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Co-expression analysis of differentially expressed genes in hepatitis C virus-induced hepatocellular carcinoma.

Song Q, Zhao C, Ou S, Meng Z, Kang P, Fan L, Qi F, Ma Y - Mol Med Rep (2014)

Bottom Line: There were 22 time series genes which were clustered into 3 expression patterns, and the demarcation point of the 2 expression patterns that 401 overlapping DEGs at 24 and 48 h clustered into was 24 h post-infection. tRNA synthesis-related biological processes emerged at 24 and 48 h.Replication and assembly of HCV in HCV-infected Huh7 cells occurred mainly at 24 h post-infection.In view of this, the screened time series genes have the potential to become candidate target molecules for monitoring, diagnosing and treating HCV-induced HCC.

View Article: PubMed Central - PubMed

Affiliation: Department of Interventional Radiology, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China.

ABSTRACT
The aim of the current study was to investigate the molecular mechanisms underlying hepatitis C virus (HCV)-induced hepatocellular carcinoma (HCC) using the expression profiles of HCV-infected Huh7 cells at different time points. The differentially expressed genes (DEGs) were identified with the Samr package in R software once the data were normalized. Functional and pathway enrichment analysis of the identified DEGs was also performed. Subsequently, MCODE in Cytoscape software was applied to conduct module analysis of the constructed co-expression networks. A total of 1,100 DEGs were identified between the HCV-infected and control samples at 12, 18, 24 and 48 h post-infection. DEGs at 24 and 48 h were involved in the same signaling pathways and biological processes, including sterol biosynthetic processes and tRNA amino-acylation. There were 22 time series genes which were clustered into 3 expression patterns, and the demarcation point of the 2 expression patterns that 401 overlapping DEGs at 24 and 48 h clustered into was 24 h post-infection. tRNA synthesis-related biological processes emerged at 24 and 48 h. Replication and assembly of HCV in HCV-infected Huh7 cells occurred mainly at 24 h post-infection. In view of this, the screened time series genes have the potential to become candidate target molecules for monitoring, diagnosing and treating HCV-induced HCC.

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Related in: MedlinePlus

Overlapping of differentially expressed genes (DEGs) at different time points. The blue, yellow, green and red oval diagrams represent the DEGs at 12, 18, 24 and 48 h post-infection, respectively. The shadows of corresponding colors represent overlapping genes of different time points. A total of 22 DEGs were simultaneously presenting at 4 time points; 401 DEGs were simultaneously presenting at 24 and 48 h post-infection.
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f1-mmr-11-01-0021: Overlapping of differentially expressed genes (DEGs) at different time points. The blue, yellow, green and red oval diagrams represent the DEGs at 12, 18, 24 and 48 h post-infection, respectively. The shadows of corresponding colors represent overlapping genes of different time points. A total of 22 DEGs were simultaneously presenting at 4 time points; 401 DEGs were simultaneously presenting at 24 and 48 h post-infection.

Mentions: In order to analyze the difference between DEGs at each time point, a Venn diagram was utilized to identify overlapping genes (Fig. 1). A total of 22 DEGs, denoted as time series genes, occurred in the HCV-infected samples at 12, 18, 24 and 48 h post-infection. To further study expression level changes of time series genes subsequent to HCV infection, the fold changes of these genes were clustered into a hierarchical diagram (Fig. 2). The 22 time series genes were clustered into three expression patterns. The expression levels of HSPA2, NCF2, CNN1 and TGFB1/1 first decreased and then increased. The expression levels of HCAR3, CYP1A1, SLC7A11, CTH, DDIT4, MTHFD2, ARRDC4, INHBE, STC2, TXNIP, PCK2, ASNS, PSAT1, CHAC1 and SNHG8 first decreased, then increased, and then stabilized. The expression levels of RASSF9, GPAM and MYC increased and then decreased. Furthermore, 401 DEGs were concurrent in Huh7 cells at 24 and 48 h post HCV-infection. These 401 DEGs were clustered into two expression patterns: i) Decreasing then increasing; and ii) increasing then decreasing. The demarcation point of the two expression patterns is at 24 h post-infection (Fig. 3). The functions of these DEGs at 24 and 48 h post HCV-infection are mainly related to cholesterol processing and amino-acyl tRNA synthetase signaling pathways (Table III).


