1
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Kim MW, Moon S, Lee S, Lee H, Kim Y, Kim JY, Kim JY, Kim SI. Exploring miRNA‑target gene profiles associated with drug resistance in patients with breast cancer receiving neoadjuvant chemotherapy. Oncol Lett 2024; 27:158. [PMID: 38426156 PMCID: PMC10902752 DOI: 10.3892/ol.2024.14291] [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: 11/28/2023] [Accepted: 01/24/2024] [Indexed: 03/02/2024] Open
Abstract
Exosomal microRNAs (miRNAs) are closely related to drug resistance in patients with breast cancer (BC); however, only a few roles of the exosomal miRNA-target gene networks have been clinically implicated in drug resistance in BC. Therefore, the present study aimed to identify the differential expression of exosomal miRNAs associated with drug resistance and their target mRNAs. In vitro microarray analysis was used to verify differentially expressed miRNAs (DEMs) in drug-resistant BC. Next, tumor-derived exosomes (TDEs) were isolated. Furthermore, it was determined whether the candidate drug-resistant miRNAs were also significant in TDEs, and then putative miRNAs in TDEs were validated in plasma samples from 35 patients with BC (20 patients with BC showing no response and 15 patients with BC showing a complete response). It was confirmed that the combination of five exosomal miRNAs, including miR-125b-5p, miR-146a-5p, miR-484, miR-1246-5p and miR-1260b, was effective for predicting therapeutic response to neoadjuvant chemotherapy, with an area under the curve value of 0.95, sensitivity of 75%, and specificity of 95%. Public datasets were analyzed to identify differentially expressed genes (DEGs) related to drug resistance and it was revealed that BAK1, NOVA1, PTGER4, RTKN2, AGO1, CAP1, and ETS1 were the target genes of exosomal miRNAs. Networks between DEMs and DEGs were highly correlated with mitosis, metabolism, drug transport, and immune responses. Consequently, these targets could be used as predictive markers and therapeutic targets for clinical applications to enhance treatment outcomes for patients with BC.
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Affiliation(s)
- Min Woo Kim
- Department of Surgery, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Sol Moon
- Department of Surgery, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Suji Lee
- Department of Surgery, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Hyojung Lee
- Department of Surgery, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Young Kim
- Department of Surgery, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Joon Ye Kim
- Department of Surgery, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Jee Ye Kim
- Department of Surgery, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Seung Il Kim
- Department of Surgery, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
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2
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Nersisyan S, Zhiyanov A, Engibaryan N, Maltseva D, Tonevitsky A. A novel approach for a joint analysis of isomiR and mRNA expression data reveals features of isomiR targeting in breast cancer. Front Genet 2022; 13:1070528. [PMID: 36531236 PMCID: PMC9751988 DOI: 10.3389/fgene.2022.1070528] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 11/21/2022] [Indexed: 07/31/2023] Open
Abstract
A widely used procedure for selecting significant miRNA-mRNA or isomiR-mRNA pairs out of predicted interactions involves calculating the correlation between expression levels of miRNAs/isomiRs and mRNAs in a series of samples. In this manuscript, we aimed to assess the validity of this procedure by comparing isomiR-mRNA correlation profiles in sets of sequence-based predicted target mRNAs and non-target mRNAs (negative controls). Target prediction was carried out using RNA22 and TargetScan algorithms. Spearman's correlation analysis was conducted using miRNA and mRNA sequencing data of The Cancer Genome Atlas Breast Invasive Carcinoma (TCGA-BRCA) project. Luminal A, luminal B, basal-like breast cancer subtypes, and adjacent normal tissue samples were analyzed separately. Using the sets of putative targets and non-targets, we introduced adjusted isomiR targeting activity (ITA)-the number of negatively correlated potential isomiR targets adjusted by the background (estimated using non-target mRNAs). We found that for most isomiRs a significant negative correlation between isomiR-mRNA expression levels appeared more often in a set of predicted targets compared to the non-targets. This trend was detected for both classical seed region binding types (8mer, 7mer-m8, 7mer-A1, 6mer) predicted by TargetScan and the non-classical ones (G:U wobbles and up to one mismatch or unpaired nucleotide within seed sequence) predicted by RNA22. Adjusted ITA distributions were similar for target sites located in 3'-UTRs and coding mRNA sequences, while 5'-UTRs had much lower scores. Finally, we observed strong cancer subtype-specific patterns of isomiR activity, highlighting the differences between breast cancer molecular subtypes and normal tissues. Surprisingly, our target prediction- and correlation-based estimates of isomiR activities were practically non-correlated with the average isomiR expression levels neither in cancerous nor in normal samples.
