scholarly journals Network Pharmacology and Bioinformatics Approach Reveals the Therapeutic Mechanism of Action of Baicalein in Hepatocellular Carcinoma

2019 ◽  
Vol 2019 ◽  
pp. 1-15 ◽  
Author(s):  
Chongyang Ma ◽  
Tian Xu ◽  
Xiaoguang Sun ◽  
Shuang Zhang ◽  
Shuling Liu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Hepatocellular Carcinoma ◽  
Overall Survival ◽  
Disease Free Survival ◽  
Network Pharmacology ◽  
Therapeutic Effects ◽  
Potential Candidate ◽  
Ppi Network ◽  
Free Survival ◽  
Disease Free

Liver cancer is the fourth leading cause of cancer death worldwide, and hepatocellular carcinoma (HCC) accounts for the greatest proportion of these deaths. Baicalein, a flavonoid isolated from the root of Scutellariae radix, is considered a potential candidate to treat HCC. However, the underlying molecular mechanisms remain poorly understood. In the present study, a network pharmacological approach was combined with microarray data (GSE95504) acquired from the Gene Expression Omnibus database to reveal the therapeutic mechanisms of action of baicalein at a systemic level. We identified 38 baicalein targets and 76 differently expressed genes (DEGs) following treatment with baicalein, including 55 upregulated and 21 downregulated genes. The DEGs were significantly enriched in the biological functions of apoptosis, endoplasmic reticulum stress, and PERK-mediated unfolded protein response. Protein-protein interaction (PPI) network construction and topological screening revealed a core module of PPIs including two baicalein targets, TP53 and CDK1, and two downregulated DEGs, HSPA1A and HSPA1B. Expression and survival data for these genes in the module derived from Gene Expression Profiling Interactive Analysis (GEPIA) were subjected to Kaplan–Meier analysis of overall survival and disease-free survival. Overexpression of CDK1, BRCA1, TUBB, HSPA1A, HSPA1B, and HSPA4 was associated with significantly worse overall survival, while overexpression of CDK1, CLU7, BRCA1, and TUBB was associated with significantly worse disease-free survival. These data suggest that baicalein exerts therapeutic effects against HCC via a PPI network involving TP53, CDK1, HSPA1A, and HSPA1B.

scholarly journals Identification of special key genes for alcohol-related hepatocellular carcinoma through bioinformatic analysis

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6375 ◽  
Author(s):  
Xiuzhi Zhang ◽  
Chunyan Kang ◽  
Ningning Li ◽  
Xiaoli Liu ◽  
Jinzhong Zhang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Risk Factors ◽  
Hepatocellular Carcinoma ◽  
Overall Survival ◽  
Prognostic Factor ◽  
Disease Free Survival ◽  
Free Survival ◽  
Oncomine Database ◽  
Key Genes ◽  
Disease Free

