Prognostic potential of the small GTPase Ran and its methylation in hepatocellular carcinoma

Validation of Two Prognostic Gene Scores in Patients Undergoing Liver Resection for Hepatocellular Carcinoma

Background/Aims

Several prognostic gene signatures have been proposed as predictors of the prognosis of hepatocellular carcinoma (HCC), yet none are implemented in the clinical setting. We aimed to validate two gene scores previously derived from European cohorts.

Methods

The patients who underwent liver resection for HCC at Copenhagen University Hospital, Rigshospitalet from 2014 to 2018 were included. RNA sequencing determined the expression of genes in the '5-gene score' (HN1, RAN, RAMP3, KRT19, TAF9B) and 'HepatoPredict' (CLU, DPT, SPRY2, CAPSN1). Univariable Cox regression assessed associations with overall and disease-free survival. These parameters were also analyzed in the The Cancer Genome Atlas Liver Hepatocellular Carcinoma (TCGA-LIHC) (n = 359) and National Institute of Health (NIH) (n = 178) cohorts.

Results

Among 51 patients (88% male), 59% had no underlying liver disease and 25% had cirrhosis. No individual genes were significantly associated with overall survival in the Danish cohort. In the TCGA-LIHC cohort, CLU was linked to better overall survival, and in the NIH cohort, high expression of SPRY2 was associated with poorer overall survival. In the TCGA-LIHC cohort, HN1, RAN, and TAF9B were associated with poorer overall survival, while RAMP3 was linked to better overall survival. No genes were associated with disease-free survival.

Conclusion

Few individual genes significantly predicted survival in the larger cohorts, and none in the Danish cohort. However, the clinical implication of this needs further investigation.

Ran drives pancreatic cancer metastasis by activating the osteopontin-PI3K/AKT-androgen receptor signaling cascade

The small GTPase Ran has emerged as a key player in cancer metastasis. Our previous studies demonstrated that Ran drives pancreatic cancer metastasis by modulating androgen receptor (AR) expression. However, the detailed mechanisms by which Ran regulates AR expression remain unclear. This study aimed to elucidate the regulatory mechanisms through which Ran influences AR expression in the context of pancreatic cancer metastasis. We observed elevated levels of Ran, osteopontin (OPN), and AR in metastatic lymph node tissues, with OPN positively correlated with either Ran or AR expression. Ran silencing led to decreased levels of OPN and AR, whereas Ran upregulation increased their expression. Notably, OPN overexpression restored AR levels in Ran-silenced cells, whereas OPN knockdown diminished the inductive effect of Ran on AR expression. Additionally, OPN knockdown decreased AR expression and was associated with reduced activation of the PI3K/AKT signaling pathway. Functional assays revealed that silencing OPN significantly impaired the mobility and invasion of pancreatic cancer cells and restricted hepatic metastasis. Conversely, OPN overexpression restored the impaired metastasis caused by Ran knockdown. Furthermore, inhibiting PI3K/AKT signaling abolished the promoting effects of either Ran or OPN on pancreatic cancer metastasis. Importantly, re-expressing AR reversed the inhibitory effects of Ran or OPN silencing on the mobility and invasion of pancreatic cancer cells. In summary, Ran induces AR expression through the regulation of the OPN-PI3K/AKT signaling cascade. The Ran-OPN-PI3K/AKT-AR signaling pathway is crucial for driving pancreatic cancer metastasis.

Integrative analysis of bulk and single-cell transcriptomic data reveals novel insights into lipid metabolism and prognostic factors in hepatocellular carcinoma

Hepatocellular carcinoma (HCC) is associated with high mortality rate. This study investigated the status of lipid metabolism-related genes in HCC. Bulk transcriptomic and single-cell sequencing data for HCC were retrieved from public databases. The single-cell sequencing data was subjected to dimensionality reduction, which facilitated the annotation of distinct cell subpopulations and marker gene expression analysis within each subpopulation. Genes associated with lipid metabolism in liver cells were identified, and a machine-learning model was developed using the bulk transcriptomic data randomly partitioned into training and validation sets. The efficacy of the model was validated using these two sets. A multifactorial Cox analysis on the model genes combined with clinical features, led to the identification of age, HMGCS2, HNRNPU, and RAN as independent prognostic factors, which were included in the nomogram model construction and validation. A weighted gene co-expression analysis of all genes of the bulk transcriptome samples revealed the correlation between gene modules and risk score. Genes with cor > 0.4 in the highest-expressing module were selected for Gene Ontology and Kyoto Encyclopedia of Genes and Genomes functional enrichment analysis. Immune-related analysis was conducted based on seven algorithms for immune cell infiltration prediction. For the genes in the nomogram model, the expression in clinical pathological factors was also analyzed. The drug sensitivity analysis offered a reference for the selection of targeting drugs. This investigation provides novel insights and a theoretical basis for the prognosis, treatment, and pharmaceutical advancements for patients diagnosed with HCC.

Methylation-regulated tumor suppressor gene PDE7B promotes HCC invasion and metastasis through the PI3K/AKT signaling pathway

BACKGROUND

Hepatocellular carcinoma (HCC) has a high mortality rate, and the mechanisms underlying tumor development and progression remain unclear. However, inactivated tumor suppressor genes might play key roles. DNA methylation is a critical regulatory mechanism for inactivating tumor suppressor genes in HCC. Therefore, this study investigated methylation-related tumor suppressors in HCC to identify potential biomarkers and therapeutic targets.

