Identification of Prognostic Genes in the Tumor Microenvironment of Hepatocellular Carcinoma
Background: Hepatocellular carcinoma (HCC) is one of the most common malignant tumors in the world. The efficacy of immunotherapy usually depends on the interaction of immunomodulation in the tumor microenvironment (TME). This study aimed to explore the potential stromal-immune score-based prognosti...
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| Published in | Frontiers in immunology Vol. 12; p. 653836 |
|---|---|
| Main Authors | , , , , , , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
Switzerland
Frontiers Media S.A
07.04.2021
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| Abstract | Background:
Hepatocellular carcinoma (HCC) is one of the most common malignant tumors in the world. The efficacy of immunotherapy usually depends on the interaction of immunomodulation in the tumor microenvironment (TME). This study aimed to explore the potential stromal-immune score-based prognostic genes related to immunotherapy in HCC through bioinformatics analysis.
Methods:
ESTIMATE algorithm was applied to calculate the immune/stromal/Estimate scores and tumor purity of HCC using the Cancer Genome Atlas (TCGA) transcriptome data. Functional enrichment analysis of differentially expressed genes (DEGs) was analyzed by the Database for Annotation, Visualization, and Integrated Discovery database (DAVID). Univariate and multivariate Cox regression analysis and least absolute shrinkage and selection operator (LASSO) regression analysis were performed for prognostic gene screening. The expression and prognostic value of these genes were further verified by KM-plotter database and the Human Protein Atlas (HPA) database. The correlation of the selected genes and the immune cell infiltration were analyzed by single sample gene set enrichment analysis (ssGSEA) algorithm and Tumor Immune Estimation Resource (TIMER).
Results:
Data analysis revealed that higher immune/stromal/Estimate scores were significantly associated with better survival benefits in HCC within 7 years, while the tumor purity showed a reverse trend. DEGs based on both immune and stromal scores primarily affected the cytokine–cytokine receptor interaction signaling pathway. Among the DEGs, three genes (CASKIN1, EMR3, and GBP5) were found most significantly associated with survival. Moreover, the expression levels of CASKIN1, EMR3, and GBP5 genes were significantly correlated with immune/stromal/Estimate scores or tumor purity and multiple immune cell infiltration. Among them, GBP5 genes were highly related to immune infiltration.
Conclusion:
This study identified three key genes which were related to the TME and had prognostic significance in HCC, which may be promising markers for predicting immunotherapy outcomes. |
|---|---|
| AbstractList | Background:
Hepatocellular carcinoma (HCC) is one of the most common malignant tumors in the world. The efficacy of immunotherapy usually depends on the interaction of immunomodulation in the tumor microenvironment (TME). This study aimed to explore the potential stromal-immune score-based prognostic genes related to immunotherapy in HCC through bioinformatics analysis.
Methods:
ESTIMATE algorithm was applied to calculate the immune/stromal/Estimate scores and tumor purity of HCC using the Cancer Genome Atlas (TCGA) transcriptome data. Functional enrichment analysis of differentially expressed genes (DEGs) was analyzed by the Database for Annotation, Visualization, and Integrated Discovery database (DAVID). Univariate and multivariate Cox regression analysis and least absolute shrinkage and selection operator (LASSO) regression analysis were performed for prognostic gene screening. The expression and prognostic value of these genes were further verified by KM-plotter database and the Human Protein Atlas (HPA) database. The correlation of the selected genes and the immune cell infiltration were analyzed by single sample gene set enrichment analysis (ssGSEA) algorithm and Tumor Immune Estimation Resource (TIMER).
Results:
Data analysis revealed that higher immune/stromal/Estimate scores were significantly associated with better survival benefits in HCC within 7 years, while the tumor purity showed a reverse trend. DEGs based on both immune and stromal scores primarily affected the cytokine–cytokine receptor interaction signaling pathway. Among the DEGs, three genes (CASKIN1, EMR3, and GBP5) were found most significantly associated with survival. Moreover, the expression levels of CASKIN1, EMR3, and GBP5 genes were significantly correlated with immune/stromal/Estimate scores or tumor purity and multiple immune cell infiltration. Among them, GBP5 genes were highly related to immune infiltration.
