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Warden CD, Wu X. Critical Differential Expression Assessment for Individual Bulk RNA-Seq Projects. bioRxiv 2024:2024.02.10.579728. [PMID: 38405814 PMCID: PMC10888899 DOI: 10.1101/2024.02.10.579728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Finding the right balance of quality and quantity can be important, and it is essential that project quality does not drop below the level where important main conclusions are missed or misstated. We use knock-out and over-expression studies as a simplification to test recovery of a known causal gene in RNA-Seq cell line experiments. When single-end RNA-Seq reads are aligned with STAR and quantified with htseq-count, we found potential value in testing the use of the Generalized Linear Model (GLM) implementation of edgeR with robust dispersion estimation more frequently for either single-variate or multi-variate 2-group comparisons (with the possibility of defining criteria less stringent than |fold-change| > 1.5 and FDR < 0.05). When considering a limited number of patient sample comparisons with larger sample size, there might be some decreased variability between methods (except for DESeq1). However, at the same time, the ranking of the gene identified using immunohistochemistry (for ER/PR/HER2 in breast cancer samples from The Cancer Genome Atlas) showed as possible shift in performance compared to the cell line comparisons, potentially highlighting utility for standard statistical tests and/or limma-based analysis with larger sample sizes. If this continues to be true in additional studies and comparisons, then that could be consistent with the possibility that it may be important to allocate time for potential methods troubleshooting for genomics projects. Analysis of public data presented in this study does not consider all experimental designs, and presentation of downstream analysis is limited. So, any estimate from this simplification would be an underestimation of the true need for some methods testing for every project. Additionally, this set of independent cell line experiments has a limitation in being able to determine the frequency of missing a highly important gene if the problem is rare (such as 10% or lower). For example, if there was an assumption that only one method can be tested for "initial" analysis, then it is not completely clear to the extent that using edgeR-robust might perform better than DESeq2 in the cell line experiments. Importantly, we do not wish to cause undue concern, and we believe that it should often be possible to define a gene expression differential expression workflow that is suitable for some purposes for many samples. Nevertheless, at the same time, we provide a variety of measures that we believe emphasize the need to critically assess every individual project and maximize confidence in published results.
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Affiliation(s)
- Charles D Warden
- Integrative Genomics Core, Department of Molecular and Cellular Biology, City of Hope National Medical Center, Duarte, CA
| | - Xiwei Wu
- Integrative Genomics Core, Department of Molecular and Cellular Biology, City of Hope National Medical Center, Duarte, CA
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O’Connor LM, O’Connor BA, Zeng J, Lo CH. Data Mining of Microarray Datasets in Translational Neuroscience. Brain Sci 2023; 13:1318. [PMID: 37759919 PMCID: PMC10527016 DOI: 10.3390/brainsci13091318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 09/04/2023] [Accepted: 09/10/2023] [Indexed: 09/29/2023] Open
Abstract
Data mining involves the computational analysis of a plethora of publicly available datasets to generate new hypotheses that can be further validated by experiments for the improved understanding of the pathogenesis of neurodegenerative diseases. Although the number of sequencing datasets is on the rise, microarray analysis conducted on diverse biological samples represent a large collection of datasets with multiple web-based programs that enable efficient and convenient data analysis. In this review, we first discuss the selection of biological samples associated with neurological disorders, and the possibility of a combination of datasets, from various types of samples, to conduct an integrated analysis in order to achieve a holistic understanding of the alterations in the examined biological system. We then summarize key approaches and studies that have made use of the data mining of microarray datasets to obtain insights into translational neuroscience applications, including biomarker discovery, therapeutic development, and the elucidation of the pathogenic mechanisms of neurodegenerative diseases. We further discuss the gap to be bridged between microarray and sequencing studies to improve the utilization and combination of different types of datasets, together with experimental validation, for more comprehensive analyses. We conclude by providing future perspectives on integrating multi-omics, to advance precision phenotyping and personalized medicine for neurodegenerative diseases.
