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Wagner V, Meese E, Keller A. The intricacies of isomiRs: from classification to clinical relevance. Trends Genet 2024:S0168-9525(24)00124-0. [PMID: 38862304 DOI: 10.1016/j.tig.2024.05.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 05/14/2024] [Accepted: 05/15/2024] [Indexed: 06/13/2024]
Abstract
MicroRNAs (miRNAs) and isoforms of their archetype, called isomiRs, regulate gene expression via complementary base-pair binding to messenger RNAs (mRNAs). The partially evolutionarily conserved isomiR sequence variations are differentially expressed among tissues, populations, and genders, and between healthy and diseased states. Aiming towards the clinical use of isomiRs as diagnostic biomarkers and for therapeutic purposes, several challenges need to be addressed, including (i) clarification of isomiR definition, (ii) improved annotation in databases with new standardization (such as the mirGFF3 format), and (iii) improved methods of isomiR detection, functional verification, and in silico analysis. In this review we discuss the respective challenges, and highlight the opportunities for clinical use of isomiRs, especially in the light of increasing amounts of next-generation sequencing (NGS) data.
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Affiliation(s)
- Viktoria Wagner
- Chair for Clinical Bioinformatics, Center for Bioinformatics, Saarland University, 66123 Saarbrücken, Germany; Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Saarland University Campus, 66123 Saarbrücken, Germany
| | - Eckart Meese
- Department of Human Genetics, Saarland University, 66421 Homburg/Saar, Germany
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Center for Bioinformatics, Saarland University, 66123 Saarbrücken, Germany; Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Saarland University Campus, 66123 Saarbrücken, Germany.
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2
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Do VQ, Hoang-Thi C, Pham TT, Bui NL, Kim DT, Chu DT. Computational tools supporting known miRNA identification. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 203:225-242. [PMID: 38360000 DOI: 10.1016/bs.pmbts.2023.12.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
The study of small RNAs is a field that is expanding quickly. Other functional short RNA molecules other than microRNAs, and gene expression regulators, have been found in animals and plants. MicroRNAs play a significant role in host-microbe interactions, and parasite microRNAs may affect the host's innate immunity. Furthermore, short RNAs are intriguing non-invasive biomarker possibilities because they can be found in physiological fluids. These trends suggest that for many researchers, quick and simple techniques for expression profiling and subsequent downstream analysis of miRNA-seq data are crucial. We selected sRNAtoolbox to make integrated sRNA research easier. Each tool can be used separately or to explore and analyze sRNAbench results in further depth. A special focus was placed on the tools' usability. We review available miRNA research tools to have an overview of the evaluation of the tools. Mainly we evaluate the tool sRNAtoolbox.
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Affiliation(s)
- Van-Quy Do
- Faculty of Applied Sciences, International School, Vietnam National University, Hanoi, Vietnam; Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam
| | - Chuc Hoang-Thi
- Faculty of Applied Sciences, International School, Vietnam National University, Hanoi, Vietnam; Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam
| | - Thanh-Truong Pham
- Faculty of Applied Sciences, International School, Vietnam National University, Hanoi, Vietnam; Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam
| | - Nhat-Le Bui
- Faculty of Applied Sciences, International School, Vietnam National University, Hanoi, Vietnam; Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam
| | - Dinh-Thai Kim
- Faculty of Applied Sciences, International School, Vietnam National University, Hanoi, Vietnam.
| | - Dinh-Toi Chu
- Faculty of Applied Sciences, International School, Vietnam National University, Hanoi, Vietnam; Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam.
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3
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Solaguren-Beascoa M, Gámez-Valero A, Escaramís G, Herrero-Lorenzo M, Ortiz AM, Minguet C, Gonzalo R, Bravo MI, Costa M, Martí E. Phospho-RNA-Seq Highlights Specific Small RNA Profiles in Plasma Extracellular Vesicles. Int J Mol Sci 2023; 24:11653. [PMID: 37511412 PMCID: PMC10380198 DOI: 10.3390/ijms241411653] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 07/04/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023] Open
Abstract
Small RNAs (sRNAs) are bioactive molecules that can be detected in biofluids, reflecting physiological and pathological states. In plasma, sRNAs are found within extracellular vesicles (EVs) and in extravesicular compartments, offering potential sources of highly sensitive biomarkers. Deep sequencing strategies to profile sRNAs favor the detection of microRNAs (miRNAs), the best-known class of sRNAs. Phospho-RNA-seq, through the enzymatic treatment of sRNAs with T4 polynucleotide kinase (T4-PNK), has been recently developed to increase the detection of thousands of previously inaccessible RNAs. In this study, we investigated the value of phospho-RNA-seq on both the EVs and extravesicular plasma subfractions. Phospho-RNA-seq increased the proportion of sRNAs used for alignment and highlighted the diversity of the sRNA transcriptome. Unsupervised clustering analysis using sRNA counts matrices correctly classified the EVs and extravesicular samples only in the T4-PNK treated samples, indicating that phospho-RNA-seq stresses the features of sRNAs in each plasma subfraction. Furthermore, T4-PNK treatment emphasized specific miRNA variants differing in the 5'-end (5'-isomiRs) and certain types of tRNA fragments in each plasma fraction. Phospho-RNA-seq increased the number of tissue-specific messenger RNA (mRNA) fragments in the EVs compared with the extravesicular fraction, suggesting that phospho-RNA-seq favors the discovery of tissue-specific sRNAs in EVs. Overall, the present data emphasizes the value of phospho-RNA-seq in uncovering RNA-based biomarkers in EVs.
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Affiliation(s)
- Maria Solaguren-Beascoa
- Department de Biomedicina, Facultat de Medicina i Ciències de la Salut, Institut de Neurociències, Universitat de Barcelona, C/Casanova 143, 08036 Barcelona, Spain
| | - Ana Gámez-Valero
- Department de Biomedicina, Facultat de Medicina i Ciències de la Salut, Institut de Neurociències, Universitat de Barcelona, C/Casanova 143, 08036 Barcelona, Spain
- Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Ministerio de Ciencia Innovación y Universidades, 28029 Madrid, Spain
| | - Georgia Escaramís
- Department de Biomedicina, Facultat de Medicina i Ciències de la Salut, Institut de Neurociències, Universitat de Barcelona, C/Casanova 143, 08036 Barcelona, Spain
- Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Ministerio de Ciencia Innovación y Universidades, 28029 Madrid, Spain
| | - Marina Herrero-Lorenzo
- Department de Biomedicina, Facultat de Medicina i Ciències de la Salut, Institut de Neurociències, Universitat de Barcelona, C/Casanova 143, 08036 Barcelona, Spain
| | - Ana M Ortiz
- Grifols Scientific Innovation Office, 08022 Barcelona, Spain
| | - Carla Minguet
- Grifols Scientific Innovation Office, 08022 Barcelona, Spain
| | - Ricardo Gonzalo
- Grifols Scientific Innovation Office, 08022 Barcelona, Spain
| | | | | | - Eulàlia Martí
- Department de Biomedicina, Facultat de Medicina i Ciències de la Salut, Institut de Neurociències, Universitat de Barcelona, C/Casanova 143, 08036 Barcelona, Spain
- Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Ministerio de Ciencia Innovación y Universidades, 28029 Madrid, Spain
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4
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Scheper M, Romagnolo A, Besharat ZM, Iyer AM, Moavero R, Hertzberg C, Weschke B, Riney K, Feucht M, Scholl T, Petrak B, Maulisova A, Nabbout R, Jansen AC, Jansen FE, Lagae L, Urbanska M, Ferretti E, Tempes A, Blazejczyk M, Jaworski J, Kwiatkowski DJ, Jozwiak S, Kotulska K, Sadowski K, Borkowska J, Curatolo P, Mills JD, Aronica E. miRNAs and isomiRs: Serum-Based Biomarkers for the Development of Intellectual Disability and Autism Spectrum Disorder in Tuberous Sclerosis Complex. Biomedicines 2022; 10:biomedicines10081838. [PMID: 36009385 PMCID: PMC9405248 DOI: 10.3390/biomedicines10081838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 07/22/2022] [Accepted: 07/28/2022] [Indexed: 11/16/2022] Open
Abstract
Tuberous sclerosis complex (TSC) is a rare multi-system genetic disorder characterized by a high incidence of epilepsy and neuropsychiatric manifestations known as tuberous-sclerosis-associated neuropsychiatric disorders (TANDs), including autism spectrum disorder (ASD) and intellectual disability (ID). MicroRNAs (miRNAs) are small regulatory non-coding RNAs that regulate the expression of more than 60% of all protein-coding genes in humans and have been reported to be dysregulated in several diseases, including TSC. In the current study, RNA sequencing analysis was performed to define the miRNA and isoform (isomiR) expression patterns in serum. A Receiver Operating Characteristic (ROC) curve analysis was used to identify circulating molecular biomarkers, miRNAs, and isomiRs, able to discriminate the development of neuropsychiatric comorbidity, either ASD, ID, or ASD + ID, in patients with TSC. Part of our bioinformatics predictions was verified with RT-qPCR performed on RNA isolated from patients’ serum. Our results support the notion that circulating miRNAs and isomiRs have the potential to aid standard clinical testing in the early risk assessment of ASD and ID development in TSC patients.
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Affiliation(s)
- Mirte Scheper
- Department of (Neuro)Pathology Amsterdam Neuroscience, Amsterdam UMC Location University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; (M.S.); (A.R.); (A.M.I.)
| | - Alessia Romagnolo
- Department of (Neuro)Pathology Amsterdam Neuroscience, Amsterdam UMC Location University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; (M.S.); (A.R.); (A.M.I.)
| | - Zein Mersini Besharat
- Department of Experimental Medicine, Sapienza University of Rome, 00161 Rome, Italy; (Z.M.B.); (E.F.)
| | - Anand M. Iyer
- Department of (Neuro)Pathology Amsterdam Neuroscience, Amsterdam UMC Location University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; (M.S.); (A.R.); (A.M.I.)
- Internal Medicine, Erasmus MC, 3015 GD Rotterdam, The Netherlands
| | - Romina Moavero
- Child Neurology and Psychiatry Unit, Systems Medicine Department, Tor Vergata University, 00133 Rome, Italy; (R.M.); (P.C.)
- Child Neurology Unit, Neuroscience Department, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy
| | - Christoph Hertzberg
- Diagnose-und Behandlungszentrum für Kinder, Vivantes-Klinikum Neukölln, 12351 Berlin, Germany;
| | - Bernhard Weschke
- Department of Neuropediatrics, Charité University Medicine Berlin, 13353 Berlin, Germany;
| | - Kate Riney
- Faculty of Medicine, The University of Queensland, Herston, QLD 4029, Australia;
- Neurosciences Unit, Queensland Children’s Hospital, South Brisbane, QLD 4101, Australia
| | - Martha Feucht
- Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, “Member of ERN EpiCARE”, 1090 Vienna, Austria; (M.F.); (T.S.)
| | - Theresa Scholl
- Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, “Member of ERN EpiCARE”, 1090 Vienna, Austria; (M.F.); (T.S.)
| | - Borivoj Petrak
- Motol University Hospital, Charles University, 15000 Prague, Czech Republic; (B.P.); (A.M.)
| | - Alice Maulisova
- Motol University Hospital, Charles University, 15000 Prague, Czech Republic; (B.P.); (A.M.)
| | - Rima Nabbout
- Reference Centre for Rare Epilepsies, Department of Pediatric Neurology, Necker Enfants Malades University Hospital, APHP, Member of ERN EpiCARE, Université de Paris, 149 Rue de Sèvres, 75015 Paris, France;
| | - Anna C. Jansen
- Department of Translational Neurosciences, University of Antwerp, 2000 Antwerp, Belgium;
| | - Floor E. Jansen
- Department of Child Neurology, Brain Center University Medical Center, Member of ERN EpiCare, 3584 BA Utrecht, The Netherlands;
| | - Lieven Lagae
- Department of Development and Regeneration Section Pediatric Neurology, University Hospitals KU Leuven, 3000 Leuven, Belgium;
| | - Malgorzata Urbanska
- Department of Neurology and Epileptology, The Children’s Memorial Health Institute, 04-730 Warsaw, Poland; (M.U.); (S.J.); (K.K.); (K.S.); (J.B.)
| | - Elisabetta Ferretti
- Department of Experimental Medicine, Sapienza University of Rome, 00161 Rome, Italy; (Z.M.B.); (E.F.)
| | - Aleksandra Tempes
- International Institute of Molecular and Cell Biology, 02-109 Warsaw, Poland; (A.T.); (M.B.); (J.J.)
| | - Magdalena Blazejczyk
- International Institute of Molecular and Cell Biology, 02-109 Warsaw, Poland; (A.T.); (M.B.); (J.J.)
| | - Jacek Jaworski
- International Institute of Molecular and Cell Biology, 02-109 Warsaw, Poland; (A.T.); (M.B.); (J.J.)
| | | | - Sergiusz Jozwiak
- Department of Neurology and Epileptology, The Children’s Memorial Health Institute, 04-730 Warsaw, Poland; (M.U.); (S.J.); (K.K.); (K.S.); (J.B.)
- Department of Child Neurology, Medical University of Warsaw, 02-097 Warsaw, Poland
| | - Katarzyna Kotulska
- Department of Neurology and Epileptology, The Children’s Memorial Health Institute, 04-730 Warsaw, Poland; (M.U.); (S.J.); (K.K.); (K.S.); (J.B.)
| | - Krzysztof Sadowski
- Department of Neurology and Epileptology, The Children’s Memorial Health Institute, 04-730 Warsaw, Poland; (M.U.); (S.J.); (K.K.); (K.S.); (J.B.)
| | - Julita Borkowska
- Department of Neurology and Epileptology, The Children’s Memorial Health Institute, 04-730 Warsaw, Poland; (M.U.); (S.J.); (K.K.); (K.S.); (J.B.)
| | - Paolo Curatolo
- Child Neurology and Psychiatry Unit, Systems Medicine Department, Tor Vergata University, 00133 Rome, Italy; (R.M.); (P.C.)
| | - James D. Mills
- Department of (Neuro)Pathology Amsterdam Neuroscience, Amsterdam UMC Location University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; (M.S.); (A.R.); (A.M.I.)