Conclusion:
This study identified three key genes which were related to the TME and had prognostic significance in HCC, which may be promising markers for predicting immunotherapy outcomes. Hepatocellular carcinoma (HCC) is one of the most common malignant tumors in the world. The efficacy of immunotherapy usually depends on the interaction of immunomodulation in the tumor microenvironment (TME). This study aimed to explore the potential stromal-immune score-based prognostic genes related to immunotherapy in HCC through bioinformatics analysis. ESTIMATE algorithm was applied to calculate the immune/stromal/Estimate scores and tumor purity of HCC using the Cancer Genome Atlas (TCGA) transcriptome data. Functional enrichment analysis of differentially expressed genes (DEGs) was analyzed by the Database for Annotation, Visualization, and Integrated Discovery database (DAVID). Univariate and multivariate Cox regression analysis and least absolute shrinkage and selection operator (LASSO) regression analysis were performed for prognostic gene screening. The expression and prognostic value of these genes were further verified by KM-plotter database and the Human Protein Atlas (HPA) database. The correlation of the selected genes and the immune cell infiltration were analyzed by single sample gene set enrichment analysis (ssGSEA) algorithm and Tumor Immune Estimation Resource (TIMER). Data analysis revealed that higher immune/stromal/Estimate scores were significantly associated with better survival benefits in HCC within 7 years, while the tumor purity showed a reverse trend. DEGs based on both immune and stromal scores primarily affected the cytokine-cytokine receptor interaction signaling pathway. Among the DEGs, three genes (CASKIN1, EMR3, and GBP5) were found most significantly associated with survival. Moreover, the expression levels of CASKIN1, EMR3, and GBP5 genes were significantly correlated with immune/stromal/Estimate scores or tumor purity and multiple immune cell infiltration. Among them, GBP5 genes were highly related to immune infiltration. This study identified three key genes which were related to the TME and had prognostic significance in HCC, which may be promising markers for predicting immunotherapy outcomes. Background: Hepatocellular carcinoma (HCC) is one of the most common malignant tumors in the world. The efficacy of immunotherapy usually depends on the interaction of immunomodulation in the tumor microenvironment (TME). This study aimed to explore the potential stromal-immune score-based prognostic genes related to immunotherapy in HCC through bioinformatics analysis.Methods: ESTIMATE algorithm was applied to calculate the immune/stromal/Estimate scores and tumor purity of HCC using the Cancer Genome Atlas (TCGA) transcriptome data. Functional enrichment analysis of differentially expressed genes (DEGs) was analyzed by the Database for Annotation, Visualization, and Integrated Discovery database (DAVID). Univariate and multivariate Cox regression analysis and least absolute shrinkage and selection operator (LASSO) regression analysis were performed for prognostic gene screening. The expression and prognostic value of these genes were further verified by KM-plotter database and the Human Protein Atlas (HPA) database. The correlation of the selected genes and the immune cell infiltration were analyzed by single sample gene set enrichment analysis (ssGSEA) algorithm and Tumor Immune Estimation Resource (TIMER).Results: Data analysis revealed that higher immune/stromal/Estimate scores were significantly associated with better survival benefits in HCC within 7 years, while the tumor purity showed a reverse trend. DEGs based on both immune and stromal scores primarily affected the cytokine–cytokine receptor interaction signaling pathway. Among the DEGs, three genes (CASKIN1, EMR3, and GBP5) were found most significantly associated with survival. Moreover, the expression levels of CASKIN1, EMR3, and GBP5 genes were significantly correlated with immune/stromal/Estimate scores or tumor purity and multiple immune cell infiltration. Among them, GBP5 genes were highly related to immune infiltration.Conclusion: This study identified three key genes which were