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Affiliation(s)
- Lance M. O’Connor
- College of Biological Sciences, University of Minnesota, Minneapolis, MN 55455, USA;
| | - Blake A. O’Connor
- School of Pharmacy, University of Wisconsin, Madison, WI 53705, USA;
| | - Jialiu Zeng
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308232, Singapore;
| | - Chih Hung Lo
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308232, Singapore;
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Chavdoula E, Anastas V, Ferlita AL, Aldana J, Carota G, Spampinato M, Soysal B, Cosentini I, Parashar S, Sircar A, Nigita G, Sehgal L, Freitas MA, Tsichlis PN. Transcriptional regulation of amino acid metabolism by KDM2B, in the context of ncPRC1.1 and in concert with MYC and ATF4. bioRxiv 2023:2023.07.07.548031. [PMID: 37461630 PMCID: PMC10350079 DOI: 10.1101/2023.07.07.548031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Introduction KDM2B encodes a JmjC domain-containing histone lysine demethylase, which functions as an oncogene in several types of tumors, including TNBC. This study was initiated to address the cancer relevance of the results of our earlier work, which had shown that overexpression of KDM2B renders mouse embryonic fibroblasts (MEFs) resistant to oxidative stress by regulating antioxidant mechanisms. Methods We mainly employed a multi-omics strategy consisting of RNA-Seq, quantitative TMT proteomics, Mass-spectrometry-based global metabolomics, ATAC-Seq and ChIP-seq, to explore the role of KDM2B in the resistance to oxidative stress and intermediary metabolism. These data and data from existing patient datasets were analyzed using bioinformatic tools, including exon-intron-split analysis (EISA), FLUFF and clustering analyses. The main genetic strategy we employed was gene silencing with shRNAs. ROS were measured by flow cytometry, following staining with CellROX and various metabolites were measured with biochemical assays, using commercially available kits. Gene expression was monitored with qRT-PCR and immunoblotting, as indicated. Results The knockdown of KDM2B in basal-like breast cancer cell lines lowers the levels of GSH and sensitizes the cells to ROS inducers, GSH targeting molecules, and DUB inhibitors. To address the mechanism of GSH regulation, we knocked down KDM2B in MDA-MB-231 cells and we examined the effects of the knockdown, using a multi-omics strategy. The results showed that KDM2B, functioning in the context of ncPRC1.1, regulates a network of epigenetic and transcription factors, which control a host of metabolic enzymes, including those involved in the SGOC, glutamate, and GSH metabolism. They also showed that KDM2B enhances the chromatin accessibility and expression of MYC and ATF4, and that it binds in concert with MYC and ATF4, the promoters of a large number of transcriptionally active genes, including many, encoding metabolic enzymes. Additionally, MYC and ATF4 binding sites were enriched in genes whose accessibility depends on KDM2B, and analysis of a cohort of TNBCs expressing high or low levels of KDM2B, but similar levels of MYC and ATF4 identified a subset of MYC targets, whose expression correlates with the expression of KDM2B. Further analyses of basal-like TNBCs in the same cohort, revealed that tumors expressing high levels of all three regulators exhibit a distinct metabolic signature that carries a poor prognosis. Conclusions The present study links KDM2B, ATF4, and MYC in a transcriptional network that regulates the expression of multiple metabolic enzymes, including those that control the interconnected SGOC, glutamate, and GSH metabolic pathways. The co-occupancy of the promoters of many transcriptionally active genes, by all three factors, the enrichment of MYC binding sites in genes whose chromatin accessibility depends on KDM2B, and the correlation of the levels of KDM2B with the expression of a subset of MYC target genes in tumors that express similar levels of MYC, suggest that KDM2B regulates both the expression and the transcriptional activity of MYC. Importantly, the concerted expression of all three factors also defines a distinct metabolic subset of TNBCs with poor prognosis. Overall, this study identifies novel mechanisms of SGOC regulation, suggests novel KDM2B-dependent metabolic vulnerabilities in TNBC, and provides new insights into the role of KDM2B in the epigenetic regulation of transcription.
