Bioinformatics Analysis of Candidate Genes and Pathways Related to Hepatocellular Carcinoma in China: A Study Based on Public Databases

Unmasking early colorectal cancer clues: in silico and in vitro investigation of downregulated IGF2, SOCS1, MLH1, and CACNA1G in SSA polyps

BACKGROUND AND AIM

Colorectal cancer (CRC) originates from pre-existing polyps in the colon. The development of different subtypes of CRC is influenced by various genetic and epigenetic characteristics. CpG island methylator phenotype (CIMP) is found in about 15-20% of sporadic CRCs and is associated with hypermethylation of certain gene promoters. This study aims to find prognostic genes and compare their expression and methylation status as potential biomarkers in patients with serrated sessile adenomas/polyps (SSAP) and CRC, in order to evaluate which, one is a better predictor of disease.

METHOD

This study employed a multi-phase approach to investigate genes associated with CRC and SSAP. Initially, two gene expression datasets were analyzed using R and Limma package to identify differentially expressed genes (DEGs). Venn diagram analysis further refined the selection, revealing four genes from the Weissenberg panel with significant changes. These genes, underwent thorough in silico evaluations. Once confirmed, they proceeded to wet lab experimentation, focusing on expression and methylation status. This comprehensive methodology ensured a robust examination of the genes involved in CRC and SSAP.

RESULT

This study identified cancer-specific genes, with 8,351 and 1,769 genes specifically down-regulated in SSAP and CRC tissues, respectively. The down-regulated genes were associated with cell adhesion, negative regulation of cell proliferation, and drug response. Four highly downregulated genes in the Weissenberg panel, including CACNA1G, IGF2, MLH1, and SOCS1. In vitro analysis showed that they are hypermethylated in both SSAP and CRC samples while their expressions decreased only in CRC samples.

CONCLUSION

This suggests that the decrease in gene expression could help determine whether a polyp will become cancerous. Using both methylation status and gene expression status of genes in the Weissenberg panel in prognostic tests may lead to better prognoses for patients.

The role of kinesin family members in hepatobiliary carcinomas: from bench to bedside

As a major component of the digestive system malignancies, tumors originating from the hepatic and biliary ducts seriously endanger public health. The kinesins (KIFs) are molecular motors that enable the microtubule-dependent intracellular trafficking necessary for mitosis and meiosis. Normally, the stability of KIFs is essential to maintain cell proliferation and genetic homeostasis. However, aberrant KIFs activity may destroy this dynamic stability, leading to uncontrolled cell division and tumor initiation. In this work, we have made an integral summarization of the specific roles of KIFs in hepatocellular and biliary duct carcinogenesis, referring to aberrant signal transduction and the potential for prognostic evaluation. Additionally, current clinical applications of KIFs-targeted inhibitors have also been discussed, including their efficacy advantages, relationship with drug sensitivity or resistance, the feasibility of combination chemotherapy or other targeted agents, as well as the corresponding clinical trials. In conclusion, the abnormally activated KIFs participate in the regulation of tumor progression via a diverse range of mechanisms and are closely associated with tumor prognosis. Meanwhile, KIFs-aimed inhibitors also carry out a promising tumor-targeted therapeutic strategy that deserves to be further investigated in hepatobiliary carcinoma (HBC).