related to the TME and had prognostic significance in HCC, which may be promising markers for predicting immunotherapy outcomes. Background: Hepatocellular carcinoma (HCC) is one of the most common malignant tumors in the world. The efficacy of immunotherapy usually depends on the interaction of immunomodulation in the tumor microenvironment (TME). This study aimed to explore the potential stromal-immune score-based prognostic genes related to immunotherapy in HCC through bioinformatics analysis. Methods: ESTIMATE algorithm was applied to calculate the immune/stromal/Estimate scores and tumor purity of HCC using the Cancer Genome Atlas (TCGA) transcriptome data. Functional enrichment analysis of differentially expressed genes (DEGs) was analyzed by the Database for Annotation, Visualization, and Integrated Discovery database (DAVID). Univariate and multivariate Cox regression analysis and least absolute shrinkage and selection operator (LASSO) regression analysis were performed for prognostic gene screening. The expression and prognostic value of these genes were further verified by KM-plotter database and the Human Protein Atlas (HPA) database. The correlation of the selected genes and the immune cell infiltration were analyzed by single sample gene set enrichment analysis (ssGSEA) algorithm and Tumor Immune Estimation Resource (TIMER). Results: Data analysis revealed that higher immune/stromal/Estimate scores were significantly associated with better survival benefits in HCC within 7 years, while the tumor purity showed a reverse trend. DEGs based on both immune and stromal scores primarily affected the cytokine-cytokine receptor interaction signaling pathway. Among the DEGs, three genes (CASKIN1, EMR3, and GBP5) were found most significantly associated with survival. Moreover, the expression levels of CASKIN1, EMR3, and GBP5 genes were significantly correlated with immune/stromal/Estimate scores or tumor purity and multiple immune cell infiltration. Among them, GBP5 genes were highly related to immune infiltration. Conclusion: This study identified three key genes which were related to the TME and had prognostic significance in HCC, which may be promising markers for predicting immunotherapy outcomes.Background: Hepatocellular carcinoma (HCC) is one of the most common malignant tumors in the world. The efficacy of immunotherapy usually depends on the interaction of immunomodulation in the tumor microenvironment (TME). This study aimed to explore the potential stromal-immune score-based prognostic genes related to immunotherapy in HCC through bioinformatics analysis. Methods: ESTIMATE algorithm was applied to calculate the immune/stromal/Estimate scores and tumor purity of HCC using the Cancer Genome Atlas (TCGA) transcriptome data. Functional enrichment analysis of differentially expressed genes (DEGs) was analyzed by the Database for Annotation, Visualization, and Integrated Discovery database (DAVID). Univariate and multivariate Cox regression analysis and least absolute shrinkage and selection operator (LASSO) regression analysis were performed for prognostic gene screening. The expression and prognostic value of these genes were further verified by KM-plotter database and the Human Protein Atlas (HPA) database. The correlation of the selected genes and the immune cell infiltration were analyzed by single sample gene set enrichment analysis (ssGSEA) algorithm and Tumor Immune Estimation Resource (TIMER). Results: Data analysis revealed that higher immune/stromal/Estimate scores were significantly associated with better survival benefits in HCC within 7 years, while the tumor purity showed a reverse trend. DEGs based on both immune and stromal scores primarily affected the cytokine-cytokine receptor interaction signaling pathway. Among the DEGs, three genes (CASKIN1, EMR3, and GBP5) were found most significantly associated with survival. Moreover, the expression levels of CASKIN1, EMR3, and GBP5 genes were significantly correlated with immune/stromal/Estimate scores or tumor purity and multiple immune cell infiltration. Among them, GBP5 genes were highly related to immune infiltration. Conclusion: This study identified three key genes which were related to the TME and had prognostic significance in HCC, which may be promising markers for predicting immunotherapy outcomes. |