- Department of Clinical and Experimental Epilepsy, UCL Queen Square Institute of Neurology, London WC1E 6BT, UK
- Chalfont Centre for Epilepsy, Chalfont St Peter SL9 0RJ, UK
- Correspondence: (J.D.M.); (E.A.)
| | - Eleonora Aronica
- Department of (Neuro)Pathology Amsterdam Neuroscience, Amsterdam UMC Location University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; (M.S.); (A.R.); (A.M.I.)
- Correspondence: (J.D.M.); (E.A.)
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5
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Simeone I, Rubolino C, Noviello T, Farinello D, Cerulo L, Marzi M, Nicassio F. OUP accepted manuscript. Nucleic Acids Res 2022; 50:2019-2035. [PMID: 35137158 PMCID: PMC8887481 DOI: 10.1093/nar/gkac057] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 01/14/2022] [Accepted: 01/25/2022] [Indexed: 12/04/2022] Open
Abstract
It is currently unknown how many RNA transcripts are able to induce degradation of microRNAs (miRNA) via the mechanism known as target-directed miRNA degradation (TDMD). We developed TDMDfinder, a computational pipeline that identifies ‘high confidence’ TDMD interactions in the Human and Mouse transcriptomes by combining sequence alignment and feature selection approaches. Our predictions suggested that TDMD is widespread, with potentially every miRNA controlled by endogenous targets. We experimentally tested 37 TDMDfinder predictions, of which 17 showed TDMD effects as measured by RT-qPCR and small RNA sequencing, linking the miR-17, miR-19, miR-30, miR-221, miR-26 and miR-23 families to novel endogenous TDMDs. In some cases, TDMD was found to affect different members of the same miRNA family selectively. Features like complementarity to the miRNA 3′ region, bulge size and hybridization energy appeared to be the main factors determining sensitivity. Computational analyses performed using the multiomic TCGA platform substantiated the involvement of many TDMD transcripts in human cancer and highlighted 36 highly significant interactions, suggesting TDMD as a new potential oncogenic mechanism. In conclusion, TDMDfinder provides the first inventory of bona fide human and mouse TDMDs. Available as a free webtool, TDMDfinder allows users to search for any TDMD interaction of interest by customizing its selection criteria.
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Affiliation(s)
| | | | - Teresa Maria Rosaria Noviello
- Department of Electrical Engineering and Information Technology, University of Naples “Federico II”, Via Claudio 21, Naples 80128, Italy
- BioGeM, Institute of Genetic Research “Gaetano Salvatore”, Via Camporeale, Ariano Irpino (AV) 83031, Italy
| | - Diego Farinello
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT)—Via Adamello 16, 20139 Milan, Italy
| | - Luigi Cerulo
- Dep. of Science and Technology, University of Sannio, via de Sanctis, 11, Benevento 82100, Italy
- BioGeM, Institute of Genetic Research “Gaetano Salvatore”, Via Camporeale, Ariano Irpino (AV) 83031, Italy
| | - Matteo Jacopo Marzi
- Correspondence may also be addressed to Matteo Jacopo Marzi. Tel: +39 0294375192;
| | - Francesco Nicassio
- To whom correspondence should be addressed. Tel: +39 0294375174; Fax +39 0294375991;
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6
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Schmauch E, Levonen AL, Linna-Kuosmanen S. Global MicroRNA Profiling of Vascular Endothelial Cells. Methods Mol Biol 2022; 2475:157-186. [PMID: 35451756 DOI: 10.1007/978-1-0716-2217-9_11] [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] [Indexed: 06/14/2023]
Abstract
MicroRNA sequencing (miRNA-seq) enables the detection and characterization of the cell miRNome, including miRNA isoforms (isomiRs) and novel miRNA species. In roughly half of the cases, the most abundant isomiR in the cells is not the reference miRNA given in miRBase, which highlights the importance of isomiR-specific analysis. Here, we describe a gel-free protocol for global miRNA profiling in vascular endothelial cells and the main steps of the subsequent data analysis with two alternative analysis methods. In addition to endothelial cells, the protocol is suitable for other cell and tissue types and has been successfully used to obtain miRNA-seq data from human cardiac tissue, plasma, pericardial fluid, and biofluid exosomes.
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Affiliation(s)
- Eloi Schmauch
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Anna-Liisa Levonen
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Suvi Linna-Kuosmanen
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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7
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Zelli V, Compagnoni C, Capelli R, Corrente A, Cornice J, Vecchiotti D, Di Padova M, Zazzeroni F, Alesse E, Tessitore A. Emerging Role of isomiRs in Cancer: State of the Art and Recent Advances. Genes (Basel) 2021; 12:genes12091447. [PMID: 34573429 PMCID: PMC8469436 DOI: 10.3390/genes12091447] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 09/16/2021] [Accepted: 09/17/2021] [Indexed: 12/12/2022] Open
Abstract
The advent of Next Generation Sequencing technologies brought with it the discovery of several microRNA (miRNA) variants of heterogeneous lengths and/or sequences. Initially ascribed to sequencing errors/artifacts, these isoforms, named isomiRs, are now considered non-canonical variants that originate from physiological processes affecting the canonical miRNA biogenesis. To date, accurate IsomiRs abundance, biological activity, and functions are not completely understood; however, the study of isomiR biology is an area of great interest due to their high frequency in the human miRNome, their putative functions in cooperating with the canonical miRNAs, and potential for exhibiting novel functional roles. The discovery of isomiRs highlighted the complexity of the small RNA transcriptional landscape in several diseases, including cancer. In this field, the study of isomiRs could provide further insights into the miRNA biology and its implication in oncogenesis, possibly providing putative new cancer diagnostic, prognostic, and predictive biomarkers as well. In this review, a comprehensive overview of the state of research on isomiRs in different cancer types, including the most common tumors such as breast cancer, colorectal cancer, melanoma, and prostate cancer, as well as in the less frequent tumors, as for example brain tumors and hematological malignancies, will be summarized and discussed.
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Affiliation(s)
- Veronica Zelli
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (A.C.); (J.C.); (D.V.); (M.D.P.); (F.Z.); (E.A.)
- Center for Molecular Diagnostics and Advanced Therapies, University of L’Aquila, Via Petrini, 67100 L’Aquila, Italy
| | - Chiara Compagnoni
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (A.C.); (J.C.); (D.V.); (M.D.P.); (F.Z.); (E.A.)
| | - Roberta Capelli
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (A.C.); (J.C.); (D.V.); (M.D.P.); (F.Z.); (E.A.)
| | - Alessandra Corrente
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (A.C.); (J.C.); (D.V.); (M.D.P.); (F.Z.); (E.A.)
| | - Jessica Cornice
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (A.C.); (J.C.); (D.V.); (M.D.P.); (F.Z.); (E.A.)
| | - Davide Vecchiotti
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (A.C.); (J.C.); (D.V.); (M.D.P.); (F.Z.); (E.A.)
| | - Monica Di Padova
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (A.C.); (J.C.); (D.V.); (M.D.P.); (F.Z.); (E.A.)
| | - Francesca Zazzeroni
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (A.C.); (J.C.); (D.V.); (M.D.P.); (F.Z.); (E.A.)
| | - Edoardo Alesse
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (A.C.); (J.C.); (D.V.); (M.D.P.); (F.Z.); (E.A.)
| | - Alessandra Tessitore
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (A.C.); (J.C.); (D.V.); (M.D.P.); (F.Z.); (E.A.)
- Center for Molecular Diagnostics and Advanced Therapies, University of L’Aquila, Via Petrini, 67100 L’Aquila, Italy
- Correspondence: ; Tel.: +39-0862433518; Fax: +39-0862433131
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8
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Rodríguez-Galán A, Dosil SG, Gómez MJ, Fernández-Delgado I, Fernández-Messina L, Sánchez-Cabo F, Sánchez-Madrid F. MiRNA post-transcriptional modification dynamics in T cell activation. iScience 2021; 24:102530. [PMID: 34142042 PMCID: PMC8188497 DOI: 10.1016/j.isci.2021.102530] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 04/06/2021] [Accepted: 05/10/2021] [Indexed: 12/15/2022] Open
Abstract
T cell activation leads to extensive changes in the miRNA repertoire. Although overall miRNA expression decreases within a few hours of T cell activation, some individual miRNAs are specifically upregulated. Using next-generation sequencing, we assessed miRNA expression and post-transcriptional modification kinetics in human primary CD4+ T cells upon T cell receptor (TCR) or type I interferon stimulation. This analysis identified differential expression of multiple miRNAs not previously linked to T cell activation. Remarkably, upregulated miRNAs showed a higher frequency of 3' adenylation. TCR stimulation was followed by increased expression of RNA modifying enzymes and the RNA degrading enzymes Dis3L2 and Eri1. In the midst of this adverse environment, 3' adenylation may serve a protective function that could be exploited to improve miRNA stability for T cell-targeted therapy.
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Affiliation(s)
- Ana Rodríguez-Galán
- Servicio de Inmunología. Hospital Universitario La Princesa, Instituto Investigación Sanitaria Princesa (IIS-IP), Universidad Autónoma de Madrid (UAM), 28006 Madrid, Spain
- Vascular Pathophysiology Area. Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28029 Madrid, Spain
| | - Sara G. Dosil
- Servicio de Inmunología. Hospital Universitario La Princesa, Instituto Investigación Sanitaria Princesa (IIS-IP), Universidad Autónoma de Madrid (UAM), 28006 Madrid, Spain
- Vascular Pathophysiology Area. Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28029 Madrid, Spain
| | - Manuel José Gómez
- Vascular Pathophysiology Area. Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28029 Madrid, Spain
| | - Irene Fernández-Delgado
- Servicio de Inmunología. Hospital Universitario La Princesa, Instituto Investigación Sanitaria Princesa (IIS-IP), Universidad Autónoma de Madrid (UAM), 28006 Madrid, Spain
- Vascular Pathophysiology Area. Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28029 Madrid, Spain
| | - Lola Fernández-Messina
- Servicio de Inmunología. Hospital Universitario La Princesa, Instituto Investigación Sanitaria Princesa (IIS-IP), Universidad Autónoma de Madrid (UAM), 28006 Madrid, Spain
- Vascular Pathophysiology Area. Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28029 Madrid, Spain
- CIBER de Enfermedades Cardiovasculares. Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Fátima Sánchez-Cabo
- Vascular Pathophysiology Area. Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28029 Madrid, Spain
| | - Francisco Sánchez-Madrid
- Servicio de Inmunología. Hospital Universitario La Princesa, Instituto Investigación Sanitaria Princesa (IIS-IP), Universidad Autónoma de Madrid (UAM), 28006 Madrid, Spain
- Vascular Pathophysiology Area. Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28029 Madrid, Spain
- CIBER de Enfermedades Cardiovasculares. Instituto de Salud Carlos III, 28029 Madrid, Spain
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9
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Chen Y, Wu T, Zhu Z, Huang H, Zhang L, Goel A, Yang M, Wang X. An integrated workflow for biomarker development using microRNAs in extracellular vesicles for cancer precision medicine. Semin Cancer Biol 2021; 74:134-155. [PMID: 33766650 DOI: 10.1016/j.semcancer.2021.03.011] [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: 12/07/2020] [Revised: 03/13/2021] [Accepted: 03/16/2021] [Indexed: 02/06/2023]
Abstract
EV-miRNAs are microRNA (miRNA) molecules encapsulated in extracellular vesicles (EVs), which play crucial roles in tumor pathogenesis, progression, and metastasis. Recent studies about EV-miRNAs have gained novel insights into cancer biology and have demonstrated a great potential to develop novel liquid biopsy assays for various applications. Notably, compared to conventional liquid biomarkers, EV-miRNAs are more advantageous in representing host-cell molecular architecture and exhibiting higher stability and specificity. Despite various available techniques for EV-miRNA separation, concentration, profiling, and data analysis, a standardized approach for EV-miRNA biomarker development is yet lacking. In this review, we performed a substantial literature review and distilled an integrated workflow encompassing important steps for EV-miRNA biomarker development, including sample collection and EV isolation, EV-miRNA extraction and quantification, high-throughput data preprocessing, biomarker prioritization and model construction, functional analysis, as well as validation. With the rapid growth of "big data", we highlight the importance of efficient mining of high-throughput data for the discovery of EV-miRNA biomarkers and integrating multiple independent datasets for in silico and experimental validations to increase the robustness and reproducibility. Furthermore, as an efficient strategy in systems biology, network inference provides insights into the regulatory mechanisms and can be used to select functionally important EV-miRNAs to refine the biomarker candidates. Despite the encouraging development in the field, a number of challenges still hinder the clinical translation. We finally summarize several common challenges in various biomarker studies and discuss potential opportunities emerging in the related fields.
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Affiliation(s)
- Yu Chen
- Department of Biomedical Sciences, City University of Hong Kong, 31 To Yuen Street, Kowloon Tong, Hong Kong
| | - Tan Wu
- Department of Biomedical Sciences, City University of Hong Kong, 31 To Yuen Street, Kowloon Tong, Hong Kong
| | - Zhongxu Zhu
- Department of Biomedical Sciences, City University of Hong Kong, 31 To Yuen Street, Kowloon Tong, Hong Kong
| | - Hao Huang
- Department of Biomedical Sciences, City University of Hong Kong, 31 To Yuen Street, Kowloon Tong, Hong Kong
| | - Liang Zhang
- Department of Biomedical Sciences, City University of Hong Kong, 31 To Yuen Street, Kowloon Tong, Hong Kong; Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong; Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute, City University of Hong Kong, Shenzhen, Guangdong Province, China
| | - Ajay Goel
- Department of Molecular Diagnostics and Experimental Therapeutics, Beckman Research Institute of City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Mengsu Yang
- Department of Biomedical Sciences, City University of Hong Kong, 31 To Yuen Street, Kowloon Tong, Hong Kong; Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong; Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute, City University of Hong Kong, Shenzhen, Guangdong Province, China
| | - Xin Wang
- Department of Biomedical Sciences, City University of Hong Kong, 31 To Yuen Street, Kowloon Tong, Hong Kong; Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong; Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute, City University of Hong Kong, Shenzhen, Guangdong Province, China.
