scholarly journals Discovery of Differentially Expressed Genes Related to Histological Subtype of Hepatocellular Carcinoma

2003 ◽  
Vol 19 (3) ◽  
pp. 1011-1015 ◽  
Author(s):  
D. Lee ◽  
S.W. Choi ◽  
M. Kim ◽  
J.H. Park ◽  
M. Kim ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Differentially Expressed Genes ◽  
Differentially Expressed ◽  
Histological Subtype

scholarly journals Prognostic Value and Regulatory Network of Immune-Related Genes in Hepatocellular Carcinoma

2020 ◽  
Author(s):  
Xiang Zhou ◽  
Keying Zhang ◽  
Fa Yang ◽  
Chao Xu ◽  
Jianhua Jiao ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Regression Analysis ◽  
Differentially Expressed Genes ◽  
Molecular Mechanisms ◽  
Risk Model ◽  
Cox Regression ◽  
Wilcoxon Test ◽  
Differentially Expressed ◽  
Cox Regression Analysis ◽  
Immune Related Genes

Abstract Background: Hepatocellular carcinoma (HCC) is a disease with higher morbidity, mortality, and poor prognosis in the whole world. Understanding the crosslink between HCC and the immune system is essential for people to uncover a few potential and valuable therapeutic strategies. This study aimed to reveal the correlation between HCC and immune-related genes and establish a clinical evaluation model. Methods: We had analyzed the clinical information consisted of 373 HCC and 49 normal samples from the cancer genome atlas (TCGA). The differentially expressed genes (DEGs) were selected by the Wilcoxon test and the immune-related differentially expressed genes (IRDEGs) in DEGs were identified by matching DEGs with immune-related genes downloaded from the ImmPort database. Furthermore, the univariate Cox regression analysis and multivariate Cox regression analysis were performed to construct a prognostic risk model. Then, twenty-two types of tumor immune-infiltrating cells (TIICs) were downloaded from Tumor Immune Estimation Resource (TIMER) and were used to construct the correlational graphs between the TIICs and risk score by the CIBERSORT. Subsequently, the transcription factors (TFs) were gained in the Cistrome website and the differentially expressed TFs (DETFs) were achieved. Finally, the KEGG pathway analysis and GO analysis were performed to further understand the molecular mechanisms between DETFs and PDIRGs.Results: In our study, 5839 DEGs, 326 IRDEGs, and 31 prognosis-related IRDEGs (PIRDEGs) were identified. And 8 optimal PIRDEGs were employed to construct a prognostic risk model by multivariate Cox regression analysis. The correlation between risk genes and clinical characterizations and TIICs has verified that the prognostic model was effective in predicting the prognosis of HCC patients. Finally, several important immune-related pathways and molecular functions of the eight PIRDEGs were significantly enriched and there was a distinct association between the risk IRDEGs and TFs. Conclusion: The prognostic risk model showed a more valuable predicting role for HCC patients, and produced many novel therapeutic targets and strategies for HCC.

scholarly journals Dihydroartemisinin Inhibits Proliferation and Induces Apoptosis of Human Hepatocellular Carcinoma Cell by Upregulating Tumor Necrosis Factor via JNK/NF-κB Pathways

2019 ◽  
Vol 2019 ◽  
pp. 1-9 ◽  
Author(s):  
Long Wu ◽  
Yanlei Cheng ◽  
Junjian Deng ◽  
Weiping Tao ◽  
Junjie Ye
Keyword(s):  
Hepatocellular Carcinoma ◽  
Cell Proliferation ◽  
Differentially Expressed Genes ◽  
Carcinoma Cell ◽  
Expression Profiles ◽  
Human Hepatocellular Carcinoma ◽  
Differentially Expressed ◽  
Venn Diagram ◽  
Dependent Manner ◽  
Hepatocellular Carcinoma Cell

Background. Dihydroartemisinin (DHA) is a predominant compound in Artemisia annua L., and it has been shown to inhibit tumorigenesis. Methods. In this study, the antitumor potential of DHA was investigated in the MHCC97-L hepatocellular carcinoma cell line. Cells were treated at various concentrations of DHA, and then the cell cycle, viability, and DNA synthesis were measured to evaluate cell proliferation. Furthermore, the expression of genes and proteins related to proliferation and apoptosis was measured to determine the effects of DHA. Finally, the mechanism was investigated using RNA-sequencing to identify differentially expressed genes and signaling pathways, and JNK/NF-κB pathways were evaluated with Western blotting. Results. Cells were treated with a concentration range of DHA from 1 to 100 μM, and cell proliferation was suppressed in a dose-dependent manner. In addition, the genes and proteins involved in typical cellular functions of MHCC97-L cells were significantly inhibited. DHA treatment downregulated the angiogenic gene ANGPTL2 and the cell proliferation genes CCND1, E2F1, PCNA, and BCL2. DHA treatment significantly upregulated the apoptotic genes CASP3, CASP8, CASP9, and TNF. Global gene expression profiles identified 2064 differentially expressed genes (DEGs). Among them, 744 were upregulated and 1320 were downregulated. Furthermore, MAPK, NF-kappa B, and TNF pathways were enriched based on the DEGs, and the consensus DEG was identified as TNF using a Venn diagram of those pathways. DHA promoted phosphorylation of JNK, inhibited nuclear p65, and then significantly induced TNF-α synthesis. Conclusion. DHA inhibited cell proliferation and induced apoptosis in human hepatocellular carcinoma cells by upregulating TNF expression via JNK/NF-κB pathways.

scholarly journals Integrative molecular analysis of metastatic hepatocellular carcinoma