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Affiliation(s)
- Stepan Nersisyan
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
| | - Anton Zhiyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Narek Engibaryan
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
| | - Diana Maltseva
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
| | - Alexander Tonevitsky
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Art Photonics GmbH, Berlin, Germany
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3
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Nersisyan S, Gorbonos A, Makhonin A, Zhiyanov A, Shkurnikov M, Tonevitsky A. isomiRTar: a comprehensive portal of pan-cancer 5'-isomiR targeting. PeerJ 2022; 10:e14205. [PMID: 36275459 PMCID: PMC9583861 DOI: 10.7717/peerj.14205] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 09/19/2022] [Indexed: 01/24/2023] Open
Abstract
Inaccurate cleavage of pri- and pre-miRNA hairpins by Drosha and Dicer results in the generation of miRNA isoforms known as isomiRs. isomiRs with 5'-end variations (5'-isomiRs) create a new dimension in miRNA research since they have different seed regions and distinct targetomes. We developed isomiRTar (https://isomirtar.hse.ru)-a comprehensive portal that allows one to analyze expression profiles and targeting activity of 5'-isomiRs in cancer. Using the Cancer Genome Atlas sequencing data, we compiled the list of 1022 5'-isomiRs expressed in 9282 tumor samples across 31 cancer types. Sequences of these isomiRs were used to predict target genes with miRDB and TargetScan. The putative interactions were then subjected to the co-expression analysis in each cancer type to identify isomiR-target pairs supported by significant negative correlations. Downstream analysis of the data deposited in isomiRTar revealed both cancer-specific and cancer-conserved 5'-isomiR expression landscapes. Pairs of isomiRs differing in one nucleotide shift from 5'-end had poorly overlapping targetomes with the median Jaccard index of 0.06. The analysis of colorectal cancer 5'-isomiR-mediated regulatory networks revealed promising candidate tumor suppressor isomiRs: hsa-miR-203a-3p-+1, hsa-miR-192-5p-+1 and hsa-miR-148a-3p-0. In summary, we believe that isomiRTar will help researchers find novel mechanisms of isomiR-mediated gene silencing in different types of cancer.
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Affiliation(s)
- Stepan Nersisyan
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia,Institute of Molecular Biology, The National Academy of Sciences of the Republic of Armenia, Yerevan, Armenia,Armenian Bioinformatics Institute (ABI), Yerevan, Armenia,Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
| | | | - Alexey Makhonin
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
| | - Anton Zhiyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia,Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
| | - Maxim Shkurnikov
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
| | - Alexander Tonevitsky
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia,Faculty of Biology and Biotechnology, HSE University, Moscow, Russia,Art Photonics GmbH, Berlin, Germany
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4
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Mehta TK, Penso-Dolfin L, Nash W, Roy S, Di-Palma F, Haerty W. Evolution of miRNA binding sites and regulatory networks in cichlids. Mol Biol Evol 2022; 39:6617238. [PMID: 35748824 PMCID: PMC9260339 DOI: 10.1093/molbev/msac146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The divergence of regulatory regions and gene regulatory network (GRN) rewiring is a key driver of cichlid phenotypic diversity. However, the contribution of miRNA binding site turnover has yet to be linked to GRN evolution across cichlids. Here, we extend our previous studies by analysing the selective constraints driving evolution of miRNA and transcription factor (TF) binding sites of target genes, to infer instances of cichlid GRN rewiring associated with regulatory binding site turnover. Comparative analyses identified increased species-specific networks that are functionally associated to traits of cichlid phenotypic diversity. The evolutionary rewiring is associated with differential models of miRNA and TF binding site turnover, driven by a high proportion of fast-evolving polymorphic sites in adaptive trait genes compared to subsets of random genes. Positive selection acting upon discrete mutations in these regulatory regions is likely to be an important mechanism in rewiring GRNs in rapidly radiating cichlids. Regulatory variants of functionally associated miRNA and TF binding sites of visual opsin genes differentially segregate according to phylogeny and ecology of Lake Malawi species, identifying both rewired e.g. clade-specific and conserved network motifs of adaptive trait associated GRNs. Our approach revealed several novel candidate regulators, regulatory regions and three-node motifs across cichlid genomes with previously reported associations to known adaptive evolutionary traits.
