12:E2198. [PMID: 32781574 PMCID: PMC7465134 DOI: 10.3390/cancers12082198] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 07/27/2020] [Accepted: 07/28/2020] [Indexed: 12/23/2022] Open
Abstract
Adrenocortical Carcinoma (ACC) is a rare but aggressive malignancy with poor prognosis and limited response to available systemic therapies. Although complete surgical resection gives the best chance for long-term survival, ACC has a two-year recurrence rate of 50%, which poses a therapeutic challenge. High throughput analyses focused on characterizing the molecular signature of ACC have revealed specific micro-RNAs (miRNAs) that are associated with aggressive tumor phenotypes. MiRNAs are small non-coding RNA molecules that regulate gene expression by inhibiting mRNA translation or degrading mRNA transcripts and have been generally implicated in carcinogenesis. This review summarizes the current insights into dysregulated miRNAs in ACC tumorigenesis, their known functions, and specific targetomes. In addition, we explore the possibility of particular miRNAs to be exploited as clinical biomarkers in ACC and as potential therapeutics.
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Affiliation(s)
- Marthe Chehade
- Cancer Genetics Laboratory, Kolling Institute, Northern Sydney Local Health District, St. Leonards, NSW 2065, Australia; (M.C.); (M.B.); (A.G.)
- Sydney Medical School Northern, Royal North Shore Hospital, University of Sydney, Sydney, NSW 2065, Australia
| | - Martyn Bullock
- Cancer Genetics Laboratory, Kolling Institute, Northern Sydney Local Health District, St. Leonards, NSW 2065, Australia; (M.C.); (M.B.); (A.G.)
- Sydney Medical School Northern, Royal North Shore Hospital, University of Sydney, Sydney, NSW 2065, Australia
| | - Anthony Glover
- Cancer Genetics Laboratory, Kolling Institute, Northern Sydney Local Health District, St. Leonards, NSW 2065, Australia; (M.C.); (M.B.); (A.G.)
- Sydney Medical School Northern, Royal North Shore Hospital, University of Sydney, Sydney, NSW 2065, Australia
- Endocrine Surgery Unit, Royal North Shore Hospital, Northern Clinical School, Faculty of Medicine and Health, The University of Sydney, St. Leonards, Sydney, NSW 2007, Australia
| | - Gyorgy Hutvagner
- School of Biomedical Engineering, Faculty of Engineering and Information Technology, University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Stan Sidhu
- Cancer Genetics Laboratory, Kolling Institute, Northern Sydney Local Health District, St. Leonards, NSW 2065, Australia; (M.C.); (M.B.); (A.G.)
- Sydney Medical School Northern, Royal North Shore Hospital, University of Sydney, Sydney, NSW 2065, Australia
- Endocrine Surgery Unit, Royal North Shore Hospital, Northern Clinical School, Faculty of Medicine and Health, The University of Sydney, St. Leonards, Sydney, NSW 2007, Australia
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72
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Fan D, Ran L, Hu J, Ye X, Xu D, Li J, Su H, Wang X, Ren S, Luo K. miR319a/TCP module and DELLA protein regulate trichome initiation synergistically and improve insect defenses in Populus tomentosa. THE NEW PHYTOLOGIST 2020; 227:867-883. [PMID: 32270484 DOI: 10.1111/nph.16585] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 03/16/2020] [Indexed: 05/20/2023]
Abstract
Trichomes are specialized epidermal cells that contribute to plant resistance against herbivores. Their formation is controlled precisely by multiple genetic and environmental signals. Previous studies have shown that microRNA319 (miR319) and gibberellin (GA) signaling are involved in trichome development in Arabidopsis, but little is known about their interaction between these factors. Here we reported that the miR319a/TEOSINTE BRANCHED/CYCLOIDEA/PCF (TCP) module participates in trichome initiation synergistically with GA signaling in Populus tomentosa. We demonstrated that overexpression of miR319a decreased transcription levels of its targeted TCPs and significantly elevated leaf trichome density in transgenic poplar, resulting in decreasing insect herbivory. Conversely, repressing miR319a by short tandem target mimics (STTM) elevated TCP expression levels and decreased trichome density in transgenic plants. The trichome phenotype of 35S:miR319a plants could be abolished by introducing a miR319a-resistant form of TCP19. Furthermore, the miR319a-targeted TCP19 interacted directly with REPRESSOR OF ga1-3 (RGA), a downstream repressor of GA signaling. TCP19 and RGA synergistically inhibited the GLABROUS1 (GL1)-induced expression of trichome marker gene GLABRA2 (GL2), thereby repressing leaf trichome initiation. Our results provide an insight into the molecular mechanism by which miR319/TCP19 module and GA signaling coordinated regulating trichome initiation in P. tomentosa.
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Affiliation(s)
- Di Fan
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, Chongqing, 400715, China
- Key Laboratory of Eco-environments of Three Gorges Reservoir Region, Ministry of Education, Southwest University, Chongqing, 400715, China
| | - Lingyu Ran
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Jian Hu
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Xiao Ye
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Dan Xu
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Jianqiu Li
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Huili Su
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Xianqiang Wang
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Sha Ren
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, Chongqing, 400715, China
- Key Laboratory of Eco-environments of Three Gorges Reservoir Region, Ministry of Education, Southwest University, Chongqing, 400715, China
| | - Keming Luo
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, Chongqing, 400715, China
- Key Laboratory of Eco-environments of Three Gorges Reservoir Region, Ministry of Education, Southwest University, Chongqing, 400715, China
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Wong L, You ZH, Guo ZH, Yi HC, Chen ZH, Cao MY. MIPDH: A Novel Computational Model for Predicting microRNA-mRNA Interactions by DeepWalk on a Heterogeneous Network. ACS OMEGA 2020; 5:17022-17032. [PMID: 32715187 PMCID: PMC7376568 DOI: 10.1021/acsomega.9b04195] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Accepted: 03/06/2020] [Indexed: 06/11/2023]
Abstract
Analysis of miRNA-target mRNA interaction (MTI) is of crucial significance in discovering new target candidates for miRNAs. However, the biological experiments for identifying MTIs have a high false positive rate and are high-priced, time-consuming, and arduous. It is an urgent task to develop effective computational approaches to enhance the investigation of miRNA-target mRNA relationships. In this study, a novel method called MIPDH is developed for miRNA-mRNA interaction prediction by using DeepWalk on a heterogeneous network. More specifically, MIPDH extracts two kinds of features, in which a biological behavior feature is learned using a network embedding algorithm on a constructed heterogeneous network derived from 17 kinds of associations among drug, disease, and 6 kinds of biomolecules, and the attribute feature is learned using the k-mer method on sequences of miRNAs and target mRNAs. Then, a random forest classifier is trained on the features combined with the biological behavior feature and attribute feature. When implementing a 5-fold cross-validation experiment, MIPDH achieved an average accuracy, sensitivity, specificity and AUC of 75.85, 74.37, 77.33%, and 0.8044, respectively. To further evaluate the performance of MIPDH, other classifiers and feature descriptors are conducted for comparisons. MIPDH can achieve a better performance. Additionally, case studies on hsa-miR-106b-5p, hsa-let-7d-5p, and hsa-let-7e-5p are also implemented. As a result, 14, 9, and 9 out of the top 15 targets that interacted with these miRNAs were verified using the experimental literature or other databases. All these prediction results indicate that MIPDH is an effective method for predicting miRNA-target mRNA interactions.
