Integrative analysis of h-prune as a potential therapeutic target for hepatocellular carcinoma

Unraveling the causal relationship and underlying mechanisms between cathepsins on liver cancer: findings from mendelian randomization and bioinformatics analysis

BACKGROUND

Hepatocellular carcinoma (HCC) and cholangiocarcinoma (CCA) are two major types of primary liver cancer (PLC). Earlier research has indicated a potential link between cathepsins and liver cancer. Nonetheless, there have been limited clinical trials examining the connection between cathepsins and PLC. Therefore, we conducted a two-sample Mendelian randomization (MR) study to evaluate the causal relationship between cathepsins and PLC.

METHODS

Data from genome-wide association studies (GWAS) focusing on cathepsins was collected. Additionally, summary data for GCST90018803 (Hepatic bile duct cancer, HBDC), and GCST90018858 (related to hepatic cancer, HC), were employed in the discovery and validation phases of the study, respectively. The inverse variance weighted (IVW) method was served as the primary analytical method in our Mendelian randomization (MR) study, supplemented by the MR-Egger, weighted median, simple mode, and weighted mode methods. To assess heterogeneity and pleiotropy, we conducted the MR-Egger intercept test, Cochran's Q test, as well as the MR-Pleiotropy RESidual Sum and Outlier (MR-PRESSO) analysis, along with the leave-one-out analysis. After that, bioinformatic analysis based on the Gene Expression Omnibus (GEO) databases were utilized, Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional enrichment analysis were utilized for exploring the underlying mechanisms. Additionally, protein-protein docking was employed to confirm the interaction between related proteins.

RESULTS

The results showed that cathepsin F (CTSF), was causally associated with HBDC. CTSF decrease the risk of HBDC (OR = 0.826, 95% CI 0.711-0.959, P = 0.012). CTSF may play protective roles in patients with HBDC. No heterogeneity or pleiotropy was observed. Additionally, the expression of CTSF genes is lower in patients with HBDC, GO and KEGG functional enrichment analysis revealed CTSF were mainly related to cell cycle, and P53 pathway in HBDC. Docking results showed that CTSF had good binding ability with MDM2, the most well-established negative regulator of p53.

CONCLUSION

This study provided new evidence of the relationship between CTSF and HBDC, suggesting that CTSF plays an inhibition role in HBDC progression. CTSF could be a novel and effective way to for HDBC treatment.

Functional Genomics of PRUNE1 in Neurodevelopmental Disorders (NDDs) Tied to Medulloblastoma (MB) and Other Tumors

We analyze the fundamental functions of Prune_1 in brain pathophysiology. We discuss the importance and maintenance of the function of Prune_1 and how its perturbation influences both brain pathological conditions, neurodevelopmental disorder with microcephaly, hypotonia, and variable brain anomalies (NMIHBA; OMIM: 617481), and tumorigenesis of medulloblastoma (MB) with functional correlations to other tumors. A therapeutic view underlying recent discoveries identified small molecules and cell penetrating peptides to impair the interaction of Prune_1 with protein partners (e.g., Nm23-H1), thus further impairing intracellular and extracellular signaling (i.e., canonical Wnt and TGF-β pathways). Identifying the mechanism of action of Prune_1 as responsible for neurodevelopmental disorders (NDDs), we have recognized other genes which are found overexpressed in brain tumors (e.g., MB) with functional implications in neurodevelopmental processes, as mainly linked to changes in mitotic cell cycle processes. Thus, with Prune_1 being a significant target in NDDs, we discuss how its network of action can be dysregulated during brain development, thus generating cancer and metastatic dissemination.

ARHGEF11 promotes proliferation and epithelial-mesenchymal transition of hepatocellular carcinoma through activation of β-catenin pathway

Rho guanine nucleotide exchange factor 11 (ARHGEF11) has been proved to promote tumor metastasis in glioblastoma and ovarian carcinoma. However, the role of ARHGEF11 in hepatocellular carcinoma (HCC) progression is largely unknown. Here, we found that ARHGEF11 was upregulated in HCC samples and highly metastatic hepatoma cell lines. Knockdown of ARHGEFF11 inhibited the cell proliferation and invasion in both HCCLM3 and SKHEP1 cell lines. Subsequent mechanistic investigation showed that downregulation of ARHGEF11 significantly attenuated β-catenin nuclear translocation, thereafter repressed the expression of ZEB1 and cyclinD1, finally contributing to inhibition of epithelial-mesenchymal transition (EMT) and cell cycle arrest. Moreover, high levels of ARHGEF11 were found to be associated with shorter disease free and overall survival. A prognostic nomogram model that integrated ARHGEF11, tumor size and BCLC classification showed good performance in predicting clinical outcomes of HCC patients. Overall, this study demonstrated that ARHGEF11 could promote proliferation and metastasis of HCC via activating β-catenin pathway, suggesting that ARHGEF11 might serve as a potential prognostic biomarker for HCC.

HN1 as a diagnostic and prognostic biomarker for liver cancer

BACKGROUND

The present study aimed to examine the diagnostic and prognostic value of HN1 in terms of overall survival (OS) and recurrence-free survival (RFS) in liver cancer and its potential regulatory signaling pathway.