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Affiliation(s)
- Evangelia Chavdoula
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, United States
- The Ohio State University, Comprehensive Cancer Center, Columbus, OH, United States
| | - Vollter Anastas
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, United States
- The Ohio State University, Comprehensive Cancer Center, Columbus, OH, United States
- Tufts Graduate School of Biomedical Sciences, Program in Genetics, Boston, MA, United States
| | - Alessandro La Ferlita
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, United States
- The Ohio State University, Comprehensive Cancer Center, Columbus, OH, United States
| | - Julian Aldana
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, United States
- The Ohio State University, Comprehensive Cancer Center, Columbus, OH, United States
| | - Giuseppe Carota
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Mariarita Spampinato
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Burak Soysal
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, United States
- The Ohio State University, Comprehensive Cancer Center, Columbus, OH, United States
| | - Ilaria Cosentini
- Department of Clinical and Experimental Medicine, Bioinformatics Unit, University of Catania, Catania, Italy
| | - Sameer Parashar
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, United States
- The Ohio State University, Comprehensive Cancer Center, Columbus, OH, United States
| | - Anuvrat Sircar
- The Ohio State University, Comprehensive Cancer Center, Columbus, OH, United States
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, United States
| | - Giovanni Nigita
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, United States
- The Ohio State University, Comprehensive Cancer Center, Columbus, OH, United States
| | - Lalit Sehgal
- The Ohio State University, Comprehensive Cancer Center, Columbus, OH, United States
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, United States
| | - Michael A. Freitas
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, United States
- The Ohio State University, Comprehensive Cancer Center, Columbus, OH, United States
| | - Philip N. Tsichlis
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, United States
- The Ohio State University, Comprehensive Cancer Center, Columbus, OH, United States
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Kanaya N, Kitamura Y, Vazquez ML, Franco A, Chen KS, van Schaik TA, Farzani TA, Borges P, Ichinose T, Seddiq W, Kuroda S, Boland G, Jahan N, Fisher D, Wakimoto H, Shah K. Gene-edited and -engineered stem cell platform drives immunotherapy for brain metastatic melanomas. Sci Transl Med 2023; 15:eade8732. [PMID: 37256936 PMCID: PMC10799631 DOI: 10.1126/scitranslmed.ade8732] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 05/10/2023] [Indexed: 06/02/2023]
Abstract
Oncolytic virus therapy has shown activity against primary melanomas; however, its efficacy in brain metastases remains challenging, mainly because of the delivery and immunosuppressive nature of tumors in the brain. To address this challenge, we first established PTEN-deficient melanoma brain metastasis mouse models and characterized them to be more immunosuppressive compared with primary melanoma, mimicking the clinical settings. Next, we developed an allogeneic twin stem cell (TSC) system composed of two tumor-targeting stem cell (SC) populations. One SC was loaded with oncolytic herpes simplex virus (oHSV), and the other SC was CRISPR-Cas9 gene-edited to knock out nectin 1 (N1) receptor (N1KO) to acquire resistance to oHSV and release immunomodulators, such as granulocyte-macrophage colony-stimulating factor (GM-CSF). Using mouse models of brain metastatic BRAFV600E/PTEN-/- and BRAFV600E/wt/PTEN-/- mutant melanomas, we show that locoregional delivery of TSCs releasing oHSV and GM-CSF (TSC-G) activated dendritic cell- and T cell-mediated immune responses. In addition, our strategy exhibited greater therapeutic efficacy when compared with the existing oncolytic viral therapeutic approaches. Moreover, the TSCs composed of SC-oHSV and SCN1KO-releasing GM-CSF and single-chain variable fragment anti-PD-1 (TSC-G/P) had therapeutic efficacy in both syngeneic and patient-derived humanized mouse models of leptomeningeal metastasis. Our findings provide a promising allogeneic SC-based immunotherapeutic strategy against melanomas in the CNS and a road map toward clinical translation.