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Affiliation(s)
- Leon Wong
- The
Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Urumqi 830011, China
- University
of Chinese Academy of Sciences, Beijing 100049, China
- XinJiang
Laboratory of Minority Speech and Language Information Processing, Chinese Academy of Sciences, Urumqi 830011, China
| | - Zhu-Hong You
- The
Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Urumqi 830011, China
- University
of Chinese Academy of Sciences, Beijing 100049, China
- XinJiang
Laboratory of Minority Speech and Language Information Processing, Chinese Academy of Sciences, Urumqi 830011, China
| | - Zhen-Hao Guo
- The
Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Urumqi 830011, China
- University
of Chinese Academy of Sciences, Beijing 100049, China
- XinJiang
Laboratory of Minority Speech and Language Information Processing, Chinese Academy of Sciences, Urumqi 830011, China
| | - Hai-Cheng Yi
- The
Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Urumqi 830011, China
- University
of Chinese Academy of Sciences, Beijing 100049, China
- XinJiang
Laboratory of Minority Speech and Language Information Processing, Chinese Academy of Sciences, Urumqi 830011, China
| | - Zhan-Heng Chen
- The
Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Urumqi 830011, China
- University
of Chinese Academy of Sciences, Beijing 100049, China
- XinJiang
Laboratory of Minority Speech and Language Information Processing, Chinese Academy of Sciences, Urumqi 830011, China
| | - Mei-Yuan Cao
- Guang
Dong Polytechnic College, Zhaoqing 526100, Guangdong, China
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74
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Kyrollos DG, Reid B, Dick K, Green JR. RPmirDIP: Reciprocal Perspective improves miRNA targeting prediction. Sci Rep 2020; 10:11770. [PMID: 32678114 PMCID: PMC7366700 DOI: 10.1038/s41598-020-68251-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 06/15/2020] [Indexed: 12/16/2022] Open
Abstract
MicroRNAs (miRNAs) are short, non-coding RNAs that interact with messenger RNA (mRNA) to accomplish critical cellular activities such as the regulation of gene expression. Several machine learning methods have been developed to improve classification accuracy and reduce validation costs by predicting which miRNA will target which gene. Application of these predictors to large numbers of unique miRNA-gene pairs has resulted in datasets comprising tens of millions of scored interactions; the largest among these is mirDIP. We here demonstrate that miRNA target prediction can be significantly improved ([Formula: see text]) through the application of the Reciprocal Perspective (RP) method, a cascaded, semi-supervised machine learning method originally developed for protein-protein interaction prediction. The RP method, aptly named RPmirDIP, augments the original mirDIP prediction scores by leveraging local thresholds from the two complimentary views available to each miRNA-gene pair, rather than apply a traditional global decision threshold. Application of this novel RPmirDIP predictor promises to help identify new, unexpected miRNA-gene interactions. A dataset of RPmirDIP-scored interactions are made available to the scientific community at cu-bic.ca/RPmirDIP and https://doi.org/10.5683/SP2/LD8JKJ.
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Affiliation(s)
- Daniel G Kyrollos
- Department of Systems and Computer Engineering, Carleton University, Ottawa, Canada
| | - Bradley Reid
- Department of Systems and Computer Engineering, Carleton University, Ottawa, Canada
| | - Kevin Dick
- Department of Systems and Computer Engineering, Carleton University, Ottawa, Canada
- Institute of Data Science, Carleton University, Ottawa, Canada
| | - James R Green
- Department of Systems and Computer Engineering, Carleton University, Ottawa, Canada.
- Institute of Data Science, Carleton University, Ottawa, Canada.
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75
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Ladak SS, Roebuck E, Powell J, Fisher AJ, Ward C, Ali S. The Role of miR-200b-3p in Modulating TGF-β1-induced Injury in Human Bronchial Epithelial Cells. Transplantation 2020; 103:2275-2286. [PMID: 31283671 DOI: 10.1097/tp.0000000000002845] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND Dysregulation of microRNAs (miRNAs) has been implicated in airway diseases where transforming growth factor-β (TGF-β)-induced epithelial-mesenchymal transition (EMT) may contribute to pathophysiology. Our study investigated the role of miRNA-200b in TGF-β1-induced EMT in human bronchial epithelial cells. METHODS NanoString nCounter miRNA assay was used to profile miRNA in control versus TGF-β1 (1, 4, and 24 h) stimulated BEAS-2B cells. Immortalized primary bronchial epithelial cell line (BEAS-2B cells), human primary bronchial epithelial cells (PBECs), and PBECs derived post-lung transplant were transfected with miR-200b-3p mimics and EMT marker expression was examined at RNA and protein level. miRNA target studies were performed and validated using computational tools and luciferase assay. In situ hybridization was done on normal lung tissue to localize miR-200b-3p in airway epithelium. RESULTS miR-200b-3p was downregulated post-TGF-β1 treatment compared with control in BEAS-2B. miR-200b-3p mimic transfection before TGF-β1 stimulation maintained epithelial marker expression and downregulated mesenchymal cell markers at RNA and protein level in BEAS-2B cells and PBECs. Furthermore, miR-200b-3p mimics reversed established TGF-β1-induced EMT in BEAS-2B cells. miR-200b-3p targets, ZNF532, and ZEB2 were validated as direct targets using luciferase assay. miR-200b-3p mimics suppress TGF-β1-induced EMT via inhibition of ZNF532 and ZEB2. In situ hybridization showed that miR-200b-3p is expressed in the normal lung epithelium. Additionally, miR-200b-3p mimics inhibit EMT in the presence of TGF-β1 in PBECs derived from lung allograft. CONCLUSIONS We provide proof of concept that miR-200b-3p protects airway epithelial cells from EMT. Manipulating miR-200b-3p expression may represent a novel therapeutic modulator in airway pathophysiology.
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Affiliation(s)
- Shameem S Ladak
- Institute of Cellular Medicine, Medical School, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Eliott Roebuck
- Institute of Cellular Medicine, Medical School, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Jason Powell
- Institute of Cellular Medicine, Medical School, Newcastle University, Newcastle upon Tyne, United Kingdom.,Department of Otolaryngology, Head and Neck Surgery, Freeman Hospital, Newcastle upon Tyne, United Kingdom
| | - Andrew J Fisher
- Institute of Cellular Medicine, Medical School, Newcastle University, Newcastle upon Tyne, United Kingdom.,Institute of Transplantation, Newcastle Upon Tyne Hospitals, Newcastle upon Tyne, United Kingdom
| | - Chris Ward
- Institute of Cellular Medicine, Medical School, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Simi Ali
- Institute of Cellular Medicine, Medical School, Newcastle University, Newcastle upon Tyne, United Kingdom
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76
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MicroRNAs in hematopoietic stem cell aging. Mech Ageing Dev 2020; 189:111281. [PMID: 32512019 DOI: 10.1016/j.mad.2020.111281] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 04/17/2020] [Accepted: 06/01/2020] [Indexed: 12/23/2022]
Abstract
The functional decline that is observed in HSCs upon aging is attributed mainly to cell intrinsic factors that regulate quiescence, self-renewal and differentiation. MicroRNAs (miRs) have an indispensable role in the regulation of HSCs and have been shown to also regulate processes related to tissue aging in specific cell types. Here we discuss the role of miRs in the regulation of HSC self-renewal and differentiation throughout life and its implications for future research.