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10
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Heydarzadeh S, Ranjbar M, Karimi F, Seif F, Alivand MR. Overview of host miRNA properties and their association with epigenetics, long non-coding RNAs, and Xeno-infectious factors. Cell Biosci 2021; 11:43. [PMID: 33632341 PMCID: PMC7905430 DOI: 10.1186/s13578-021-00552-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 02/06/2021] [Indexed: 12/19/2022] Open
Abstract
MicroRNA-derived structures play impressive roles in various biological processes. So dysregulation of miRNAs can lead to different human diseases. Recent studies have extended our comprehension of the control of miRNA function and features. Here, we overview some remarkable miRNA properties that have potential implications for the miRNA functions, including different variants of a miRNA called isomiRs, miRNA arm selection/arm switching, and the effect of these factors on miRNA target selection. Besides, we review some aspects of miRNA interactions such as the interaction between epigenetics and miRNA (different miRNAs and their related processing enzymes are epigenetically regulated by multiple DNA methylation enzymes. moreover, DNA methylation could be controlled by diverse mechanisms related to miRNAs), direct and indirect crosstalk between miRNA and lnc (Long Non-Coding) RNAs as a further approach to conduct intercellular regulation called "competing endogenous RNA" (ceRNA) that is involved in the pathogenesis of different diseases, and the interaction of miRNA activities and some Xeno-infectious (virus/bacteria/parasite) factors, which result in modulation of the pathogenesis of infections. This review provides some related studies to a better understanding of miRNA involvement mechanisms and overcoming the complexity of related diseases that may be applicable and useful to prognostic, diagnostic, therapeutic purposes and personalized medicine in the future.
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Affiliation(s)
- Samaneh Heydarzadeh
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Maryam Ranjbar
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Farokh Karimi
- Department of Biotechnology, Faculty of Science, University of Maragheh, Maragheh, Iran
| | - Farhad Seif
- Department of Immunology and Allergy, Academic Center for Education, Culture, and Research (ACECR), Tehran, Iran
- Neuroscience Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Alivand
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
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11
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Vasconcelos AM, Carmo MB, Ferreira B, Viegas I, Gama-Carvalho M, Ferreira A, Amaral AJ. IsomiR_Window: a system for analyzing small-RNA-seq data in an integrative and user-friendly manner. BMC Bioinformatics 2021; 22:37. [PMID: 33522913 PMCID: PMC7852101 DOI: 10.1186/s12859-021-03955-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 01/01/2021] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND IsomiRs are miRNA variants that vary in length and/or sequence when compared to their canonical forms. These variants display differences in length and/or sequence, including additions or deletions of one or more nucleotides (nts) at the 5' and/or 3' end, internal editings or untemplated 3' end additions. Most available tools for small RNA-seq data analysis do not allow the identification of isomiRs and often require advanced knowledge of bioinformatics. To overcome this, we have developed IsomiR Window, a platform that supports the systematic identification, quantification and functional exploration of isomiR expression in small RNA-seq datasets, accessible to users with no computational skills. METHODS IsomiR Window enables the discovery of isomiRs and identification of all annotated non-coding RNAs in RNA-seq datasets from animals and plants. It comprises two main components: the IsomiR Window pipeline for data processing; and the IsomiR Window Browser interface. It integrates over ten third-party softwares for the analysis of small-RNA-seq data and holds a new algorithm that allows the detection of all possible types of isomiRs. These include 3' and 5'end isomiRs, 3' end tailings, isomiRs with single nucleotide polymorphisms (SNPs) or potential RNA editings, as well as all possible fuzzy combinations. IsomiR Window includes all required databases for analysis and annotation, and is freely distributed as a Linux virtual machine, including all required software. RESULTS IsomiR Window processes several datasets in an automated manner, without restrictions of input file size. It generates high quality interactive figures and tables which can be exported into different formats. The performance of isomiR detection and quantification was assessed using simulated small-RNA-seq data. For correctly mapped reads, it identified different types of isomiRs with high confidence and 100% accuracy. The analysis of a small RNA-seq data from Basal Cell Carcinomas (BCCs) using isomiR Window confirmed that miR-183-5p is up-regulated in Nodular BCCs, but revealed that this effect was predominantly due to a novel 5'end variant. This variant displays a different seed region motif and 1756 isoform-exclusive mRNA targets that are significantly associated with disease pathways, underscoring the biological relevance of isomiR-focused analysis. IsomiR Window is available at https://isomir.fc.ul.pt/ .
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Affiliation(s)
- Ana M Vasconcelos
- Lasige - Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | | | - Beatriz Ferreira
- BioISI - Biosystems & Integrative Sciences Institute, University of Lisboa, Faculty of Sciences, Lisbon, Portugal
| | - Inês Viegas
- BioISI - Biosystems & Integrative Sciences Institute, University of Lisboa, Faculty of Sciences, Lisbon, Portugal
| | - Margarida Gama-Carvalho
- BioISI - Biosystems & Integrative Sciences Institute, University of Lisboa, Faculty of Sciences, Lisbon, Portugal
| | - António Ferreira
- Lasige - Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Andreia J Amaral
- CIISA - Centro de Investigação Interdisciplinar Em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, Lisbon, Portugal.
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12
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A longitudinal study defined circulating microRNAs as reliable biomarkers for disease prognosis and progression in ALS human patients. Cell Death Discov 2021; 7:4. [PMID: 33431881 PMCID: PMC7801652 DOI: 10.1038/s41420-020-00397-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 11/11/2020] [Accepted: 12/15/2020] [Indexed: 12/12/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease associated with motor neuron degeneration, muscle atrophy and paralysis. To date, multiple panels of biomarkers have been described in ALS patients and murine models. Nevertheless, none of them has sufficient specificity and thus the molecular signature for ALS prognosis and progression remains to be elucidated. Here we overcome this limitation through a longitudinal study, analyzing serum levels of circulating miRNAs, stable molecules that are recently used as promising biomarkers for many types of human disorders, in ALS patients during the progression of the pathology. We performed next-generation sequencing (NGS) analysis and absolute RT quantification of serum samples of ALS patients and healthy controls. The expression levels of five selected miRNAs were quantitatively analyzed during disease progression in each patient and we demonstrated that high levels of miR-206, miR-133a and miR-151a-5p can predict a slower clinical decline of patient functionality. In particular, we found that miR-206 and miR-151a-5p serum levels were significantly up-regulated at the mild stage of ALS pathology, to decrease in the following moderate and severe stages, whereas the expression levels of miR-133a and miR-199a-5p remained low throughout the course of the disease, showing a diagnostic significance in moderate and severe stages for miR-133a and in mild and terminal ones for miR-199a-5p. Moreover, we found that miR-423–3p and 151a-5p were significantly downregulated respectively in mild and terminal stages of the disease. These data suggest that these miRNAs represent potential prognostic markers for ALS disease.
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13
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Huang S, Yoshitake K, Asaduzzaman M, Kinoshita S, Watabe S, Asakawa S. Discovery and functional understanding of MiRNAs in molluscs: a genome-wide profiling approach. RNA Biol 2021; 18:1702-1715. [PMID: 33356816 DOI: 10.1080/15476286.2020.1867798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
Small non-coding RNAs play a pivotal role in gene regulation, repression of transposable element and viral activity in various organisms. Among the various categories of these small non-coding RNAs, microRNAs (miRNAs) guide post-translational gene regulation in cellular development, proliferation, apoptosis, oncogenesis, and differentiation. Here, we performed a genome-wide computational prediction of miRNAs to improve the understanding of miRNA observation and function in molluscs. As an initial step, hundreds of conserved miRNAs were predicted in 35 species of molluscs through genome scanning. Afterwards, the miRNAs' population, isoforms, organization, and function were characterized in detail. Furthermore, the key miRNA biogenesis factors, including AGO2, DGCR8, DICER, DROSHA, TRABP2, RAN, and XPO5, were elucidated based on homologue sequence searching. We also summarized the miRNAs' function in biomineralization, immune and stress response, as well as growth and development in molluscs. Because miRNAs play a vital role in various lifeforms, this study will provide insight into miRNA biogenesis and function in molluscs, as well as other invertebrates.
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Affiliation(s)
- Songqian Huang
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Kazutoshi Yoshitake
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Md Asaduzzaman
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Shigeharu Kinoshita
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Shugo Watabe
- School of Marine Biosciences, Kitasato University, Sagamihara, Kanagawa, Japan
| | - Shuichi Asakawa
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
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14
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MicroRNAs Regulating Autophagy in Neurodegeneration. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1208:191-264. [PMID: 34260028 DOI: 10.1007/978-981-16-2830-6_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Social and economic impacts of neurodegenerative diseases (NDs) become more prominent in our constantly aging population. Currently, due to the lack of knowledge about the aetiology of most NDs, only symptomatic treatment is available for patients. Hence, researchers and clinicians are in need of solid studies on pathological mechanisms of NDs. Autophagy promotes degradation of pathogenic proteins in NDs, while microRNAs post-transcriptionally regulate multiple signalling networks including autophagy. This chapter will critically discuss current research advancements in the area of microRNAs regulating autophagy in NDs. Moreover, we will introduce basic strategies and techniques used in microRNA research. Delineation of the mechanisms contributing to NDs will result in development of better approaches for their early diagnosis and effective treatment.
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15
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isomiRs-Hidden Soldiers in the miRNA Regulatory Army, and How to Find Them? Biomolecules 2020; 11:biom11010041. [PMID: 33396892 PMCID: PMC7823672 DOI: 10.3390/biom11010041] [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: 11/27/2020] [Revised: 12/22/2020] [Accepted: 12/26/2020] [Indexed: 02/06/2023] Open
Abstract
Numerous studies on microRNAs (miRNA) in cancer and other diseases have been accompanied by diverse computational approaches and experimental methods to predict and validate miRNA biological and clinical significance as easily accessible disease biomarkers. In recent years, the application of the next-generation deep sequencing for the analysis and discovery of novel RNA biomarkers has clearly shown an expanding repertoire of diverse sequence variants of mature miRNAs, or isomiRs, resulting from alternative post-transcriptional processing events, and affected by (patho)physiological changes, population origin, individual's gender, and age. Here, we provide an in-depth overview of currently available bioinformatics approaches for the detection and visualization of both mature miRNA and cognate isomiR sequences. An attempt has been made to present in a systematic way the advantages and downsides of in silico approaches in terms of their sensitivity and accuracy performance, as well as used methods, workflows, and processing steps, and end output dataset overlapping issues. The focus is given to the challenges and pitfalls of isomiR expression analysis. Specifically, we address the availability of tools enabling research without extensive bioinformatics background to explore this fascinating corner of the small RNAome universe that may facilitate the discovery of new and more reliable disease biomarkers.
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16
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Vivek AT, Kumar S. Computational methods for annotation of plant regulatory non-coding RNAs using RNA-seq. Brief Bioinform 2020; 22:6041165. [PMID: 33333550 DOI: 10.1093/bib/bbaa322] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 10/19/2020] [Accepted: 10/20/2020] [Indexed: 12/19/2022] Open
Abstract
Plant transcriptome encompasses numerous endogenous, regulatory non-coding RNAs (ncRNAs) that play a major biological role in regulating key physiological mechanisms. While studies have shown that ncRNAs are extremely diverse and ubiquitous, the functions of the vast majority of ncRNAs are still unknown. With ever-increasing ncRNAs under study, it is essential to identify, categorize and annotate these ncRNAs on a genome-wide scale. The use of high-throughput RNA sequencing (RNA-seq) technologies provides a broader picture of the non-coding component of transcriptome, enabling the comprehensive identification and annotation of all major ncRNAs across samples. However, the detection of known and emerging class of ncRNAs from RNA-seq data demands complex computational methods owing to their unique as well as similar characteristics. Here, we discuss major plant endogenous, regulatory ncRNAs in an RNA sample followed by computational strategies applied to discover each class of ncRNAs using RNA-seq. We also provide a collection of relevant software packages and databases to present a comprehensive bioinformatics toolbox for plant ncRNA researchers. We assume that the discussions in this review will provide a rationale for the discovery of all major categories of plant ncRNAs.
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Affiliation(s)
- A T Vivek
- National Institute of Plant Genome Research in New Delhi, India
| | - Shailesh Kumar
- National Institute of Plant Genome Research in New Delhi
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17
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Schmartz GP, Kern F, Fehlmann T, Wagner V, Fromm B, Keller A. Encyclopedia of tools for the analysis of miRNA isoforms. Brief Bioinform 2020; 22:6032629. [PMID: 33313643 DOI: 10.1093/bib/bbaa346] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 10/15/2020] [Accepted: 10/29/2020] [Indexed: 12/14/2022] Open
Abstract
RNA sequencing data sets rapidly increase in quantity. For microRNAs (miRNAs), frequently dozens to hundreds of billion reads are generated per study. The quantification of annotated miRNAs and the prediction of new miRNAs are leading computational tasks. Now, the increased depth of coverage allows to gain deeper insights into the variability of miRNAs. The analysis of isoforms of miRNAs (isomiRs) is a trending topic, and a range of computational tools for the analysis of isomiRs has been developed. We provide an overview on 27 available computational solutions for the analysis of isomiRs. These include both stand-alone programs (17 tools) and web-based solutions (10 tools) and span a publication time range from 2010 to 2020. Seven of the tools were published in 2019 and 2020, confirming the rising importance of the topic. While most of the analyzed tools work for a broad range of organisms or are completely independent of a reference organism, several tools have been tailored for the analysis of human miRNA data or for plants. While 14 of the tools are general analysis tools of miRNAs, and isomiR analysis is one of their features, the remaining 13 tools have specifically been developed for isomiR analysis. A direct comparison on 20 deep sequencing data sets for selected tools provides insights into the heterogeneity of results. With our work, we provide users a comprehensive overview on the landscape of isomiR analysis tools and in that support the selection of the most appropriate tool for their respective research task.
