scholarly journals Key Candidate Prognostic Biomarkers Correlated with Immune Infiltration in Hepatocellular Carcinoma

2021 ◽  
Vol Volume 8 ◽  
pp. 1607-1622
Author(s):  
Zenghua Deng ◽  
Kanghua Huang ◽  
Dongfang Liu ◽  
Nan Luo ◽  
Tingting Liu ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Prognostic Biomarkers ◽  
Immune Infiltration

scholarly journals Identification of PDCD1 and PDCD1LG2 as Prognostic Biomarkers and Associated with Immune Infiltration in Hepatocellular Carcinoma

2022 ◽  
Vol Volume 15 ◽  
pp. 437-449
Author(s):  
Wang Li ◽  
Mei Mei ◽  
Tian Liu ◽  
ShuWen Zhang ◽  
ZeYu Wang ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Prognostic Biomarkers ◽  
Immune Infiltration

scholarly journals Identification of Prognostic Biomarkers and Correlation With Immune Infiltrates in Hepatocellular Carcinoma Based on a Competing Endogenous RNA Network

2021 ◽  
Vol 12 ◽  
Author(s):  
Zhangya Pu ◽  
Yuanyuan Zhu ◽  
Xiaofang Wang ◽  
Yun Zhong ◽  
Fang Peng ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
T Cells ◽  
Survival Analysis ◽  
Immune Cell ◽  
Cox Regression ◽  
Quantitative Polymerase Chain Reaction ◽  
Prognostic Biomarkers ◽  
Hub Genes ◽  
Immune Infiltration ◽  
Cerna Network

BackgroundHepatocellular carcinoma (HCC) is one of the most common malignant tumors worldwide. Recently, competing endogenous RNAs (ceRNA) have revealed a significant role in the progression of HCC. Herein, we aimed to construct a ceRNA network to identify potential biomarkers and illustrate its correlation with immune infiltration in HCC.MethodsRNA sequencing data and clinical traits of HCC patients were downloaded from TCGA. The limma R package was used to identify differentially expressed (DE) RNAs. The predicted prognostic model was established using univariate and multivariate Cox regression. A K-M curve, TISIDB and GEPIA website were utilized for survival analysis. Functional annotation was determined using Enrichr and Reactome. Protein-to-protein network analysis was implemented using SRTNG and Cytoscape. Hub gene expression was validated by quantitative polymerase chain reaction, Oncomine and the Hunan Protein Atlas database. Immune infiltration was analyzed by TIMMER, and Drugbank was exploited to identify bioactive compounds.ResultsThe predicted model that was established revealed significant efficacy with 3- and 5-years of the area under ROC at 0.804 and 0.744, respectively. Eleven DEmiRNAs were screened out by a K-M survival analysis. Then, we constructed a ceRNA network, including 56 DElncRNAs, 6 DEmiRNAs, and 28 DEmRNAs. The 28 DEmRNAs were enriched in cancer-related pathways, for example, the TNF signaling pathway. Moreover, six hub genes, CEP55, DEPDC1, KIF23, CLSPN, MYBL2, and RACGAP1, were all overexpressed in HCC tissues and independently correlated with survival rate. Furthermore, expression of hub genes was related to immune cell infiltration in HCC, including B cells, CD8+ T cells, CD4+ T cells, monocytes, macrophages, neutrophils, and dendritic cells.ConclusionThe findings from this study demonstrate that CEP55, DEPDC1, KIF23, CLSPN, MYBL2, and RACGAP1 are closely associated with prognosis and immune infiltration, representing potential therapeutic targets or prognostic biomarkers in HCC.

scholarly journals CDK1, CCNB1, and CCNB2 are Prognostic Biomarkers and Correlated with Immune Infiltration in Hepatocellular Carcinoma

2020 ◽  
Vol 26 ◽  
Author(s):  
Yiping Zou ◽  
Shiye Ruan ◽  
Liang Jin ◽  
Zhihong Chen ◽  
Hongwei Han ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Prognostic Biomarkers ◽  
Immune Infiltration

scholarly journals Arp2/3 Complex Subunits as Prognostic Biomarkers and Their Correlations With Immune Infiltration in Hepatocellular Carcinoma