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77
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Ratti M, Lampis A, Ghidini M, Salati M, Mirchev MB, Valeri N, Hahne JC. MicroRNAs (miRNAs) and Long Non-Coding RNAs (lncRNAs) as New Tools for Cancer Therapy: First Steps from Bench to Bedside. Target Oncol 2020; 15:261-278. [PMID: 32451752 PMCID: PMC7283209 DOI: 10.1007/s11523-020-00717-x] [Citation(s) in RCA: 195] [Impact Index Per Article: 48.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Non-coding RNAs represent a significant proportion of the human genome. After having been considered as 'junk' for a long time, non-coding RNAs are now well established as playing important roles in maintaining cellular homeostasis and functions. Some non-coding RNAs show cell- and tissue-specific expression patterns and are specifically deregulated under pathological conditions (e.g. cancer). Therefore, non-coding RNAs have been extensively studied as potential biomarkers in the context of different diseases with a focus on microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) for several years. Since their discovery, miRNAs have attracted more attention than lncRNAs in research studies; however, both families of non-coding RNAs have been established to play an important role in gene expression control, either as transcriptional or post-transcriptional regulators. Both miRNAs and lncRNAs can regulate key genes involved in the development of cancer, thus influencing tumour growth, invasion, and metastasis by increasing the activation of oncogenic pathways and limiting the expression of tumour suppressors. Furthermore, miRNAs and lncRNAs are also emerging as important mediators in drug-sensitivity and drug-resistance mechanisms. In the light of these premises, a number of pre-clinical and early clinical studies are exploring the potential of non-coding RNAs as new therapeutics. The aim of this review is to summarise the latest knowledge of the use of miRNAs and lncRNAs as therapeutic tools for cancer treatment.
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Affiliation(s)
- Margherita Ratti
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Medical Department, Division of Oncology, ASST di Cremona, Ospedale di Cremona, Cremona, Italy
| | - Andrea Lampis
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Michele Ghidini
- Division of Medical Oncology, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Massimiliano Salati
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Milko B Mirchev
- Clinic of Gastroenterology, Medical University, Varna, Bulgaria
| | - Nicola Valeri
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Department of Medicine, The Royal Marsden NHS Foundation Trust, London, UK
| | - Jens C Hahne
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK.
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK.
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78
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Babicola L, Pietrosanto M, Ielpo D, D'Addario SL, Cabib S, Ventura R, Ferlazzo F, Helmer-Citterich M, Andolina D, Lo Iacono L. RISC RNA sequencing in the Dorsal Raphè reveals microRNAs regulatory activities associated with behavioral and functional adaptations to chronic stress. Brain Res 2020; 1736:146763. [DOI: 10.1016/j.brainres.2020.146763] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 03/03/2020] [Accepted: 03/08/2020] [Indexed: 01/06/2023]
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79
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Yuan F, Zhang S, Xie W, Yang S, Lin T, Chen X. Effect and mechanism of miR-146a on malignant biological behaviors of lung adenocarcinoma cell line. Oncol Lett 2020; 19:3643-3652. [PMID: 32382320 PMCID: PMC7202298 DOI: 10.3892/ol.2020.11474] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Accepted: 06/28/2019] [Indexed: 12/28/2022] Open
Abstract
The aim of the present study was to assess the expression of microRNA-146a (miR-146a) in human lung adenocarcinoma cells, its effect on cellular behaviors, and the underlying molecular mechanisms. Reverse transcription-quantitative PCR (RT-qPCR) was used to measure miR-146a expression in the human normal lung epithelial cell line, BEAS-2B, and human lung adenocarcinoma cell lines, A549, PC-9 and H1299, to determine whether miR-146a acts as an oncogene or anti-oncogene. miR-146a mimics were transfected into target cells to observe the proliferation, apoptosis, invasion and migration of human lung adenocarcinoma cells. The target genes of miR-146a were predicted using bioinformatics analysis, and binding sites were validated by dual-luciferase reporter assay. Target gene expression at the mRNA and protein levels was measured by RT-qPCR and western blot analysis, respectively. The expression levels of miR-146a in human lung adenocarcinoma cell lines were lower than its expression in BEAS-2B (P<0.01). A549 cell line is a EGFR wild-type lung adenocarcinoma cell line, which is also the most widely studied in NSCLC, and therefore this was chosen as the target cell line for further investigation. Overexpression of miR-146a in A549 cells can inhibit cell proliferation (P<0.05), promote apoptosis (P<0.05), and reduce the cells' migratory ability (P<0.01). Bioinformatics prediction indicated that interleukin-1 receptor-associated kinase 1 (IRAK1) and TNF receptor associated factor 6 (TRAF6) are the target genes of miR-146a. Dual-luciferase reporter assay showed that miR-146a could specifically bind to 3′-untranslated regions of IRAK1 and TRAF6. The protein and mRNA levels of IRAK1 and TRAF6 were significantly downregulated after miR-146a overexpression in A549 cells (P<0.01). The results of this study demonstrated that the expression of miR-146a in human lung adenocarcinoma cells was significantly lower than in normal lung epithelial cells, indicating that miR-146a acts as an anti-oncogene. miR-146a suppresses the proliferation and migration of human lung adenocarcinoma cells by downregulating the expression of IRAK1 and TRAF6.
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Affiliation(s)
- Fang Yuan
- Department of Respiratory Medicine, Fujian Medical University Union Hospital, Fuzhou, Fujian 350001, P.R. China.,Department of Respiratory, The First Hospital of Jiujiang City, Jiujiang, Jiangxi 332000, P.R. China
| | - Suyun Zhang
- Department of Oncology, Fujian Medical University Union Hospital, Fuzhou, Fujian 350001, P.R. China
| | - Wenying Xie
- Department of Oncology, Fujian Medical University Union Hospital, Fuzhou, Fujian 350001, P.R. China
| | - Sheng Yang
- Department of Oncology, Fujian Medical University Union Hospital, Fuzhou, Fujian 350001, P.R. China
| | - Tingyan Lin
- Department of Respiratory Medicine, Fujian Medical University Union Hospital, Fuzhou, Fujian 350001, P.R. China
| | - Xiangqi Chen
- Department of Respiratory Medicine, Fujian Medical University Union Hospital, Fuzhou, Fujian 350001, P.R. China
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Christoforidou E, Joilin G, Hafezparast M. Potential of activated microglia as a source of dysregulated extracellular microRNAs contributing to neurodegeneration in amyotrophic lateral sclerosis. J Neuroinflammation 2020; 17:135. [PMID: 32345319 PMCID: PMC7187511 DOI: 10.1186/s12974-020-01822-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 04/21/2020] [Indexed: 02/07/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is the most common form of motor neuron degeneration in adults, and several mechanisms underlying the disease pathology have been proposed. It has been shown that glia communicate with other cells by releasing extracellular vesicles containing proteins and nucleic acids, including microRNAs (miRNAs), which play a role in the post-transcriptional regulation of gene expression. Dysregulation of miRNAs is commonly observed in ALS patients, together with inflammation and an altered microglial phenotype. However, the role of miRNA-containing vesicles in microglia-to-neuron communication in the context of ALS has not been explored in depth. This review summarises the evidence for the presence of inflammation, pro-inflammatory microglia and dysregulated miRNAs in ALS, then explores how microglia may potentially be responsible for this miRNA dysregulation. The possibility of pro-inflammatory ALS microglia releasing miRNAs which may then enter neuronal cells to contribute to degeneration is also explored. Based on the literature reviewed here, microglia are a likely source of dysregulated miRNAs and potential mediators of neurodegenerative processes. Therefore, dysregulated miRNAs may be promising candidates for the development of therapeutic strategies.
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Affiliation(s)
| | - Greig Joilin
- School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9QG, UK
| | - Majid Hafezparast
- School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9QG, UK.