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Affiliation(s)
| | - Luca Penso-Dolfin
- Silence Therapeutics GmbH, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | | | - Sushmita Roy
- Dept. of Biostatistics and Medical Informatics, UW Madison, Madison, USA.,Wisconsin Institute for Discovery (WID), Madison, USA.,Dept. of Computer Sciences, UW Madison, Madison, USA
| | - Federica Di-Palma
- School of Biological Sciences, University of East Anglia, Norwich, UK.,Genome British Columbia, Vancouver, Canada
| | - Wilfried Haerty
- Earlham Institute (EI), Norwich, UK.,School of Biological Sciences, University of East Anglia, Norwich, UK
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5
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Monfort-Lanzas P, Gronauer R, Madersbacher L, Schatz C, Rieder D, Hackl H. MIO: MicroRNA target analysis system for Immuno-Oncology. Bioinformatics 2022; 38:3665-3667. [PMID: 35642895 PMCID: PMC9272810 DOI: 10.1093/bioinformatics/btac366] [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: 01/13/2022] [Revised: 04/25/2022] [Indexed: 11/13/2022] Open
Abstract
Summary MicroRNAs have been shown to be able to modulate the tumor microenvironment and the immune response and hence could be interesting biomarkers and therapeutic targets in immuno-oncology; however, dedicated analysis tools are missing. Here, we present a user-friendly web platform MIO and a Python toolkit miopy integrating various methods for visualization and analysis of provided or custom bulk microRNA and gene expression data. We include regularized regression and survival analysis and provide information of 40 microRNA target prediction tools as well as a collection of curated immune related gene and microRNA signatures and processed TCGA data including estimations of infiltrated immune cells and the immunophenoscore. The integration of several machine learning methods enables the selection of prognostic and predictive microRNAs and gene interaction network biomarkers. Availability and implementation https://mio.icbi.at, https://github.com/icbi-lab/mio and https://github.com/icbi-lab/miopy. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Pablo Monfort-Lanzas
- Institute of Bioinformatics, Biocenter, Medical University of Innsbruck, Innrain 80, Innsbruck, 6020, Austria.,Institute of Medical Biochemistry, Biocenter, Medical University of Innsbruck, Innrain 80, 6020, Austria Innsbruck
| | - Raphael Gronauer
- Institute of Bioinformatics, Biocenter, Medical University of Innsbruck, Innrain 80, Innsbruck, 6020, Austria
| | - Leonie Madersbacher
- Institute of Bioinformatics, Biocenter, Medical University of Innsbruck, Innrain 80, Innsbruck, 6020, Austria
| | - Christoph Schatz
- Institute of Pathology, Neuropathology and Molecular Pathology, Medical University of Innsbruck, Müllerstraße 44, Innsbruck, 6020, Austria
| | - Dietmar Rieder
- Institute of Bioinformatics, Biocenter, Medical University of Innsbruck, Innrain 80, Innsbruck, 6020, Austria
| | - Hubert Hackl
- Institute of Bioinformatics, Biocenter, Medical University of Innsbruck, Innrain 80, Innsbruck, 6020, Austria
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6
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Nersisyan SA. Isoforms of miR-148a and miR-203a are putative suppressors of colorectal cancer. BULLETIN OF RUSSIAN STATE MEDICAL UNIVERSITY 2022. [DOI: 10.24075/brsmu.2022.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
MicroRNAs are short non-coding molecules which regulate translation in a gene-specific manner. MicroRNA isoforms that differ by few extra or missing nucleotides at the 5'-terminus (5'-isomiR) show strikingly different target specificity. This study aimed to identify functional roles of 5′-isomiR in colorectal cancers. Transcriptomic targets of microRNA isoforms were predicted using bioinformatics tools miRDB and TargetScan. The sets of putative targets identified for 5′-isomiR were integrated with mRNA and microRNA sequencing data for primary colorectal tumors retrieved from The Cancer Genome Atlas Colon Adenocarcinoma (TCGA-COAD) database. The network of interactions among miRNA, their targets and transcription factors was built using the miRGTF-net algorithm. The results indicate that microRNA isoforms highly expressed in colorectal cancer and differing by a single nucleotide position at the 5'-terminus have ≤ 30% common targets. The regulatory network of interactions enables identification of the most engaged microRNA isoforms. Anti-correlated expression levels of canonical microRNA hsa-miR-148a-3p and its putative targets including CSF1, ETS1, FLT1, ITGA5, MEIS1, MITF and RUNX2 proliferation regulators suggest an anti-tumor role for this molecule. The canonical microRNA hsa-miR-203a-3p|0 and its 5′-isoform bind different sets of anti-correlated putative targets, although both of them interact with genes involved in the epithelial-mesenchymal transition: SNAI2 and TNC.