2021 ◽  
Author(s):  
Shenglan Huang ◽  
Dan Li ◽  
LingLing Zhuang ◽  
Liying Sun ◽  
Jianbing WU
Keyword(s):  
Hepatocellular Carcinoma ◽  
Expression Patterns ◽  
Family Members ◽  
Enrichment Analysis ◽  
Normal Liver ◽  
Gene Set Enrichment Analysis ◽  
Prognostic Biomarkers ◽  
Migration And Invasion ◽  
Multiple Cancer ◽  
Immune Infiltration

Abstract Introduction: Actin‐related protein 2/3 complex (Arp2/3) is a major actin nucleator containing seven subunits in humans, which has been widely reported that Arp2/3 plays an important role in promoting migration and invasion of various kinds of cancers. Nevertheless, the expression patterns and prognostic values of Arp2/3 subunits and the correlation between ARP2/3 subunits with immune infiltration in hepatocellular carcinoma remains unclear.Methods: TCGA-FPKM dataset, Oncomine, CCLE and UCSC Xena database was used to obtained mRNA expression and clinical information of Arp2/3 subunits in HCC. The Arp2/3 subunits differential expression in HCC tissues and cell lines was analyzed by utilizing the Perl 5.30.0 and R 4.0.4 software. The protein expression data of Arp2/3 subunits was obtained from The Human Protein Atlas (HPA). The prognostic value of each individual Arp2/3 subunits was identified by R 4.0.4 software. The association between the mRNA expressions of Arp2/3 members in HCC tissues with their clinicopathologic parameters was analyzed by UALCAN. The relevance between tumor immunocyte infiltration and the Arp2/3 complex members were determined by the TIMER 2.0 platform and GEPIA database. A gene set enrichment analysis (GSEA) was performed to explore the potential mechanism of Arp2/3 complex members in the carcinogenesis of HCC.Results：The results revealed that expression of Arp2/3 family members(ACTR2,ACTR3,ARPC1A, APRC1B,ARPC2,ARPC3,ARPC4, ARPC5, ARPC5L) were up-regulated in hepatocellular carcinoma (HCC). Moreover, higher protein expressions of of ACTR3, ARPC1A, ARPC1B, ARPC2 were found in HCC tissues compared with normal liver tissues. The higher expression of of Arp2/3 family members were significantly correlated with poor survival and cancer stages in HCC patients. Multivariate analysis also demonstrated that ACTR3, ARPC2 and ARPC5 were independent prognostic biomarkers of survival in HCC patients. Meanwhile, ACTR3, ARPC2 and ARPC5 in HCC has positive significant correlations with the infiltration of immune cells. The GSEA results indicated that Arp2/3 members significantly involve in multiple cancer-related pathways by which promoted development of HCC. Conclusions：Various analysis indicated that certain Arp2/3 complex subunits were noticeably upregulated and predicted worse survival in HCC, which may be applied as promising molecular targets for diagnosis and therapy of HCC in the future.

scholarly journals Identification of Prognostic Biomarkers and Correlation with Immune Infiltrates in Hepatocellular Carcinoma Based on a Competing Endogenous RNA Network

2020 ◽  
Author(s):  
Zhangya Pu ◽  
Yuanyuan Zhu ◽  
Xiaofang Wang ◽  
Yun Zhong ◽  
Fang Peng ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
T Cells ◽  
Survival Analysis ◽  
Immune Cell ◽  
Cox Regression ◽  
Malignant Tumors ◽  
Prognostic Biomarkers ◽  
Hub Genes ◽  
Immune Infiltration ◽  
Cerna Network