2019 ◽  
Vol 12 (1) ◽  
Author(s):  
Dongfang Wang ◽  
Yanjing Zhu ◽  
Jing Tang ◽  
Qiuyu Lian ◽  
Guijuan Luo ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Differentially Expressed Genes ◽  
Primary Tumor ◽  
Integrative Analysis ◽  
Differentially Expressed ◽  
Focal Region ◽  
Differential Analysis ◽  
Gene Expressions ◽  
Molecular Alterations ◽  
Matched Primary Tumor

Abstract Background Hepatocellular carcinoma (HCC) is the major type of primary liver cancer. Intrahepatic metastasis, such as portal vein tumor thrombosis (PVTT), strongly indicates poor prognosis of HCC. But now, there are limited understandings of the molecular features and mechanisms of those metastatic HCCs. Methods To characterize the molecular alterations of the metastatic HCCs, we implemented an integrative analysis of the copy number variations (CNVs), DNA methylations and transcriptomes of matched adjacent normal, primary tumor and PVTT samples from 19 HCC patients. Results CNV analysis identified a frequently amplified focal region chr11q13.3 and a novel deletion peak chr19q13.41 containing three miRNAs. The integrative analysis with RNA-seq data suggests that CNVs and differential promoter methylations regulate distinct oncogenic processes. Then, we used individualized differential analysis to identify the differentially expressed genes between matched primary tumor and PVTT of each patient. Results show that 5 out of 19 studied patients acquire evidential progressive alterations of gene expressions (more than 1000 differentially expressed genes were identified in each patient). While, another subset of eight patients have nearly identical gene expressions between the corresponding matched primary tumor and PVTT. Twenty genes were found to be recurrently and progressively differentially expressed in multiple patients. These genes are mainly associated with focal adhesion, xenobiotics metabolism by cytochrome P450 and amino acid metabolism. For several differentially expressed genes in metabolic pathways, their expressions are significantly associated with overall survivals and vascular invasions of HCC patients. The following transwell assay experiments validate that they can regulate invasive phenotypes of HCC cells. Conclusions The metastatic HCCs with PVTTs have significant molecular alterations comparing with adjacent normal tissues. The recurrent alteration patterns are similar to several previously published general HCC cohorts, but usually with higher severity. By an individualized differential analysis strategy, the progressively differentially expressed genes between the primary tumor and PVTT were identified for each patient. A few patients aquire evidential progressive alterations of gene expressions. And, experiments show that several recurrently differentially expressed genes can strongly regulate HCC cell invasions.

scholarly journals Mast Cells Resting-Related Prognostic Signature in Hepatocellular Carcinoma

2021 ◽  
Vol 2021 ◽  
pp. 1-9
Author(s):  
Hao Zhang ◽  
Lin Sun ◽  
Xiao Hu
Keyword(s):  
Hepatocellular Carcinoma ◽  
Mast Cells ◽  
Liver Cancer ◽  
Differentially Expressed Genes ◽  
High Risk Group ◽  
The Cancer Genome Atlas ◽  
Differentially Expressed ◽  
Immune Checkpoints ◽  
New Ideas ◽  
Cancer Genome Atlas

The immune microenvironment of liver cancer is of great significance for the treatment of liver cancer. After evaluating the content of mast cells resting in the transcriptome data of The Cancer Genome Atlas database by CIBERSORT analysis, this study aimed to group the samples according to the content of mast cells resting in different samples to find the differentially expressed genes in the two groups. Significant prognostic differences were found between high and low mast cells resting infiltration groups. The prognostic model was constructed according to the differentially expressed genes. The model was validated using external independent datasets. The results revealed that the constructed model was reliable. It could well distinguish the prognostic differences of patients in different characteristic groups. The high-risk group was mainly concentrated in metabolic pathways. The risk score of this model was closely related to some immune cells, immune function, and immune checkpoints. Therefore, this model may provide new ideas for immunotherapy of hepatocellular carcinoma.

scholarly journals Identification of a Subtype of Hepatocellular Carcinoma with Poor Prognosis Based on Expression of Genes within the Glucose Metabolic Pathway

Cancers ◽  
2019 ◽  
Vol 11 (12) ◽  
pp. 2023 ◽  
Author(s):  
Xiaoli Zhang ◽  
Jin Li ◽  
Kalpana Ghoshal ◽  
Soledad Fernandez ◽  
Lang Li
Keyword(s):  
Hepatocellular Carcinoma ◽  
Differentially Expressed Genes ◽  
Metabolic Pathway ◽  
Poor Prognosis ◽  
Clinical Stage ◽  
Differentially Expressed ◽  
Liver Malignancy ◽  
Advanced Clinical Stage ◽  
Metabolic Genes ◽  
Expression Of Genes

Hepatocellular carcinoma (HCC) is the most prevalent primary cancer and a highly aggressive liver malignancy. Liver cancer cells reprogram their metabolism to meet their needs for rapid proliferation and tumor growth. In the present study, we investigated the alterations in the expression of the genes involved in glucose metabolic pathways as well as their association with the clinical stage and survival of HCC patients. We found that the expressions of around 30% of genes involved in the glucose metabolic pathway are consistently dysregulated with a predominant down-regulation in HCC tumors. Moreover, the differentially expressed genes are associated with an advanced clinical stage and a poor prognosis. More importantly, unsupervised clustering analysis with the differentially expressed genes that were also associated with overall survival (OS) revealed a subgroup of patients with a worse prognosis including reduced OS, disease specific survival, and recurrence-free survival. This aggressive subtype had significantly increased expression of stemness-related genes and down-regulated metabolic genes, as well as increased immune infiltrates that contribute to a poor prognosis. Collectively, this integrative study indicates that expressions of the glucose metabolic genes could be used as potential prognostic markers and/or therapeutic targets, which might be helpful in developing precise treatment for patients with HCC.

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