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81
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Jiang H, Yang M, Chen X, Li M, Li Y, Wang J. miRTMC: A miRNA Target Prediction Method Based on Matrix Completion Algorithm. IEEE J Biomed Health Inform 2020; 24:3630-3641. [PMID: 32287029 DOI: 10.1109/jbhi.2020.2987034] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
microRNAs (miRNAs) are small non-coding RNAs which modulate the stability of gene targets and their rates of translation into proteins at transcriptional level and post-transcriptional level. miRNA dysfunctions can lead to human diseases because of dysregulation of their targets. Correct miRNA target prediction will lead to better understanding of the mechanisms of human diseases and provide hints on curing them. In recent years, computational miRNA target prediction methods have been proposed according to the interaction rules between miRNAs and targets. However, these methods suffer from high false positive rates due to the complicated relationship between miRNAs and their targets. The rapidly growing number of experimentally validated miRNA targets enables predicting miRNA targets with high precision via accurate data analysis. Taking advantage of these known miRNA targets, a novel recommendation system model (miRTMC) for miRNA target prediction is established using a new matrix completion algorithm. In miRTMC, a heterogeneous network is constructed by integrating the miRNA similarity network, the gene similarity network, and the miRNA-gene interaction network. Our assumption is that the latent factors determining whether a gene is the target of miRNA or not are highly correlated, i.e., the adjacency matrix of the heterogeneous network is low-rank, which is then completed by using a nuclear norm regularized linear least squares model under non-negative constraints. Alternating direction method of multipliers (ADMM) is adopted to numerically solve the matrix completion problem. Our results show that miRTMC outperforms the competing methods in terms of various evaluation metrics. Our software package is available at https://github.com/hjiangcsu/miRTMC.
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82
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Fan D, Li C, Fan C, Hu J, Li J, Yao S, Lu W, Yan Y, Luo K. MicroRNA6443-mediated regulation of FERULATE 5-HYDROXYLASE gene alters lignin composition and enhances saccharification in Populus tomentosa. THE NEW PHYTOLOGIST 2020; 226:410-425. [PMID: 31849071 DOI: 10.1111/nph.16379] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 12/01/2019] [Indexed: 05/22/2023]
Abstract
Ferulate 5-hydroxylase (F5H) is a limiting enzyme involved in biosynthesizing sinapyl (S) monolignol in angiosperms. Genetic regulation of F5H can influence S monolignol synthesis and therefore improve saccharification efficiency and biofuel production. To date, little is known about whether F5H is post-transcriptionally regulated by endogenous microRNAs (miRNAs) in woody plants. Here, we report that a microRNA, miR6443, specifically regulates S lignin biosynthesis during stem development in Populus tomentosa. In situ hybridization showed that miR6443 is preferentially expressed in vascular tissues. We further identified that F5H2 is the direct target of miR6443. Overexpression of miR6443 decreased the transcript level of F5H2 in transgenic plants, resulting in a significant reduction in S lignin content. Conversely, reduced miR6443 expression by short tandem target mimics (STTM) elevated F5H2 transcripts, therefore increasing S lignin composition. Introduction of a miR6443-resistant form of F5H2 into miR6443-overexpression plants restored lignin ectopic composition, supporting that miR6443 specifically regulated S lignin biosynthesis by repressing F5H2 in P. tomentosa. Furthermore, saccharification assays revealed decreased hexose yields by 7.5-24.5% in miR6443-overexpression plants compared with the wild-type control, and increased hexoses yields by 13.2-14.6% in STTM6443-overexpression plants. Collectively, we demonstrate that miR6443 modulates S lignin biosynthesis by specially regulating F5H2 in P. tomentosa.
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Affiliation(s)
- Di Fan
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Chaofeng Li
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Chunfen Fan
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, Chongqing, 400715, China
- Key Laboratory of Eco-environments of Three Gorges Reservoir Region, Ministry of Education, Southwest University, Chongqing, 400715, China
| | - Jian Hu
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Jianqiu Li
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Shu Yao
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Wanxiang Lu
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Yangyang Yan
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Keming Luo
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, Chongqing, 400715, China
- Key Laboratory of Eco-environments of Three Gorges Reservoir Region, Ministry of Education, Southwest University, Chongqing, 400715, China
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83
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Agarwal S, Kashaw SK. Potential target identification for breast cancer and screening of small molecule inhibitors: A bioinformatics approach. J Biomol Struct Dyn 2020; 39:1975-1989. [PMID: 32186248 DOI: 10.1080/07391102.2020.1743757] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
In the current study, we investigated the role of PAK1 (P21 (RAC1) Activated Kinase 1) gene in breast cancer and to this end, we performed differential gene expression analysis of PAK1 in breast cancer tissues compared to the normal adjacent tissue. We also studied its significance in protein-protein interaction (PPI) network, and analysed biological pathways, cellular processes, and role of PAK1 in different diseases. We found PAK1 to have significant role in breast cancer pathways such as integrin signaling, axonal guidance signaling, signaling by Rho family GTPases, ERK5 signaling. Additionally, it has been found as hub gene in PPI network, suggesting its possible regulatory role in breast carcinogenesis. Moreover, PAK1 had role in progression of various diseases as neoplasia, tumorigenesis, lymphatic neoplasia. Thereby, PAK1 can be used as a therapeutic target in breast cancer. Further, we put our efforts in identification of potential small molecules inhibitors against PAK1 by developing a composite virtual screening protocol involving molecular dynamics (MD) and molecular docking. The chemical library of compounds from NCI diversity sets, Pubchem and eMolecules were screened against PAK1 protein and hits which showed good binding affinity were considered for MD simulation study. Moreover, to assess binding of selected hits, MMGBSA (Molecular Mechanics-Generalized Born Surface Area) analysis was performed using AMBER (Assisted Model Building with Energy Refinement) package. MMGBSA calculations exhibited that the identified ligands showed good binding affinity with PAK1. HighlightsThe PAK1 has been found to be upregulated in breast cancer samples and is a potential oncogene playing role in different cellular functions and processes.The molecular docking studies revealed ligands showed good binding affinity towards PAK1 protein.The residues Glu345, Leu347, Thr406, Asp299, Asp393 and Gly350 were found to make H-bond interactions with small molecule inhibitors.The residues Ile276, Val284, Ala297, Tyr346, Leu396 and Asp407 were found to make hydrophobic interactions.The RMSD analysis confirmed stability of complexes throughout 40 ns production period.The MD simulations studies revealed the binding site flexibility, binding free energy of complexes and per-residue contribution in ligand binding.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shivangi Agarwal
- Department of Pharmaceutical Sciences, Dr. Harisingh Gour University (A Central University), Sagar, MP, India
| | - Sushil K Kashaw
- Department of Pharmaceutical Sciences, Dr. Harisingh Gour University (A Central University), Sagar, MP, India
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84
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Contributions of Gene Modules Regulated by Essential Noncoding RNA in Colon Adenocarcinoma Progression. BIOMED RESEARCH INTERNATIONAL 2020; 2020:8595473. [PMID: 32280704 PMCID: PMC7128050 DOI: 10.1155/2020/8595473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 02/26/2020] [Accepted: 03/04/2020] [Indexed: 11/17/2022]
Abstract
Noncoding RNAs (ncRNAs), especially microRNA (miRNA) and long noncoding RNA (lncRNA), have an impact on a variety of important biological processes during colon adenocarcinoma (COAD) progression. This includes chromatin organization, transcriptional and posttranscriptional regulation, and cell-cell signaling. The aim of this study is to identify the ncRNA-regulated modules that accompany the progression of COAD and to analyze their mechanisms, in order to screen the potential prognostic biomarkers for COAD. An integrative molecular analysis was carried out to identify the crosstalks of gene modules between different COAD stages, as well as the essential ncRNAs in the posttranscriptional regulation of these modules. 31 ncRNA regulatory modules were found to be significantly associated with overall survival in COAD patients. 17 out of the 31 modules (in which ncRNAs played essential roles) had improved the predictive ability for COAD patient survival compared to only the mRNAs of those modules, which were enriched in the core cancer hallmark pathways with closer interactions. These suggest that the ncRNAs' regulatory modules not only exhibit close relation to COAD progression but also reflect the dynamic significant crosstalk of genes in the modules to the different malignant extent of COAD.
