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Lawarde A, Sharif Rahmani E, Nath A, Lavogina D, Jaal J, Salumets A, Modhukur V. ExplORRNet: An interactive web tool to explore stage-wise miRNA expression profiles and their interactions with mRNA and lncRNA in human breast and gynecological cancers. Noncoding RNA Res 2024; 9:125-140. [PMID: 38035042 PMCID: PMC10686811 DOI: 10.1016/j.ncrna.2023.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 10/09/2023] [Accepted: 10/10/2023] [Indexed: 12/02/2023] Open
Abstract
Background MicroRNAs (miRNAs) are key regulators of gene expression that have been implicated in gynecological and breast cancers. Understanding the cancer stage-wise expression patterns of miRNAs and their interactions with other RNA molecules in cancer is crucial to improve cancer diagnosis and treatment planning. Comprehensive web tools that integrate data on the transcriptome, circulating miRNAs, and their validated targets to derive beneficial conclusions in cancer research are lacking. Methods Using the Shiny R package, we developed a web tool called ExplORRNet that integrates transcriptomic profiles from The Cancer Genome Atlas and miRNA expression data derived from various sources, including tissues, cell lines, exosomes, serum, and plasma, available in the Gene Expression Omnibus database. Differential expression analyses between normal and tumor tissue samples as well as different stages of cancer, accompanied by gene enrichment and survival analyses, can be performed using specialized R packages. Additionally, a miRNA-messenger RNA (mRNA)-long non-coding RNA (lncRNA) networks are constructed to identify regulatory modules. Results Our tool identifies cancer stage-wise differentially regulated miRNAs, mRNAs, and lncRNAs in gynecological and breast cancers. Survival analysis identifies miRNAs associated with patient survival, and functional enrichment analysis provides insights into dysregulated miRNA-related biological processes and pathways. The miRNA-mRNA-lncRNA networks highlight interconnected regulatory molecular modules driving cancer progression. Case studies demonstrate the utility of the ExplORRNet for studying gynecological and breast cancers. Conclusion ExplORRNet is an intuitive and user-friendly web tool that provides a deeper understanding of dysregulated miRNAs and their functional implications in gynecological and breast cancers. We hope our ExplORRNet tool has potential utility among the clinical and basic researchers and will be beneficial to the entire cancer genomics community to encourage and facilitate mining the rapidly growing public databases to progress the field of precision oncology. The ExplORRNet is available at https://mirna.cs.ut.ee.
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Affiliation(s)
- Ankita Lawarde
- Competence Centre on Health Technologies, Tartu, Estonia
- Department of Obstetrics and Gynecology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | | | - Adhiraj Nath
- Bioengineering Research Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, North Guwahati, Assam, India
| | - Darja Lavogina
- Competence Centre on Health Technologies, Tartu, Estonia
- Institute of Clinical Medicine, Faculty of Medicine, University of Tartu, Estonia
- Institute of Chemistry, University of Tartu, Estonia
| | - Jana Jaal
- Institute of Clinical Medicine, Faculty of Medicine, University of Tartu, Estonia
- Haematology and Oncology Clinic, Tartu University Hospital, Tartu, Estonia
| | - Andres Salumets
- Competence Centre on Health Technologies, Tartu, Estonia
- Department of Obstetrics and Gynecology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
- Division of Obstetrics and Gynecology, Department of Clinical Science, Intervention and Technology, Karolinska Institute and Karolinska University Hospital, Stockholm, Sweden
| | - Vijayachitra Modhukur
- Competence Centre on Health Technologies, Tartu, Estonia
- Department of Obstetrics and Gynecology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
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Urso A, Fiannaca A, La Rosa M, La Paglia L, Lo Bosco G, Rizzo R. BITS2019: the sixteenth annual meeting of the Italian society of bioinformatics. BMC Bioinformatics 2020; 21:363. [PMID: 32938383 PMCID: PMC7493178 DOI: 10.1186/s12859-020-03708-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The 16th Annual Meeting of the Bioinformatics Italian Society was held in Palermo, Italy, on June 26-28, 2019. More than 80 scientific contributions were presented, including 4 keynote lectures, 31 oral communications and 49 posters. Also, three workshops were organised before and during the meeting. Full papers from some of the works presented in Palermo were submitted for this Supplement of BMC Bioinformatics. Here, we provide an overview of meeting aims and scope. We also shortly introduce selected papers that have been accepted for publication in this Supplement, for a complete presentation of the outcomes of the meeting.