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Affiliation(s)
- SA Nersisyan
- National Research University Higher School of Economics (HSE), Moscow, Russia
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7
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Raigorodskaya MP, Zhiyanov AP, Averinskaya DA, Tonevitsky EA. Changes in the Expression of miRNA Isoforms and Their Targets in HT-29 Cells after Hypoxic Exposure. Bull Exp Biol Med 2022; 173:123-127. [PMID: 35624351 DOI: 10.1007/s10517-022-05506-2] [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: 12/21/2021] [Indexed: 11/28/2022]
Abstract
Tumor hypoxia is one of the main causes of progression and metastasis of colorectal cancer. Changes in the expression of miRNA responsible for post-translation regulation of gene expression is an important molecular mechanism of cell response to hypoxia. We performed sequencing of miRNA and mRNA of human colorectal adenocarcinoma HT-29 cells treated with two chemical agents mimicking hypoxia: cobalt (II) chloride and oxyquinoline. Bioinformatics analysis revealed differentially expressed miRNA isoforms (hsa-miR-210-3p|0, hsa-miR- 22-3p|0, hsa-let-7a-3p|0, hsa-miR-615-3p|0, and hsa-miR-4521|0) and their targets that changed their expression in both models of hypoxia. Thus, we identified new regulatory mechanisms of cell response to hypoxia.
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Affiliation(s)
- M P Raigorodskaya
- Faculty of Biology and Biotechnologies, Higher School of Economics (HSE University), Moscow, Russia
| | - A P Zhiyanov
- Faculty of Biology and Biotechnologies, Higher School of Economics (HSE University), Moscow, Russia.
| | - D A Averinskaya
- Faculty of Biology and Biotechnologies, Higher School of Economics (HSE University), Moscow, Russia
| | - E A Tonevitsky
- Faculty of Biology and Biotechnologies, Higher School of Economics (HSE University), Moscow, Russia
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8
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Novosad VO, Polikanova IS, Tonevitsky EA, Maltseva DV. Expression of CD44 Isoforms in Tumor Samples and Cell Lines of Human Colorectal Cancer. Bull Exp Biol Med 2022; 173:155-159. [PMID: 35618971 DOI: 10.1007/s10517-022-05512-4] [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: 12/21/2021] [Indexed: 10/18/2022]
Abstract
Detection of colorectal cancer biomarkers (CRC) remains an urgent task for the diagnosis and prediction of the disease course. A promising approach is the study of cancer stem cell markers. The cell surface glycoprotein CD44 is very important for CRC and its stem cells. Alternative splicing of 9 variable exons of CD44 mRNA leads to the formation of various isoforms of the protein with different roles in the progression of cancer. Studies of the functions of CD44 isoforms require adequate models considering the distribution of CD44 isoforms in real tumor samples. In the present study, the expression profile of CD44 isoforms in CRC was assessed based on the publicly available mRNA sequencing data of patient tumors from the TCGA-COAD database. It was shown that normal tissues predominantly expressed isoforms 3 and 4 at nearly equal levels, whereas tumors mainly expressed isoforms 2, 3, and 4; isoform 3 was expressed at the highest level. Further, the most relevant cell lines for studying the role of CD44 in CRC were identified based on the analysis of mRNA sequencing data of 55 CRC cell lines form CCLE database.