| Author | Xiang, Shixin Li, Mingxing Li, Jing Cho, Chi Hin Yi, Tao Yang, Xiao Zheng, Yuan Du, Fukuan Wu, Xu Shen, Jing Kaboli, Parham Jabbarzadeh Xiao, Zhangang Zhao, Yueshui Wen, Qinglian |
| AuthorAffiliation | 1 Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University , Luzhou , China 2 South Sichuan Institute of Translational Medicine , Luzhou , China 4 Neijiang Health and Health Vocational College , Neijiang , China 3 Department of Oncology and Hematology, Hospital (T.C.M) Affiliated to Southwest Medical University , Luzhou , China 6 Faculty of Medicine, School of Biomedical Sciences, The Chinese University of Hong Kong , Hong Kong , China 5 Department of Oncology, Affiliated Hospital of Southwest Medical University , Luzhou , China 7 School of Chinese Medicine, Hong Kong Baptist University , Hong Kong , China 8 Department of Pharmacy, The Affiliated Hospital of Southwest Medical University , Luzhou , China |
| AuthorAffiliation_xml | – name: 6 Faculty of Medicine, School of Biomedical Sciences, The Chinese University of Hong Kong , Hong Kong , China – name: 8 Department of Pharmacy, The Affiliated Hospital of Southwest Medical University , Luzhou , China – name: 2 South Sichuan Institute of Translational Medicine , Luzhou , China – name: 1 Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University , Luzhou , China – name: 3 Department of Oncology and Hematology, Hospital (T.C.M) Affiliated to Southwest Medical University , Luzhou , China – name: 5 Department of Oncology, Affiliated Hospital of Southwest Medical University , Luzhou , China – name: 7 School of Chinese Medicine, Hong Kong Baptist University , Hong Kong , China – name: 4 Neijiang Health and Health Vocational College , Neijiang , China |
| Author_xml | – sequence: 1 givenname: Shixin surname: Xiang fullname: Xiang, Shixin – sequence: 2 givenname: Jing surname: Li fullname: Li, Jing – sequence: 3 givenname: Jing surname: Shen fullname: Shen, Jing – sequence: 4 givenname: Yueshui surname: Zhao fullname: Zhao, Yueshui – sequence: 5 givenname: Xu surname: Wu fullname: Wu, Xu – sequence: 6 givenname: Mingxing surname: Li fullname: Li, Mingxing – sequence: 7 givenname: Xiao surname: Yang fullname: Yang, Xiao – sequence: 8 givenname: Parham Jabbarzadeh surname: Kaboli fullname: Kaboli, Parham Jabbarzadeh – sequence: 9 givenname: Fukuan surname: Du fullname: Du, Fukuan – sequence: 10 givenname: Yuan surname: Zheng fullname: Zheng, Yuan – sequence: 11 givenname: Qinglian surname: Wen fullname: Wen, Qinglian – sequence: 12 givenname: Chi Hin surname: Cho fullname: Cho, Chi Hin – sequence: 13 givenname: Tao surname: Yi fullname: Yi, Tao – sequence: 14 givenname: Zhangang surname: Xiao fullname: Xiao, Zhangang |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/33897701$$D View this record in MEDLINE/PubMed |
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| Cites_doi | 10.1002/hep.27246 10.1200/JCO.2004.08.186 10.1007/978-3-319-41523-9_15 10.1111/j.1365-2893.2010.01269.x 10.1186/s12935-020-01351-3 10.1038/s41598-018-27641-5 10.18632/aging.102820 10.1016/j.toxlet.2018.03.003 10.1038/ncomms3612 10.3322/caac.21583 10.12659/MSM.922159 10.3389/fonc.2018.00269 10.1038/nprot.2008.211 10.1186/s40425-019-0647-4 10.1155/2019/2408348 10.1111/his.13504 10.1007/s00262-014-1627-7 10.3109/01677069009107113 10.3748/wjg.v26.i8.789 10.1038/nrc1934 10.3748/wjg.v26.i2.134 10.1097/MD.0000000000021287 10.1038/s41588-018-0312-8 10.1016/j.jhep.2019.01.028 10.1016/j.pharmthera.2017.02.005 10.1038/nm.3394 10.3892/ol.2018.8306 10.1007/978-1-4939-3578-9_6 10.18632/aging.102233 10.3389/fonc.2018.00634 10.3390/ijms18020412 10.3390/genes10080630 10.1186/s13045-019-0739-0 10.1016/j.phrs.2017.05.004 10.1126/science.aaa1348 10.18632/aging.101415 10.1097/WNR.0b013e32833f19f2 10.1002/ijc.32343 10.1016/j.cell.2018.03.042 10.1007/978-3-642-71967-7_12 10.1093/annonc/mdy495 10.3390/ijms20174131 10.18632/aging.103115 10.1186/1471-2105-14-7 10.1016/j.exger.2018.04.023 10.1038/bjc.2017.208 10.1038/s41571-019-0203-7 10.1056/NEJMc1415938 10.1186/s13046-019-1396-4 10.15252/embj.2018100926 10.18637/jss.v033.i01 10.1373/clinchem.2014.224360 10.1038/s41591-018-0134-3 10.1038/s41598-017-10649-8 10.1016/j.ctrv.2018.02.004 10.3389/fgene.2019.01119 10.1016/j.csbj.2017.07.004 10.1001/jamaoncol.2019.2996 |