AhR may be involved in Th17 cell differentiation in chronic hepatitis B

Th17 cells which are crucial for host immunity have been demonstrated to increase HBV infection. However, the mechanism of the Th17 cell increase is unknown. Hence, the mechanism of Th17 cell enhancement is important to provide a theoretical foundation for chronic hepatitis B immunotherapy. This study included 15 instances in the healthy control (HC) and 15 cohorts in the chronic hepatitis B (CHB). Their CD4+ T cells were isolated from their peripheral blood and then subjected to RNA transcriptome sequencing. Then, to identify target genes linked to Th17-cell differentiation, DEGs associated with CHB were convergent with the Th17-cell-associated genes from the KEGG database. Hub genes of DEG and target genes linked to Th17 cells were analysed for correlation. The AhR-related genes were located using the GeneMANIA database. To analyse the function of the genes, GO and KEGG pathways were employed. Protein-protein interaction network analysis employed the Metascape, STRING and Cytoscape databases. Finally, Western blotting and RT-qPCR were used to validate AhR. A total of 348 differential genes were identified in CHB patients. CytoHubba was used for screening five hub genes associated with CHB: CXCL10, RACGAP1, TPX2, FN1 and GZMA. This study aimed to determine the mechanism of elevated Th17 cells in CHB. As a result, further investigation using the convergence of DGEs and Th17 cell-related genes identified three target genes: AhR, HLA-DQA1 and HLA-DQB1, all of which were elevated in CHB. The three genes were primarily involved in immune response-related processes, according to the GO enrichment analysis. Correlation analysis of CXCL10, RACGAP1, TPX2, FN1 and GZMA genes with AhR, HLA-DQA1 and HLA-DQB1 revealed that AhR was positively associated with CXCL10 and GZMA genes, which best respond to the severity of CHB disease. Combined with the role of AhR in Th17 cell differentiation, the genes AhR was chosen for confirmation by RT-qPCR and WB in this study. The results showed that the CHB group had higher expression levels of AhR at both RT-qPCR and WB levels. Furthermore, this study's findings revealed that AhR may contribute to the development of CHB by affecting the differentiation of Th17 cells.

Therapeutic targeting of the TPX2/TTK network in colorectal cancer

BACKGROUND

While the increased screening, changes in lifestyle, and recent advances in treatment regimen have decreased colorectal cancer (CRC) mortality, metastatic disease and recurrence remains a major clinical challenge. In the era of precision medicine, the identification of actionable novel therapeutic targets could ultimately offer an alternative treatment strategy for CRC.

METHODS

RNA-Seq was conducted using the illumina platform, while bioinformatics analyses were conducted using CLC genomics workbench and iDEP.951. Colony forming unit, flow cytometry, and fluorescent microscopy were used to assess cell proliferation, cell cycle distribution, and cell death, respectively. The growth potential of CRC cells under 3-dimensional (3D) conditions was assessed using Matrigel. STRING database (v11.5) and Ingenuity Pathway Analysis (IPA) tool were used for network and pathway analyses. CRISPR-Cas9 perturbational effects database was used to identify potential therapeutic targets for CRC, through integration with gene-drug interaction database. Structural modeling and molecular docking were used to assess the interaction between candidate drugs and their targets.

RESULTS

In the current study, we investigated the therapeutic potential of targeting TPX2, TTK, DDX39A, and LRP8, commonly upregulated genes in CRC identified through differential expression analysis in CRC and adjacent non-cancerous tissue. Targeted depletion of TPX2 and TTK impaired CRC proliferation, cell cycle progression, and organoid formation under 3D culture conditions, while suppression of DDX39A and LRP8 had modest effects on CRC colony formation. Differential expression analysis and bioinformatics on TPX2 and TTK-deficient cells identified cell cycle regulation as the hallmark associated with loss of TPX2 and TTK. Elevated expression of TPX2 and TTK correlated with an oncogenic state in tumor tissue from patients with colon adenocarcinoma, thus corroborating an oncogenic role for the TPX2/TTK network in the pathogenesis of CRC. Gene set enrichment and pathway analysis of TPX2high/TTKhigh CRC identified numerous additional gene targets as integral components of the TPX2/TTK network. Integration of TPX2/TTK enriched network with CRISPR-Cas9 functional screen data identified numerous novel dependencies for CRC. Additionally, gene-drug interaction analysis identified several druggable gene targets enriched in the TPX2/TTK network, including AURKA, TOP2A, CDK1, BIRC5, and many others.

CONCLUSIONS

Our data has implicated an essential role for TPX2 and TTK in CRC pathogenesis and identified numerous potential therapeutic targets and their drug interactions, suggesting their potential clinical use as a novel therapeutic strategy for patients with CRC. Video Abstract.