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Affiliation(s)
| | | | | | | | - Bastian Fromm
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Andreas Keller
- Saarland Center for Bioinformatics and Chair for Clinical Bioinformatics, Saarland University Building E2.1, 66123 Saarbrücken, Germany
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18
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Nersisyan SA, Shkurnikov MY, Knyazev EN. Factors Involved in miRNA Processing Change Its Expression Level during Imitation of Hypoxia in BeWo b30 Cells. DOKL BIOCHEM BIOPHYS 2020; 493:205-207. [PMID: 32894466 DOI: 10.1134/s1607672920040110] [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: 03/30/2020] [Revised: 04/17/2020] [Accepted: 04/17/2020] [Indexed: 11/23/2022]
Abstract
One of the main complications of pregnancy and causes of maternal and perinatal mortality is preeclampsia. The pathophysiology of preeclampsia is associated with the development of placenta and fetal hypoxia and secretion of a number of effective molecules. The human choriocarcinoma cell line BeWo b30 is often used as a model of the placental barrier. It was shown that oxyquinoline derivatives can mimic hypoxia by suppressing HIF-prolyl hydroxylases and the accumulation of HIF-1α. This effect also leads to a change in the expression of microRNAs and their target genes. However, with hypoxia in cells, not only the level of individual miRNAs but also the ratio of miRNA isoforms (isomiRs) can change, presumably due to inaccuracies in the work of the Drosha and Dicer enzymes. In this work, we showed a change in the expression of the factors involved in the maturation of miRNAs when simulating hypoxia in BeWo b30 cells with an oxyquinoline derivative, which may be one of the causes for the change in the ratio of miRNA isoforms.
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Affiliation(s)
- S A Nersisyan
- Faculty of Biology and Biotechnology, National Research University Higher School of Economics, Moscow, Russia.,Faculty of Mechanics and Mathematics, Moscow State University, Moscow, Russia
| | - M Yu Shkurnikov
- Hertsen Moscow Oncology Research Center, Branch of the National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Moscow, Russia
| | - E N Knyazev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia. .,Translational Technology Center, Moscow, Russia.
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19
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Morgado L, Johannes F. Computational tools for plant small RNA detection and categorization. Brief Bioinform 2020; 20:1181-1192. [PMID: 29059285 PMCID: PMC6781577 DOI: 10.1093/bib/bbx136] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 09/09/2017] [Indexed: 01/06/2023] Open
Abstract
Small RNAs (sRNAs) are important short-length molecules with regulatory functions essential for plant development and plasticity. High-throughput sequencing of total sRNA populations has revealed that the largest share of sRNA remains uncategorized. To better understand the role of sRNA-mediated cellular regulation, it is necessary to create accurate and comprehensive catalogues of sRNA and their sequence features, a task that currently relies on nontrivial bioinformatic approaches. Although a large number of computational tools have been developed to predict features of sRNA sequences, these tools are mostly dedicated to microRNAs and none integrates the functionalities necessary to describe units from all sRNA pathways thus far discovered in plants. Here, we review the different classes of sRNA found in plants and describe available bioinformatics tools that can help in their detection and categorization.
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Affiliation(s)
- Lionel Morgado
- Corresponding author: Lionel Morgado, Groningen Bioinformatics Centre, University of Groningen, Nijenborgh 25 7, 9747 AG Groningen, The Netherlands. Tel.: +31 685 585 827; E-mail:
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20
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Zhao D. Single nucleotide alterations in MicroRNAs and human cancer-A not fully explored field. Noncoding RNA Res 2020; 5:27-31. [PMID: 32128468 PMCID: PMC7044681 DOI: 10.1016/j.ncrna.2020.02.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 02/16/2020] [Accepted: 02/16/2020] [Indexed: 12/17/2022] Open
Abstract
MicroRNAs are ~20 nt long small noncoding RNAs that are processed from stem-looped precursors and function mainly as posttranscriptional regulators of protein coding genes through binding to 3'-untranslated regions of messenger RNAs to inhibit the translation or cause RNA degradation. It is predicted microRNAs could regulate up to half of all human genes and are proved to play important roles in human diseases including cancer. They bind to target mRNAs based on complementary binding which is dominated by the so-called "seed" region which are the 5' 2-8 bases of the microRNA. Due to the small size in nature, even a single nucleotide variation in the precursor region especially those located in the seed regions could show big influence. Here, I summarized and reviewed the current knowledge of these single nucleotide alterations in microRNAs in human cancer including (i) common SNPs in the precursor region, (ii) isomiRs, (iii) somatic mutations of microRNAs. Briefly, this is an underexploited field and clearly, warrants further studies to reveal their biological and clinical significances. I believe they will be key to advancing personalized medicine.
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Affiliation(s)
- Dan Zhao
- Department of Genetics and Cell Biology, Nankai University School of Life Sciences, Tianjin, 300071, China
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21
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Correia de Sousa M, Gjorgjieva M, Dolicka D, Sobolewski C, Foti M. Deciphering miRNAs' Action through miRNA Editing. Int J Mol Sci 2019; 20:E6249. [PMID: 31835747 PMCID: PMC6941098 DOI: 10.3390/ijms20246249] [Citation(s) in RCA: 502] [Impact Index Per Article: 100.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 12/04/2019] [Accepted: 12/06/2019] [Indexed: 12/13/2022] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs with the capability of modulating gene expression at the post-transcriptional level either by inhibiting messenger RNA (mRNA) translation or by promoting mRNA degradation. The outcome of a myriad of physiological processes and pathologies, including cancer, cardiovascular and metabolic diseases, relies highly on miRNAs. However, deciphering the precise roles of specific miRNAs in these pathophysiological contexts is challenging due to the high levels of complexity of their actions. Indeed, regulation of mRNA expression by miRNAs is frequently cell/organ specific; highly dependent on the stress and metabolic status of the organism; and often poorly correlated with miRNA expression levels. Such biological features of miRNAs suggest that various regulatory mechanisms control not only their expression, but also their activity and/or bioavailability. Several mechanisms have been described to modulate miRNA action, including genetic polymorphisms, methylation of miRNA promoters, asymmetric miRNA strand selection, interactions with RNA-binding proteins (RBPs) or other coding/non-coding RNAs. Moreover, nucleotide modifications (A-to-I or C-to-U) within the miRNA sequences at different stages of their maturation are also critical for their functionality. This regulatory mechanism called "RNA editing" involves specific enzymes of the adenosine/cytidine deaminase family, which trigger single nucleotide changes in primary miRNAs. These nucleotide modifications greatly influence a miRNA's stability, maturation and activity by changing its specificity towards target mRNAs. Understanding how editing events impact miRNA's ability to regulate stress responses in cells and organs, or the development of specific pathologies, e.g., metabolic diseases or cancer, should not only deepen our knowledge of molecular mechanisms underlying complex diseases, but can also facilitate the design of new therapeutic approaches based on miRNA targeting. Herein, we will discuss the current knowledge on miRNA editing and how this mechanism regulates miRNA biogenesis and activity.
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Affiliation(s)
| | | | | | | | - Michelangelo Foti
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland; (M.C.d.S.); (M.G.); (D.D.); (C.S.)
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22
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An Approach to Identify Individual Functional Single Nucleotide Polymorphisms and Isoform MicroRNAs. BIOMED RESEARCH INTERNATIONAL 2019; 2019:6193673. [PMID: 31467902 PMCID: PMC6699389 DOI: 10.1155/2019/6193673] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 05/28/2019] [Accepted: 06/24/2019] [Indexed: 01/08/2023]
Abstract
MicroRNAs (miRNAs) and single nucleotide polymorphisms (SNPs) play important roles in disease risk and development, especially cancer. Importantly, when SNPs are located in pre-miRNAs, they affect their splicing mechanism and change the function of miRNAs. To improve disease risk assessment, we propose an approach and developed a software tool, IsomiR_Find, to identify disease/phenotype-related SNPs and isomiRs in individuals. Our approach is based on the individual's samples, with SNP information extracted from the 1000 Genomes Project. SNPs were mapped to pre-miRNAs based on whole-genome coordinates and then SNP-pre-miRNA sequences were constructed. Moreover, we developed matpred2, a software tool to identify the four splicing sites of mature miRNAs. Using matpred2, we identified isomiRs and then verified them by searching within individual miRNA sequencing data. Our approach yielded biomarkers for biological experiments, mined functions of miRNAs and SNPs, improved disease risk assessment, and provided a way to achieve individualized precision medicine.
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Grisard E, Coan M, Cesaratto L, Rigo I, Zandonà L, Paulitti A, Andreuzzi E, Rampioni Vinciguerra GL, Poletto E, Del Ben F, Brisotto G, Biscontin E, Turetta M, Dassi E, Mirnezami A, Canzonieri V, Vecchione A, Baldassarre G, Mongiat M, Spizzo R, Nicoloso MS. Sleeping beauty genetic screen identifies miR-23b::BTBD7 gene interaction as crucial for colorectal cancer metastasis. EBioMedicine 2019; 46:79-93. [PMID: 31303496 PMCID: PMC6710852 DOI: 10.1016/j.ebiom.2019.06.044] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 06/21/2019] [Accepted: 06/21/2019] [Indexed: 12/12/2022] Open
Abstract
Background Metastatic colorectal cancer (CRC) remains a deadly disease. Identifying locally advanced CRC patients with high risk of developing metastasis and improving outcome of metastatic CRC patients require discovering master regulators of metastasis. In this context, the non-coding part of the human genome is still largely unexplored. Methods To interrogate the non-coding part of the human genome and disclose regulators of CRC metastasis, we combined a transposon-based forward genetic screen with a novel in vitro assay, which forces cells to grow deprived of cell-substrate and cell-cell contacts (i.e. forced single cell suspension assay - fSCS). Findings We proved that fSCS selects CRC cells with mesenchymal and pro-metastatic traits. Moreover, we found that the transposon insertions conferred CRC cells resistance to fSCS and thus metastatic advantage. Among the retrieved transposon insertions, we demonstrated that the one located in the 3′UTR of BTBD7 disrupts miR-23b::BTBD7 interaction and contributes to pro-metastatic traits. In addition, miR-23b and BTBD7 correlate with CRC metastasis both in preclinical experiments and in clinical samples. Interpretation fSCS is a simple and scalable in vitro assay to investigate pro-metastatic traits and transposon-based genetic screens can interrogate the non-coding part of the human genome (e.g. miRNA::target interactions). Finally, both Btbd7 and miR-23b represent promising prognostic biomarkers and therapeutic targets in CRC. Fund This work was supported by Marie Curie Actions (CIG n. 303877) and Friuli Venezia Giulia region (Grant Agreement n°245574), Italian Association for Cancer Research (AIRC, MFAG n°13589), Italian Ministry of Health (GR-2010-2319387 and PE-2016-02361040) and 5x1000 to CRO Aviano.
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Affiliation(s)
- Eleonora Grisard
- Division of Molecular Oncology, Department of Translational Research, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Italy
| | - Michela Coan
- Division of Molecular Oncology, Department of Translational Research, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Italy; Department of Life and Reproduction Sciences, University of Verona, Verona, Italy
| | - Laura Cesaratto
- Division of Molecular Oncology, Department of Translational Research, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Italy
| | - Ilenia Rigo
- Division of Molecular Oncology, Department of Translational Research, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Italy
| | - Luigi Zandonà
- Division of Molecular Oncology, Department of Translational Research, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Italy
| | - Alice Paulitti
- Division of Molecular Oncology, Department of Translational Research, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Italy
| | - Eva Andreuzzi
- Division of Molecular Oncology, Department of Translational Research, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Italy
| | - Gian Luca Rampioni Vinciguerra
- Division of Molecular Oncology, Department of Translational Research, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Italy; Faculty of Medicine and Psychology, Department of Clinical and Molecular Medicine, University of Rome "Sapienza", Santo Andrea Hospital, 00189 Rome, Italy
| | - Evelina Poletto
- Division of Molecular Oncology, Department of Translational Research, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Italy
| | - Fabio Del Ben
- Immunopathology and Cancer Biomarkers, Department of Translational Research, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Italy
| | - Giulia Brisotto
- Immunopathology and Cancer Biomarkers, Department of Translational Research, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Italy; Veneto Institute of Oncology IOV-IRCCS, Comprehensive Cancer Centre, Department of Surgery, Oncology and Gastroenterology, University of Padova, Italy
| | - Eva Biscontin
- Immunopathology and Cancer Biomarkers, Department of Translational Research, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Italy
| | - Matteo Turetta
- Pathology Department, University Hospital of Udine, Italy
| | - Erik Dassi
- Laboratory of Translational Genomics, Centre for Integrative Biology, University of Trento, Italy
| | - Alex Mirnezami
- Cancer Sciences, University Surgical Unit, University of Southampton, UK
| | - Vincenzo Canzonieri
- Pathology Unit, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Italy; Department of Medical, Surgical and Health Sciences, University of Trieste Medical School, Trieste, Italy
| | - Andrea Vecchione
- Faculty of Medicine and Psychology, Department of Clinical and Molecular Medicine, University of Rome "Sapienza", Santo Andrea Hospital, 00189 Rome, Italy
| | - Gustavo Baldassarre
- Division of Molecular Oncology, Department of Translational Research, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Italy
| | - Maurizio Mongiat
- Division of Molecular Oncology, Department of Translational Research, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Italy
| | - Riccardo Spizzo
- Division of Molecular Oncology, Department of Translational Research, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Italy.
| | - Milena S Nicoloso
- Division of Molecular Oncology, Department of Translational Research, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Italy
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Computational Resources for Prediction and Analysis of Functional miRNA and Their Targetome. Methods Mol Biol 2019; 1912:215-250. [PMID: 30635896 DOI: 10.1007/978-1-4939-8982-9_9] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
microRNAs are evolutionarily conserved, endogenously produced, noncoding RNAs (ncRNAs) of approximately 19-24 nucleotides (nts) in length known to exhibit gene silencing of complementary target sequence. Their deregulated expression is reported in various disease conditions and thus has therapeutic implications. In the last decade, various computational resources are published in this field. In this chapter, we have reviewed bioinformatics resources, i.e., miRNA-centered databases, algorithms, and tools to predict miRNA targets. First section has enlisted more than 75 databases, which mainly covers information regarding miRNA registries, targets, disease associations, differential expression, interactions with other noncoding RNAs, and all-in-one resources. In the algorithms section, we have compiled about 140 algorithms from eight subcategories, viz. for the prediction of precursor (pre-) and mature miRNAs. These algorithms are developed on various sequence, structure, and thermodynamic based features incorporated into different machine learning techniques (MLTs). In addition, computational identification of miRNAs from high-throughput next generation sequencing (NGS) data and their variants, viz. isomiRs, differential expression, miR-SNPs, and functional annotation, are discussed. Prediction and analysis of miRNAs and their associated targets are also evaluated under miR-targets section providing knowledge regarding novel miRNA targets and complex host-pathogen interactions. In conclusion, we have provided comprehensive review of in silico resources published in miRNA research to help scientific community be updated and choose the appropriate tool according to their needs.