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85
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Hoang NT, Tóth K, Stacey G. The role of microRNAs in the legume-Rhizobium nitrogen-fixing symbiosis. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:1668-1680. [PMID: 32163588 DOI: 10.1093/jxb/eraa018] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 01/10/2020] [Indexed: 06/10/2023]
Abstract
Under nitrogen starvation, most legume plants form a nitrogen-fixing symbiosis with Rhizobium bacteria. The bacteria induce the formation of a novel organ called the nodule in which rhizobia reside as intracellular symbionts and convert atmospheric nitrogen into ammonia. During this symbiosis, miRNAs are essential for coordinating the various plant processes required for nodule formation and function. miRNAs are non-coding, endogenous RNA molecules, typically 20-24 nucleotides long, that negatively regulate the expression of their target mRNAs. Some miRNAs can move systemically within plant tissues through the vascular system, which mediates, for example, communication between the stem/leaf tissues and the roots. In this review, we summarize the growing number of miRNAs that function during legume nodulation focusing on two model legumes, Lotus japonicus and Medicago truncatula, and two important legume crops, soybean (Glycine max) and common bean (Phaseolus vulgaris). This regulation impacts a variety of physiological processes including hormone signaling and spatial regulation of gene expression. The role of mobile miRNAs in regulating legume nodule number is also highlighted.
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Affiliation(s)
- Nhung T Hoang
- C.S. Bond Life Sciences Center, Divisions of Plant Science and Biochemistry, University of Missouri-Columbia, MO, USA
| | - Katalin Tóth
- C.S. Bond Life Sciences Center, Divisions of Plant Science and Biochemistry, University of Missouri-Columbia, MO, USA
| | - Gary Stacey
- C.S. Bond Life Sciences Center, Divisions of Plant Science and Biochemistry, University of Missouri-Columbia, MO, USA
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86
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Integrated miRNA/mRNA Counter-Expression Analysis Highlights Oxidative Stress-Related Genes CCR7 and FOXO1 as Blood Markers of Coronary Arterial Disease. Int J Mol Sci 2020; 21:ijms21061943. [PMID: 32178422 PMCID: PMC7139611 DOI: 10.3390/ijms21061943] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 03/10/2020] [Indexed: 11/23/2022] Open
Abstract
Our interest in the mechanisms of atherosclerosis progression (ATHp) has led to the recent identification of 13 miRNAs and 1285 mRNAs whose expression was altered during ATHp. Here, we deepen the functional relationship among these 13 miRNAs and genes associated to oxidative stress, a crucial step in the onset and progression of vascular disease. We first compiled a list of genes associated to the response to oxidative stress (Oxstress genes) by performing a reverse Gene Ontology analysis (rGO, from the GO terms to the genes) with the GO terms GO0006979, GO1902882, GO1902883 and GO1902884, which included a total of 417 unique Oxstress genes. Next, we identified 108 putative targets of the 13 miRNAs among these unique Oxstress genes, which were validated by an integrated miRNA/mRNA counter-expression analysis with the 1285 mRNAs that yielded 14 genes, Map2k1, Mapk1, Mapk9, Dapk1, Atp2a2, Gata4, Fos, Egfr, Foxo1, Ccr7, Vkorc1l1, Rnf7, Kcnh3, and Mgat3. GO enrichment analysis and a protein–protein-interaction network analysis (PPI) identified most of the validated Oxstress transcripts as components of signaling pathways, highlighting a role for MAP signaling in ATHp. Lastly, expression of these Oxstress transcripts was measured in PBMCs from patients suffering severe coronary artery disease, a serious consequence of ATHp. This allowed the identification of FOXO1 and CCR7 as blood markers downregulated in CAD. These results are discussed in the context of the interaction of the Oxstress transcripts with the ATHp-associated miRNAs.
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87
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Teuber-Hanselmann S, Meinl E, Junker A. MicroRNAs in gray and white matter multiple sclerosis lesions: impact on pathophysiology. J Pathol 2020; 250:496-509. [PMID: 32073139 DOI: 10.1002/path.5399] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 02/05/2020] [Accepted: 02/11/2020] [Indexed: 12/12/2022]
Abstract
Multiple sclerosis (MS) is a chronic disease of the CNS, hallmarked by inflammation and demyelination. Early stages of the disease frequently show active lesions containing numerous foamy macrophages and inflammatory cells. Disease progression is highlighted by increasing numbers of mixed active/inactive or inactive lesions showing sparse inflammation and pronounced astrogliosis. Furthermore, gray matter lesions increase in number and extent during disease progression. MicroRNAs (miRNAs) comprise a group of several thousand (in humans more than 2000), small non-coding RNA molecules with a fundamental influence on about one-third of all protein-coding genes. Furthermore, miRNAs have been detected in body fluids, including spinal fluid, and they are assumed to participate in intercellular communications. Several studies have determined miRNA profiles from dissected white and gray matter lesions of autoptic MS patients. In this review, we summarize in detail the current knowledge of individual miRNAs in gray and white matter lesions of MS patients and present the concepts of MS tissue lesion development based on the altered miRNA profiles. © 2020 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.
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Affiliation(s)
| | - Edgar Meinl
- Institute of Clinical Neuroimmunology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Andreas Junker
- Institute of Neuropathology, University Hospital Essen, Essen, Germany
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88
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Schäfer M, Ciaudo C. Prediction of the miRNA interactome - Established methods and upcoming perspectives. Comput Struct Biotechnol J 2020; 18:548-557. [PMID: 32211130 PMCID: PMC7082591 DOI: 10.1016/j.csbj.2020.02.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 02/21/2020] [Accepted: 02/27/2020] [Indexed: 01/21/2023] Open
Abstract
MicroRNAs (miRNAs) are well-studied small noncoding RNAs involved in post-transcriptional gene regulation in a wide range of organisms, including mammals. Their function is mediated by base pairing with their target RNAs. Although many features required for miRNA-mediated repression have been described, the identification of functional interactions is still challenging. In the last two decades, numerous Machine Learning (ML) models have been developed to predict their putative targets. In this review, we summarize the biological knowledge and the experimental data used to develop these ML models. Recently, Deep Neural Network-based models have also emerged in miRNA interaction modeling. We thus outline established and emerging models to give a perspective on the future developments needed to improve the identification of genes directly regulated by miRNAs.
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Affiliation(s)
- Moritz Schäfer
- Swiss Federal Institute of Technology Zurich, Department of Biology, Institute of Molecular Health Sciences, CH-8093 Zurich, Switzerland
- Life Science Zurich Graduate School, Systems Biology Program, University of Zurich, CH-8047 Zurich, Switzerland
| | - Constance Ciaudo
- Swiss Federal Institute of Technology Zurich, Department of Biology, Institute of Molecular Health Sciences, CH-8093 Zurich, Switzerland
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89
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Bjerke GA, Yi R. Integrated analysis of directly captured microRNA targets reveals the impact of microRNAs on mammalian transcriptome. RNA (NEW YORK, N.Y.) 2020; 26:306-323. [PMID: 31900330 PMCID: PMC7025510 DOI: 10.1261/rna.073635.119] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 12/27/2019] [Indexed: 05/16/2023]
Abstract
MicroRNA (miRNA)-mediated regulation is widespread, relatively mild but functionally important. It remains challenging to unequivocally identify miRNA targeted RNAs at a genomic scale and determine how changes in miRNA levels affect the transcriptome. Here, we captured individual miRNAs and their targeted RNA sites in wild-type, miR-200 family knockout and induced epithelial cells. We detected 1797 miRNAs interacting with 13,830 transcripts at 616,127 sites by sequencing 1,230,019 unique miRNA:RNA chimeras. Although mRNA sites that are bound by miRNAs and contain matches to seed sequences confer the strongest regulation, ∼40%-60% of miRNA bound regions do not contain seed matches. Different miRNAs have different preferences to seed matches and 3' end base-pairing. For individual miRNAs, the effectiveness of mRNA regulation is highly correlated with the number of captured miRNA:mRNA chimeras. Notably, elevated miR-200 expression robustly represses existing targets with little impact on newly recognized targets. Global analysis of directly captured mRNA targets reveals pathways that are involved in cancer and cell adhesion and signaling pathways that are highly regulated by many different miRNAs in epithelial cells. Comparison between experimentally captured and TargetScan predicted targets indicates that our approach is more effective in identifying bona fide targets by reducing false positive and negative predictions. This study reveals the global binding landscape and impact of miRNAs on the mammalian transcriptome.