C18ORF54 promotes immune infiltration and poor prognosis as a potential biomarker for hepatocellular carcinoma

OBJECTIVE

The morbidity of hepatocellular carcinoma (HCC) is increasing annually. The aim of this study is to investigate the molecular mechanisms of upregulated genes in HCC using bioinformatic methods, so as to identify new potential biological markers.

METHODS

The Gene Expression Omnibus database (GEO database) was mined for HCC datasets, which were screened for hub genes and subjected to (Gene Ontology) GO and (Kyoto Encyclopedia of Genes and Genomes) KEGG enrichment analysis. The hub genes were analyzed in terms of Receiver Operating Characteristic (ROC) and methylation levels. Validation of hub genes was completed through basic pathological alterations based on the protein and gene expression level of hub genes. The correlation of genes with immune infiltration in HCC was analyzed based on the database Timer 2.0, and the prognosis as well as survival of hub genes in HCC was analyzed using R studio software. Finally, we performed a gene combination drug analysis on the potential therapeutic targets in HCC.

RESULTS

Expression-up-regulated genes were screened via differential analysis, which were mainly enriched in cell cycles and DNA replication pathways. Five hub genes, BRCA1 associated RING domain 1 (BARD1), Mismatch Repair Protein (MSH2), Recombinant H2A Histone Family, Member X (H2AFX), Recombinant H2A Histone Family, Member z (H2AFZ) and Chromosome 18 Open Reading Frame 54 (C18orf54) were identified using a Protein-Protein Interaction Networks (PPI). After a comprehensive analysis of ROC curves and methylation gene mutation sites, C18orf54 was localized followed by basic experiments, so as to verify the C18orf54 upregulated in HCC. Based on the online database Timer 2.0, the immune infiltration of C18orf54 gene in HCC was analyzed, which was found to be negatively correlated with CD4+ T cells and macrophages in HCC, meanwhile a further refinement of the immune checkpoint correlation analysis revealed that C18orf54 was mainly correlated with Hepatitis A virus cellular receptor 2 (HAVCR2), T cell immunoreceptor with Ig and ITIM domains (TIGIT) and Cytotoxic T lymphocyte associate protein-4 (CTLA4). The prognosis and survival of patients with HCC expressing C18orf54 were also analyzed, and it was found that such patients had a higher incidence of adjacent liver tissue inflammation, a higher child-Pugh grade score and a higher rate of residual tumor recurrence. Similarly, the prognosis was worse in the subset of patients with C18orf54. Finally, we performed a combined genetic analysis, which suggested that cyclosporine, quercetin, testosterone and calcitriol might be effective in reducing C18orf54 mRNA expression.

CONCLUSION

C18orf54 is involved in the immune infiltration and promotes the poor prognosis of HCC, which could be a candidate biomarker for HCC.

Differentially expressed discriminative genes and significant meta-hub genes based key genes identification for hepatocellular carcinoma using statistical machine learning

Hepatocellular carcinoma (HCC) is the most common lethal malignancy of the liver worldwide. Thus, it is important to dig the key genes for uncovering the molecular mechanisms and to improve diagnostic and therapeutic options for HCC. This study aimed to encompass a set of statistical and machine learning computational approaches for identifying the key candidate genes for HCC. Three microarray datasets were used in this work, which were downloaded from the Gene Expression Omnibus Database. At first, normalization and differentially expressed genes (DEGs) identification were performed using limma for each dataset. Then, support vector machine (SVM) was implemented to determine the differentially expressed discriminative genes (DEDGs) from DEGs of each dataset and select overlapping DEDGs genes among identified three sets of DEDGs. Enrichment analysis was performed on common DEDGs using DAVID. A protein-protein interaction (PPI) network was constructed using STRING and the central hub genes were identified depending on the degree, maximum neighborhood component (MNC), maximal clique centrality (MCC), centralities of closeness, and betweenness criteria using CytoHubba. Simultaneously, significant modules were selected using MCODE scores and identified their associated genes from the PPI networks. Moreover, metadata were created by listing all hub genes from previous studies and identified significant meta-hub genes whose occurrence frequency was greater than 3 among previous studies. Finally, six key candidate genes (TOP2A, CDC20, ASPM, PRC1, NUSAP1, and UBE2C) were determined by intersecting shared genes among central hub genes, hub module genes, and significant meta-hub genes. Two independent test datasets (GSE76427 and TCGA-LIHC) were utilized to validate these key candidate genes using the area under the curve. Moreover, the prognostic potential of these six key candidate genes was also evaluated on the TCGA-LIHC cohort using survival analysis.