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Affiliation(s)
- Alfonso Urso
- ICAR-CNR, Institute for high performance computing and networking, National Research Council of Italy, Palermo, 90146, Italy.
| | - Antonino Fiannaca
- ICAR-CNR, Institute for high performance computing and networking, National Research Council of Italy, Palermo, 90146, Italy
| | - Massimo La Rosa
- ICAR-CNR, Institute for high performance computing and networking, National Research Council of Italy, Palermo, 90146, Italy
| | - Laura La Paglia
- ICAR-CNR, Institute for high performance computing and networking, National Research Council of Italy, Palermo, 90146, Italy
| | - Giosue' Lo Bosco
- Department of Mathematics and Computer Science, University of Palermo, Palermo, 90128, Italy
| | - Riccardo Rizzo
- ICAR-CNR, Institute for high performance computing and networking, National Research Council of Italy, Palermo, 90146, Italy
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Fiannaca A, Paglia LL, Rosa ML, Rizzo R, Urso A. miRTissue ce: extending miRTissue web service with the analysis of ceRNA-ceRNA interactions. BMC Bioinformatics 2020; 21:199. [PMID: 32938402 PMCID: PMC7493844 DOI: 10.1186/s12859-020-3520-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Accepted: 04/29/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Non-coding RNAs include different classes of molecules with regulatory functions. The most studied are microRNAs (miRNAs) that act directly inhibiting mRNA expression or protein translation through the interaction with a miRNAs-response element. Other RNA molecules participate in the complex network of gene regulation. They behave as competitive endogenous RNA (ceRNA), acting as natural miRNA sponges to inhibit miRNA functions and modulate the expression of RNA messenger (mRNA). It became evident that understanding the ceRNA-miRNA-mRNA crosstalk would increase the functional information across the transcriptome, contributing to identify new potential biomarkers for translational medicine. RESULTS We present miRTissue ce, an improvement of our original miRTissue web service. By introducing a novel computational pipeline, miRTissue ce provides an easy way to search for ceRNA interactions in several cancer tissue types. Moreover it extends the functionalities of previous miRTissue release about miRNA-target interaction in order to provide a complete insight about miRNA mediated regulation processes. miRTissue ce is freely available at http://tblab.pa.icar.cnr.it/mirtissue.html . CONCLUSIONS The study of ceRNA networks and its dynamics in cancer tissue could be applied in many fields of translational biology, as the investigation of new cancer biomarker, both diagnostic and prognostic, and also in the investigation of new therapeutic strategies of intervention. In this scenario, miRTissue ce can offer a powerful instrument for the analysis and characterization of ceRNA-ceRNA interactions in different tissue types, representing a fundamental step in order to understand more complex regulation mechanisms.
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Affiliation(s)
- Antonino Fiannaca
- CNR-ICAR, National Research Council of Italy, via Ugo La Malfa 153, Palermo, 90146 Italy
| | - Laura La Paglia
- CNR-ICAR, National Research Council of Italy, via Ugo La Malfa 153, Palermo, 90146 Italy
| | - Massimo La Rosa
- CNR-ICAR, National Research Council of Italy, via Ugo La Malfa 153, Palermo, 90146 Italy
| | - Riccardo Rizzo
- CNR-ICAR, National Research Council of Italy, via Ugo La Malfa 153, Palermo, 90146 Italy
| | - Alfonso Urso
- CNR-ICAR, National Research Council of Italy, via Ugo La Malfa 153, Palermo, 90146 Italy
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Jishnu PV, Jayaram P, Shukla V, Varghese VK, Pandey D, Sharan K, Chakrabarty S, Satyamoorthy K, Kabekkodu SP. Prognostic role of 14q32.31 miRNA cluster in various carcinomas: a systematic review and meta-analysis. Clin Exp Metastasis 2020; 37:31-46. [PMID: 31813069 DOI: 10.1007/s10585-019-10013-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 12/02/2019] [Indexed: 12/15/2022]
Abstract
Deregulated miR-379/miR-656 cluster expression is considered as important for carcinogenesis and can be used as a potential prognostic marker. Hence, the meta-analysis was conducted to test the utility of miR-379/miR-656 cluster as a prognostic marker in various cancers. A literature search was performed using Web of Science, PubMed and Cochrane Library to obtain relevant studies and were subjected to various subgroup and bioinformatics analyses. Selected twenty-three studies contained 13 cancer types comprising of 3294 patients from 7 nations. Univariate and multivariate data showed an association of high expression of miRNAs with the poor prognosis of cancer patients (p < 0.001). The subgroup analysis showed that lung cancer, breast cancer and papillary renal cell carcinoma (p < 0.001) have a negative association with the survival of patients. Our study is the first meta-analysis showing the association of miR-379/miR-656 cluster expression and overall survival, suggesting its potential as a prognostic indicator in multiple cancers.