Background Alcohol-related hepatocellular carcinoma (HCC) was reported to be diagnosed at a later stage, but the mechanism was unknown. This study aimed to identify special key genes (SKGs) during alcohol-related HCC development and progression. Methods The mRNA data of 369 HCC patients and the clinical information were downloaded from the Cancer Genome Atlas project (TCGA). The 310 patients with certain HCC-related risk factors were included for analysis and divided into seven groups according to the risk factors. Survival analyses were applied for the HCC patients of different groups. The patients with hepatitis B virus or hepatitis C virus infection only were combined into the HCC-V group for further analysis. The differentially expressed genes (DEGs) between the HCCs with alcohol consumption only (HCC-A) and HCC-V tumors were identified through limma package in R with cutoff criteria│log2 fold change (logFC)|>1.0 and p < 0.05. The DEGs between eight alcohol-related HCCs and their paired normal livers of GSE59259 from the Gene Expression Omnibus (GEO) were identified through GEO2R (a built-in tool in GEO database) with cutoff criteria |logFC|> 2.0 and adj.p < 0.05. The intersection of the two sets of DEGs was considered SKGs which were then investigated for their specificity through comparisons between HCC-A and other four HCC groups. The SKGs were analyzed for their correlations with HCC-A stage and grade and their prognostic power for HCC-A patients. The expressional differences of the SKGs in the HCCs in whole were also investigated through Gene Expression Profiling Interactive Analysis (GEPIA). The SKGs in HCC were validated through Oncomine database analysis. Results Pathological stage is an independent prognostic factor for HCC patients. HCC-A patients were diagnosed later than HCC patients with other risk factors. Ten SKGs were identified and nine of them were confirmed for their differences in paired samples of HCC-A patients. Three (SLC22A10, CD5L, and UROC1) and four (SLC22A10, UROC1, CSAG3, and CSMD1) confirmed genes were correlated with HCC-A stage and grade, respectively. SPP2 had a lower trend in HCC-A tumors and was negatively correlated with HCC-A stage and grade. The SKGs each was differentially expressed between HCC-A and at least one of other HCC groups. CD5L was identified to be favorable prognostic factor for overall survival while CSMD1 unfavorable prognostic factor for disease-free survival for HCC-A patients and HCC patients in whole. Through Oncomine database, the dysregulations of the SKGs in HCC and their clinical significance were confirmed. Conclusion The poor prognosis of HCC-A patients might be due to their later diagnosis. The SKGs, especially the four stage-correlated genes (CD5L, SLC22A10, UROC1, and SPP2) might play important roles in HCC development, especially alcohol-related HCC development and progression. CD5L might be useful for overall survival and CSMD1 for disease-free survival predication in HCC, especially alcohol-related HCC.

scholarly journals Bioinformatics Analysis of the Expression of ATP binding cassette subfamily C member 3 (ABCC3) in Human Glioma

Open Medicine ◽  
2020 ◽  
Vol 15 (1) ◽  
pp. 107-113 ◽  
Author(s):  
Zelin Sun ◽  
Xiaoyuan Qi ◽  
Yan Zhang
Keyword(s):  
Gene Expression ◽  
Overall Survival ◽  
Disease Free Survival ◽  
Expression Level ◽  
Normal Brain ◽  
Human Glioma ◽  
Ppi Network ◽  
Free Survival ◽  
Disease Free ◽  
Low Expression

AbstractObjectiveTo investigate the expression of the ABCC3 gene in human glioma and its correlation with the patient’s prognosis.MethodsThe cancer genome atlas (TCGA) database was used to analyze the differential expression of the ABCC3 gene in human glioma. The STRING database was used to construct the protein-protein interaction (PPI) network of the ABCC3 gene coding protein. The co-expression genes relevant to the ABCC3 gene were analyzed by the Pearson correlation test. A log-rank test was used to analyze the difference of overall survival (OS) and disease-free survival (DFS) between the high and low ABCC3 gene expression groups.ResultsThe expression level of the ABCC3 gene in glioma tissues was lower than that of corresponding normal brain tissues. The PPI network contains 51 nodes with the average node degree of 13.3 and the local clustering coefficient of 0.72 which indicated that the PPI enrichment was significant (p<0.001). Ten hub genes (ABCC3,NR1I2,NR1H4,-CYP7A1,SLC10A1,CYP3A4,UGT1A1,UGT1A8,UGT1A6 and ALB) were identified by the cytoscape software. The KEGG analysis was enriched in drug metabolism - cytochrome P450 and PPAR signaling pathway. CFI gene expression level was positive correlated with the ABCC3 expression level (r=0.71, p<0.05). And the CNRIP1 gene expressed was negative correlated with ABCC3 expression (r=-0.43, p<0.05). The overall survival (HR=2.8, P<0.05) and disease-free survival rates (HR=2.0, P<0.05) of patients with ABCC3 low expression glioma were significantly higher than those of patients with high expression of ABCC3. Conclusion The expression level of the ABCC3 gene in glioma was decreased compared to normal brain tissue. The overall survival and disease-free survival of in the ABCC3 low-expression group was significant decreased.

Efficacy trend of hepatic resection for hepatocellular carcinoma with large multinodular tumor or macrovascular invasion.