Integrated analysis of ferroptosis-related gene signature for overall survival prediction in Asian patients with hepatocellular carcinoma

PURPOSE

Hepatocellular carcinoma (HCC) is one of the most prevalent types of cancers in Asia. Accumulating evidence suggests that ferroptosis is a non-apoptotic form of cell death, and has played an important role in cancer biology.

METHODS

Based on the manually curated ferroptosis-related gene set and TCGA-LIHC dataset of Asian patients, we used DESeq2, Kaplan-Meier analysis, and univariate Cox regression to identify differentially expressed ferroptosis-related genes with significantly prognostic capacity. A risk signature was constructed based on the selected genes for predicting the survival of HCC patients in Asia. The survival prediction accuracy was confirmed by the time-dependent receiver operating characteristic (ROC) curve analysis. Gene set variation analysis (GSVA) was used to explore the functional associations of the signature. Ferroptosis potential index (FPI) and xCell algorithm was applied to quantify ferroptosis and immune cell infiltration, respectively. Two independent datasets from the GEO and the ICGC database were used for external validation.

RESULTS

The ferroptosis-related signature could accurately predict the survival outcomes of HCC patients in Asian (p value < 0.0001). We showed that the signature was an independent factor and was beneficial in elevating risk stratification of current clinicopathologic features, such as the amount of alpha-fetoprotein (AFP) and residual tumor classification. Functional characterization showed that critical processes in tumorigenesis belonged to the high-risk groups, for example inflammatory response, which may be the main driver of HCC. The high-risk group had higher FPIs and infiltrations of macrophages and T-helper cells than the low-risk group. Furthermore, two independent cohorts confirmed the prognostic value of our signature.

CONCLUSION

Overall, our results demonstrated potential application of ferroptosis-related genes as independent biomarkers in Asian HCC patients. Targeting ferroptosis may be clinically useful beyond known clinicopathological factors and provide benefit in immunotherapy.

Identification of Potential Hub Genes Related to Aflatoxin B1, Liver Fibrosis and Hepatocellular Carcinoma via Integrated Bioinformatics Analysis

The molecular mechanism of the hepatotoxicant aflatoxin B1 to induce liver fibrosis and hepatocellular carcinoma (HCC) remains unclear, to offer fresh perspectives on the molecular mechanisms underlying the onset and progression of AFB1-Fibrosis-HCC, which may offer novel targets for the detection and therapy of HCC caused by AFB1. In this study, expression profiles of AFB1, liver fibrosis and liver cancer-related datasets were downloaded from the Gene Expression Omnibus (GEO), and differentially expressed genes (DEGs) were identified by the GEO2R tool. The STRING database, CytoHubba, and Cytoscape software were used to create the protein-protein interaction and hub genes of the combined genes, and the ssGSEA score for inflammatory cells related gene sets, the signaling pathway, and immunotherapy were identified using R software and the GSEA database. The findings revealed that AFB1-associated liver fibrosis and HCC combined genes were linked to cell process disruptions, the BUB1B and RRM2 genes were identified as hub genes, and the BUB1B gene was significantly increased in JAK-STAT signaling gene sets pathways as well as having an immunotherapy-related impact. In conclusion, BUB1B and RRM2 were identified as potential biomarkers for AFB1-induced fibrosis and HCC progression.