| ContentType | Journal Article |
| Copyright | Copyright © 2021 Xiang, Li, Shen, Zhao, Wu, Li, Yang, Kaboli, Du, Zheng, Wen, Cho, Yi and Xiao. Copyright © 2021 Xiang, Li, Shen, Zhao, Wu, Li, Yang, Kaboli, Du, Zheng, Wen, Cho, Yi and Xiao. 2021 Xiang, Li, Shen, Zhao, Wu, Li, Yang, Kaboli, Du, Zheng, Wen, Cho, Yi and Xiao |
| Copyright_xml | – notice: Copyright © 2021 Xiang, Li, Shen, Zhao, Wu, Li, Yang, Kaboli, Du, Zheng, Wen, Cho, Yi and Xiao. – notice: Copyright © 2021 Xiang, Li, Shen, Zhao, Wu, Li, Yang, Kaboli, Du, Zheng, Wen, Cho, Yi and Xiao. 2021 Xiang, Li, Shen, Zhao, Wu, Li, Yang, Kaboli, Du, Zheng, Wen, Cho, Yi and Xiao |
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| Keywords | Hepatocellular carcinoma Prognosis tumor microenvironment ESTIMATE algorithm TCGA |
| Language | English |
| License | Copyright © 2021 Xiang, Li, Shen, Zhao, Wu, Li, Yang, Kaboli, Du, Zheng, Wen, Cho, Yi and Xiao. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
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| Notes | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 These authors have contributed equally to this work Edited by: Huanfa Yi, Jilin University, China Reviewed by: Zheng Liu, Virginia Commonwealth University, United States; Tao Su, Guangzhou University of Chinese Medicine, China This article was submitted to Cancer Immunity and Immunotherapy, a section of the journal Frontiers in Immunology |
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| References | Kane (B53) 2010; 21 Jia (B10) 2018; 10 Pan (B40) 2020; 26 Huang (B27) 2009; 4 Hsiao (B39) 2019; 10 Laplane (B35) 2019; 145 Oliver (B17) 2015; 61 Hutter (B25) 2018; 173 Gandara (B46) 2018; 24 Li (B12) 2019; 16 Belli (B13) 2018; 65 Olsen (B20) 2014; 63 Llovet (B3) 2019; 70 Patil (B54) 2018; 73 Yoshihara (B23) 2013; 4 Hanzelmann (B32) 2013; 14 Li (B29) 2019; 10 Friedman (B30) 2010; 33 Wang (B26) 2016; 1418 Rizvi (B43) 2015; 348 Wang (B52) 2004; 22 Deng (B36) 2020; 12 Hamann (B51) 2016; 234 Zhang (B50) 2020; 26 Farazi (B2) 2006; 6 Tian (B42) 2020; 26 Wang (B56) 2018; 15 Deng (B38) 2019; 2019 Hato (B7) 2014; 60 DeSantis (B4) 2019; 69 Samstein (B44) 2019; 51 Bolzetta (B31) 2018; 108 Snyder (B45) 2015; 372 Hohenberger (B19) 1998; 146 Shrestha (B47) 2018; 8 Quail (B11) 2013; 19 Chan (B33) 2019; 30 Fisch (B59) 2019; 38 Xu (B9) 2019; 11 Abate (B5) 2019; 5 Zhou (B16) 2020; 20 Chen (B58) 2018; 289 Eggert (B14) 2017; 173 Lao (B28) 2017; 7 Pineiro Fernandez (B48) 2019; 20 Fu (B6) 2019; 38 Yin (B18) 2017; 15 Alonso (B24) 2017; 117 Fancello (B34) 2019; 7 Kiprenskii (B37) 1992; 3 Wu (B49) 2019; 12 Zanjani (B41) 1990; 6 He (B57) 2020; 99 Chen (B55) 2020; 12 Fu (B1) 2018; 8 He (B21) 2017; 18 Zhang (B8) 2010; 17 Yang (B15) 2017; 126 Wu (B22) 2018; 8 |
| References_xml | – volume: 60 start-page: 1776 year: 2014 ident: B7 article-title: Immune checkpoint blockade in hepatocellular carcinoma: current progress and future directions publication-title: Hepatology. doi: 10.1002/hep.27246 – volume: 22 start-page: 1564 year: 2004 ident: B52 article-title: Gene expression profiles and molecular markers to predict recurrence of Dukes' B colon cancer publication-title: J Clin Oncol. doi: 10.1200/JCO.2004.08.186 – volume: 234 start-page: 329 year: 2016 ident: B51 article-title: Adhesion GPCRs as modulators of immune cell function publication-title: Handb Exp Pharmacol. doi: 10.1007/978-3-319-41523-9_15 – volume: 17 start-page: 34 year: 2010 ident: B8 article-title: Regulatory T cells in chronic hepatitis B patients affect the immunopathogenesis of hepatocellular carcinoma by suppressing the anti-tumour immune responses publication-title: J Viral Hepat. doi: 10.1111/j.1365-2893.2010.01269.x – volume: 20 start-page: 264 year: 2020 ident: B16 article-title: Exploring TCGA database for identification of potential prognostic genes in stomach adenocarcinoma publication-title: Cancer Cell Int. doi: 10.1186/s12935-020-01351-3 – volume: 8 start-page: 9395 year: 2018 ident: B1 article-title: Author correction: a novel microRNA signature predicts survival in liver hepatocellular