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Affiliation(s)
- V O Novosad
- Faculty of Biology and Biotechnologies, National Research University Higher School of Economics (HSE University), Moscow, Russia.
| | - I S Polikanova
- Faculty of Biology and Biotechnologies, National Research University Higher School of Economics (HSE University), Moscow, Russia
| | - E A Tonevitsky
- Faculty of Biology and Biotechnologies, National Research University Higher School of Economics (HSE University), Moscow, Russia
| | - D V Maltseva
- Faculty of Biology and Biotechnologies, National Research University Higher School of Economics (HSE University), Moscow, Russia
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9
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Yousef M, Goy G, Bakir-Gungor B. miRModuleNet: Detecting miRNA-mRNA Regulatory Modules. Front Genet 2022; 13:767455. [PMID: 35495139 PMCID: PMC9039401 DOI: 10.3389/fgene.2022.767455] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 03/24/2022] [Indexed: 12/13/2022] Open
Abstract
Increasing evidence that microRNAs (miRNAs) play a key role in carcinogenesis has revealed the need for elucidating the mechanisms of miRNA regulation and the roles of miRNAs in gene-regulatory networks. A better understanding of the interactions between miRNAs and their mRNA targets will provide a better understanding of the complex biological processes that occur during carcinogenesis. Increased efforts to reveal these interactions have led to the development of a variety of tools to detect and understand these interactions. We have recently described a machine learning approach miRcorrNet, based on grouping and scoring (ranking) groups of genes, where each group is associated with a miRNA and the group members are genes with expression patterns that are correlated with this specific miRNA. The miRcorrNet tool requires two types of -omics data, miRNA and mRNA expression profiles, as an input file. In this study we describe miRModuleNet, which groups mRNA (genes) that are correlated with each miRNA to form a star shape, which we identify as a miRNA-mRNA regulatory module. A scoring procedure is then applied to each module to further assess their contribution in terms of classification. An important output of miRModuleNet is that it provides a hierarchical list of significant miRNA-mRNA regulatory modules. miRModuleNet was further validated on external datasets for their disease associations, and functional enrichment analysis was also performed. The application of miRModuleNet aids the identification of functional relationships between significant biomarkers and reveals essential pathways involved in cancer pathogenesis. The miRModuleNet tool and all other supplementary files are available at https://github.com/malikyousef/miRModuleNet/
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Affiliation(s)
- Malik Yousef
- Department of Information Systems, Zefat Academic College, Zefat, Israel
- *Correspondence: Malik Yousef,
| | - Gokhan Goy
- Department of Computer Engineering, Faculty of Engineering, Abdullah Gul University, Kayseri, Turkey
- The Scientific and Technological Research Council of Turkey, Ankara, Turkey
| | - Burcu Bakir-Gungor
- Department of Computer Engineering, Faculty of Engineering, Abdullah Gul University, Kayseri, Turkey
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10
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Nersisyan S, Novosad V, Galatenko A, Sokolov A, Bokov G, Konovalov A, Alekseev D, Tonevitsky A. ExhauFS: exhaustive search-based feature selection for classification and survival regression. PeerJ 2022; 10:e13200. [PMID: 35378930 PMCID: PMC8976470 DOI: 10.7717/peerj.13200] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 03/09/2022] [Indexed: 01/12/2023] Open
Abstract
Feature selection is one of the main techniques used to prevent overfitting in machine learning applications. The most straightforward approach for feature selection is an exhaustive search: one can go over all possible feature combinations and pick up the model with the highest accuracy. This method together with its optimizations were actively used in biomedical research, however, publicly available implementation is missing. We present ExhauFS-the user-friendly command-line implementation of the exhaustive search approach for classification and survival regression. Aside from tool description, we included three application examples in the manuscript to comprehensively review the implemented functionality. First, we executed ExhauFS on a toy cervical cancer dataset to illustrate basic concepts. Then, multi-cohort microarray breast cancer datasets were used to construct gene signatures for 5-year recurrence classification. The vast majority of signatures constructed by ExhauFS passed 0.65 threshold of sensitivity and specificity on all datasets, including the validation one. Moreover, a number of gene signatures demonstrated reliable performance on independent RNA-seq dataset without any coefficient re-tuning, i.e., turned out to be cross-platform. Finally, Cox survival regression models were used to fit isomiR signatures for overall survival prediction for patients with colorectal cancer. Similarly to the previous example, the major part of models passed the pre-defined concordance index threshold 0.65 on all datasets. In both real-world scenarios (breast and colorectal cancer datasets), ExhauFS was benchmarked against state-of-the-art feature selection models, including L1-regularized sparse models. In case of breast cancer, we were unable to construct reliable cross-platform classifiers using alternative feature selection approaches. In case of colorectal cancer not a single model passed the same 0.65 threshold. Source codes and documentation of ExhauFS are available on GitHub: https://github.com/s-a-nersisyan/ExhauFS.