METHODS

We assessed genome-wide DNA methylation in HCC using whole genome bisulfite sequencing (WGBS) and RNA sequencing, respectively, and identified the differential expression of methylation-related genes, and finally screened phosphodiesterase 7B (PDE7B) for the study. The correlation between PDE7B expression and clinical features was then assessed. We then analyzed the changes of PDE7B expression in HCC cells before and after DNA methyltransferase inhibitor treatment by MassArray nucleic acid mass spectrometry. Furthermore, HCC cell lines overexpressing PDE7B were constructed to investigate its effect on HCC cell function. Finally, GO and KEGG were applied for the enrichment analysis of PDE7B-related pathways, and their effects on the expression of pathway proteins and EMT-related factors in HCC cells were preliminarily explored.

RESULTS

HCC exhibited a genome-wide hypomethylation pattern. We screened 713 hypomethylated and 362 hypermethylated mCG regions in HCC and adjacent normal tissues. GO analysis showed that the main molecular functions of hypermethylation and hypomethylation were "DNA-binding transcriptional activator activity" and "structural component of ribosomes", respectively, whereas KEGG analysis showed that they were enriched in "bile secretion" and "Ras-associated protein-1 (Rap1) signaling pathway", respectively. PDE7B expression was significantly down-regulated in HCC tissues, and this low expression was negatively correlated with recurrence and prognosis of HCC. In addition, DNA methylation regulates PDE7B expression in HCC. On the contrary, overexpression of PDE7B inhibited tumor proliferation and metastasis in vitro. In addition, PDE7B-related genes were mainly enriched in the PI3K/ATK signaling pathway, and PDE7B overexpression inhibited the progression of PI3K/ATK signaling pathway-related proteins and EMT.

CONCLUSION

PDE7B expression in HCC may be regulated by promoter methylation. PDE7B can regulate the EMT process in HCC cells through the PI3K/AKT pathway, which in turn affects HCC metastasis and invasion.

PRMT5 Mediated HIF1α Signaling and Ras-Related Nuclear Protein as Promising Biomarker in Hepatocellular Carcinoma

Protein arginine N-methyltransferase 5 (PRMT5) has been identified as a potential therapeutic target for various cancer types. However, its role in regulating the hepatocellular carcinoma (HCC) transcriptome remains poorly understood. In this study, publicly available databases were employed to investigate PRMT5 expression, its correlation with overall survival, targeted pathways, and genes of interest in HCC. Additionally, we utilized in-house generated NGS data to explore PRMT5 expression in dysplastic nodules compared to hepatocellular carcinoma. Our findings revealed that PRMT5 is significantly overexpressed in HCC compared to normal liver, and elevated expression correlates with poor overall survival. To gain insights into the mechanism driving PRMT5 overexpression in HCC, we analyzed promoter CpG islands and methylation status in HCC compared to normal tissues. Pathway analysis of PRMT5 knockdown in the HCC cells revealed a connection between PRMT5 expression and genes related to the HIF1α pathway. Additionally, by filtering PRMT5-correlated genes within the HIF1α pathway and selecting up/downregulated genes in HCC patients, we identified Ras-related nuclear protein (RAN) as a target associated with overall survival. For the first time, we report that PRMT5 is implicated in the regulation of HIF1A and RAN genes, suggesting the potential prognostic utility of PRMT5 in HCC.

Hypomethylation of glycine dehydrogenase promoter in peripheral blood mononuclear cells is a new diagnostic marker of hepatitis B virus-associated hepatocellular carcinoma

BACKGROUND

Glycine dehydrogenase (GLDC) plays an important role in the initiation and proliferation of several human cancers. In this study, we aimed to detect the methylation status of GLDC promoter and its diagnostic value for hepatitis B virus-associated hepatocellular carcinoma (HBV-HCC).

METHODS

We enrolled 197 patients, 111 with HBV-HCC, 51 with chronic hepatitis B (CHB), and 35 healthy controls (HCs). The methylation status of GLDC promoter in peripheral mononuclear cells (PBMCs) was identified by methylation specific polymerase chain reaction (MSP). The mRNA expression was examined using real-time quantitative polymerase chain reaction (qPCR).

RESULTS

The methylation frequency of the GLDC promoter was significantly lower in HBV-HCC patients (27.0%) compared to that in CHB patients (68.6%) and HCs (74.3%) (P < 0.001). The methylated group had lower alanine aminotransferase level (P = 0.035) and lower rates of tumor node metastasis (TNM) III/IV (P = 0.043) and T3/T4 (P = 0.026). TNM stage was identified to be an independent factor for GLDC promoter methylation. GLDC mRNA levels in CHB patients and HCs were significantly lower than those in HBV-HCC patients (P = 0.022 and P < 0.001, respectively). GLDC mRNA levels were significantly higher in HBV-HCC patients with unmethylated GLDC promoters than those with methylated GLDC promoters (P = 0.003). The diagnostic accuracy of alpha-fetoprotein (AFP) combined with GLDC promoter methylation for HBV-HCC was improved compared with that of AFP alone (AUC: 0.782 vs. 0.630, P < 0.001). In addition, GLDC promoter methylation was an independent predictor for overall survival of HBV-HCC patients (P = 0.038).

CONCLUSIONS

The methylation frequency of GLDC promoter was lower in PBMCs from HBV-HCC patients than that from patients with CHB and HCs. The combination of AFP and GLDC promoter hypomethylation significantly improved the diagnostic accuracy of HBV-HCC.