2015 ◽  
Vol 33 (3_suppl) ◽  
pp. 427-427 ◽  
Author(s):  
Jian-Hong Zhong ◽  
Le-Qun Li ◽  
Xin-Ping Ye ◽  
Yang Ke ◽  
Lin Wang ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Overall Survival ◽  
Liver Function ◽  
Hepatic Resection ◽  
Tertiary Care ◽  
Disease Free Survival ◽  
Recent Decade ◽  
Free Survival ◽  
Disease Free

427 Background: Official guidelines and retrospective studies have different view on the role of hepatic resection (HR) for patients with large (≥5 cm) multinodular (≥2) hepatocellular carcinoma (HCC) and those involving macrovascular invasion (MVI). We aim to evaluate the efficacy and its variation trend and the safety of HR for these patients in three tertiary care settings. Methods: A consecutive sample of 1,824 patients with Child-Pugh A liver function and large/multinodular HCC or involving MVI and who underwent initial HR were divided into four groups: large/multinodular HCC of the previous (2000-2004, n = 496) and recent five years (2005-2010, n = 765), involving MVI of the previous (n = 242) and recent five years (n = 321). Results: Among our patient sample, the hospital mortality was less than 5% and had a downward trend. Moreover, patients in recent five years have statistically significant longer survival time. Among patients with large/multinodular HCC, patients in recent five years showed a significantly better overall survival than those in previous five years at 1-year (92% vs. 84%), 3-year (69% vs. 61%), and 5-year (45% vs. 40%) (P = 0.004). Moreover, among patients involving MVI, overall survival in recent five years was significantly higher at 1-year (83% vs. 78%), 3-year (50% vs. 41%), and 5-year (25% vs. 17%) (P= 0.033). However, the disease-free survival of recent five years was only slightly higher than that of the previous five years in the two subgroups. Conclusions: HR offers good overall survival for patients with resectable large/multinodular HCC or those involving MVI and with preserved liver function. Outcomes have tended to improve in recent decade.

Prognosis of hepatic failure with the albumin-bilirubin model for hepatocellular carcinoma after stereotactic body radiotherapy with and without transplant.

2018 ◽  
Vol 36 (4_suppl) ◽  
pp. 384-384
Author(s):  
Shaakir Hasan ◽  
Alexander V. Kirichenko ◽  
Paul Renz ◽  
Vijay Kudithipudi ◽  
Molly Vincent ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Overall Survival ◽  
Hepatic Failure ◽  
Stereotactic Body Radiotherapy ◽  
Disease Free Survival ◽  
Median Dose ◽  
Free Survival ◽  
Prognostic Assessment ◽  
Disease Free

384 Background: The Albumin-Bilirubin (ALBI) model is a validated prognostic assessment of cirrhosis in hepatocellular carcinoma (HCC), stratifying patients to grades 1(ALBI-1), 2(ALBI-2), or 3(ALBI-3). We reported that ALBI distinguishes patients at higher risk for hepatic failure(HF) after stereotactic body radiotherapy (SBRT) within the Child Pugh(CP) A population. We now apply the ALBI model to both CP-A and CP-B patients after SBRT with or without orthotropic liver transplant (OLT), and assess its prognostic capability of overall survival (OS) and HF relative to the CP model. Methods: From 2009-2017, 68 patients with 81 HCC lesions and CP-A (45) or CP-B (23) cirrhosis completed SBRT in this IRB approved study. The median dose was 45 Gy (35 - 57 Gy) in 4-7 fractions. Initial ALBI and CP scores were measured against OS and progression of CP class, which was recorded every 3-4 months. Median follow-up = 18 months. Results: The median age = 62 and tumor size = 3.5 cm (1.1 Ð 11 cm). 26 patients were ALBI-1, 31 ALBI-2, and 11 ALBI-3 prior to SBRT. For all patients, 2-year local control was 96%. 1 and 2 year OS was 77% and 54%, disease free survival was 71% and 40%, and freedom from CP progression was 71% and 56%, respectively. OS was significantly different between ALBI-1, ALBI-2, and ALBI-3 patients (P = 0.01), as was progression of CP class (P<0.001). When stratified by initial CP class, there were no significant differences in survival or CP progression [Table 1]. In a subset of 37 CP-A and 15 CP-B without OLT, rates of progressive cirrhosis were better predicted by ALBI (P<0.001) than CP class (P=0.09). Conclusions: Compared to the CP model, the ALBI index more precisely predicted HF and OS in HCC patients for both early and intermediate cirrhosis. Its application may help better select candidates for OLT after SBRT, who may be at higher risk for HF than initially predicted. [Table: see text]

scholarly journals Network Pharmacology and Bioinformatics Methods Reveal the Mechanism of Zao-Jiao-Ci in the Treatment of LSCC