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25
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Yang K, Wen X, Mudunuri S, Varma GPS, Sablok G. Diff isomiRs: Large-scale detection of differential isomiRs for understanding non-coding regulated stress omics in plants. Sci Rep 2019; 9:1406. [PMID: 30723229 PMCID: PMC6363768 DOI: 10.1038/s41598-019-38932-w] [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: 07/27/2018] [Accepted: 01/14/2019] [Indexed: 11/11/2022] Open
Abstract
Plants have an amazing ability to cope with wide variety of stresses by regulating the expression of genes and thus by altering the physiological status. In the past few years, canonical microRNA variants (isomiRs) have been shown to play pivotal roles by acting as regulators of the transcriptional machinery. In the present research, we present Diff isomiRs, a web-based exploratory repository of differential isomiRs across 16 sequenced plant species representing a total of 433 datasets across 21 different stresses and 158 experimental states. Diff isomiRs provides the high-throughput detection of differential isomiRs using mapping-based and model-based differential analysis revealing a total of 16,157 and 2,028 differential isomiRs, respectively. Easy-to-use and web-based exploration of differential isomiRs provides several features such as browsing of the differential isomiRs according to stress or species, as well as association of the differential isomiRs to targets and plant endogenous target mimics (PeTMs). Diff isomiRs also provides the relationship between the canonical miRNAs, isomiRs and the miRNA-target interactions. This is the first web-based large-scale repository for browsing differential isomiRs and will facilitate better understanding of the regulatory role of the isomiRs with respect to the canonical microRNAs. Diff isomiRs can be accessed at: www.mcr.org.in/diffisomirs.
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Affiliation(s)
- Kun Yang
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Guizhou University), Ministry of Education, Institute of Agro-bioengineering/College of Life Sciences, Guizhou University, Guiyang, 550025, Guizhou Province, P. R. China
| | - Xiaopeng Wen
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Guizhou University), Ministry of Education, Institute of Agro-bioengineering/College of Life Sciences, Guizhou University, Guiyang, 550025, Guizhou Province, P. R. China.
| | - Suresh Mudunuri
- Centre for Bioinformatics Research, SRKR Engineering College, Chinna Amiram, Bhimavaram, West Godavari District, Andhra Pradesh, 534204, India
| | - G P Saradhi Varma
- Centre for Bioinformatics Research, SRKR Engineering College, Chinna Amiram, Bhimavaram, West Godavari District, Andhra Pradesh, 534204, India
| | - Gaurav Sablok
- Finnish Museum of Natural History, Helsinki, Finland. .,Organismal and Evolutionary Biology (OEB) Research Programme, Department of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.
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Buñay J, Larriba E, Patiño-Garcia D, Urriola-Muñoz P, Moreno RD, del Mazo J. Combined proteomic and miRNome analyses of mouse testis exposed to an endocrine disruptors chemicals mixture reveals altered toxicological pathways involved in male infertility. ACTA ACUST UNITED AC 2019; 25:156-169. [DOI: 10.1093/molehr/gaz003] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Revised: 12/23/2018] [Accepted: 01/24/2019] [Indexed: 12/20/2022]
Affiliation(s)
- Julio Buñay
- Department of Physiology, Faculty of Biological Sciences, Pontificia Universidad Catolica de Chile (PUC), Santiago, Chile
| | - Eduardo Larriba
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biologicas (CIB-CSIC), Madrid, Spain
| | - Daniel Patiño-Garcia
- Department of Physiology, Faculty of Biological Sciences, Pontificia Universidad Catolica de Chile (PUC), Santiago, Chile
| | - Paulina Urriola-Muñoz
- Department of Physiology, Faculty of Biological Sciences, Pontificia Universidad Catolica de Chile (PUC), Santiago, Chile
- Chemistry Institute, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Ricardo D Moreno
- Department of Physiology, Faculty of Biological Sciences, Pontificia Universidad Catolica de Chile (PUC), Santiago, Chile
| | - Jesús del Mazo
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biologicas (CIB-CSIC), Madrid, Spain
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Armenta-Medina A, Gillmor CS. An Introduction to Methods for Discovery and Functional Analysis of MicroRNAs in Plants. Methods Mol Biol 2019; 1932:1-14. [PMID: 30701488 DOI: 10.1007/978-1-4939-9042-9_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
MicroRNAs play important roles in posttranscriptional regulation of plant development, metabolism, and abiotic stress responses. The recent generation of massive amounts of small RNA sequence data, along with development of bioinformatic tools to identify miRNAs and their mRNA targets, has led to an explosion of newly identified putative miRNAs in plants. Genome editing techniques like CRISPR-Cas9 will allow us to study the biological role of these potential novel miRNAs by efficiently targeting both the miRNA and its mRNA target. In this chapter, we review bioinformatic tools and experimental methods for the identification and functional characterization of miRNAs and their target mRNAs in plants.
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Affiliation(s)
- Alma Armenta-Medina
- Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato, Mexico
| | - C Stewart Gillmor
- Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato, Mexico.
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An integrative piRNA analysis of mouse gametes and zygotes reveals new potential origins and gene regulatory roles. Sci Rep 2018; 8:12832. [PMID: 30150632 PMCID: PMC6110870 DOI: 10.1038/s41598-018-31032-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 08/08/2018] [Indexed: 12/14/2022] Open
Abstract
Piwi-interacting RNAs (piRNAs) are a subclass of the small non-coding RNAs (sncRNAs). Their main reported function was to exert control over transposable elements (TEs) in mammalian germline. In this study undertaking a deeper bioinformatics analysis of piRNAs present in mouse oocytes, sperm cells and zygotes, we first elaborated a new piRNA database based on sequences identified as piRNAs by immunoprecipitation with PIWI proteins. Our bioinformatics analysis revealed that, at least in gametes and zygotes, piRNAs could encompass multifunctional cell-dependent regulatory molecules. Indeed, genome analysis of the piRNA mapping density (reads/kb) evidenced in all samples an enrichment of intron-derived piRNAs. Further, piRNA population was classified into sequences not associated to TEs or repeats (NRapiRNAs) and associated to repetitive genome elements (RapiRNAs). In oocytes most of the NRapiRNAs mapped to the 5′UTRs of coding mRNAs, while higher proportion of NRapiRNAs was detected in sperm cells associated to the 3′UTRs of mRNAs. This piRNA complementarity to mRNA UTRs suggests key post-transcriptional regulatory roles over mRNAs such as those encoding MHC genes. In addition, a striking association of RapiRNA with long non-coding RNAs (lncRNAs) was identified. piRNAs associated with relevant lncRNAs such as: Rab26os and GAS5 and key mRNAs, were particularly assessed.
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29
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Identifying and characterizing functional 3' nucleotide addition in the miRNA pathway. Methods 2018; 152:23-30. [PMID: 30138674 DOI: 10.1016/j.ymeth.2018.08.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 08/02/2018] [Accepted: 08/14/2018] [Indexed: 02/07/2023] Open
Abstract
Over the past decade, modifications to microRNAs (miRNAs) via 3' end nucleotide addition have gone from a deep-sequencing curiosity to experimentally confirmed drivers of a range of regulatory activities. Here we overview the methods that have been deployed by researchers seeking to untangle these diverse functional roles and include characterizing not only the nucleotidyl transferases catalyzing the additions but also the nucleotides being added, and the timing of their addition during the miRNA pathway. These methods and their further development are key to clarifying the diverse and sometimes contradictory functional findings presently attributed to these nucleotide additions.
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30
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Endogenous transcripts control miRNA levels and activity in mammalian cells by target-directed miRNA degradation. Nat Commun 2018; 9:3119. [PMID: 30087332 PMCID: PMC6081425 DOI: 10.1038/s41467-018-05182-9] [Citation(s) in RCA: 105] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 06/19/2018] [Indexed: 01/19/2023] Open
Abstract
Little is known about miRNA decay. A target-directed miRNA degradation mechanism (TDMD) has been suggested, but further investigation on endogenous targets is necessary. Here, we identify hundreds of targets eligible for TDMD and show that an endogenous RNA (Serpine1) controls the degradation of two miRNAs (miR-30b-5p and miR-30c-5p) in mouse fibroblasts. In our study, TDMD occurs when the target is expressed at relatively low levels, similar in range to those of its miRNAs (100-200 copies per cell), and becomes more effective at high target:miRNA ratios (>10:1). We employ CRISPR/Cas9 to delete the miR-30 responsive element within Serpine1 3'UTR and interfere with TDMD. TDMD suppression increases miR-30b/c levels and boosts their activity towards other targets, modulating gene expression and cellular phenotypes (i.e., cell cycle re-entry and apoptosis). In conclusion, a sophisticated regulatory layer of miRNA and gene expression mediated by specific endogenous targets exists in mammalian cells.
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Menezes MR, Balzeau J, Hagan JP. 3' RNA Uridylation in Epitranscriptomics, Gene Regulation, and Disease. Front Mol Biosci 2018; 5:61. [PMID: 30057901 PMCID: PMC6053540 DOI: 10.3389/fmolb.2018.00061] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2018] [Accepted: 06/14/2018] [Indexed: 12/31/2022] Open
Abstract
Emerging evidence implicates a wide range of post-transcriptional RNA modifications that play crucial roles in fundamental biological processes including regulating gene expression. Collectively, they are known as epitranscriptomics. Recent studies implicate 3' RNA uridylation, the non-templated addition of uridine(s) to the terminal end of RNA, as a key player in epitranscriptomics. In this review, we describe the functional roles and significance of 3' terminal RNA uridylation that has diverse functions in regulating both mRNAs and non-coding RNAs. In mammals, three Terminal Uridylyl Transferases (TUTases) are primarily responsible for 3' RNA uridylation. These enzymes are also referred to as polyU polymerases. TUTase 1 (TUT1) is implicated in U6 snRNA maturation via uridylation. The TUTases TUT4 and/or TUT7 are the predominant mediators of all other cellular uridylation. Terminal uridylation promotes turnover for many polyadenylated mRNAs, replication-dependent histone mRNAs that lack polyA-tails, and aberrant structured noncoding RNAs. In addition, uridylation regulates biogenesis of a subset of microRNAs and generates isomiRs, sequent variant microRNAs that have altered function in specific cases. For example, the RNA binding protein and proto-oncogene LIN28A and TUT4 work together to polyuridylate pre-let-7, thereby blocking biogenesis and function of the tumor suppressor let-7 microRNA family. In contrast, monouridylation of Group II pre-miRNAs creates an optimal 3' overhang that promotes recognition and subsequent cleavage by the Dicer-TRBP complex that then yields the mature microRNA. Also, uridylation may play a role in non-canonical microRNA biogenesis. The overall significance of 3' RNA uridylation is discussed with an emphasis on mammalian development, gene regulation, and disease, including cancer and Perlman syndrome. We also introduce recent changes to the HUGO-approved gene names for multiple terminal nucleotidyl transferases that affects in part TUTase nomenclature (TUT1/TENT1, TENT2/PAPD4/GLD2, TUT4/ZCCHC11/TENT3A, TUT7/ZCCHC6/TENT3B, TENT4A/PAPD7, TENT4B/PAPD5, TENT5A/FAM46A, TENT5B/FAM46B, TENT5C/FAM46C, TENT5D/FAM46D, MTPAP/TENT6/PAPD1).