carcinoma after hepatectomy publication-title: Sci Rep. doi: 10.1038/s41598-018-27641-5 – volume: 12 start-page: 3431 year: 2020 ident: B36 article-title: Development and validation of a prognostic classifier based on HIF-1 signaling for hepatocellular carcinoma publication-title: Aging. doi: 10.18632/aging.102820 – volume: 289 start-page: 42 year: 2018 ident: B58 article-title: Gene expression network regulated by DNA methylation and microRNA during microcystin-leucine arginine induced malignant transformation in human hepatocyte L02 cells publication-title: Toxicol Lett. doi: 10.1016/j.toxlet.2018.03.003 – volume: 4 start-page: 2612 year: 2013 ident: B23 article-title: Inferring tumour purity and stromal and immune cell admixture from expression data publication-title: Nat Commun. doi: 10.1038/ncomms3612 – volume: 69 start-page: 438 year: 2019 ident: B4 article-title: Breast cancer statistics, 2019 publication-title: CA Cancer J Clin. doi: 10.3322/caac.21583 – volume: 26 start-page: e922159 year: 2020 ident: B42 article-title: Bioinformatics analysis of prognostic tumor microenvironment-related genes in the tumor microenvironment of hepatocellular carcinoma publication-title: Med Sci Monit. doi: 10.12659/MSM.922159 – volume: 8 start-page: 269 year: 2018 ident: B47 article-title: Monitoring immune checkpoint regulators as predictive biomarkers in hepatocellular carcinoma publication-title: Front Oncol. doi: 10.3389/fonc.2018.00269 – volume: 4 start-page: 44 year: 2009 ident: B27 article-title: Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources publication-title: Nat Protoc. doi: 10.1038/nprot.2008.211 – volume: 7 start-page: 183 year: 2019 ident: B34 article-title: Tumor mutational burden quantification from targeted gene panels: major advancements and challenges publication-title: J Immunother Cancer. doi: 10.1186/s40425-019-0647-4 – volume: 2019 start-page: 2408348 year: 2019 ident: B38 article-title: Mining TCGA database for tumor microenvironment-related genes of prognostic value in hepatocellular carcinoma publication-title: Biomed Res Int. doi: 10.1155/2019/2408348 – volume: 73 start-page: 124 year: 2018 ident: B54 article-title: Expression of PD-L1, indoleamine 2,3-dioxygenase and the immune microenvironment in gastric adenocarcinoma publication-title: Histopathology. doi: 10.1111/his.13504 – volume: 63 start-page: 1235 year: 2014 ident: B20 article-title: Bioinformatics for cancer immunotherapy target discovery publication-title: Cancer Immunol Immunother. doi: 10.1007/s00262-014-1627-7 – volume: 6 start-page: 229 year: 1990 ident: B41 article-title: Cell loss in the inferior olive of the staggerer mutant mouse is an indirect effect of the gene publication-title: J Neurogenet. doi: 10.3109/01677069009107113 – volume: 26 start-page: 789 year: 2020 ident: B40 article-title: Promising key genes associated with tumor microenvironments and prognosis of hepatocellular carcinoma publication-title: World J Gastroenterol. doi: 10.3748/wjg.v26.i8.789 – volume: 6 start-page: 674 year: 2006 ident: B2 article-title: Hepatocellular carcinoma pathogenesis: from genes to environment publication-title: Nat Rev Cancer. doi: 10.1038/nrc1934 – volume: 26 start-page: 134 year: 2020 ident: B50 article-title: Construction of a risk score prognosis model based on hepatocellular carcinoma microenvironment publication-title: World J Gastroenterol. doi: 10.3748/wjg.v26.i2.134 – volume: 99 start-page: e21287 year: 2020 ident: B57 article-title: Relationship between a 7-mRNA signature of the pancreatic adenocarcinoma microenvironment and patient prognosis (a STROBE-compliant article) publication-title: Medicine. doi: 10.1097/MD.0000000000021287 – volume: 51 start-page: 202 year: 2019 ident: B44 article-title: Tumor mutational load predicts survival after immunotherapy across multiple cancer types publication-title: Nat Genet. doi: 10.1038/s41588-018-0312-8 – volume: 70 start-page: 1262 year: 2019 ident: B3 article-title: Randomized trials and endpoints in advanced HCC: role of PFS as a surrogate of survival publication-title: J Hepatol. doi: 10.1016/j.jhep.2019.01.028 – volume: 173 start-page: 47 year: 2017 ident: B14 article-title: Tumor regulation of the tissue environment in the