Identification of Key Functional Modules and Immunomodulatory Regulators of Hepatocellular Carcinoma
Despite the advances in the treatment of hepatocellular carcinoma (HCC), the prognosis of HCC patients remains unsatisfactory due to postsurgical recurrence and treatment resistance. Therefore, it is important to reveal the mechanisms underlying HCC and identify potential therapeutic targets against...
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| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Wiley
2021-01-01
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| Series: | Journal of Immunology Research |
| Online Access: | http://dx.doi.org/10.1155/2021/1801873 |
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| author | Ding Luo Xiang Zhang Xiao-Kai Li Gang Chen |
| author_facet | Ding Luo Xiang Zhang Xiao-Kai Li Gang Chen |
| author_sort | Ding Luo |
| collection | DOAJ |
| description | Despite the advances in the treatment of hepatocellular carcinoma (HCC), the prognosis of HCC patients remains unsatisfactory due to postsurgical recurrence and treatment resistance. Therefore, it is important to reveal the mechanisms underlying HCC and identify potential therapeutic targets against HCC, which could facilitate the development of novel therapies. Based on 12 HCC samples and 12 paired paracancerous normal tissues, we identified differentially expressed mRNAs and lncRNAs using the “limma” package in R software. Moreover, we used the weighted gene coexpression network analysis (WGCNA) to analyze the expression data and screened hub genes. Furthermore, we performed pathway enrichment analysis based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. In addition, the relative abundance of a given gene set was estimated by single-sample Gene Set Enrichment Analysis. We identified 687 differentially expressed mRNAs and 260 differentially expressed lncRNAs. A total of 6 modules were revealed by WGCNA, and MT1M and MT1E genes from the red module were identified as hub genes. Moreover, pathway analysis revealed the top 10 enriched KEGG pathways of upregulated or downregulated genes. Additionally, we also found that CD58 might act as an immune checkpoint gene in HCC via PD1/CTLA4 pathways and regulate the levels of tumor-infiltrating immune cells in HCC tissues, which might be an immunotherapeutic target in HCC. Our research identified key functional modules and immunomodulatory regulators for HCC, which might offer novel diagnostic biomarkers and/or therapeutic targets for cancer immunotherapy. |
| format | Article |
| id | doaj-art-045e378af0d0470f8abb7acae3df5a18 |
| institution | OA Journals |
| issn | 2314-8861 2314-7156 |
| language | English |
| publishDate | 2021-01-01 |
| publisher | Wiley |
| record_format | Article |
| series | Journal of Immunology Research |
| spelling | doaj-art-045e378af0d0470f8abb7acae3df5a182025-08-20T02:03:08ZengWileyJournal of Immunology Research2314-88612314-71562021-01-01202110.1155/2021/18018731801873Identification of Key Functional Modules and Immunomodulatory Regulators of Hepatocellular CarcinomaDing Luo0Xiang Zhang1Xiao-Kai Li2Gang Chen3Department of Hepatobiliary Surgery, The First People’s Hospital of Kunming City & Ganmei Affiliated Hospital of Kunming Medical University, No. 504 Youth Road, Kunming 650000, ChinaDepartment of Hepatobiliary Surgery, The First People’s Hospital of Kunming City & Ganmei Affiliated Hospital of Kunming Medical University, No. 504 Youth Road, Kunming 650000, ChinaDepartment of Hepatobiliary Surgery, First Affiliated Hospital of Kunming Medical University, No. 295 Xichang Road, Kunming 650032, ChinaDepartment of Hepatobiliary Surgery, The First People’s Hospital of Kunming City & Ganmei Affiliated Hospital of Kunming Medical University, No. 504 Youth Road, Kunming 650000, ChinaDespite the advances in the treatment of hepatocellular carcinoma (HCC), the prognosis of HCC patients remains unsatisfactory due to postsurgical recurrence and treatment resistance. Therefore, it is important to reveal the mechanisms underlying HCC and identify potential therapeutic targets against HCC, which could facilitate the development of novel therapies. Based on 12 HCC samples and 12 paired paracancerous normal tissues, we identified differentially expressed mRNAs and lncRNAs using the “limma” package in R software. Moreover, we used the weighted gene coexpression network analysis (WGCNA) to analyze the expression data and screened hub genes. Furthermore, we performed pathway enrichment analysis based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. In addition, the relative abundance of a given gene set was estimated by single-sample Gene Set Enrichment Analysis. We identified 687 differentially expressed mRNAs and 260 differentially expressed lncRNAs. A total of 6 modules were revealed by WGCNA, and MT1M and MT1E genes from the red module were identified as hub genes. Moreover, pathway analysis revealed the top 10 enriched KEGG pathways of upregulated or downregulated genes. Additionally, we also found that CD58 might act as an immune checkpoint gene in HCC via PD1/CTLA4 pathways and regulate the levels of tumor-infiltrating immune cells in HCC tissues, which might be an immunotherapeutic target in HCC. Our research identified key functional modules and immunomodulatory regulators for HCC, which might offer novel diagnostic biomarkers and/or therapeutic targets for cancer immunotherapy.http://dx.doi.org/10.1155/2021/1801873 |
| spellingShingle | Ding Luo Xiang Zhang Xiao-Kai Li Gang Chen Identification of Key Functional Modules and Immunomodulatory Regulators of Hepatocellular Carcinoma Journal of Immunology Research |
| title | Identification of Key Functional Modules and Immunomodulatory Regulators of Hepatocellular Carcinoma |
| title_full | Identification of Key Functional Modules and Immunomodulatory Regulators of Hepatocellular Carcinoma |
| title_fullStr | Identification of Key Functional Modules and Immunomodulatory Regulators of Hepatocellular Carcinoma |
| title_full_unstemmed | Identification of Key Functional Modules and Immunomodulatory Regulators of Hepatocellular Carcinoma |
| title_short | Identification of Key Functional Modules and Immunomodulatory Regulators of Hepatocellular Carcinoma |
| title_sort | identification of key functional modules and immunomodulatory regulators of hepatocellular carcinoma |
| url | http://dx.doi.org/10.1155/2021/1801873 |
| work_keys_str_mv | AT dingluo identificationofkeyfunctionalmodulesandimmunomodulatoryregulatorsofhepatocellularcarcinoma AT xiangzhang identificationofkeyfunctionalmodulesandimmunomodulatoryregulatorsofhepatocellularcarcinoma AT xiaokaili identificationofkeyfunctionalmodulesandimmunomodulatoryregulatorsofhepatocellularcarcinoma AT gangchen identificationofkeyfunctionalmodulesandimmunomodulatoryregulatorsofhepatocellularcarcinoma |