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Affiliation(s)
- Miriam R Menezes
- Department of Neurosurgery, University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Julien Balzeau
- Department of Neurosurgery, University of Texas Health Science Center at Houston, Houston, TX, United States
| | - John P Hagan
- Department of Neurosurgery, University of Texas Health Science Center at Houston, Houston, TX, United States
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Wu CW, Evans JM, Huang S, Mahoney DW, Dukek BA, Taylor WR, Yab TC, Smyrk TC, Jen J, Kisiel JB, Ahlquist DA. A Comprehensive Approach to Sequence-oriented IsomiR annotation (CASMIR): demonstration with IsomiR profiling in colorectal neoplasia. BMC Genomics 2018; 19:401. [PMID: 29801434 PMCID: PMC5970459 DOI: 10.1186/s12864-018-4794-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 05/14/2018] [Indexed: 01/14/2023] Open
Abstract
Background MicroRNA (miRNA) profiling is an important step in studying biological associations and identifying marker candidates. miRNA exists in isoforms, called isomiRs, which may exhibit distinct properties. With conventional profiling methods, limitations in assay and analysis platforms may compromise isomiR interrogation. Results We introduce a comprehensive approach to sequence-oriented isomiR annotation (CASMIR) to allow unbiased identification of global isomiRs from small RNA sequencing data. In this approach, small RNA reads are maintained as independent sequences instead of being summarized under miRNA names. IsomiR features are identified through step-wise local alignment against canonical forms and precursor sequences. Through customizing the reference database, CASMIR is applicable to isomiR annotation across species. To demonstrate its application, we investigated isomiR profiles in normal and neoplastic human colorectal epithelia. We also ran miRDeep2, a popular miRNA analysis algorithm to validate isomiRs annotated by CASMIR. With CASMIR, specific and biologically relevant isomiR patterns could be identified. We note that specific isomiRs are often more abundant than their canonical forms. We identify isomiRs that are commonly up-regulated in both colorectal cancer and advanced adenoma, and illustrate advantages in targeting isomiRs as potential biomarkers over canonical forms. Conclusions Studying miRNAs at the isomiR level could reveal new insight into miRNA biology and inform assay design for specific isomiRs. CASMIR facilitates comprehensive annotation of isomiR features in small RNA sequencing data for isomiR profiling and differential expression analysis. Electronic supplementary material The online version of this article (10.1186/s12864-018-4794-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chung Wah Wu
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Jared M Evans
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA
| | - Shengbing Huang
- Division of Bioinformatics and Computational Biology, University of Minnesota Rochester, Rochester, MN, USA
| | - Douglas W Mahoney
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA
| | - Brian A Dukek
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - William R Taylor
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Tracy C Yab
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Thomas C Smyrk
- Division of Anatomic Pathology, Mayo Clinic, Rochester, MN, USA
| | - Jin Jen
- Genome Analysis Core, Medical Genome Facility, Mayo Clinic, Rochester, MN, USA.,Division of Experimental Pathology, Mayo Clinic, Rochester, MN, USA
| | - John B Kisiel
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - David A Ahlquist
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA.
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Kavitha N, Vijayarathna S, Oon CE, Chen Y, Kanwar JR, Punj V, Sasidharan S. MicroRNA profiling in MDA-MB-231 human breast cancer cell exposed to the Phaleria macrocarpa (Boerl.) fruit ethyl acetate fraction (PMEAF) through IIlumina Hi-Seq technologies and various in silico bioinformatics tools. JOURNAL OF ETHNOPHARMACOLOGY 2018; 213:118-131. [PMID: 29154802 DOI: 10.1016/j.jep.2017.11.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Revised: 11/06/2017] [Accepted: 11/09/2017] [Indexed: 06/07/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Phaleria macrocarpa (Scheff) Boerl, is a famous traditional medicinal plant which exhibited cytotoxicity against various cancerous cells. Traditionally, P. macrocarpa has been used to control cancer, impotency, hemorrhoids, diabetes mellitus, allergies, liver and heart disease, kidney disorders, blood diseases, acne, stroke, migraine, and various skin diseases. AIM OF THE STUDY Recent studies have demonstrated a potent anticancer potential of P. macrocarpa, especially against HeLa cell. The objective of this study was to investigate the regulation of miRNAs on MDA-MB-231 treated with P. macrocarpa ethyl acetate fraction (PMEAF). MATERIALS AND METHODS The regulation of miRNAs on MDA-MB-231 cells treated with PMEAF was studied through IIlumina, Hi-Seq. 2000 platform of Next Generation Sequencing (NGS) and various in silico bioinformatics tools. RESULTS The PMEAF treatment against MDA-MB-231 cells identified 10 upregulated and 10 downregulated miRNAs. A set of 606 target genes of 10 upregulated miRNAs and 517 target genes of 10 downregulated miRNAs were predicted based on computational and validated databases by using miRGate DB Query. Meanwhile, results from DAVID Bioinformatics Resources 6.8 specified the functional annotation of the upregulated miRNAs involvement in cancer pathway by suppressing the oncogenes and downregulating miRNAs by expressing the tumour suppressor genes in the regulation of apoptosis pathway. CONCLUSION In conclusion, the results of this study proved that PMEAF is a promising anticancer agent with high cytotoxicity against MDA-MB-231 breast cancer cells and it induced apoptotic cell death mechanism through the regulation of miRNAs. PMEAF might be the best candidate for developing more potent anticancer drugs or chemo preventive supplements.
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Affiliation(s)
- Nowroji Kavitha
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, USM, 11800 Pulau Pinang, Malaysia
| | - Soundararajan Vijayarathna
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, USM, 11800 Pulau Pinang, Malaysia
| | - Chern Ein Oon
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, USM, 11800 Pulau Pinang, Malaysia
| | - Yeng Chen
- Dental Research & Training Unit, and Oral Cancer Research and Coordinating Centre (OCRCC), Faculty of Dentistry, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Jagat R Kanwar
- Nanomedicine-Laboratory of Immunology and Molecular Biomedical Research (LIMBR), School of Medicine (SoM), Faculty of Health, Deakin University, Waurn Ponds, Geelong, VIC 3216, Australia
| | - Vasu Punj
- Department of Medicine, Norris Comprehensive Cancer Center, University of Southern California at Los Angeles, Los Angeles, CA 90089, USA
| | - Sreenivasan Sasidharan
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, USM, 11800 Pulau Pinang, Malaysia.
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Tripathi A, Chacon O, Singla-Pareek SL, Sopory SK, Sanan-Mishra N. Mapping the microRNA Expression Profiles in Glyoxalase Over-expressing Salinity Tolerant Rice. Curr Genomics 2018; 19:21-35. [PMID: 29491730 PMCID: PMC5817874 DOI: 10.2174/1389202918666170228134530] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 09/08/2016] [Accepted: 09/20/2016] [Indexed: 12/01/2022] Open
Abstract
In the recent years, glyoxalase pathway has been an active area of research in both human and plants. This pathway is reported to confer stress tolerance in plants, by modulating the glutathione homeostasis to achieve detoxification of a potent cytotoxic and mutagenic compound, methylglyoxal. The microRNAs (miRNAs) are also reported to play significant role in stress tolerance for plants. However, the cross-talk of miRNAs with the metabolism regulated by glyoxalase in the salinity-tolerance is unexplored. We therefore investigated whether expression profiles of miRNAs are altered in response to glyoxalase overexpression, and if any of these are also responsible for modulating the stress responses of plants. In this study, the Next Generation Sequencing (NGS) was employed to profile miRNA expression levels from glyoxalase overexpressing transgenic lines. The associated targets of differentially expressed miRNAs were predicted and their functional annotation was carried out using Gene Ontology (GO) and KEGG Orthology (KO), which showed their involvement in several crucial biological pathways. The analysis of NGS datasets also identified other isoforms or isomiRs of selected miRNAs, which may have an active role in developing tolerance against salt stress. Different aspects of miRNA modifications were also studied in glyoxalase overexpressing lines.
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Affiliation(s)
- Anita Tripathi
- International Center for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
| | - Osmani Chacon
- International Center for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
| | - Sneh Lata Singla-Pareek
- International Center for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
| | - Sudhir K. Sopory
- International Center for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
| | - Neeti Sanan-Mishra
- International Center for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
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35
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Marzi MJ, Nicassio F. Uncovering the Stability of Mature miRNAs by 4-Thio-Uridine Metabolic Labeling. Methods Mol Biol 2018; 1823:141-152. [PMID: 29959679 DOI: 10.1007/978-1-4939-8624-8_11] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
MicroRNAs (miRNAs) are an evolutionary conserved class of short, single-stranded noncoding RNAs (<18-22 nt in length) that act in posttranscriptional regulation of gene expression in higher eukaryotes. The abundance of a miRNA is a key feature in control of its activity and, therefore, a number of mechanisms finely regulate miRNA levels, acting at both transcriptional and posttranscriptional level. Recent evidences, including our research, highlighted the role of miRNA decay as a mechanism controlling the miRNA pool. We describe in this chapter an optimized methodology to determine miRNA degradation rates in mammalian cells. Our approach is based on metabolic pulse labeling with 4-thiouridine (4sU), a uridine analog that is incorporated in nascent RNA and allows thiol-specific biotinylation and selective pull-down of labeled RNA. In particular, given the long average half-life and the complex biogenetic process of miRNAs, we developed a "pulse-chase" protocol where 4sU is removed from the medium after a long labeling period (2-3 h pulse), and labeled RNA is purified at different time points to measure the decay of labeled molecules. By combining the 4sU-based "pulse-chase" approach with high-throughput small RNA sequencing (sRNAseq), it is possible to quantify at genome-wide level miRNA degradation rates.
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Affiliation(s)
- Matteo J Marzi
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), Milan, Italy.
| | - Francesco Nicassio
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), Milan, Italy.
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Yang K, Wen X, Mudunuri SB, Sablok G. Plant IsomiR Atlas: Large Scale Detection, Profiling, and Target Repertoire of IsomiRs in Plants. FRONTIERS IN PLANT SCIENCE 2018; 9:1881. [PMID: 30723486 PMCID: PMC6349829 DOI: 10.3389/fpls.2018.01881] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 12/05/2018] [Indexed: 05/15/2023]
Abstract
microRNAs (miRNAs) play an important role as key regulators controlling the post-transcriptional events in plants across development, abiotic and biotic stress, tissue polarity and also in defining the evolutionary basis of the origin of the post-transcriptional machinery. Identifying patterns of regulated and co-regulated small RNAs, in particular miRNAs and their sequence variants with the availability of next generation sequencing approaches has widely demonstrated the role of miRNAs and their temporal regulation in maintaining plant development and their response to stress conditions. Although the role of canonical miRNAs has been widely explored and functional diversity is revealed, those works for isomiRs are still limited and urgent to be carried out across plants. This relative lack of information with respect to isomiRs might be attributed to the non-availability of large-scale detection of isomiRs across wide plant species. In the present research, we addressed this by developing Plant isomiR Atlas, which provides large-scale detection of isomiRs across 23 plant species utilizing 677 smallRNAs datasets and reveals a total of 98,374 templated and non-templated isomiRs from 6,167 precursors. Plant isomiR Atlas provides several visualization features such as species specific isomiRs, isomiRs and canonical miRNAs overlap, terminal modification classifications, target identification using psRNATarget and TargetFinder and also canonical miRNAs:target interactions. Plant isomiR Atlas will play a key role in understanding the regulatory nature of miRNAome and will accelerate to understand the functional role of isomiRs. Plant isomiR Atlas is available at www.mcr.org.in/isomir. One Sentence Summary Plant isomiR Atlas will play a key role in understanding the regulatory nature of miRNAome and will accelerate the understanding and diversity of functional targets of plants isomiRs.
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Affiliation(s)
- Kun Yang
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Guizhou University), Ministry of Education, Institute of Agro-Bioengineering, College of Life Sciences, Guizhou University, Guiyang, China
| | - Xiaopeng Wen
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Guizhou University), Ministry of Education, Institute of Agro-Bioengineering, College of Life Sciences, Guizhou University, Guiyang, China
- *Correspondence: Xiaopeng Wen
| | - Suresh B. Mudunuri
- Centre for Bioinformatics Research, SRKR Engineering College, Bhimavaram, India
| | - Gaurav Sablok
- Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
- Organismal and Evolutionary Biology (OEB) Research Programme, Department of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- Gaurav Sablok
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Amsel D, Vilcinskas A, Billion A. Evaluation of high-throughput isomiR identification tools: illuminating the early isomiRome of Tribolium castaneum. BMC Bioinformatics 2017; 18:359. [PMID: 28774263 PMCID: PMC5543545 DOI: 10.1186/s12859-017-1772-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 07/30/2017] [Indexed: 01/01/2023] Open
Abstract
Background MicroRNAs carry out post-transcriptional gene regulation in animals by binding to the 3' untranslated regions of mRNAs, causing their degradation or translational repression. MicroRNAs influence many biological functions, and dysregulation can therefore disrupt development or even cause death. High-throughput sequencing and the mining of animal small RNA data has shown that microRNA genes can yield differentially expressed isoforms, known as isomiRs. Such isoforms are particularly relevant during early development, and the extension or truncation of the 5' end can change the profile of mRNA targets compared to the original mature sequence. We used the publicly available small RNA dataset of the model beetle Tribolium castaneum to create the first comparative isomiRome of early developmental stages in this species. Standard microRNA analysis software does not specifically account for isomiRs. We therefore carried out the first comparative evaluation of the specialized tools isomiRID, isomiR-SEA and miraligner, which can be downloaded for local use and can handle next generation sequencing data. Results We compared the performance of isomiRID, isomiR-SEA and miraligner using simulated Illumina HiSeq2000 and MiSeq data to test the impact of technical errors. We also created artificial microRNA isoforms to determine the effect of biological variants on the performance of each algorithm. We found that isomiRID achieved the best true positive rate among the three algorithms, but only accounted for one mutation at a time. In contrast, miraligner reported all variations simultaneously but with 78% sensitivity, yielding isomiRs with 3' or 5' deletions. Finally, isomiR-SEA achieved a sensitivity of 25–33% when the seed region was mutated or partly deleted, but was the only tool that could accommodate more than one mismatch. Using the best tool, we performed a complete isomiRome analysis of the early developmental stages of T. castaneum. Conclusions Our findings will help researchers to select the most suitable isomiR analysis tools for their experiments. We confirmed the dynamic expression of 3′ non-template isomiRs and expanded the isomiRome by all known isomiR modifications during the early development of T. castaneum. Electronic supplementary material The online version of this article (doi:10.1186/s12859-017-1772-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Daniel Amsel
- Fraunhofer Institute for Molecular Biology and Applied Ecology, Department of Bioresources, Winchester Str. 2, 35394, Giessen, Germany.
| | - Andreas Vilcinskas
- Fraunhofer Institute for Molecular Biology and Applied Ecology, Department of Bioresources, Winchester Str. 2, 35394, Giessen, Germany.,Institute for Insect Biotechnology, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | - André Billion
- Fraunhofer Institute for Molecular Biology and Applied Ecology, Department of Bioresources, Winchester Str. 2, 35394, Giessen, Germany
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Buñay J, Larriba E, Moreno RD, Del Mazo J. Chronic low-dose exposure to a mixture of environmental endocrine disruptors induces microRNAs/isomiRs deregulation in mouse concomitant with intratesticular estradiol reduction. Sci Rep 2017; 7:3373. [PMID: 28611354 PMCID: PMC5469815 DOI: 10.1038/s41598-017-02752-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 04/18/2017] [Indexed: 12/31/2022] Open
Abstract
Humans are environmentally exposed not only to single endocrine-disrupting chemicals (EDCs) but to mixtures that affect their reproductive health. In reproductive tissues, microRNAs (miRNAs) are emerging as key targets of EDCs. Here, we analysed changes in the testis "miRNome" (and their biogenesis mechanism) in chronically exposed adult mice to a cocktail of five EDCs containing 0.3 mg/kg-body weight (BW)/day of each phthalate (DEHP, DBP, BBP) and 0.05 mg/kg-BW/day of each alkylphenol (NP, OP), from conception to adulthood. The testis "miRNome" was characterised using next-generation sequencing (NGS). Expression levels of genes involved in miRNA biogenesis were measured by RT-qPCR, as well as several physiological and cytological parameters. We found two up-regulated, and eight down-regulated miRNAs and thirty-six differentially expressed isomiRs along with an over-expression of Drosha, Adar and Zcchc11. A significant decrease of intratesticular estradiol but not testosterone was detected. Functional analysis showed altered spermatogenesis, germ cell apoptosis and negative correlation of miR-18a-5p with Nr1h2 involved in the deregulation of the steroidogenesis pathway. Here, we present the first association between miRNA/isomiRs deregulation, their mechanisms of biogenesis and histopathological and hormonal alterations in testes of adult mice exposed to a mixture of low-dose EDCs, which can play a role in male infertility.