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Affiliation(s)
- Nobuhiko Kanaya
- Center for Stem Cell and Translational Immunotherapy, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Yohei Kitamura
- Center for Stem Cell and Translational Immunotherapy, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Maria Lopez Vazquez
- Center for Stem Cell and Translational Immunotherapy, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Arnaldo Franco
- Center for Stem Cell and Translational Immunotherapy, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Kok-Siong Chen
- Center for Stem Cell and Translational Immunotherapy, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Thijs A. van Schaik
- Center for Stem Cell and Translational Immunotherapy, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Touraj Aligholipour Farzani
- Center for Stem Cell and Translational Immunotherapy, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Paulo Borges
- Center for Stem Cell and Translational Immunotherapy, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Toru Ichinose
- Center for Stem Cell and Translational Immunotherapy, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Waleed Seddiq
- Center for Stem Cell and Translational Immunotherapy, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Shinji Kuroda
- Department of Gastroenterological Surgery, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama 700-8558, Japan
| | - Genevieve Boland
- Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Nusrat Jahan
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - David Fisher
- Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Hiroaki Wakimoto
- Center for Stem Cell and Translational Immunotherapy, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Khalid Shah
- Center for Stem Cell and Translational Immunotherapy, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
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Zhu J, Sun YH, Ouyang Z, Li K, Negi S, Piya S, Hu W, Zavodszky MI, Yalamanchili H, Chen Y, Zhang X, Casey F, Zhang B. RNASequest: An End-to-End Reproducible RNAseq Data Analysis and Publishing Framework. J Mol Biol 2023:168017. [PMID: 36806691 DOI: 10.1016/j.jmb.2023.168017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 02/03/2023] [Accepted: 02/12/2023] [Indexed: 02/18/2023]
Abstract
We present RNASequest, a customizable RNA sequencing (RNAseq) analysis, app management, and result publishing framework. Its three-in-one RNAseq data analysis ecosystem consists of (1) a reproducible, configurable expression analysis (EA) module, (2) multi-faceted result presentation in R Shiny, a Bookdown document and an online slide deck, and (3) a centralized data management system. In principle, following up our well-received omics data visualization tool Quickomics, RNASequest automates the differential gene expression analysis step, eases statistical model design by built-in covariates testing module, and further provides a web-based tool, ShinyOne, to manage apps powered by Quickomics and reports generated by running the pipeline on multiple projects in one place. Researchers can experience the functionalities by exploring demo data sets hosted at http://shinyone.bxgenomics.com or following the tutorial, https://interactivereport.github.io/RNASequest/tutorial/docs/introduction.html to set up the framework locally to process private RNAseq datasets. The source code released under MIT open-source license is provided at https://github.com/interactivereport/RNASequest.
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Affiliation(s)
- Jing Zhu
- Translational Sciences, Biogen Inc, Cambridge, MA 02142, USA.
| | - Yu H Sun
- Translational Sciences, Biogen Inc, Cambridge, MA 02142, USA.
| | | | - Kejie Li
- Translational Sciences, Biogen Inc, Cambridge, MA 02142, USA.
| | - Soumya Negi
- Translational Sciences, Biogen Inc, Cambridge, MA 02142, USA.
| | - Sarbottam Piya
- Translational Sciences, Biogen Inc, Cambridge, MA 02142, USA.
| | - Wenxing Hu
- Translational Sciences, Biogen Inc, Cambridge, MA 02142, USA.
| | | | | | - Yirui Chen
- Translational Sciences, Biogen Inc, Cambridge, MA 02142, USA.
| | - Xinmin Zhang
- Data Science, BioInfoRx Inc, Madison, WI 53719, USA.
| | - Fergal Casey
- Translational Sciences, Biogen Inc, Cambridge, MA 02142, USA.
| | - Baohong Zhang
- Translational Sciences, Biogen Inc, Cambridge, MA 02142, USA.
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Filetti V, Lombardo C, Loreto C, Dounias G, Bracci M, Matera S, Rapisarda L, Rapisarda V, Ledda C, Vitale E. Small RNA-Seq Transcriptome Profiling of Mesothelial and Mesothelioma Cell Lines Revealed microRNA Dysregulation after Exposure to Asbestos-like Fibers. Biomedicines 2023; 11:biomedicines11020538. [PMID: 36831074 PMCID: PMC9953340 DOI: 10.3390/biomedicines11020538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/06/2023] [Accepted: 02/10/2023] [Indexed: 02/15/2023] Open
Abstract
Environmental exposure to fibers of respirable size has been identified as a risk for public health. Experimental evidence has revealed that a variety of fibers, including fluoro-edenite, can develop chronic respiratory diseases and elicit carcinogenic effects in humans. Fluoro-edenite (FE) is a silicate mineral first found in Biancavilla (Sicily, Italy) in 1997. Environmental exposure to its fibers has been correlated with a cluster of malignant pleural mesotheliomas. This neoplasm represents a public health problem due to its long latency and to its aggression not alerted by specific symptoms. Having several biomarkers providing us with data on the health state of those exposed to FE fibers or allowing an early diagnosis on malignant pleural mesothelioma, still asymptomatic patients, would be a remarkable goal. To these purposes, we reported the miRNA transcriptome in human normal mesothelial cell line (MeT-5A) and in the human malignant mesothelioma cell line (JU77) exposed and not exposed to FE fibers. The results showed a difference in the number of deregulated miRNAs between tumor and nontumor samples both exposed and not exposed to FE fibers. As a matter of fact, the effect of exposure to FE fibers is more evident in the expression of miRNA in the tumor samples than in the nontumor samples. In the present paper, several pathways involved in the pathogenesis of malignant pleural mesothelioma have been analyzed. We especially noticed the involvement of pathways that have important functions in inflammatory processes, angiogenesis, apoptosis, and necrosis. Besides this amount of data, further studies will be designed for the selection of the most significant miRNAs to test and validate their diagnostic potential, alone or in combination with other protein biomarkers, in high-risk individuals' liquid biopsy to have a noninvasive tool of diagnosis for this neoplasm.