MiR-155 regulates M2 polarization of hepatitis B virus-infected tumour-associated macrophages which in turn regulates the malignant progression of hepatocellular carcinoma

Hepatocellular carcinoma (HCC) initiated by hepatitis B virus (HBV) infection is a complicated process. MiR-155 can alter the immune microenvironment to affect the host's anti-infective ability. This study investigated the mechanism by which miR-155 affects tumour-associated macrophage (TAM) polarization at a molecular level, thus affecting the malignant progression of HBV⁺ HCC. MiR-155 and TAM-related cytokine expression were analysed by qRT-PCR. The distribution of TAMs was detected by immunohistochemistry. The effect of the aberrant miR-155 expression on macrophage polarization was examined by flow cytometry. The targeted relationship was verified by dual-luciferase assay, and the protein level of src homology 2 domain-containing inositol polyphosphate 5-phosphatase 1 (SHIP1) was detected by western blot. The proliferation of HCC cells was examined by CCK-8 and colony formation assays. Invasion and migration of HCC cells were detected by transwell assay. In HBV⁺ HCC tissues, miR-155 was significantly highly expressed and the number of CD206-positive TAM (CD206⁺ TAM) and CD68-positive TAM (CD68⁺ TAM) were higher than those in HBV^- HCC tissues. In addition, miR-155 overexpression significantly promoted M2-type macrophage polarization, whilst miR-155 silencing expression significantly promoted M1-type macrophage polarization. Besides, the miR-155/SHIP1 axis accelerated HCC cell invasion, proliferation and migration by inducing M2-type macrophage polarization. MiR-155 accelerates HCC cell proliferation, migration and invasion by targeting SHIP1 expression and inducing macrophage M2 polarization. This finding provides new insights into the development of novel therapeutic strategies for combatting HBV⁺ HCC and a new reference for exploring anti-tumour immunotherapy.

Construction and validation of prognostic signature for hepatocellular carcinoma basing on hepatitis B virus related specific genes

BACKGROUND

Hepatocellular carcinoma (HCC) is a frequent primary liver cancer, and it is one of the leading cause of cancer-related deaths. Hepatitis B virus (HBV) infection is a crucial risk factor for HCC. Thus, this study aimed to explore the prognostic role of HBV-positive HCC related specific genes in HCC.

METHODS

The HCC related data were downloaded from three databases, including The Cancer Genome Atlas (TCGA), International Cancer Genome Consortium (ICGC), and Gene Expression Omnibus (GEO). Univariate Cox regression analysis and LASSO Cox regression analysis were conducted to build the Risk score. Multivariate Cox regression analysis and survival analysis determined the independent prognostic indicators.

RESULTS

After cross analysis of differentially expressed genes (DEGs), we have identified 106 overlapped DEGs, which were probably HBV-positive HCC related specific genes. These 106 DEGs were significantly enriched in 213 GO terms and 8 KEGG pathways. Among that, 11 optimal genes were selected to build a Risk score, and Risk score was an independent prognostic factor for HCC. High risk HCC patients had worse OS. Moreover, five kinds of immune cells were differentially infiltrated between high and low risk HCC patients.

CONCLUSION

The prognostic signature, based on HMMR, MCM6, TPX2, KIF20A, CCL20, RGS2, NUSAP1, FABP5, FZD6, PBK, and STK39, is conducive to distinguish different prognosis of HCC patients.