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Affiliation(s)
- Julio Buñay
- Department of Physiology, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Eduardo Larriba
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas (CSIC), Madrid, Spain
| | - Ricardo D Moreno
- Department of Physiology, Pontificia Universidad Católica de Chile, Santiago, Chile.
| | - Jesús Del Mazo
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas (CSIC), Madrid, Spain.
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Krauskopf J, de Kok TM, Schomaker SJ, Gosink M, Burt DA, Chandler P, Warner RL, Johnson KJ, Caiment F, Kleinjans JC, Aubrecht J. Serum microRNA signatures as "liquid biopsies" for interrogating hepatotoxic mechanisms and liver pathogenesis in human. PLoS One 2017; 12:e0177928. [PMID: 28545106 PMCID: PMC5435338 DOI: 10.1371/journal.pone.0177928] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 05/05/2017] [Indexed: 12/13/2022] Open
Abstract
MicroRNAs (miRNAs) released into the peripheral circulation upon cellular injury have shown a promise as a new class of tissue-specific biomarkers. We were first to demonstrate that next-generation sequencing analysis of serum from human subjects with acetaminophen-induced liver injury revealed a specific signature of circulating miRNAs. We consequently hypothesized that different types of hepatic liver impairments might feature distinct signatures of circulating miRNAs and that this approach might be useful as minimally invasive diagnostic "liquid biopsies" enabling the interrogation of underlying molecular mechanisms of injury in distant tissues. Therefore we examined serum circulating miRNAs in a total of 72 serum samples from a group of 53 subjects that included patients with accidental acetaminophen overdose, hepatitis B infection, liver cirrhosis and type 2 diabetes as well as gender- and age-matched healthy subjects with no evidence of liver disease. The miRNA signatures were identified using next-generation sequencing that provided analysis for the whole miRNome, including miRNA isoforms. Compared to the healthy subjects, a total of 179 miRNAs showed altered serum levels across the diseased subjects. Although many subjects have elevated alanine aminotransferase suggesting liver impairments, we identified distinct miRNA signatures for different impairments with minimum overlap. Furthermore, the bioinformatics analysis of miRNA signatures revealed relevant molecular pathways associated with the mechanisms of toxicity and or pathogenesis of disease. Interestingly, the high proportion of miRNA isoforms present in the respective signatures indicated a new level of complexity in cellular response to stress or disease. Our study demonstrates for the first time that signatures of circulating miRNAs show specificity for liver injury phenotypes and, once validated, might become useful for diagnosis of organ pathologies as "liquid biopsies".
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Affiliation(s)
- Julian Krauskopf
- Department of Toxicogenomics, Maastricht University, Maastricht, the Netherlands
- * E-mail:
| | - Theo M. de Kok
- Department of Toxicogenomics, Maastricht University, Maastricht, the Netherlands
| | - Shelli J. Schomaker
- Drug Safety Research and Development, Pfizer Inc., Groton, Connecticut, United States of America
| | - Mark Gosink
- Drug Safety Research and Development, Pfizer Inc., Groton, Connecticut, United States of America
| | - Deborah A. Burt
- Drug Safety Research and Development, Pfizer Inc., Groton, Connecticut, United States of America
| | - Patricia Chandler
- Clinical Research Unit, Pfizer Inc., New Haven, Connecticut, United States of America
| | - Roscoe L. Warner
- Pathology Department, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Kent J. Johnson
- Pathology Department, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Florian Caiment
- Department of Toxicogenomics, Maastricht University, Maastricht, the Netherlands
| | - Jos C. Kleinjans
- Department of Toxicogenomics, Maastricht University, Maastricht, the Netherlands
| | - Jiri Aubrecht
- Drug Safety Research and Development, Pfizer Inc., Groton, Connecticut, United States of America
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40
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Marinaro F, Marzi MJ, Hoffmann N, Amin H, Pelizzoli R, Niola F, Nicassio F, De Pietri Tonelli D. MicroRNA-independent functions of DGCR8 are essential for neocortical development and TBR1 expression. EMBO Rep 2017; 18:603-618. [PMID: 28232627 DOI: 10.15252/embr.201642800] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 01/16/2017] [Accepted: 01/19/2017] [Indexed: 12/31/2022] Open
Abstract
Recent evidence indicates that the miRNA biogenesis factors DROSHA, DGCR8, and DICER exert non-overlapping functions, and have also roles in miRNA-independent regulatory mechanisms. However, it is currently unknown whether miRNA-independent functions of DGCR8 play any role in the maintenance of neuronal progenitors and during corticogenesis. Here, by phenotypic comparison of cortices from conditional Dgcr8 and Dicer knockout mice, we show that Dgcr8 deletion, in contrast to Dicer depletion, leads to premature differentiation of neural progenitor cells and overproduction of TBR1-positive neurons. Remarkably, depletion of miRNAs upon DCGR8 loss is reduced compared to DICER loss, indicating that these phenotypic differences are mediated by miRNA-independent functions of DGCR8. We show that Dgcr8 mutations induce an earlier and stronger phenotype in the developing nervous system compared to Dicer mutants and that miRNA-independent functions of DGCR8 are critical for corticogenesis. Finally, our data also suggest that the Microprocessor complex, with DROSHA and DGCR8 as core components, directly regulates the Tbr1 transcript, containing evolutionarily conserved hairpins that resemble miRNA precursors, independently of miRNAs.
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Affiliation(s)
- Federica Marinaro
- Neuroscience and Brain Technologies Department, Istituto Italiano di Tecnologia, Genoa, Italy
| | - Matteo J Marzi
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia, Milan, Italy
| | - Nadin Hoffmann
- Neuroscience and Brain Technologies Department, Istituto Italiano di Tecnologia, Genoa, Italy
| | - Hayder Amin
- Neuroscience and Brain Technologies Department, Istituto Italiano di Tecnologia, Genoa, Italy
| | - Roberta Pelizzoli
- Neuroscience and Brain Technologies Department, Istituto Italiano di Tecnologia, Genoa, Italy
| | - Francesco Niola
- Neuroscience and Brain Technologies Department, Istituto Italiano di Tecnologia, Genoa, Italy
| | - Francesco Nicassio
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia, Milan, Italy
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Zhang Y, Zang Q, Zhang H, Ban R, Yang Y, Iqbal F, Li A, Shi Q. DeAnnIso: a tool for online detection and annotation of isomiRs from small RNA sequencing data. Nucleic Acids Res 2016; 44:W166-75. [PMID: 27179030 PMCID: PMC4987950 DOI: 10.1093/nar/gkw427] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 05/05/2016] [Indexed: 12/19/2022] Open
Abstract
Small RNA (sRNA) Sequencing technology has revealed that microRNAs (miRNAs) are capable of exhibiting frequent variations from their canonical sequences, generating multiple variants: the isoforms of miRNAs (isomiRs). However, integrated tool to precisely detect and systematically annotate isomiRs from sRNA sequencing data is still in great demand. Here, we present an online tool, DeAnnIso (Detection and Annotation of IsomiRs from sRNA sequencing data). DeAnnIso can detect all the isomiRs in an uploaded sample, and can extract the differentially expressing isomiRs from paired or multiple samples. Once the isomiRs detection is accomplished, detailed annotation information, including isomiRs expression, isomiRs classification, SNPs in miRNAs and tissue specific isomiR expression are provided to users. Furthermore, DeAnnIso provides a comprehensive module of target analysis and enrichment analysis for the selected isomiRs. Taken together, DeAnnIso is convenient for users to screen for isomiRs of their interest and useful for further functional studies. The server is implemented in PHP + Perl + R and available to all users for free at: http://mcg.ustc.edu.cn/bsc/deanniso/ and http://mcg2.ustc.edu.cn/bsc/deanniso/.
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Affiliation(s)
- Yuanwei Zhang
- Molecular and Cell Genetics Laboratory, The CAS Key Laboratory of Innate Immunity and Chronic Disease, Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei 230027, China Hefei Institute of Physical Science, China Academy of Science, Hefei 230027, China
| | - Qiguang Zang
- School of Information Science and Technology, University of Science and Technology of China, Hefei 230027, China
| | - Huan Zhang
- Molecular and Cell Genetics Laboratory, The CAS Key Laboratory of Innate Immunity and Chronic Disease, Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Rongjun Ban
- School of Information Science and Technology, University of Science and Technology of China, Hefei 230027, China
| | - Yifan Yang
- Department of statistics, University of Kentucky, Lexington, KY 40536, USA
| | - Furhan Iqbal
- Molecular and Cell Genetics Laboratory, The CAS Key Laboratory of Innate Immunity and Chronic Disease, Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei 230027, China Institute of Pure and Applied Biology, Bahauddin Zakariya University, Multan 60800, Pakistan
| | - Ao Li
- School of Information Science and Technology, University of Science and Technology of China, Hefei 230027, China Research Centers for Biomedical Engineering, University of Science and Technology of China, Hefei 230027, China
| | - Qinghua Shi
- Molecular and Cell Genetics Laboratory, The CAS Key Laboratory of Innate Immunity and Chronic Disease, Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei 230027, China Hefei Institute of Physical Science, China Academy of Science, Hefei 230027, China
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43
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Guo L, Yu J, Liang T, Zou Q. miR-isomiRExp: a web-server for the analysis of expression of miRNA at the miRNA/isomiR levels. Sci Rep 2016; 6:23700. [PMID: 27009551 PMCID: PMC4806314 DOI: 10.1038/srep23700] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 03/09/2016] [Indexed: 12/22/2022] Open
Abstract
MicroRNA (miRNA) locus has been found that can generate a series of varied isomiR sequences. Most studies always focus on determining miRNA level, however, the canonical miRNA sequence is only a specific member in the multiple isomiRs. Some studies have shown that isomiR sequences play versatile roles in biological progress, and the analysis and research should be simultaneously performed at the miRNA/isomiR levels. Based on the biological characteristics of miRNA and isomiR, we developed miR-isomiRExp to analyze expression pattern of miRNA at the miRNA/isomiR levels, provide insights into tracking miRNA/isomiR maturation and processing mechanisms, and reveal functional characteristics of miRNA/isomiR. Simultaneously, we also performed expression analysis of specific human diseases using public small RNA sequencing datasets based on the analysis platform, which may help in surveying the potential deregulated miRNA/isomiR expression profiles, especially sequence and function-related isomiRs for further interaction analysis and study. The miR-isomiRExp platform provides miRNA/isomiR expression patterns and more information to study deregulated miRNA loci and detailed isomiR sequences. This comprehensive analysis will enrich experimental miRNA studies. miR-isomiRExp is available at http://server.malab.cn/miRisomiRExp/.
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Affiliation(s)
- Li Guo
- Department of Bioinformatics, School of Geographic and Biologic Information, Nanjing University of Posts and Telecommunications, Nanjing, 210023, China
| | - Jiafeng Yu
- Shandong Provincial Key Laboratory of Functional Macromolecular Biophysics, Institute of Biophysics, Dezhou University, Dezhou, 253023, China
| | - Tingming Liang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, 210023, China
| | - Quan Zou
- School of Computer Science and Technology, Tianjin University, Tianjin, 300072, China
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44
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Marzi MJ, Ghini F, Cerruti B, de Pretis S, Bonetti P, Giacomelli C, Gorski MM, Kress T, Pelizzola M, Muller H, Amati B, Nicassio F. Degradation dynamics of microRNAs revealed by a novel pulse-chase approach. Genome Res 2016; 26:554-65. [PMID: 26821571 PMCID: PMC4817778 DOI: 10.1101/gr.198788.115] [Citation(s) in RCA: 123] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 01/19/2016] [Indexed: 12/22/2022]
Abstract
The regulation of miRNAs is critical to the definition of cell identity and behavior in normal physiology and disease. To date, the dynamics of miRNA degradation and the mechanisms involved in remain largely obscure, in particular, in higher organisms. Here, we developed a pulse-chase approach based on metabolic RNA labeling to calculate miRNA decay rates at genome-wide scale in mammalian cells. Our analysis revealed heterogeneous miRNA half-lives, with many species behaving as stable molecules (T1/2 > 24 h), while others, including passenger miRNAs and a number (25/129) of guide miRNAs, are quickly turned over (T1/2 = 4–14 h). Decay rates were coupled with other features, including genomic organization, transcription rates, structural heterogeneity (isomiRs), and target abundance, measured through quantitative experimental approaches. This comprehensive analysis highlighted functional mechanisms that mediate miRNA degradation, as well as the importance of decay dynamics in the regulation of the miRNA pool under both steady-state conditions and during cell transitions.