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Affiliation(s)
- Stepan Nersisyan
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
| | - Victor Novosad
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia
| | - Alexei Galatenko
- Faculty of Mechanics and Mathematics, Lomonosov Moscow State University, Moscow, Russia,Moscow Center for Fundamental and Applied Mathematics, Moscow, Russia
| | - Andrey Sokolov
- Faculty of Mechanics and Mathematics, Lomonosov Moscow State University, Moscow, Russia,Moscow Center for Fundamental and Applied Mathematics, Moscow, Russia
| | - Grigoriy Bokov
- Faculty of Mechanics and Mathematics, Lomonosov Moscow State University, Moscow, Russia,Moscow Center for Fundamental and Applied Mathematics, Moscow, Russia
| | - Alexander Konovalov
- Faculty of Mechanics and Mathematics, Lomonosov Moscow State University, Moscow, Russia,Moscow Center for Fundamental and Applied Mathematics, Moscow, Russia
| | - Dmitry Alekseev
- Faculty of Mechanics and Mathematics, Lomonosov Moscow State University, Moscow, Russia,Moscow Center for Fundamental and Applied Mathematics, Moscow, Russia
| | - Alexander Tonevitsky
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia,Institute of Nanotechnologies of Microelectronics RAS, Moscow, Russia
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11
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Santo GD, Frasca M, Bertoli G, Castiglioni I, Cava C. Identification of key miRNAs in prostate cancer progression based on miRNA-mRNA network construction. Comput Struct Biotechnol J 2022; 20:864-873. [PMID: 35222845 PMCID: PMC8844601 DOI: 10.1016/j.csbj.2022.02.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 02/03/2022] [Accepted: 02/03/2022] [Indexed: 01/09/2023] Open
Abstract
Prostate cancer (PC) is one of the major male cancers. Differential diagnosis of PC is indispensable for the individual therapy, i.e., Gleason score (GS) that describes the grade of cancer can be used to choose the appropriate therapy. However, the current techniques for PC diagnosis and prognosis are not always effective. To identify potential markers that could be used for differential diagnosis of PC, we analyzed miRNA-mRNA interactions and we build specific networks for PC onset and progression. Key differentially expressed miRNAs for each GS were selected by calculating three parameters of network topology measures: the number of their single regulated mRNAs (NSR), the number of target genes (NTG) and NSR/NTG. miRNAs that obtained a high statistically significant value of these three parameters were chosen as potential biomarkers for computational validation and pathway analysis. 20 miRNAs were identified as key candidates for PC. 8 out of 20 miRNAs (miR-25-3p, miR-93-3p, miR-122-5p, miR-183-5p, miR-615-3p, miR-7-5p, miR-375, and miR-92a-3p) were differentially expressed in all GS and proposed as biomarkers for PC onset. In addition, "Extracellular-receptor interaction", "Focal adhesion", and "microRNAs in cancer" were significantly enriched by the differentially expressed target genes of the identified miRNAs. miR-10a-5p was found to be differentially expressed in GS 6, 7, and 8 in PC samples. 3 miRNAs were identified as PC GS-specific differentially expressed miRNAs: miR-155-5p was identified in PC samples with GS 6, and miR-142-3p and miR-296-3p in PC samples with GS 9. The efficacy of 20 miRNAs as potential biomarkers was revealed with a Random Forest classification using an independent dataset. The results demonstrated our 20 miRNAs achieved a better performance (AUC: 0.73) than miRNAs selected with Boruta algorithm (AUC: 0.55), a method for the automated feature extraction. Studying miRNA-mRNA associations, key miRNAs were identified with a computational approach for PC onset and progression. Further experimental validations are needed for future translational development.