2021 ◽  
Vol 2021 ◽  
pp. 1-15
Author(s):  
Feng Xiang ◽  
Linman Li ◽  
Jieling Lin ◽  
Shasha Li ◽  
Guiyuan Peng
Keyword(s):  
Cell Cycle ◽  
Overall Survival ◽  
Disease Free Survival ◽  
Network Pharmacology ◽  
Signal Pathways ◽  
Core Network ◽  
Free Survival ◽  
The Core ◽  
Ppi Networks ◽  
Disease Free

Objective. Zao-Jiao-Ci (ZJC), a traditional Chinese medicine, is considered as a promising candidate to treat laryngeal squamous cell carcinoma (LSCC). However, the underlying molecular mechanism remains unclear. Methods. Gene expression profiles of GSE36668 were available from the GEO database, and differentially expressed genes (DEGs) of LSCC were obtained by R package; subsequently, enrichment analysis on KEGG and GO of DEGs was performed. The active ingredients of ZJC were screened from the TCMSP database, and the matched candidate targets were obtained by PharmMapper. Furthermore, we constructed protein-protein interaction (PPI) networks of DEGs and candidate targets, respectively, and we screened the core network from the merged network through combining the two PPI networks using Cytoscape 3.7.2. The key targets derived from the core network were analyzed to find out the associated KEGG signal enrichment pathway. By the GEPIA online website, Kaplan–Meier analysis was used to complete the overall survival and disease-free survival of the selected genes in the core module. Results. We identified 96 candidate targets of ZJC and 86 DEGs of LSCC, the latter including 50 upregulated genes and 36 downregulated genes. DEGs were obviously enriched in the following biological functions: extracellular structure organization, the extracellular matrix organization, and endodermal cell differentiation. The 60 key targets from the core network were enriched in the signal pathways including transcriptional misregulation cancer, cell cycle, and so on. We found that LSCC patients with high expression of HIST1H3J, HIST1H3F, and ITGA4 had worse overall survival, while higher expression of NTRK1, COPS5, HIST1H3A, and HIST1H3G had significantly worse disease-free survival. Conclusion. It suggested that the interaction between ZJC and LSCC was related to the signal pathways of transcriptional misregulation cancer and cell cycle, revealing that it may be the mechanism of ZJC in the treatment of LSCC.

scholarly journals FAM83D is associated with gender, AJCC stage, overall survival and disease-free survival in hepatocellular carcinoma

2019 ◽  
Vol 39 (5) ◽  
Author(s):  
Xuling Liu ◽  
Hong Gao ◽  
Jie Zhang ◽  
Dongying Xue
Keyword(s):  
Hepatocellular Carcinoma ◽  
Overall Survival ◽  
Sequence Similarity ◽  
Prognostic Significance ◽  
Disease Free Survival ◽  
High Expression ◽  
Mrna Levels ◽  
Free Survival ◽  
Ajcc Stage ◽  
Disease Free