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Affiliation(s)
- Glen A Bjerke
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, Colorado 80309, USA
| | - Rui Yi
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, Colorado 80309, USA
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90
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Cheray M, Etcheverry A, Jacques C, Pacaud R, Bougras-Cartron G, Aubry M, Denoual F, Peterlongo P, Nadaradjane A, Briand J, Akcha F, Heymann D, Vallette FM, Mosser J, Ory B, Cartron PF. Cytosine methylation of mature microRNAs inhibits their functions and is associated with poor prognosis in glioblastoma multiforme. Mol Cancer 2020; 19:36. [PMID: 32098627 PMCID: PMC7041276 DOI: 10.1186/s12943-020-01155-z] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 02/13/2020] [Indexed: 12/23/2022] Open
Abstract
Background Literature reports that mature microRNA (miRNA) can be methylated at adenosine, guanosine and cytosine. However, the molecular mechanisms involved in cytosine methylation of miRNAs have not yet been fully elucidated. Here we investigated the biological role and underlying mechanism of cytosine methylation in miRNAs in glioblastoma multiforme (GBM). Methods RNA immunoprecipitation with the anti-5methylcytosine (5mC) antibody followed by Array, ELISA, dot blot, incorporation of a radio-labelled methyl group in miRNA, and miRNA bisulfite sequencing were perfomred to detect the cytosine methylation in mature miRNA. Cross-Linking immunoprecipiation qPCR, transfection with methylation/unmethylated mimic miRNA, luciferase promoter reporter plasmid, Biotin-tagged 3’UTR/mRNA or miRNA experiments and in vivo assays were used to investigate the role of methylated miRNAs. Finally, the prognostic value of methylated miRNAs was analyzed in a cohorte of GBM pateints. Results Our study reveals that a significant fraction of miRNAs contains 5mC. Cellular experiments show that DNMT3A/AGO4 methylated miRNAs at cytosine residues inhibit the formation of miRNA/mRNA duplex and leading to the loss of their repressive function towards gene expression. In vivo experiments show that cytosine-methylation of miRNA abolishes the tumor suppressor function of miRNA-181a-5p miRNA for example. Our study also reveals that cytosine-methylation of miRNA-181a-5p results is associated a poor prognosis in GBM patients. Conclusion Together, our results indicate that the DNMT3A/AGO4-mediated cytosine methylation of miRNA negatively. Graphical abstract ![]()
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Affiliation(s)
- Mathilde Cheray
- CRCINA, INSERM, Université de Nantes, Nantes, France.,Faculté de Médecine, Université de Nantes, Nantes, France.,Present address: Department of Oncology-Pathology, Cancer Centrum Karolinska (CCK), R8:03, Karolinska Institutet, SE-171 76, Stockholm, Sweden
| | - Amandine Etcheverry
- CNRS, UMR 6290, Institut de Génétique et Développement de Rennes (IGdR), F-35043, Rennes, France.,Université Rennes1, UEB, UMS 3480 Biosit, Faculté de Médecine, F-35043, Rennes, France.,Plate-forme Génomique Environnementale et Humaine Biosit, Université Rennes1, F-35043, Rennes, France.,CHU Rennes, Service de Génétique Moléculaire et Génomique, F-35033, Rennes, France
| | - Camille Jacques
- INSERM, UMR 1238, équipe labellisée ligue 2012, 1 Rue Gaston Veil, 44035, Nantes, France
| | - Romain Pacaud
- CRCINA, INSERM, Université de Nantes, Nantes, France.,Faculté de Médecine, Université de Nantes, Nantes, France.,LaBCT, Institut de Cancérologie de l'Ouest, Saint Herblain, France.,LabEx IGO "Immunotherapy, Graft, Oncology", Nantes, France
| | - Gwenola Bougras-Cartron
- CRCINA, INSERM, Université de Nantes, Nantes, France.,LaBCT, Institut de Cancérologie de l'Ouest, Saint Herblain, France.,Cancéropole Grand-Ouest, réseau Epigénétique (RepiCGO), Nantes, France.,EpiSAVMEN, Epigenetic consortium Pays de la Loire, Nantes, France
| | - Marc Aubry
- CNRS, UMR 6290, Institut de Génétique et Développement de Rennes (IGdR), F-35043, Rennes, France.,Université Rennes1, UEB, UMS 3480 Biosit, Faculté de Médecine, F-35043, Rennes, France.,Plate-forme Génomique Environnementale et Humaine Biosit, Université Rennes1, F-35043, Rennes, France
| | - Florent Denoual
- CHU Rennes, Service de Génétique Moléculaire et Génomique, F-35033, Rennes, France
| | - Pierre Peterlongo
- IRISA Inria Rennes Bretagne Atlantique, équipe GenScale, Campus de Beaulieu, 35042, Rennes, France
| | - Arulraj Nadaradjane
- CRCINA, INSERM, Université de Nantes, Nantes, France.,Faculté de Médecine, Université de Nantes, Nantes, France.,Cancéropole Grand-Ouest, réseau Epigénétique (RepiCGO), Nantes, France.,EpiSAVMEN, Epigenetic consortium Pays de la Loire, Nantes, France
| | - Joséphine Briand
- CRCINA, INSERM, Université de Nantes, Nantes, France.,Faculté de Médecine, Université de Nantes, Nantes, France.,LaBCT, Institut de Cancérologie de l'Ouest, Saint Herblain, France.,Cancéropole Grand-Ouest, réseau Epigénétique (RepiCGO), Nantes, France.,EpiSAVMEN, Epigenetic consortium Pays de la Loire, Nantes, France
| | - Farida Akcha
- EpiSAVMEN, Epigenetic consortium Pays de la Loire, Nantes, France.,Ifremer, Laboratoire d'Ecotoxicologie, Rue de l'Ile d'Yeu, BP21105, cedex 03 44311, . Nantes, France
| | - Dominique Heymann
- CRCINA, INSERM, Université de Nantes, Nantes, France.,Faculté de Médecine, Université de Nantes, Nantes, France.,LaBCT, Institut de Cancérologie de l'Ouest, Saint Herblain, France
| | - François M Vallette
- CRCINA, INSERM, Université de Nantes, Nantes, France.,Faculté de Médecine, Université de Nantes, Nantes, France.,LaBCT, Institut de Cancérologie de l'Ouest, Saint Herblain, France.,LabEx IGO "Immunotherapy, Graft, Oncology", Nantes, France
| | - Jean Mosser
- CNRS, UMR 6290, Institut de Génétique et Développement de Rennes (IGdR), F-35043, Rennes, France.,Université Rennes1, UEB, UMS 3480 Biosit, Faculté de Médecine, F-35043, Rennes, France.,Plate-forme Génomique Environnementale et Humaine Biosit, Université Rennes1, F-35043, Rennes, France.,CHU Rennes, Service de Génétique Moléculaire et Génomique, F-35033, Rennes, France.,Cancéropole Grand-Ouest, réseau Epigénétique (RepiCGO), Nantes, France
| | - Benjamin Ory
- INSERM, UMR 1238, équipe labellisée ligue 2012, 1 Rue Gaston Veil, 44035, Nantes, France.,Cancéropole Grand-Ouest, réseau Epigénétique (RepiCGO), Nantes, France.,EpiSAVMEN, Epigenetic consortium Pays de la Loire, Nantes, France
| | - Pierre-François Cartron
- CRCINA, INSERM, Université de Nantes, Nantes, France. .,Faculté de Médecine, Université de Nantes, Nantes, France. .,LaBCT, Institut de Cancérologie de l'Ouest, Saint Herblain, France. .,LabEx IGO "Immunotherapy, Graft, Oncology", Nantes, France. .,Cancéropole Grand-Ouest, réseau Epigénétique (RepiCGO), Nantes, France. .,EpiSAVMEN, Epigenetic consortium Pays de la Loire, Nantes, France. .,Institut de Cancérologie de l'Ouest, CRCINA INSERM U1232, Equipe 9 -Apoptose et Progression tumorale, LaBCT, Boulevard du Pr J Monod, 44805, Saint-Herblain, France.