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Affiliation(s)
- Matteo J Marzi
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), 20139 Milan, Italy
| | - Francesco Ghini
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), 20139 Milan, Italy
| | - Benedetta Cerruti
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), 20139 Milan, Italy
| | - Stefano de Pretis
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), 20139 Milan, Italy
| | - Paola Bonetti
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), 20139 Milan, Italy
| | - Chiara Giacomelli
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), 20139 Milan, Italy
| | - Marcin M Gorski
- Department of Experimental Oncology, European Institute of Oncology (IEO), 20139 Milan, Italy
| | - Theresia Kress
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), 20139 Milan, Italy; Department of Experimental Oncology, European Institute of Oncology (IEO), 20139 Milan, Italy
| | - Mattia Pelizzola
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), 20139 Milan, Italy
| | - Heiko Muller
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), 20139 Milan, Italy
| | - Bruno Amati
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), 20139 Milan, Italy; Department of Experimental Oncology, European Institute of Oncology (IEO), 20139 Milan, Italy
| | - Francesco Nicassio
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), 20139 Milan, Italy
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Klinge CM. miRNAs regulated by estrogens, tamoxifen, and endocrine disruptors and their downstream gene targets. Mol Cell Endocrinol 2015; 418 Pt 3:273-97. [PMID: 25659536 PMCID: PMC4523495 DOI: 10.1016/j.mce.2015.01.035] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 01/22/2015] [Accepted: 01/23/2015] [Indexed: 02/07/2023]
Abstract
MicroRNAs (miRNAs) are short (22 nucleotides), single-stranded, non-coding RNAs that form complimentary base-pairs with the 3' untranslated region of target mRNAs within the RNA-induced silencing complex (RISC) and block translation and/or stimulate mRNA transcript degradation. The non-coding miRBase (release 21, June 2014) reports that human genome contains ∼ 2588 mature miRNAs which regulate ∼ 60% of human protein-coding mRNAs. Dysregulation of miRNA expression has been implicated in estrogen-related diseases including breast cancer and endometrial cancer. The mechanism for estrogen regulation of miRNA expression and the role of estrogen-regulated miRNAs in normal homeostasis, reproduction, lactation, and in cancer is an area of great research and clinical interest. Estrogens regulate miRNA transcription through estrogen receptors α and β in a tissue-specific and cell-dependent manner. This review focuses primarily on the regulation of miRNA expression by ligand-activated ERs and their bona fide gene targets and includes miRNA regulation by tamoxifen and endocrine disrupting chemicals (EDCs) in breast cancer and cell lines.
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Affiliation(s)
- Carolyn M Klinge
- Department of Biochemistry & Molecular Biology, Center for Genetics and Molecular Medicine, University of Louisville School of Medicine, Louisville, KY 40292, USA.
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46
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Saiselet M, Gacquer D, Spinette A, Craciun L, Decaussin-Petrucci M, Andry G, Detours V, Maenhaut C. New global analysis of the microRNA transcriptome of primary tumors and lymph node metastases of papillary thyroid cancer. BMC Genomics 2015; 16:828. [PMID: 26487287 PMCID: PMC4618137 DOI: 10.1186/s12864-015-2082-3] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 10/14/2015] [Indexed: 01/21/2023] Open
Abstract
Background Papillary Thyroid Cancer (PTC) is the most prevalent type of endocrine cancer. Its incidence has rapidly increased in recent decades but little is known regarding its complete microRNA transcriptome (miRNome). In addition, there is a need for molecular biomarkers allowing improved PTC diagnosis. Methods We performed small RNA deep-sequencing of 3 PTC, their matching normal tissues and lymph node metastases (LNM). We designed a new bioinformatics framework to handle each aspect of the miRNome: whole expression profiles, isomiRs distribution, non-templated additions distributions, RNA-editing or mutation. Results were validated experimentally by qRT-PCR on normal samples, tumors and LNM from 14 independent patients and in silico using the dataset from The Cancer Genome Atlas (small RNA deepsequencing of 59 normal samples, 495 PTC, and 8 LNM). Results We performed small RNA deep-sequencing of 3 PTC, their matching normal tissues and lymph node metastases (LNM). We designed a new bioinformatics framework to handle each aspect of the miRNome: whole expression profiles, isomiRs distribution, non-templated additions distributions, RNA-editing or mutation. Results were validated experimentally by qRT-PCR on normal samples, tumors and LNM from 14 independent patients and in silico using the dataset from The Cancer Genome Atlas (small RNA deep-sequencing of 59 normal samples, 495 PTC, and 8 LNM). We confirmed already described up-regulations of microRNAs in PTC, such as miR-146b-5p or miR-222-3p, but we also identified down-regulated microRNAs, such as miR-7-5p or miR-30c-2-3p. We showed that these down-regulations are linked to the tumorigenesis process of thyrocytes. We selected the 14 most down-regulated microRNAs in PTC and we showed that they are potential biomarkers of PTC samples. Nevertheless, they can distinguish histological classical variants and follicular variants of PTC in the TCGA dataset. In addition, 12 of the 14 down-regulated microRNAs are significantly less expressed in aggressive PTC compared to non-aggressive PTC. We showed that the associated aggressive expression profile is mainly due to the presence of the BRAF V600E mutation. In general, primary tumors and LNM presented similar microRNA expression profiles but specific variations like the down-regulation of miR-7-2-3p and miR-30c-2-3p in LNM were observed. Investigations of the 5p-to-3p arm expression ratios, non-templated additions or isomiRs distributions revealed no major implication in PTC tumorigenesis process or LNM appearance. Conclusions Our results showed that down-regulated microRNAs can be used as new potential common biomarkers of PTC and to distinguish main subtypes of PTC. MicroRNA expressions can be linked to the development of LNM of PTC. The bioinformatics framework that we have developed can be used as a starting point for the global analysis of any microRNA deep-sequencing data in an unbiased way. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2082-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Manuel Saiselet
- IRIBHM, Université libre de Bruxelles, 808 route de Lennik, B-1070, Brussels, Belgium.
| | - David Gacquer
- IRIBHM, Université libre de Bruxelles, 808 route de Lennik, B-1070, Brussels, Belgium.
| | - Alex Spinette
- Tumor Bank of the J. Bordet Cancer Institute, 1000, Brussels, Belgium.
| | - Ligia Craciun
- Tumor Bank of the J. Bordet Cancer Institute, 1000, Brussels, Belgium.
| | - Myriam Decaussin-Petrucci
- Service d'anatomie et cytologie pathologiques, Centre Hospitalier Lyon Sud, 69495, Pierre Benite Cedex, France.
| | - Guy Andry
- J. Bordet Cancer Institute, Surgery Department, 1000, Brussels, Belgium.
| | - Vincent Detours
- IRIBHM, Université libre de Bruxelles, 808 route de Lennik, B-1070, Brussels, Belgium.
| | - Carine Maenhaut
- IRIBHM, Université libre de Bruxelles, 808 route de Lennik, B-1070, Brussels, Belgium. .,Welbio, Université libre de Bruxelles, Brussels, Belgium.
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47
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Kaushik A, Saraf S, Mukherjee SK, Gupta D. miRMOD: a tool for identification and analysis of 5' and 3' miRNA modifications in Next Generation Sequencing small RNA data. PeerJ 2015; 3:e1332. [PMID: 26623179 PMCID: PMC4662591 DOI: 10.7717/peerj.1332] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 09/27/2015] [Indexed: 12/27/2022] Open
Abstract
In the past decade, the microRNAs (miRNAs) have emerged to be important regulators of gene expression across various species. Several studies have confirmed different types of post-transcriptional modifications at terminal ends of miRNAs. The reports indicate that miRNA modifications are conserved and functionally significant as it may affect miRNA stability and ability to bind mRNA targets, hence affecting target gene repression. Next Generation Sequencing (NGS) of the small RNA (sRNA) provides an efficient and reliable method to explore miRNA modifications. The need for dedicated software, especially for users with little knowledge of computers, to determine and analyze miRNA modifications in sRNA NGS data, motivated us to develop miRMOD. miRMOD is a user-friendly, Microsoft Windows and Graphical User Interface (GUI) based tool for identification and analysis of 5′ and 3′ miRNA modifications (non-templated nucleotide additions and trimming) in sRNA NGS data. In addition to identification of miRNA modifications, the tool also predicts and compares the targets of query and modified miRNAs. In order to compare binding affinities for the same target, miRMOD utilizes minimum free energies of the miRNA:target and modified-miRNA:target interactions. Comparisons of the binding energies may guide experimental exploration of miRNA post-transcriptional modifications. The tool is available as a stand-alone package to overcome large data transfer problems commonly faced in web-based high-throughput (HT) sequencing data analysis tools. miRMOD package is freely available at http://bioinfo.icgeb.res.in/miRMOD.
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Affiliation(s)
- Abhinav Kaushik
- Bioinformatics Laboratory, SCB Group, International Centre for Genetic Engineering & Biotechnology, New Delhi, India
| | - Shradha Saraf
- Bioinformatics Laboratory, SCB Group, International Centre for Genetic Engineering & Biotechnology, New Delhi, India
| | - Sunil K Mukherjee
- Department of Genetics, University of Delhi, South Campus, Delhi, India
| | - Dinesh Gupta
- Bioinformatics Laboratory, SCB Group, International Centre for Genetic Engineering & Biotechnology, New Delhi, India
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48
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Fromm B, Billipp T, Peck LE, Johansen M, Tarver JE, King BL, Newcomb JM, Sempere LF, Flatmark K, Hovig E, Peterson KJ. A Uniform System for the Annotation of Vertebrate microRNA Genes and the Evolution of the Human microRNAome. Annu Rev Genet 2015; 49:213-42. [PMID: 26473382 DOI: 10.1146/annurev-genet-120213-092023] [Citation(s) in RCA: 364] [Impact Index Per Article: 40.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Although microRNAs (miRNAs) are among the most intensively studied molecules of the past 20 years, determining what is and what is not a miRNA has not been straightforward. Here, we present a uniform system for the annotation and nomenclature of miRNA genes. We show that less than a third of the 1,881 human miRBase entries, and only approximately 16% of the 7,095 metazoan miRBase entries, are robustly supported as miRNA genes. Furthermore, we show that the human repertoire of miRNAs has been shaped by periods of intense miRNA innovation and that mature gene products show a very different tempo and mode of sequence evolution than star products. We establish a new open access database--MirGeneDB ( http://mirgenedb.org )--to catalog this set of miRNAs, which complements the efforts of miRBase but differs from it by annotating the mature versus star products and by imposing an evolutionary hierarchy upon this curated and consistently named repertoire.
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Affiliation(s)
- Bastian Fromm
- Department of Tumor Biology, Institute for Cancer Research
| | - Tyler Billipp
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire 03755;
| | - Liam E Peck
- Department of Biology and Health Sciences, New England College, Henniker, New Hampshire 03242
| | | | - James E Tarver
- Department of Biology, The National University of Ireland, Maynooth, Kildare, Ireland.,School of Earth Sciences, University of Bristol, BS8 1TQ Bristol, United Kingdom
| | - Benjamin L King
- Kathryn W. Davis Center for Regenerative Biology and Medicine, Mount Desert Island Biological Laboratory, Salisbury Cove, Maine 04672
| | - James M Newcomb
- Department of Biology and Health Sciences, New England College, Henniker, New Hampshire 03242
| | - Lorenzo F Sempere
- Center for Cancer and Cell Biology, Van Andel Research Institute, Grand Rapids, Michigan 49503
| | - Kjersti Flatmark
- Department of Tumor Biology, Institute for Cancer Research.,Department of Gastroenterological Surgery.,Institute of Clinical Medicine
| | - Eivind Hovig
- Department of Tumor Biology, Institute for Cancer Research.,Institute of Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Nydalen, N-0424 Oslo, Norway.,Department of Informatics, University of Oslo, Blindern, N-0318 Oslo, Norway
| | - Kevin J Peterson
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire 03755;
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49
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Laganà A, Ferro A, Croce CM. Editorial: Bioinformatics of Non-Coding RNAs with Applications to Biomedicine: Recent Advances and Open Challenges. Front Bioeng Biotechnol 2015; 3:156. [PMID: 26501059 PMCID: PMC4597103 DOI: 10.3389/fbioe.2015.00156] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 09/25/2015] [Indexed: 11/13/2022] Open
Affiliation(s)
- Alessandro Laganà
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai , New York, NY , USA
| | - Alfredo Ferro
- Department of Clinical and Molecular Biomedicine, University of Catania , Catania , Italy
| | - Carlo Maria Croce
- Department of Molecular Virology, Immunology and Medical Genetics, Comprehensive Cancer Center, The Ohio State University , Columbus, OH , USA
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50
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mirPRo-a novel standalone program for differential expression and variation analysis of miRNAs. Sci Rep 2015; 5:14617. [PMID: 26434581 PMCID: PMC4592965 DOI: 10.1038/srep14617] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 09/02/2015] [Indexed: 12/16/2022] Open
Abstract
Being involved in many important biological processes, miRNAs can regulate gene expression by targeting mRNAs to facilitate their degradation or translational inhibition. Many miRNA sequencing studies reveal that miRNA variations such as isomiRs and “arm switching” are biologically relevant. However, existing standalone tools usually do not provide comprehensive, detailed information on miRNA variations. To deepen our understanding of miRNA variability, we developed a new standalone tool called “mirPRo” to quantify known miRNAs and predict novel miRNAs. Compared with the most widely used standalone program, miRDeep2, mirPRo offers several new functions including read cataloging based on genome annotation, optional seed region check, miRNA family expression quantification, isomiR identification and categorization, and “arm switching” detection. Our comparative data analyses using three datasets from mouse, human and chicken demonstrate that mirPRo is more accurate than miRDeep2 by avoiding over-counting of sequence reads and by implementing different approaches in adapter trimming, mapping and quantification. mirPRo is an open-source standalone program (https://sourceforge.net/projects/mirpro/).
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