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Affiliation(s)
- Padacherri Vethil Jishnu
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, 576104, India
| | - Pradyumna Jayaram
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, 576104, India
| | - Vaibhav Shukla
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, 576104, India
| | - Vinay Koshy Varghese
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, 576104, India
| | - Deeksha Pandey
- Department of Obstetrics, & Gynaecology, Kasturba Medical College, Manipal, MAHE, Manipal, India
| | - Krishna Sharan
- Department of Radiotherapy Oncology, Kasturba Medical College, Manipal, MAHE, Manipal, India
| | - Sanjiban Chakrabarty
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, 576104, India
| | - Kapaettu Satyamoorthy
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, 576104, India
| | - Shama Prasada Kabekkodu
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, 576104, India.
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Boscaino V, Fiannaca A, La Paglia L, La Rosa M, Rizzo R, Urso A. MiRNA therapeutics based on logic circuits of biological pathways. BMC Bioinformatics 2019; 20:344. [PMID: 31757209 PMCID: PMC6873406 DOI: 10.1186/s12859-019-2881-7] [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: 04/17/2019] [Accepted: 05/07/2019] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND In silico experiments, with the aid of computer simulation, speed up the process of in vitro or in vivo experiments. Cancer therapy design is often based on signalling pathway. MicroRNAs (miRNA) are small non-coding RNA molecules. In several kinds of diseases, including cancer, hepatitis and cardiovascular diseases, they are often deregulated, acting as oncogenes or tumor suppressors. miRNA therapeutics is based on two main kinds of molecules injection: miRNA mimics, which consists of injection of molecules that mimic the targeted miRNA, and antagomiR, which consists of injection of molecules inhibiting the targeted miRNA. Nowadays, the research is focused on miRNA therapeutics. This paper addresses cancer related signalling pathways to investigate miRNA therapeutics. RESULTS In order to prove our approach, we present two different case studies: non-small cell lung cancer and melanoma. KEGG signalling pathways are modelled by a digital circuit. A logic value of 1 is linked to the expression of the corresponding gene. A logic value of 0 is linked to the absence (not expressed) gene. All possible relationships provided by a signalling pathway are modelled by logic gates. Mutations, derived according to the literature, are introduced and modelled as well. The modelling approach and analysis are widely discussed within the paper. MiRNA therapeutics is investigated by the digital circuit analysis. The most effective miRNA and combination of miRNAs, in terms of reduction of pathogenic conditions, are obtained. A discussion of obtained results in comparison with literature data is provided. Results are confirmed by existing data. CONCLUSIONS The proposed study is based on drug discovery and miRNA therapeutics and uses a digital circuit simulation of a cancer pathway. Using this simulation, the most effective combination of drugs and miRNAs for mutated cancer therapy design are obtained and these results were validated by the literature. The proposed modelling and analysis approach can be applied to each human disease, starting from the corresponding signalling pathway.
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Affiliation(s)
- Valeria Boscaino
- CNR-ICAR, National Research Council of Italy, via Ugo La Malfa 153, Palermo, 90146, Italy
| | - Antonino Fiannaca
- CNR-ICAR, National Research Council of Italy, via Ugo La Malfa 153, Palermo, 90146, Italy
| | - Laura La Paglia
- CNR-ICAR, National Research Council of Italy, via Ugo La Malfa 153, Palermo, 90146, Italy
| | - Massimo La Rosa
- CNR-ICAR, National Research Council of Italy, via Ugo La Malfa 153, Palermo, 90146, Italy.
| | - Riccardo Rizzo
- CNR-ICAR, National Research Council of Italy, via Ugo La Malfa 153, Palermo, 90146, Italy
| | - Alfonso Urso
- CNR-ICAR, National Research Council of Italy, via Ugo La Malfa 153, Palermo, 90146, Italy
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