METHODS

We obtained clinical data and HN1 RNA-seq expression data of liver cancer patients from The Cancer Genome Atlas database, and analyzed the differences and clinical association of HN1 expression in different clinical features. We uesd receiver-operating characteristic curve to evaluate the diagnosis capability of HN1. We analyzed and evaluated the prognostic significance of HN1 by Kaplan-Meier curves and Cox analysis. Gene Set Enrichment Analysis (GSEA) was used to identify signaling pathways related to HN1 expression.

RESULTS

HN1 mRNA was up-regulated in liver cancer, and was associated with age, histologic grade, stage, T classification, M classification, and vital status. HN1 mRNA had ideal specificity and sensitivity for the diagnosis (AUC = 0.855). Besides, the analysis of Kaplan-Meier curves and Cox model showed that HN1 mRNA was strongly associated with the overall survival and could be well-predicted liver cancer prognosis, as an independent prognostic variable. GSEA analysis identified three signaling pathways that were enriched in the presence of high HN1 expression.

CONCLUSION

HN1 serves as a biomarker of diagnosis and prognosis in liver cancer.

Higher expression of cell division cycle-associated protein 5 predicts poorer survival outcomes in hepatocellular carcinoma

The upregulation of cell division cycle associated protein 5 (CDCA5) has been observed in various cancer types. However, the prognostic value of CDCA5 and its underlying mechanism contributing to tumorigenesis in hepatocellular carcinoma (HCC) remain poorly understood. We used tissue microarray (TMA) to evaluate the prognosis of 304 HCC samples based on their CDCA5 expression, and analyzed the genomic features correlated with CDCA5 by using dataset from The Cancer Genome Atlas (TCGA). Compared with adjacent normal tissues, increased expression of CDCA5 was found in HCC tissues. Moreover, higher expression of CDCA5 was associated with inferior OS and DFS outcomes in HCC patients. The enrichment plots showed that the gene signatures in cell cycle, DNA replication and p53 pathways were enriched in patients with higher CDCA5 expression. Meanwhile, statistically higher mutations burdens in TP53 could also be observed in CDCA5-high patients. Integrative analysis based on miRNAseq and methylation data demonstrated a potential association between CDCA5 expression and epigenetic changes. In conclusion, our study provided the evidence of CDCA5 as an oncogenic promoter in HCC and the potential function of CDCA5 in affecting tumor microenvironment.

Disrupted functional network in patients with temporal lobe epilepsy with impaired alertness

Cognitive impairment is common in patients with temporal lobe epilepsy (TLE). Alertness is an important subfunction of cognition, but it is poorly understood in TLE. We hypothesized that disruptions to underlying brain networks may affect alertness in patients with TLE. Patients with unilateral TLE were grouped into low-alertness and high-alertness groups, and they were matched with healthy controls (HCs) (n = 20 each). Functional magnetic resonance imaging (fMRI) was used to construct functional brain networks, and graph theory was used to identify topological parameters of the networks. At the global level, patients with low alertness had networks with less small-worldness and less normalized clustering than HCs. At the nodal level, patients with low alertness exhibited decreased centrality of the bilateral parahippocampal gyrus compared with HCs and increased centrality of the right postcentral gyrus compared with patients with high alertness. This study reveals a decreased separation, tending toward randomization, of the functional network in patients with TLE with impaired alertness. Our results also suggest that the parahippocampal gyrus may contribute to impaired alertness and the right postcentral gyrus plays an important role in the modulation of alertness in patients with TLE.

Identification of cancer/testis antigen 2 gene as a potential hepatocellular carcinoma therapeutic target by hub gene screening with topological analysis

The 5-year survival rate of hepatocellular carcinoma (HCC) is <20%; thus, identifying new potential therapeutic targets or novel biomarkers for prognosis prediction is crucial. The present study aimed to screen hub genes by constructing protein-protein interaction (PPI) subnetworks using topological analysis methods, as well as reveal their clinical significance through big data analytics and their association with the clinicopathological features. Firstly, the PPI subnetworks were constructed using four topological analysis methods, including the MCC, DMNC, MNC and degree methods, to obtain 6 hub genes. Subsequently, the hub gene cancer/testis antigen 2 (CTAG2), which affects the prognosis of HCC (overall survival, P=0.035), was acquired by analysing clinical data in The Cancer Genome Atlas database. Meanwhile, CTAG2 expression was significantly associated with the age at diagnosis (P=0.003), T stage (P=0.028), TNM stage (P=0.028) and α-fetoprotein (AFP) expression (P=0.045). Further immunohistochemical analysis of samples collected in our hospital revealed that the expression level of CTAG2 in 46 HCC tissues was significantly higher in comparison with that in paired adjacent tissues. The clinical data indicated that the expression of CTAG2 was significantly correlated with the hepatitis B virus status (P=0.010) and AFP expression (P=0.004). These results were then found to be consistent with the results of big data analytics. Furthermore, Gene Set Enrichment Analysis demonstrated that the function of CTAG2 in HCC may be associated with the cell cycle. Taken together, these findings suggest that CTAG2 may serve as a new potential therapeutic target for HCC patients.