Abstract Background: Hepatocellular carcinoma (HCC) is one of the most common malignant tumors worldwide. Recently, competing endogenous RNAs (ceRNA) have revealed a significant role in the progression of HCC. Herein, we aimed to construct a ceRNA network to identify potential biomarkers and illustrate its correlation with immune infiltration in HCC. Methods: RNA sequencing data and clinical traits of HCC patients were downloaded from TCGA. The limma R package was used to identify differentially expressed (DE) RNAs. The predicted prognostic model was established using univariate and multivariate Cox regression. A K-M curve and GEPIA website were utilized for survival analysis. Functional annotation was determined using Enrichr and Reactome. Protein-to-protein network analysis was implemented using SRTNG and Cytoscape. Hub gene expression was validated by Oncomine and the Hunan Protein Atlas database. Immune infiltration was analyzed by TIMMER, and Drugbank was exploited to identify bioactive compounds. Results: The predicted model that was established revealed significant efficacy with 3- and 5-years of the area under ROC at 0.804 and 0.744, respectively. Eleven DEmiRNAs were screened out by a K-M survival analysis. Then, we constructed a ceRNA network, including 56 DElncRNAs, 6 DEmiRNAs, and 28 DEmRNAs. The 28 DEmRNAs were enriched in cancer-related pathways, for example, the TNF signaling pathway. Moreover, six hub genes, CEP55, DEPDC1, KIF23, CLSPN, MYBL2, and RACGAP1, were all overexpressed in HCC tissues and independently correlated with survival rate. Furthermore, expression of hub genes was related to immune cell infiltration in HCC, including B cells, CD8 + T cells, CD4 + T cells, monocytes, macrophages, neutrophils, and dendritic cells. Conclusions: The findings from this study demonstrate that CEP55, DEPDC1, KIF23, CLSPN, MYBL2, and RACGAP1 are closely associated with prognosis and immune infiltration, representing potential therapeutic targets or prognostic biomarkers in HCC.

scholarly journals Transcript levels of spindle and kinetochore-associated complex 1/3 as prognostic biomarkers correlated with immune infiltrates in hepatocellular carcinoma

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
De-Chen Yu ◽  
Xiang-Yi Chen ◽  
Xin Li ◽  
Hai-Yu Zhou ◽  
De-Quan Yu ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Protein Complex ◽  
Immune Cell ◽  
Prognostic Significance ◽  
Tumor Development ◽  
Disease Free Survival ◽  
Tumor Grade ◽  
Tumor Stage ◽  
Prognostic Biomarkers ◽  
High Expression

AbstractThe spindle and kinetochore-associated protein complex (Ska) is an essential component in chromosome segregation. It comprises three proteins (Ska1, Ska2, and Ska3) with theorized roles in chromosomal instability and tumor development, and its overexpression has been widely reported in a variety of tumors. However, the prognostic significance and immune infiltration of Ska proteins in hepatocellular carcinoma (HCC) are not completely understood. The bioinformatics tools Oncomine, UALCAN, gene expression profiling interactive analysis 2 (GEPIA2), cBioPortal, GeneMANIA, Metascape, and TIMER were used to analyze differential expression, prognostic value, genetic alteration, and immune cell infiltration of the Ska protein complex in HCC patients. We found that the mRNA expression of the Ska complex was markedly upregulated in HCC. High expression of the Ska complex is closely correlated with tumor stage, patient race, tumor grade, and TP53 mutation status. In addition, high expression of the Ska complex was significantly correlated with poor disease-free survival, while the high expression levels of Ska1 and Ska3 were associated with shorter overall survival. The biological functions of the Ska complex in HCC primarily involve the amplification of signals from kinetochores, the mitotic spindle, and (via a MAD2 invasive signal) unattached kinetochores. Furthermore, the expression of the complex was positively correlated with tumor-infiltrating cells. These results may provide new insights into the development of immunotherapeutic targets and prognostic biomarkers for HCC.

dbPHCC: a database of prognostic biomarkers for hepatocellular carcinoma that provides online prognostic modeling

2016 ◽  
Vol 1860 (11) ◽  
pp. 2688-2695 ◽  
Author(s):  
Jian Ouyang ◽  
Ying Sun ◽  
Wei Li ◽  
Wen Zhang ◽  
Dandan Wang ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Prognostic Biomarkers ◽  
Prognostic Modeling

Four long noncoding RNAs as potential prognostic biomarkers for hepatocellular carcinoma

2018 ◽  
Vol 234 (6) ◽  
pp. 8709-8716 ◽  
Author(s):  
Jianchu Wang ◽  
Jian Pu ◽  
Tianwei Yao ◽  
Xiaojie Lu ◽  
Yibin Deng
Keyword(s):  
Hepatocellular Carcinoma ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Prognostic Biomarkers
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