liver publication-title: Pharmacol Ther. doi: 10.1016/j.pharmthera.2017.02.005 – volume: 19 start-page: 1423 year: 2013 ident: B11 article-title: Microenvironmental regulation of tumor progression and metastasis publication-title: Nat Med. doi: 10.1038/nm.3394 – volume: 15 start-page: 7914 year: 2018 ident: B56 article-title: Distinct prognostic value of mRNA expression of guanylate-binding protein genes in skin cutaneous melanoma publication-title: Oncol Lett. doi: 10.3892/ol.2018.8306 – volume: 1418 start-page: 111 year: 2016 ident: B26 article-title: A practical guide to The Cancer Genome Atlas (TCGA) publication-title: Methods Mol Biol. doi: 10.1007/978-1-4939-3578-9_6 – volume: 11 start-page: 6999 year: 2019 ident: B9 article-title: Prognostic value and immune infiltration of novel signatures in clear cell renal cell carcinoma microenvironment publication-title: Aging. doi: 10.18632/aging.102233 – volume: 8 start-page: 634 year: 2018 ident: B22 article-title: An integrated score and nomogram combining clinical and immunohistochemistry factors to predict high ISUP grade clear cell renal cell carcinoma publication-title: Front Oncol. doi: 10.3389/fonc.2018.00634 – volume: 18 start-page: 412 year: 2017 ident: B21 article-title: Big data analytics for genomic medicine publication-title: Int J Mol Sci. doi: 10.3390/ijms18020412 – volume: 10 start-page: 630 year: 2019 ident: B39 article-title: Tumor-infiltrating leukocyte composition and prognostic power in hepatitis B- and hepatitis C-related hepatocellular carcinomas publication-title: Genes. doi: 10.3390/genes10080630 – volume: 12 start-page: 53 year: 2019 ident: B49 article-title: Exosome-mediated communication in the tumor microenvironment contributes to hepatocellular carcinoma development and progression publication-title: J Hematol Oncol. doi: 10.1186/s13045-019-0739-0 – volume: 126 start-page: 97 year: 2017 ident: B15 article-title: Nanoparticles for modulating tumor microenvironment to improve drug delivery and tumor therapy publication-title: Pharmacol Res. doi: 10.1016/j.phrs.2017.05.004 – volume: 348 start-page: 124 year: 2015 ident: B43 article-title: Cancer immunology. Mutational landscape determines sensitivity to PD-1 blockade in non-small cell lung cancer publication-title: Science. doi: 10.1126/science.aaa1348 – volume: 10 start-page: 592 year: 2018 ident: B10 article-title: Mining TCGA database for genes of prognostic value in glioblastoma microenvironment publication-title: Aging. doi: 10.18632/aging.101415 – volume: 21 start-page: 1018 year: 2010 ident: B53 article-title: EMR-3: a potential mediator of invasive phenotypic variation in glioblastoma and novel therapeutic target publication-title: Neuroreport. doi: 10.1097/WNR.0b013e32833f19f2 – volume: 145 start-page: 2611 year: 2019 ident: B35 article-title: Beyond the tumour microenvironment publication-title: Int J Cancer. doi: 10.1002/ijc.32343 – volume: 173 start-page: 283 year: 2018 ident: B25 article-title: The cancer genome atlas: creating lasting value beyond its data publication-title: Cell. doi: 10.1016/j.cell.2018.03.042 – volume: 146 start-page: 127 year: 1998 ident: B19 article-title: Locoregional recurrence of rectal cancer: biological and technical aspects of surgical failure publication-title: Recent Results Cancer Res doi: 10.1007/978-3-642-71967-7_12 – volume: 30 start-page: 44 year: 2019 ident: B33 article-title: Development of tumor mutation burden as an immunotherapy biomarker: utility for the oncology clinic publication-title: Ann Oncol. doi: 10.1093/annonc/mdy495 – volume: 20 start-page: 4131 year: 2019 ident: B48 article-title: Hepatic tumor microenvironments and effects on NK cell phenotype and function publication-title: Int J Mol Sci. doi: 10.3390/ijms20174131 – volume: 12 start-page: 12703 year: 2020 ident: B55 article-title: Epigenomic and genomic analysis of transcriptome modulation in skin cutaneous melanoma publication-title: Aging. doi: 10.18632/aging.103115 – volume: 14 start-page: 7 year: 2013 ident: B32 article-title: GSVA: gene set variation analysis for microarray and RNA-seq data publication-title: BMC Bioinformatics. doi: 10.1186/1471-2105-14-7 – volume: 108 start-page: 209 year: 2018 ident: B31 article-title: The