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      Comprehensive analysis of partial epithelial mesenchymal transition‐related genes in hepatocellular carcinoma

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          Abstract

          Increasing evidence has revealed that cancer cells undergoing an intermediate state, partial epithelial mesenchymal transition (p‐EMT), tend to metastasize rather than complete EMT. We performed a comprehensive analysis of E‐cadherin and 25 p‐EMT‐related genes in HCC to explore the roles and regulatory mechanisms of them in HCC. We analysed E‐cadherin and 25 p‐EMT‐related genes in HCC and constructed an mRNA‐miRNA‐lncRNA ceRNA subnetwork containing p‐EMT‐related genes by bioinformatic approaches. IHC was used to identify the protein expression of key p‐EMT‐related genes, P4HA2, ITGA5, MMP9, MT1X and SPP1. Complete EMT is not necessary for HCC progression. Overexpression of P4HA2, ITGA5, MMP9, SPP1 and down‐regulation of MT1X were found in HCC tissues, which were significantly associated with poor prognosis of HCC patients. By means of stepwise reverse prediction and validation from mRNA to lncRNA, an mRNA‐miRNA‐lncRNA ceRNA subnetwork correlated with HCC prognosis was identified by expression and survival analysis. This study implied that key p‐EMT‐related genes P4HA2, ITGA5, MMP9, MT1X, SPP1 could be prognostic biomarkers and potential targets of therapy for HCC patients. We constructed an mRNA‐miRNA‐lncRNA subnetwork containing p‐EMT‐related genes successfully, among which each component might be utilized as a prognostic biomarker of HCC.

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          Global Cancer Statistics 2018: GLOBOCAN Estimates of Incidence and Mortality Worldwide for 36 Cancers in 185 Countries

          Ahmedin Jemal, Lindsey A Torre, Rebecca Siegel … (2018)
          This article provides a status report on the global burden of cancer worldwide using the GLOBOCAN 2018 estimates of cancer incidence and mortality produced by the International Agency for Research on Cancer, with a focus on geographic variability across 20 world regions. There will be an estimated 18.1 million new cancer cases (17.0 million excluding nonmelanoma skin cancer) and 9.6 million cancer deaths (9.5 million excluding nonmelanoma skin cancer) in 2018. In both sexes combined, lung cancer is the most commonly diagnosed cancer (11.6% of the total cases) and the leading cause of cancer death (18.4% of the total cancer deaths), closely followed by female breast cancer (11.6%), prostate cancer (7.1%), and colorectal cancer (6.1%) for incidence and colorectal cancer (9.2%), stomach cancer (8.2%), and liver cancer (8.2%) for mortality. Lung cancer is the most frequent cancer and the leading cause of cancer death among males, followed by prostate and colorectal cancer (for incidence) and liver and stomach cancer (for mortality). Among females, breast cancer is the most commonly diagnosed cancer and the leading cause of cancer death, followed by colorectal and lung cancer (for incidence), and vice versa (for mortality); cervical cancer ranks fourth for both incidence and mortality. The most frequently diagnosed cancer and the leading cause of cancer death, however, substantially vary across countries and within each country depending on the degree of economic development and associated social and life style factors. It is noteworthy that high-quality cancer registry data, the basis for planning and implementing evidence-based cancer control programs, are not available in most low- and middle-income countries. The Global Initiative for Cancer Registry Development is an international partnership that supports better estimation, as well as the collection and use of local data, to prioritize and evaluate national cancer control efforts. CA: A Cancer Journal for Clinicians 2018;0:1-31. © 2018 American Cancer Society.
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            Cytoscape: a software environment for integrated models of biomolecular interaction networks.

            Paul Shannon, Andrew Markiel, Owen Ozier … (2003)
            Cytoscape is an open source software project for integrating biomolecular interaction networks with high-throughput expression data and other molecular states into a unified conceptual framework. Although applicable to any system of molecular components and interactions, Cytoscape is most powerful when used in conjunction with large databases of protein-protein, protein-DNA, and genetic interactions that are increasingly available for humans and model organisms. Cytoscape's software Core provides basic functionality to layout and query the network; to visually integrate the network with expression profiles, phenotypes, and other molecular states; and to link the network to databases of functional annotations. The Core is extensible through a straightforward plug-in architecture, allowing rapid development of additional computational analyses and features. Several case studies of Cytoscape plug-ins are surveyed, including a search for interaction pathways correlating with changes in gene expression, a study of protein complexes involved in cellular recovery to DNA damage, inference of a combined physical/functional interaction network for Halobacterium, and an interface to detailed stochastic/kinetic gene regulatory models.
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              Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal.