Co-expression analysis of differentially expressed genes in hepatitis C virus-induced hepatocellular carcinoma.

Song Q, Zhao C, Ou S, Meng Z, Kang P, Fan L, Qi F, Ma Y - Mol Med Rep (2014)

Overlapping of differentially expressed genes (DEGs) at different time points. The blue, yellow, green and red oval diagrams represent the DEGs at 12, 18, 24 and 48 h post-infection, respectively. The shadows of corresponding colors represent overlapping genes of different time points. A total of 22 DEGs were simultaneously presenting at 4 time points; 401 DEGs were simultaneously presenting at 24 and 48 h post-infection.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4237098&req=5

f1-mmr-11-01-0021: Overlapping of differentially expressed genes (DEGs) at different time points. The blue, yellow, green and red oval diagrams represent the DEGs at 12, 18, 24 and 48 h post-infection, respectively. The shadows of corresponding colors represent overlapping genes of different time points. A total of 22 DEGs were simultaneously presenting at 4 time points; 401 DEGs were simultaneously presenting at 24 and 48 h post-infection.
Mentions: In order to analyze the difference between DEGs at each time point, a Venn diagram was utilized to identify overlapping genes (Fig. 1). A total of 22 DEGs, denoted as time series genes, occurred in the HCV-infected samples at 12, 18, 24 and 48 h post-infection. To further study expression level changes of time series genes subsequent to HCV infection, the fold changes of these genes were clustered into a hierarchical diagram (Fig. 2). The 22 time series genes were clustered into three expression patterns. The expression levels of HSPA2, NCF2, CNN1 and TGFB1/1 first decreased and then increased. The expression levels of HCAR3, CYP1A1, SLC7A11, CTH, DDIT4, MTHFD2, ARRDC4, INHBE, STC2, TXNIP, PCK2, ASNS, PSAT1, CHAC1 and SNHG8 first decreased, then increased, and then stabilized. The expression levels of RASSF9, GPAM and MYC increased and then decreased. Furthermore, 401 DEGs were concurrent in Huh7 cells at 24 and 48 h post HCV-infection. These 401 DEGs were clustered into two expression patterns: i) Decreasing then increasing; and ii) increasing then decreasing. The demarcation point of the two expression patterns is at 24 h post-infection (Fig. 3). The functions of these DEGs at 24 and 48 h post HCV-infection are mainly related to cholesterol processing and amino-acyl tRNA synthetase signaling pathways (Table III).

Bottom Line: There were 22 time series genes which were clustered into 3 expression patterns, and the demarcation point of the 2 expression patterns that 401 overlapping DEGs at 24 and 48 h clustered into was 24 h post-infection. tRNA synthesis-related biological processes emerged at 24 and 48 h.Replication and assembly of HCV in HCV-infected Huh7 cells occurred mainly at 24 h post-infection.In view of this, the screened time series genes have the potential to become candidate target molecules for monitoring, diagnosing and treating HCV-induced HCC.

View Article: PubMed Central - PubMed

Affiliation: Department of Interventional Radiology, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China.

ABSTRACT
The aim of the current study was to investigate the molecular mechanisms underlying hepatitis C virus (HCV)-induced hepatocellular carcinoma (HCC) using the expression profiles of HCV-infected Huh7 cells at different time points. The differentially expressed genes (DEGs) were identified with the Samr package in R software once the data were normalized. Functional and pathway enrichment analysis of the identified DEGs was also performed. Subsequently, MCODE in Cytoscape software was applied to conduct module analysis of the constructed co-expression networks. A total of 1,100 DEGs were identified between the HCV-infected and control samples at 12, 18, 24 and 48 h post-infection. DEGs at 24 and 48 h were involved in the same signaling pathways and biological processes, including sterol biosynthetic processes and tRNA amino-acylation. There were 22 time series genes which were clustered into 3 expression patterns, and the demarcation point of the 2 expression patterns that 401 overlapping DEGs at 24 and 48 h clustered into was 24 h post-infection. tRNA synthesis-related biological processes emerged at 24 and 48 h. Replication and assembly of HCV in HCV-infected Huh7 cells occurred mainly at 24 h post-infection. In view of this, the screened time series genes have the potential to become candidate target molecules for monitoring, diagnosing and treating HCV-induced HCC.

Show MeSH
Related in: MedlinePlus