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Affiliation(s)
- Giulia Dal Santo
- Institute of Molecular Bioimaging and Physiology, National Research Council (IBFM-CNR), Via F. Cervi 93, Segrate-Milan, 20090 Milan, Italy.,Department of Computer Science, Università degli Studi di Milano, Via Celoria 18, 20133 Milano, Italy
| | - Marco Frasca
- Department of Computer Science, Università degli Studi di Milano, Via Celoria 18, 20133 Milano, Italy
| | - Gloria Bertoli
- Institute of Molecular Bioimaging and Physiology, National Research Council (IBFM-CNR), Via F. Cervi 93, Segrate-Milan, 20090 Milan, Italy
| | - Isabella Castiglioni
- Department of Physics "Giuseppe Occhialini", University of Milan-Bicocca Piazza dell'Ateneo Nuovo, 20126 Milan, Italy
| | - Claudia Cava
- Institute of Molecular Bioimaging and Physiology, National Research Council (IBFM-CNR), Via F. Cervi 93, Segrate-Milan, 20090 Milan, Italy
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12
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Nersisyan S, Novosad V, Engibaryan N, Ushkaryov Y, Nikulin S, Tonevitsky A. ECM-Receptor Regulatory Network and Its Prognostic Role in Colorectal Cancer. Front Genet 2021; 12:782699. [PMID: 34938324 PMCID: PMC8685507 DOI: 10.3389/fgene.2021.782699] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 11/05/2021] [Indexed: 12/12/2022] Open
Abstract
Interactions of the extracellular matrix (ECM) and cellular receptors constitute one of the crucial pathways involved in colorectal cancer progression and metastasis. With the use of bioinformatics analysis, we comprehensively evaluated the prognostic information concentrated in the genes from this pathway. First, we constructed a ECM-receptor regulatory network by integrating the transcription factor (TF) and 5'-isomiR interaction databases with mRNA/miRNA-seq data from The Cancer Genome Atlas Colon Adenocarcinoma (TCGA-COAD). Notably, one-third of interactions mediated by 5'-isomiRs was represented by noncanonical isomiRs (isomiRs, whose 5'-end sequence did not match with the canonical miRBase version). Then, exhaustive search-based feature selection was used to fit prognostic signatures composed of nodes from the network for overall survival prediction. Two reliable prognostic signatures were identified and validated on the independent The Cancer Genome Atlas Rectum Adenocarcinoma (TCGA-READ) cohort. The first signature was made up by six genes, directly involved in ECM-receptor interaction: AGRN, DAG1, FN1, ITGA5, THBS3, and TNC (concordance index 0.61, logrank test p = 0.0164, 3-years ROC AUC = 0.68). The second hybrid signature was composed of three regulators: hsa-miR-32-5p, NR1H2, and SNAI1 (concordance index 0.64, logrank test p = 0.0229, 3-years ROC AUC = 0.71). While hsa-miR-32-5p exclusively regulated ECM-related genes (COL1A2 and ITGA5), NR1H2 and SNAI1 also targeted other pathways (adhesion, cell cycle, and cell division). Concordant distributions of the respective risk scores across four stages of colorectal cancer and adjacent normal mucosa additionally confirmed reliability of the models.