              J. Gao, B. A. Aksoy, U Dogrusoz … (2015)
              The cBioPortal for Cancer Genomics (http://cbioportal.org) provides a Web resource for exploring, visualizing, and analyzing multidimensional cancer genomics data. The portal reduces molecular profiling data from cancer tissues and cell lines into readily understandable genetic, epigenetic, gene expression, and proteomic events. The query interface combined with customized data storage enables researchers to interactively explore genetic alterations across samples, genes, and pathways and, when available in the underlying data, to link these to clinical outcomes. The portal provides graphical summaries of gene-level data from multiple platforms, network visualization and analysis, survival analysis, patient-centric queries, and software programmatic access. The intuitive Web interface of the portal makes complex cancer genomics profiles accessible to researchers and clinicians without requiring bioinformatics expertise, thus facilitating biological discoveries. Here, we provide a practical guide to the analysis and visualization features of the cBioPortal for Cancer Genomics.
              Article 0 comments Cited 6194 times – based on 0 reviews     Review now
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                Author and article information

                Contributors
                Dean Tian: datian@tjh.tjmu.edu.cn
                Ping Han:
                ORCID: https://orcid.org/0000-0003-3736-6340
                hanzhouping@163.com
                Journal
                Journal ID (nlm-ta): J Cell Mol Med
                Journal ID (iso-abbrev): J Cell Mol Med
                Journal ID (doi): 10.1111/(ISSN)1582-4934
                Journal ID (publisher-id): JCMM
                Title: Journal of Cellular and Molecular Medicine
                Publisher: John Wiley and Sons Inc. (Hoboken )
                ISSN (Print): 1582-1838
                ISSN (Electronic): 1582-4934
                Publication date (Electronic): 20 November 2020
                Publication date (Print): January 2021
                Volume: 25
                Issue: 1 ( doiID: 10.1111/jcmm.v25.1 )
                Pages: 448-462
                Affiliations
                [ 1 ] Department of Gastroenterology Tongji Hospital of Tongji Medical College Huazhong University of Science and Technology Wuhan China
                Author notes
                [*] [* ] Correspondence

                Dean Tian and Ping Han, Department of Gastroenterology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei Province, China.

                Emails: datian@ 123456tjh.tjmu.edu.cn (DT); hanzhouping@ 123456163.com (PH)

                Author information
                https://orcid.org/0000-0003-3736-6340
                Article
                Publisher ID: JCMM16099
                DOI: 10.1111/jcmm.16099
                PMC ID: 7810929
                PubMed ID: 33215860
                SO-VID: 54e3bbab-72c1-4880-a7e6-7ae0c556ebf9
                Copyright © © 2020 The Authors. Journal of Cellular and Molecular Medicine published by Foundation for Cellular and Molecular Medicine and John Wiley & Sons Ltd
                License:

                This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

                History
                Date received : 25 May 2020
                Date revision received : 19 October 2020
                Date accepted : 25 October 2020
                Page count
                Figures: 8, Tables: 0, Pages: 15, Words: 6605
                Funding
                Funded by: National Natural Science Foundation of China , open-funder-registry 10.13039/501100001809;
                Award ID: 81702396
                Award ID: 81772607
                Award ID: 81800547
                Categories
                Subject: Original Article
                Subject: Original Articles
                Custom metadata
                source-schema-version-number 2.0
                cover-date January 2021
                details-of-publishers-convertor Converter:WILEY_ML3GV2_TO_JATSPMC version:5.9.6 mode:remove_FC converted:16.01.2021

                ScienceOpen disciplines: Molecular medicine
                Keywords: competing endogenous rna,hepatocellular carcinoma,partial epithelial mesenchymal transition,prognosis
                Data availability:
                ScienceOpen disciplines: Molecular medicine
                Keywords: competing endogenous rna, hepatocellular carcinoma, partial epithelial mesenchymal transition, prognosis

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