relationship between different settings of medical service and incident frailty publication-title: Exp Gerontol. doi: 10.1016/j.exger.2018.04.023 – volume: 117 start-page: 421 year: 2017 ident: B24 article-title: Comprehensive analysis of copy number aberrations in microsatellite stable colon cancer in view of stromal component publication-title: Br J Cancer. doi: 10.1038/bjc.2017.208 – volume: 16 start-page: 425 year: 2019 ident: B12 article-title: Navigating metabolic pathways to enhance antitumour immunity and immunotherapy publication-title: Nat Rev Clin Oncol. doi: 10.1038/s41571-019-0203-7 – volume: 372 start-page: 783 year: 2015 ident: B45 article-title: Genetic basis for clinical response to CTLA-4 blockade publication-title: N Engl J Med. doi: 10.1056/NEJMc1415938 – volume: 38 start-page: 396 year: 2019 ident: B6 article-title: From bench to bed: the tumor immune microenvironment and current immunotherapeutic strategies for hepatocellular carcinoma publication-title: J Exp Clin Cancer Res. doi: 10.1186/s13046-019-1396-4 – volume: 38 start-page: e100926 year: 2019 ident: B59 article-title: Human GBP1 is a microbe-specific gatekeeper of macrophage apoptosis and pyroptosis publication-title: EMBO J. doi: 10.15252/embj.2018100926 – volume: 33 start-page: 1 year: 2010 ident: B30 article-title: Regularization paths for generalized linear models via coordinate descent publication-title: J Stat Softw. doi: 10.18637/jss.v033.i01 – volume: 3 start-page: 123 year: 1992 ident: B37 article-title: [The immunogenicity of different organs and the characteristics of immunosuppressive therapy during their allotransplantation] publication-title: Khirurgiia – volume: 61 start-page: 124 year: 2015 ident: B17 article-title: Bioinformatics for clinical next generation sequencing publication-title: Clin Chem. doi: 10.1373/clinchem.2014.224360 – volume: 24 start-page: 1441 year: 2018 ident: B46 article-title: Blood-based tumor mutational burden as a predictor of clinical benefit in non-small-cell lung cancer patients treated with atezolizumab publication-title: Nat Med. doi: 10.1038/s41591-018-0134-3 – volume: 7 start-page: 10353 year: 2017 ident: B28 article-title: A deep learning-based radiomics model for prediction of survival in glioblastoma multiforme publication-title: Sci Rep. doi: 10.1038/s41598-017-10649-8 – volume: 65 start-page: 22 year: 2018 ident: B13 article-title: Targeting the microenvironment in solid tumors publication-title: Cancer Treat Rev. doi: 10.1016/j.ctrv.2018.02.004 – volume: 10 start-page: 1119 year: 2019 ident: B29 article-title: Tumor characterization in breast cancer identifies immune-relevant gene signatures associated with prognosis publication-title: Front Genet. doi: 10.3389/fgene.2019.01119 – volume: 15 start-page: 403 year: 2017 ident: B18 article-title: Computing platforms for big biological data analytics: perspectives and challenges publication-title: Comput Struct Biotechnol J. doi: 10.1016/j.csbj.2017.07.004 – volume: 5 start-page: 1749 year: 2019 ident: B5 article-title: Global, regional, and national cancer incidence, mortality, years of life lost, years lived with disability, and disability-adjusted life-years for 29 cancer groups, 1990 to 2017: a systematic analysis for the Global Burden of Disease Study publication-title: JAMA Oncol. doi: 10.1001/jamaoncol.2019.2996 |
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Hepatocellular carcinoma (HCC) is one of the most common malignant tumors in the world. The efficacy of immunotherapy usually depends on the... Hepatocellular carcinoma (HCC) is one of the most common malignant tumors in the world. The efficacy of immunotherapy usually depends on the interaction of... Background: Hepatocellular carcinoma (HCC) is one of the most common malignant tumors in the world. The efficacy of immunotherapy usually depends on the... |
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| SubjectTerms | ESTIMATE algorithm Hepatocellular carcinoma Immunology Prognosis TCGA tumor microenvironment |
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| Title | Identification of Prognostic Genes in the Tumor Microenvironment of Hepatocellular Carcinoma |
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