AbstractPrognostic significance of family with sequence similarity 83, member D (FAM83D) in hepatocellular carcinoma (HCC) patients has not been well-investigated using Gene Expression Omnibus (GEO) series and TCGA database, we compared FAM83D expression levels between tumor and adjacent tissues, and correlated FAM83D in tumors with outcomes and clinico-pathological features in HCC patients. Validated in GSE33006, GSE45436, GSE84402 and TCGA, FAM83D was significantly overexpressed in tumor tissues than that in adjacent tissues (all P<0.01). FAM83D up-regulation was significantly associated with worse overall survival (OS) and disease-free survival (DFS) in HCC patients (Log rank P=0.00583 and P=4.178E-04, respectively). Cox analysis revealed that FAM83D high expression was significantly associated with OS in HCC patients [hazard ratio (HR) = 1.44, 95% confidence interval (CI) = 1.005–2.063, P=0.047]. Additionally, patients deceased or recurred/progressed had significantly higher FAM83D mRNA levels than those living or disease-free (P=0.0011 and P=0.0238, respectively). FAM83D high expression group had significantly more male patients and advanced American Joint Committee on Cancer (AJCC) stage cases (P=0.048 and P=0.047, respectively). FAM83D mRNA were significantly overexpressed in male (P=0.0193). Compared with patients with AJCC stage I, those with AJCC stage II and stage III–IV had significantly higher FAM83D mRNA levels (P = 0.0346 and P=0.0045, respectively). In conclusion, overexpressed in tumors, FAM83D is associated with gender, AJCC stage, tumor recurrence and survival in HCC.

scholarly journals HULC and H19 Played Different Roles in Overall and Disease-Free Survival from Hepatocellular Carcinoma after Curative Hepatectomy: A Preliminary Analysis from Gene Expression Omnibus

2015 ◽  
Vol 2015 ◽  
pp. 1-9 ◽  
Author(s):  
Zongguo Yang ◽  
Yunfei Lu ◽  
Qingnian Xu ◽  
Bozong Tang ◽  
Cheol-Keun Park ◽  
...  
Keyword(s):  
Gene Expression ◽  
Risk Factors ◽  
Hepatocellular Carcinoma ◽  
Vascular Invasion ◽  
Disease Free Survival ◽  
Gene Expression Omnibus ◽  
Free Survival ◽  
Cox Regression Analysis ◽  
Tumor Tissues ◽  
Disease Free

Objective. This study aimed to evaluate the relationships between long noncoding RNAs (lncRNAs) in tumor tissues and hepatocellular carcinoma (HCC) aggressiveness and survival.Methods. We correlated the lncRNAs in tumor tissues with HCC survival and clinicopathological features based on Gene Expression Omnibus expression profile GSE36376.Results. Eight lncRNAs and 240 HCC patients were included. Cox regression analysis indicated that HULC was a positive factor for HCC overall survival (HR = 0.885, 95% CI = 0.797–0.983, andP=0.023) and disease-free survival time (HR = 0.913, 95% CI = 0.835–0.998, andP=0.045). H19 and UCA1 were both demonstrated to be risk factors of HCC disease-free survival in multivariate Cox model (HR = 1.071, 95% CI = 1.01–1.137, andP=0.022and HR = 2.4, 95% CI = 1.092–5.273, andP=0.029, resp.). But Kaplan-Meier method showed no significant association between UCA1 and HCC disease-free survival (log rankP=0.616). Logistic regression demonstrated that H19 was overexpressed in HBV-infected patients (OR = 1.14, 95% CI = 1.008–1.29, andP=0.037). HULC had a significant association with vascular invasion (OR = 0.648, 95% CI = 0.523–0.803, andP<0.001). H19 and MEG3 were both considered to be risk factors for high AFP level (OR = 1.45, 95% CI = 1.277–1.646, andP<0.001and OR = 1.613, 95% CI = 1.1–2.365, andP=0.014, resp.).Conclusions. Contributing to decreased susceptibility to vascular invasion, upregulation of HULC in tumor tissues was positively associated with HCC survival. In contrast, H19 overexpression might be risk factor for HCC aggressiveness and poor outcomes.

scholarly journals Indication of Liver Transplantation for Hepatocellular Carcinoma Should Be Reconsidered in Case of Microvascular Invasion and Multilocular Tumor Occurrence

2021 ◽  
Vol 10 (6) ◽  
pp. 1155
Author(s):  
Jan-Paul Gundlach ◽  
Stephan Schmidt ◽  
Alexander Bernsmeier ◽  
Rainer Günther ◽  
Victor Kataev ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Liver Transplantation ◽  
Overall Survival ◽  
Cox Regression ◽  
Disease Free Survival ◽  
Microvascular Invasion ◽  
Simultaneous Occurrence ◽  
Free Survival ◽  
Cox Regression Analysis ◽  
Disease Free