Characteristics of Hepatitis B Virus Genotype and Sub-Genotype in Hepatocellular Cancer Patients in Vietnam

Untreated chronic hepatitis B virus (HBV) infection can lead to chronic liver disease and may progress to cirrhosis or hepatocellular carcinoma (HCC). HBV infection has been prevalent in Vietnam, but there is little information available on the genotypes, sub-genotypes, and mutations of HBV in patients with HBV-related HCC confirmed by histopathological diagnosis. We studied the molecular characteristics of HBV and its genetic variants in Vietnamese HCC patients after liver tumor resection. We conducted a descriptive cross-sectional study on 107 HBV-related HCC hospitalized patients from October 2018 to April 2019. The specimens collected included EDTA anticoagulant blood and liver tissues. Extracted HBV DNA was subjected to whole genome sequencing by the Sanger method. We discovered 62 individuals (57.9%) with genotype B and 45 patients (42.1%) with genotype C, with only sub-genotypes B4 and C1. Among the mutations, the double mutation, A1762T-G1764A, had the most significant frequency (73/107 samples; 68.2%) and was higher in genotype C than in genotype B (p < 0.001). The most common genotypes found in HCC patients in this investigation were B and C, with sub-genotypes B4 and C1 for each. The prevalence of genotype B4 was greater in HBV-infected Vietnamese HCC patients.

Analysis of multiple databases identifies crucial genes correlated with prognosis of hepatocellular carcinoma

Despite advancements made in the therapeutic strategies on hepatocellular carcinoma (HCC), the survival rate of HCC patient is not satisfactory enough. Therefore, there is an urgent need for the valuable prognostic biomarkers in HCC therapy. In this study, we aimed to screen hub genes correlated with prognosis of HCC via multiple databases. 117 HCC-related genes were obtained from the intersection of the four databases. We subsequently identify 10 hub genes (JUN, IL10, CD34, MTOR, PTGS2, PTPRC, SELE, CSF1, APOB, MUC1) from PPI network by Cytoscape software analysis. Significant differential expression of hub genes between HCC tissues and adjacent tissues were observed in UALCAN, HCCDB and HPA databases. These hub genes were significantly associated with immune cell infiltrations and immune checkpoints. The hub genes were correlated with clinical parameters and survival probability of HCC patients. 147 potential targeted therapeutic drugs for HCC were identified through the DGIdb database. These hub genes could be used as novel prognostic biomarkers for HCC therapy.

Study on the action mechanism of the peptide compounds of Wuguchong on diabetic ulcers, based on UHPLC-Q-TOF-MS, network pharmacology and experimental validation

ETHNOPHARMACOLOGICAL RELEVANCE

Diabetic foot ulcers mainly refer to people who are initially diabetic and do not have peripheral neuropathy or peripheral vascular disease, but have developed foot infection, septicemia, and ulceration. Diabetic trauma disease is characterized by high sugar and very slow wound healing, which is the reason why some patients with severe diabetic trauma require amputation. Prolonged hyperglycemia can lead to changes in bodily functions and endocrine changes, which can lead to permeability damage of epidermal tissue structure, microvascular damage and, in more severe cases, nerve damage, which are also the main causes of diabetic trauma. Small molecule peptides have various biological activities, such as: lowering blood pressure, antibacterial and wound healing activities, etc. It is a drug recorded in classical Chinese medicine, it is safer to use natural active peptides to treat wounds compared to the listed drugs, and there are no side effects in its use.The wound healing effect of Wuguchong dry product has been confirmed but the mechanism is still unclear, whether it is related to the small molecule active peptides contained in it remains to be studied.

AIM OF STUDY

Objective To investigate the potential mechanism of the peptide compounds of Wuguchong (PCW) on diabetic wound healing and the relevant targets in the pathway associated with the treatment of diabetic ulcers using a systematic pharmacological and pharmacological experimental validation approach.

METHODS

1) PCW was prepared by enzymatic digestion of TCMW and analyzed by UHPLC-Q-TOF-MS. 2) Further screening of the active chemical components of PCW using PubChem, Swiss Target Prediction data. 3) Prediction of its targets using Drug Bank, CTD, and Genecards databases. 4) Construct protein/gene interactions network diagrams for PCWs acting by using Cytoscape 3.7.0 software. 5) GO and KEGG analysis of PCW targets were performed by David database. 6) Validated by AO/EB staining, scratching and in vitro tube formation methods. 7) Explored the mechanism of PCW to promote diabetic wound healing by protein blotting and immunohistochemical detection of relevant protein expression.