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91
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miRgo: integrating various off-the-shelf tools for identification of microRNA-target interactions by heterogeneous features and a novel evaluation indicator. Sci Rep 2020; 10:1466. [PMID: 32001758 PMCID: PMC6992741 DOI: 10.1038/s41598-020-58336-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 01/15/2020] [Indexed: 12/20/2022] Open
Abstract
MicroRNAs (miRNAs) are short non-coding RNAs that regulate gene expression and biological processes through binding to messenger RNAs. Predicting the relationship between miRNAs and their targets is crucial for research and clinical applications. Many tools have been developed to predict miRNA-target interactions, but variable results among the different prediction tools have caused confusion for users. To solve this problem, we developed miRgo, an application that integrates many of these tools. To train the prediction model, extreme values and median values from four different data combinations, which were obtained via an energy distribution function, were used to find the most representative dataset. Support vector machines were used to integrate 11 prediction tools, and numerous feature types used in these tools were classified into six categories-binding energy, scoring function, evolution evidence, binding type, sequence property, and structure-to simplify feature selection. In addition, a novel evaluation indicator, the Chu-Hsieh-Liang (CHL) index, was developed to improve the prediction power in positive data for feature selection. miRgo achieved better results than all other prediction tools in evaluation by an independent testing set and by its subset of functionally important genes. The tool is available at http://predictor.nchu.edu.tw/miRgo.
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92
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Exploration of targets regulated by miR-125b in porcine adipocytes. In Vitro Cell Dev Biol Anim 2020; 56:103-111. [PMID: 31912457 DOI: 10.1007/s11626-019-00427-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 11/25/2019] [Indexed: 12/14/2022]
Abstract
MicroRNA (miRNA) has been proved to play a key role in lipid metabolism. In our previous study, miR-125b was validated to be differentially expressed in preadipocytes and adipocytes, which was also proved to involve in lipid metabolism. To explore the comprehensive targets of miR-125b in adipocytes, isobaric tag for relative and absolute quantitation (iTRAQ) analysis was performed to obtain differentially expressed proteins in adipocytes comparing negative control (NC) and miR-125b mimic, combining with digital gene expression (DGE) profiling of mRNA incorporated into RNA-induced silencing complex (RISC) pulled down by biotinylated miR-125b mimic and targets prediction of miR-125b by three algorithms, acyl-CoA dehydrogenase short chain (ACADS) and mitochondrial trans-2-enoyl-CoA reductase (MECR) were screened out as miR-125b direct targets. Luciferase reporter assay further validated that miR-125b mimic significantly inhibited the luciferase activity by targeting wild type (WT) 3'-UTR compared with NC. qPCR analysis of ACADS and MECR mRNA from adipose tissues of miR-125b knockout (KO) mice further confirmed the inhibition of miR-125b on ACADS and MECR expressions. Here we report miR-125b play a vital role in maintaining homeostasis of fatty acid metabolism by targeting key enzyme ACADS and MECR in the process of fatty acid elongation and degradation.
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93
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Kaushik K, Palanichamy JK. Potential of Tiny RNAs as a Hope to Detect Parkinson's Disease. Ann Indian Acad Neurol 2020; 23:5. [PMID: 32055111 PMCID: PMC7001424 DOI: 10.4103/aian.aian_634_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 12/16/2019] [Indexed: 11/30/2022] Open
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94
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Zebrafish embryogenesis – A framework to study regulatory RNA elements in development and disease. Dev Biol 2020; 457:172-180. [DOI: 10.1016/j.ydbio.2019.01.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 01/03/2019] [Accepted: 01/07/2019] [Indexed: 12/26/2022]
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95
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Xia X, Wang Y, Huang Y, Zhang H, Lu H, Zheng JC. Exosomal miRNAs in central nervous system diseases: biomarkers, pathological mediators, protective factors and therapeutic agents. Prog Neurobiol 2019; 183:101694. [PMID: 31542363 PMCID: PMC7323939 DOI: 10.1016/j.pneurobio.2019.101694] [Citation(s) in RCA: 120] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 06/14/2019] [Accepted: 09/09/2019] [Indexed: 12/12/2022]
Abstract
Exosomes are small bilipid layer-enclosed extracellular vesicles that can be found in tissues and biological fluids. As a key cell-to-cell and distant communication mediator, exosomes are involved in various central nervous system (CNS) diseases, potentially through transferring their contents such as proteins, lipids and nucleic acids to the target cells. Exosomal miRNAs, which are small non-coding RNAs in the exosomes, are known to be more stable than free miRNAs and therefore have lasting effects on disease-related gene expressions. There are distinct profiles of exosomal miRNAs in different types of CNS diseases even before the onset of irreversible neurological damages, indicating that exosomal miRNAs within tissues and biological fluids could serve as promising biomarkers. Emerging evidence has also demonstrated the pathological effects of several exosomal miRNAs in CNS diseases via specific modulation of disease-related factors. Moreover, exosomes carry therapeutically beneficial miRNAs across the blood-brain-barrier, which can be exploited as a powerful drug delivery tool to help alleviating multiple CNS diseases. In this review, we summarize the recent progress made in understanding the biological roles of exosomal miRNAs as potential diagnostic biomarkers, pathological regulators, and therapeutic targets/drugs for CNS diseases. A comprehensive discussion of the main concerns and challenges for the applications of exosomal miRNAs in the clinical setting is also provided.
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Affiliation(s)
- Xiaohuan Xia
- Center for Translational Neurodegeneration and Regenerative Therapy, Shanghai Tenth People's Hospital affiliated to Tongji University School of Medicine, Shanghai 200072, China
| | - Yi Wang
- Center for Translational Neurodegeneration and Regenerative Therapy, Shanghai Tenth People's Hospital affiliated to Tongji University School of Medicine, Shanghai 200072, China
| | - Yunlong Huang
- Center for Translational Neurodegeneration and Regenerative Therapy, Shanghai Tenth People's Hospital affiliated to Tongji University School of Medicine, Shanghai 200072, China; Departments of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, 68198-5930, USA
| | - Han Zhang
- Second Military Medical University, Shanghai 200433, China
| | - Hongfang Lu
- Center for Translational Neurodegeneration and Regenerative Therapy, Shanghai Tenth People's Hospital affiliated to Tongji University School of Medicine, Shanghai 200072, China
| | - Jialin C Zheng
- Center for Translational Neurodegeneration and Regenerative Therapy, Shanghai Tenth People's Hospital affiliated to Tongji University School of Medicine, Shanghai 200072, China; Collaborative Innovation Center for Brain Science, Tongji University, Shanghai 200092, China; Departments of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, 68198-5930, USA.