Liver transplantation (LT) is routinely performed for hepatocellular carcinoma (HCC) in cirrhosis without major vascular invasion. Although the adverse influence of microvascular invasion is recognized, its occurrence does not contraindicate LT. We retrospectively analyzed in our LT cohort the significance of microvascular invasion on survival and demonstrate bridging procedures. At our hospital, 346 patients were diagnosed with HCC, 171 patients were evaluated for LT, and 153 were listed at Eurotransplant during a period of 11 years. Among these, 112 patients received LT and were included in this study. Overall survival after 1, 3 and 5 years was 86.3%, 73.9%, and 67.9%, respectively. Microvascular invasion led to significantly reduced overall (p = 0.030) and disease-free survival (p = 0.002). Five-year disease-free survival with microvascular invasion was 10.5%. Multilocular tumor occurrence with simultaneous microvascular invasion revealed the worst prognosis. In our LT cohort, predominant bridging treatment was transarterial chemoembolization (TACE) and the number of TACE significantly correlated with poorer overall survival after LT (p = 0.028), which was confirmed in multiple Cox regression analysis for overall and disease-free survival (p = 0.015 and p = 0.011). Microvascular tumor invasion is significantly associated with reduced prognosis after LT, which is aggravated by simultaneous occurrence of multiple lesions. Therefore, indication strategies for LT should be reconsidered.

Prediction of Disease-free Survival in Hepatocellular Carcinoma by Gene Expression Profiling

2013 ◽  
Vol 20 (12) ◽  
pp. 3747-3753 ◽  
Author(s):  
Ho-Yeong Lim ◽  
Insuk Sohn ◽  
Shibing Deng ◽  
Jeeyun Lee ◽  
Sin Ho Jung ◽  
...  
Keyword(s):  
Gene Expression ◽  
Hepatocellular Carcinoma ◽  
Gene Expression Profiling ◽  
Expression Profiling ◽  
Disease Free Survival ◽  
Free Survival ◽  
Disease Free

scholarly journals The prognostic significance of microRNA-221 in hepatocellular carcinoma: An updated meta-analysis

2021 ◽  
Vol 36 (2) ◽  
pp. 172460082110326
Author(s):  
Wenfeng Liu ◽  
Keshu Hu ◽  
Feng Zhang ◽  
Shenxin Lu ◽  
Rongxin Chen ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Overall Survival ◽  
Meta Analysis ◽  
Prognostic Significance ◽  
Disease Free Survival ◽  
Progression Free Survival ◽  
Recurrence Free Survival ◽  
Free Survival ◽  
Hazard Ratios ◽  
Disease Free

Background Recently, microRNA-221 has been found to be abnormally expressed in hepatocellular carcinoma; however, its clinical value has not been summarised. This meta-analysis aimed to assess the prognostic significance of miR-221 in hepatocellular carcinoma. Material and Methods PubMed, Science Direct, Web of Science, Scopus, Ovid MEDLINE, EMbase, Google Scholar, the Cochrane Library, CNKI, CBM, VIP and Wanfang databases were searched for eligible articles. The endpoints included overall survival, progression-free survival, recurrence-free survival, metastasis-free survival, disease-free survival. Hazard ratios with 95% confidence intervals were used to explore the relationship between miR-221 expression and clinical survival results of liver cancer patients. Subgroup analysis and sensitivity analysis were performed. Begg’s test and Egger’s test were conducted to evaluate publication bias. Results A total of nine studies including 607 patients were recruited for this meta-analysis. The pooled hazard ratios displayed that high miR-221 expression was remarkably associated with poorer overall survival (hazard ratio = 1.91, 95% confidence interval: 1.53–2.38, p ＜ 0.01) and unfavourable progression-free survival/recurrence-free survival/metastasis-free survival/disease-free survival (hazard ratio = 2.02, 95% confidence interval: 1.58–2.57, p ＜ 0.01). The results of Begg’s test and Egger’s test did not exhibit obvious publication bias. Conclusions High expression of miR-221 can predict poor outcome of hepatocellular carcinoma. miR-221 can be used as a promising prognostic biomarker of hepatocellular carcinoma.

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