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Affiliation(s)
- Stepan Nersisyan
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
| | - Victor Novosad
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Narek Engibaryan
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
| | - Yuri Ushkaryov
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Medway School of Pharmacy, University of Kent, Chatham, United Kingdom
| | - Sergey Nikulin
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
- P. Hertsen Moscow Oncology Research Institute—Branch, National Medical Research Radiological Centre, Ministry of Health of Russian Federation, Moscow, Russia
- School of Biomedicine, Far Eastern Federal University, Vladivostok, Russia
| | - Alexander Tonevitsky
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
- SRC Bioclinicum, Moscow, Russia
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Knyazev E, Maltseva D, Raygorodskaya M, Shkurnikov M. HIF-Dependent NFATC1 Activation Upregulates ITGA5 and PLAUR in Intestinal Epithelium in Inflammatory Bowel Disease. Front Genet 2021; 12:791640. [PMID: 34858489 PMCID: PMC8632048 DOI: 10.3389/fgene.2021.791640] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 10/27/2021] [Indexed: 12/11/2022] Open
Abstract
Intestinal epithelial cells exist in physiological hypoxia, leading to hypoxia-inducible factor (HIF) activation and supporting barrier function and cell metabolism of the intestinal epithelium. In contrast, pathological hypoxia is a common feature of some chronic disorders, including inflammatory bowel disease (IBD). This work was aimed at studying HIF-associated changes in the intestinal epithelium in IBD. In the first step, a list of genes responding to chemical activation of hypoxia was obtained in an in vitro intestinal cell model with RNA sequencing. Cobalt (II) chloride and oxyquinoline treatment of both undifferentiated and differentiated Caco-2 cells activate the HIF-signaling pathway according to gene set enrichment analysis. The core gene set responding to chemical hypoxia stimulation in the intestinal model included 115 upregulated and 69 downregulated genes. Of this set, protein product was detected for 32 genes, and fold changes in proteome and RNA sequencing significantly correlate. Analysis of publicly available RNA sequencing set of the intestinal epithelial cells of patients with IBD confirmed HIF-1 signaling pathway activation in sigmoid colon of patients with ulcerative colitis and terminal ileum of patients with Crohn's disease. Of the core gene set from the gut hypoxia model, expression activation of ITGA5 and PLAUR genes encoding integrin α5 and urokinase-type plasminogen activator receptor (uPAR) was detected in IBD specimens. The interaction of these molecules can activate cell migration and regenerative processes in the epithelium. Transcription factor analysis with the previously developed miRGTF tool revealed the possible role of HIF1A and NFATC1 in the regulation of ITGA5 and PLAUR gene expression. Detected genes can serve as markers of IBD progression and intestinal hypoxia.
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Affiliation(s)
- Evgeny Knyazev
- Laboratory of Microfluidic Technologies for Biomedicine, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
| | - Diana Maltseva
- Faculty of Biology and Biotechnology, National Research University Higher School of Economics (HSE), Moscow, Russia
| | - Maria Raygorodskaya
- Laboratory of Microfluidic Technologies for Biomedicine, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
| | - Maxim Shkurnikov
- Laboratory of Microfluidic Technologies for Biomedicine, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia.,Faculty of Biology and Biotechnology, National Research University Higher School of Economics (HSE), Moscow, Russia.,National Center of Medical Radiological Research, P. Hertsen Moscow Oncology Research Institute, Moscow, Russia
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Zhiyanov A, Nersisyan S, Tonevitsky A. Hairpin sequence and structure is associated with features of isomiR biogenesis. RNA Biol 2021; 18:430-438. [PMID: 34286662 DOI: 10.1080/15476286.2021.1952759] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
MiRNA isoforms (isomiRs) are single stranded small RNAs originating from the same pri-miRNA hairpin as a result of cleavage by Drosha and Dicer enzymes. Variations at the 5'-end of a miRNA alter the seed region of the molecule, thus affecting the targetome of the miRNA. In this manuscript, we analysed the distribution of miRNA cleavage positions across 31 different cancers using miRNA sequencing data of TCGA project. As a result, we found that the processing positions are not tissue specific and that all miRNAs could be correctly classified as ones exhibiting homogeneous or heterogeneous cleavage at one of the four cleavage sites. In 42% of cases (42 out of 100 miRNAs), we observed imprecise 5'-end Dicer cleavage, while this fraction was only 14% for Drosha (14 out of 99). To the contrary, almost all cleavage sites of 3'-ends (either Drosha or Dicer) were heterogeneous. With the use of only four nucleotides surrounding a 5'-end Dicer cleavage position we built a model which allowed us to distinguish between homogeneous and heterogeneous cleavage with the reliable quality (ROC AUC = 0.68). Finally, we showed the possible applications of the study by the analysis of two 5'-end isoforms originating from the same exogeneous shRNA hairpin. It turned out that the less expressed shRNA variant was functionally active, which led to the increased off-targeting. Thus, the obtained results could be applied to the design of shRNAs whose processing will result in a single 5'-variant.
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Affiliation(s)
- Anton Zhiyanov
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
| | - Stepan Nersisyan
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
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