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96
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Lai X, Eberhardt M, Schmitz U, Vera J. Systems biology-based investigation of cooperating microRNAs as monotherapy or adjuvant therapy in cancer. Nucleic Acids Res 2019; 47:7753-7766. [PMID: 31340025 PMCID: PMC6735922 DOI: 10.1093/nar/gkz638] [Citation(s) in RCA: 118] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 07/05/2019] [Accepted: 07/13/2019] [Indexed: 12/22/2022] Open
Abstract
MicroRNAs (miRNAs) are short, noncoding RNAs that regulate gene expression by suppressing mRNA translation and reducing mRNA stability. A miRNA can potentially bind many mRNAs, thereby affecting the expression of oncogenes and tumor suppressor genes as well as the activity of whole pathways. The promise of miRNA therapeutics in cancer is to harness this evolutionarily conserved mechanism for the coordinated regulation of gene expression, and thus restoring a normal cell phenotype. However, the promiscuous binding of miRNAs can provoke unwanted off-target effects, which are usually caused by high-dose single-miRNA treatments. Thus, it is desirable to develop miRNA therapeutics with increased specificity and efficacy. To achieve that, we propose the concept of miRNA cooperativity in order to exert synergistic repression on target genes, thus lowering the required total amount of miRNAs. We first review miRNA therapies in clinical application. Next, we summarize the knowledge on the molecular mechanism and biological function of miRNA cooperativity and discuss its application in cancer therapies. We then propose and discuss a systems biology approach to investigate miRNA cooperativity for the clinical setting. Altogether, we point out the potential of miRNA cooperativity to reduce off-target effects and to complement conventional, targeted, or immune-based therapies for cancer.
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Affiliation(s)
- Xin Lai
- Laboratory of Systems Tumor Immunology, Department of Dermatology, Universitätsklinikum Erlangen, 91052 Erlangen, Germany
- Faculty of Medicine, Friedrich-Alexander University Erlangen-Nürnberg, 91052 Erlangen, Germany
| | - Martin Eberhardt
- Laboratory of Systems Tumor Immunology, Department of Dermatology, Universitätsklinikum Erlangen, 91052 Erlangen, Germany
- Faculty of Medicine, Friedrich-Alexander University Erlangen-Nürnberg, 91052 Erlangen, Germany
| | - Ulf Schmitz
- Computational BioMedicine Laboratory Centenary Institute, The University of Sydney, 2006 Camperdown, Australia
- Gene & Stem Cell Therapy Program Centenary Institute, The University of Sydney, 2006 Camperdown, Australia
- Sydney Medical School, The University of Sydney, 2006 Camperdown, Australia
| | - Julio Vera
- Laboratory of Systems Tumor Immunology, Department of Dermatology, Universitätsklinikum Erlangen, 91052 Erlangen, Germany
- Faculty of Medicine, Friedrich-Alexander University Erlangen-Nürnberg, 91052 Erlangen, Germany
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Lo Iacono L, Ielpo D, Accoto A, Di Segni M, Babicola L, D’Addario SL, Ferlazzo F, Pascucci T, Ventura R, Andolina D. MicroRNA-34a Regulates the Depression-like Behavior in Mice by Modulating the Expression of Target Genes in the Dorsal Raphè. Mol Neurobiol 2019; 57:823-836. [DOI: 10.1007/s12035-019-01750-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Accepted: 08/26/2019] [Indexed: 01/06/2023]
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Shanmugapriya, Othman N, Sasidharan S. Prediction of genes and protein-protein interaction networking for miR-221-5p using bioinformatics analysis. GENE REPORTS 2019. [DOI: 10.1016/j.genrep.2019.100426] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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Three miRNAs cooperate with host genes involved in human cardiovascular disease. Hum Genomics 2019; 13:40. [PMID: 31464655 PMCID: PMC6714460 DOI: 10.1186/s40246-019-0232-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Accepted: 08/13/2019] [Indexed: 12/03/2022] Open
Abstract
Background Understanding the roles of miRNAs in cardiovascular disease remains a challenge. Genomic linkage indicates a functional relationship between intronic miRNAs and their host genes. However, few studies have shown functional association between intronic miRNAs and their host coding genes that are genetically associated with cardiovascular disease. Methods In this study, we investigated functional relationship between three protein-coding genes genetically associated with cardiovascular disease, i.e., CDH13, SLC12A3, and CKAP5, and their intronic miRNAs using a data-driven approach. Results We found that the three protein-coding genes functionally interact with targets of their intronic miRNAs, i.e., miR-3182, miR-6863, and miR-5582, in a tissue-specific pattern. The intronic miRNAs preferentially impact important genes for the three host genes in the network, indicating their roles in maintaining the integrity of the interactome where the host genes are involved. Targets of the intronic miRNAs display functional similarity to the host genes. We furthermore present sets of target genes for future investigation on the possible miRNA-target interactions that potentially contribute to cardiovascular diseases. Conclusions Our work provides new insight into the regulatory network of the cardiovascular-associated pathways and opens the possibility for future experimental research. Electronic supplementary material The online version of this article (10.1186/s40246-019-0232-4) contains supplementary material, which is available to authorized users.
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MiR-32-5p influences high glucose-induced cardiac fibroblast proliferation and phenotypic alteration by inhibiting DUSP1. BMC Mol Biol 2019; 20:21. [PMID: 31438862 PMCID: PMC6704591 DOI: 10.1186/s12867-019-0135-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 07/25/2019] [Indexed: 12/14/2022] Open
Abstract
Background The current study aimed to investigate the effects of miR-32-5p on cardiac fibroblasts (CFs) that were induced with high levels of glucose; we also aimed to identify the potential mechanisms involved in the regulation of DUSP1 expression. Methods Human CFs were transfected with a miR-32-5p inhibitor or mimic and were treated with a normal concentration or a high concentration of glucose. Flow cytometry analysis was performed to identify cardiac fibroblasts by examining vimentin, fibronectin (FN) and α-actin expression in human CFs. qRT-PCR and western blot assays were performed to confirm the expression of miR-32-5p, DUSP1 and cardiac fibrosis relevant proteins. The proliferation of CFs was assessed by using MTT assay. An immunocytofluorescent staining assay was performed to determine the protein level of α-SMA and to investigate the degree of phenotypic changes in human CFs. The specific relationship between miR-32-5p and DUSP1 was investigated by a dual luciferase reporter assay. Cell apoptosis rates were measured with flow cytometry and the annexin V-FITC and propidine iodide (PI) staining method. Results A luciferase reporter assay indicated that miR-32-5p could directly target DUSP1. High glucose levels resulted in the overexpression of miR-32-5p, which downregulated DUSP1 expression. Both the upregulation of miR-32-5p and the downregulation of DUSP1 promoted cell apoptosis, proliferation and phenotypic changes in human CFs. Conclusions All findings in this study provide further evidence for the positive effects of miR-32-5p on cell proliferation and the phenotypic changes in CFs by inhibiting DUSP1 expression, and reveal that miR-32-5p could serve as prognostic diagnostic target for cardiac fibrosis. Electronic supplementary material The online version of this article (10.1186/s12867-019-0135-x) contains supplementary material, which is available to authorized users.
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