RESULTS

and finally: 1) After the above screening, 81 active ingredients of PCW and 94 targets acting on diabetic ulcers were obtained. 2) 30 biological processes, 30 cellular compositions and 30 molecular functions were obtained by GO analysis; 28 signaling pathways were obtained by KEGG analysis. 3) The results of AO/EB staining assay, scratch assay and in vitro tube-forming assay showed that PCW has significant pro-vascular endothelial cell proliferation and pro-angiogenic effects in vitro.

CONCLUSIONS

The results of this study confirmed the effect of the PCW in treating diabetic ulcers to a certain extent, and further revealed its mechanism of action in depth, which provides a new reference for the next step of Chinese medicine in treating diabetic ulcers.

Identification of Differentially Expressed Genes Associated with the Prognosis and Diagnosis of Hepatocellular Carcinoma by Integrated Bioinformatics Analysis

OBJECTIVE

The goal of this study was to understand the possible core genes associated with hepatocellular carcinoma (HCC) pathogenesis and prognosis.

METHODS

GEO contains datasets of gene expression, miRNA, and methylation patterns of diseased and healthy/control patients. The GSE62232 dataset was selected by employing the server Gene Expression Omnibus. A total of 91 samples were collected, including 81 HCC and 10 healthy samples as control. GSE62232 was analysed through GEO2R, and Functional Enrichment Analysis was performed to extract rational information from a set of DEGs. The Protein-Protein Relationship Networking search method has been used for extracting the interacting genes. MCC method was used to calculate the top 10 genes according to their importance. Hub genes in the network were analysed using GEPIA to estimate the effect of their differential expression on cancer progression.

RESULTS

We identified the top 10 hub genes through CytoHubba plugin. These included BUB1, BUB1B, CCNB1, CCNA2, CCNB2, CDC20, CDK1 and MAD2L1, NCAPG, and NDC80. NCAPG and NDC80 reported for the first time in this study while the remaining from a recently reported literature. The pathogenesis of HCC may be directly linked with the aforementioned genes. In this analysis, we found critical genes for HCC that showed recommendations for future prognostic and predictive biomarkers studies that could promote selective molecular therapy for HCC.

A systematic study of traditional Chinese medicine treating hepatitis B virus-related hepatocellular carcinoma based on target-driven reverse network pharmacology

Hepatocellular carcinoma (HCC) is a serious global health problem, and hepatitis B virus (HBV) infection remains the leading cause of HCC. It is standard care to administer antiviral treatment for HBV-related HCC patients with concurrent anti-cancer therapy. However, a drug with repressive effects on both HBV infection and HCC has not been discovered yet. In addition, drug resistance and side effects have made existing therapeutic regimens suboptimal. Traditional Chinese medicine (TCM) has multi-ingredient and multi-target advantages in dealing with multifactorial HBV infection and HCC. TCM has long been served as a valuable source and inspiration for discovering new drugs. In present study, a target-driven reverse network pharmacology was applied for the first time to systematically study the therapeutic potential of TCM in treating HBV-related HCC. Firstly, 47 shared targets between HBV and HCC were screened as HBV-related HCC targets. Next, starting from 47 targets, the relevant chemical components and herbs were matched. A network containing 47 targets, 913 chemical components and 469 herbs was established. Then, the validated results showed that almost 80% of the herbs listed in chronic hepatitis B guidelines and primary liver cancer guidelines were included in the 469 herbs. Furthermore, functional analysis was conducted to understand the biological processes and pathways regulated by these 47 targets. The docking results indicated that the top 50 chemical components bound well to targets. Finally, the frequency statistical analysis results showed the 469 herbs against HBV-related HCC were mainly warm in property, bitter in taste, and distributed to the liver meridians. Taken together, a small library of 913 chemical components and 469 herbs against HBV-related HCC were obtained with a target-driven approach, thus paving the way for the development of therapeutic modalities to treat HBV-related HCC.