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Affiliation(s)
- Veronica Filetti
- Occupational Medicine, Department of Clinical and Experimental Medicine, University of Catania, 95123 Catania, Italy
- Human Anatomy and Histology, Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
| | - Claudia Lombardo
- Human Anatomy, Department of Medical and Surgical Sciences and Advanced Technologies, University of Catania, 95123 Catania, Italy
| | - Carla Loreto
- Human Anatomy and Histology, Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
| | - George Dounias
- Department of Occupational and Environmental Health, University of West Attica, 10563 Athens, Greece
| | - Massimo Bracci
- Occupational Medicine, Department of Clinical and Molecular Sciences, Polytechnic University of Marche, 60126 Ancona, Italy
| | - Serena Matera
- Occupational Medicine, Department of Clinical and Experimental Medicine, University of Catania, 95123 Catania, Italy
| | - Lucia Rapisarda
- Occupational Medicine, Department of Clinical and Experimental Medicine, University of Catania, 95123 Catania, Italy
| | - Venerando Rapisarda
- Occupational Medicine, Department of Clinical and Experimental Medicine, University of Catania, 95123 Catania, Italy
- Correspondence:
| | - Caterina Ledda
- Occupational Medicine, Department of Clinical and Experimental Medicine, University of Catania, 95123 Catania, Italy
| | - Ermanno Vitale
- Occupational Medicine, Department of Clinical and Experimental Medicine, University of Catania, 95123 Catania, Italy
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Filetti V, La Ferlita A, Di Maria A, Cardile V, Graziano ACE, Rapisarda V, Ledda C, Pulvirenti A, Loreto C. Dysregulation of microRNAs and tRNA-derived ncRNAs in mesothelial and mesothelioma cell lines after asbestiform fiber exposure. Sci Rep 2022; 12:9181. [PMID: 35654808 DOI: 10.1038/s41598-022-13044-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 05/19/2022] [Indexed: 11/09/2022] Open
Abstract
Experimental evidence demonstrated that fluoro-edenite (FE) can develop chronic respiratory diseases and elicit carcinogenic effects. Environmental exposure to FE fibers is correlated with malignant pleural mesothelioma (MPM). An early diagnosis of MPM, and a comprehensive health monitoring of the patients exposed to FE fibers are two clinical issues that may be solved by the identification of specific biomarkers. We reported the microRNA (miRNA) and transfer RNA-derived non coding RNA (tRNA-derived ncRNA) transcriptome in human normal mesothelial and malignant mesothelioma cell lines exposed or not exposed to several concentration FE fibers. Furthermore, an interactive mesothelioma-based network was derived by using NetME tool. In untreated condition, the expression of miRNAs and tRNA-derived ncRNAs in tumor cells was significantly different with respect to non-tumor samples. Moreover, interesting and significant changes were found after the exposure of both cells lines to FE fibers. The network-based pathway analysis showed several signaling and metabolic pathways potentially involved in the pathogenesis of MPM. From papers analyzed by NetME, it is clear that many miRNAs can positively or negatively influence various pathways involved in MPM. For the first time, the analysis of tRNA-derived ncRNAs molecules in the context of mesothelioma has been made by using in vitro systems. Further studies will be designed to test and validate their diagnostic potential in high-risk individuals' liquid biopsies.
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