ABSTRACT
BACKGROUND The potential roles of alternative splicing (AS) in HCC remain unknown. This study aimed to identify AS signatures associated with the prognosis that influence the immune microenvironment of HCC. MATERIAL AND METHODS The SpliceSeq tool was employed for genome-wide profiling of 7 AS events in 361 HCC patients from The Cancer Genome Atlas (TCGA). A prognostic signature was built by integrating Cox regression and the least absolute shrinkage and selection operator (LASSO). The support vector machine (SVM) and receiver operating characteristic curve (ROC) were employed to analyze the AS events in the signatures to discriminate the immune microenvironment. RESULTS There were 3546 AS events highly linked to the survival of patients with HCC. The AS signature could effectively stratify HCC patients. Clustering analysis revealed 3 different immune clusters characterized with significantly different prognoses and were significantly correlated with AS signatures. The AS events in the final prognostic signature classified the immune cluster with an average AUC of the ROC (0.88). Moreover, a potential regulatory network of splicing events in HCC is presented. CONCLUSIONS We established the prognostic signature based on AS, which can effectively stratify HCC patients and predict the immune subtypes. Moreover, novel RNA splicing patterns and splicing-regulatory networks involved in HCC were discovered.
Subject(s)
Alternative Splicing/genetics , Carcinoma, Hepatocellular/genetics , Tumor Microenvironment/immunology , Biomarkers, Tumor/genetics , Carcinoma, Hepatocellular/immunology , Carcinoma, Hepatocellular/metabolism , Cluster Analysis , Databases, Genetic , Gene Expression , Gene Expression Profiling , Gene Regulatory Networks , Genome-Wide Association Study , Humans , Liver Neoplasms/genetics , Liver Neoplasms/metabolism , Prognosis , Proportional Hazards Models , RNA Splice Sites/genetics , RNA Splicing Factors/genetics , ROC Curve , Support Vector Machine , Transcriptome , Tumor Microenvironment/geneticsABSTRACT
Aberrant expression of histone deacetylases (HDACs) has been detected in a variety of cancers, which disrupts the balance between cell proliferation and apoptosis in favor of continuous growth. A previous study demonstrated that HDAC5 contributes to the proliferation of hepatocellular carcinoma (HCC) cells, but a clear understanding of the mechanism has not yet been provided. In the present work, we found that the levels of HDAC5 were significantly higher in HCC tissues and cells than in adjacent tissues and normal hepatic cells. In addition, knockdown of HDAC5 attenuated the proliferation of Hep3B and HepG2 cells. Through profiling the expressions of proliferation and apoptosis-related genes in Hep3B cells following HDAC5 knockdown, p63 and maspin were found obviously up-regulated in HDAC5-deprived cells compared with the control. Further investigations confirmed that HDAC5 knockdown induced TAp63 expression in HCC cells, accompanied with increased H3K9 acetylation at the TAp63 promoter. Overexpression of TAp63 led to proliferation inhibition by inducing cell cycle arrest. Additionally, TAp63 that was required for the maspin upregulation resulted from HDAC5 knockdown. Phenotype experiments showed that interrupting either TAp63 or maspin recovered the proliferative and tumorigenic capabilities of HCC cells with HDAC5 knockdown. Clinical analysis showed that HDAC5 was negatively correlated with TAp63 and maspin in HCC tissues. In addition, a high level of HDAC5 as well as a low level of TAp63 or maspin predicted poor survival in HCC patients. Taken together, this study proposes the existence of an aberrant HDAC5-TAp63-maspin pathway conferring HCC progression through proliferation induction, which suggests novel intervention targets for the disease.
ABSTRACT
Hypoxia plays a critical role in the progression and metastasis of hepatocellular carcinoma by activating the key transcription factor, hypoxia-inducible factor-1. This study aims to identify the novel mechanisms underlying the dysregulation of hypoxia-inducible factor-1α in hepatocellular carcinoma. We found that histone deacetylase 5, a highly expressed histone deacetylase in hepatocellular carcinoma, strengthened the migration and invasion of hepatocellular carcinoma cells under hypoxia but not normoxia condition. Furthermore, histone deacetylase 5 induced the transcription of hypoxia-inducible factor-1α by silencing homeodomain-interacting protein kinase-2 expression, which was also dependent on hypoxia. And then knockdown of hypoxia-inducible factor-1α decreased the expressions of mesenchymal markers, N-cadherin, and Vimentin, as well as matrix metalloproteinases, MMP7 and MMP9; however, the epithelial marker, E-cadherin, increased. Phenotype experiments showed that the migration and invasion of hepatocellular carcinoma cells were impaired by knockdown of histone deacetylase 5 or hypoxia-inducible factor-1α but rescued when eliminating homeodomain-interacting protein kinase-2 in hepatocellular carcinoma cells, which suggested the critical role of histone deacetylase 5-homeodomain-interacting protein kinase-2-hypoxia-inducible factor-1α pathway in hypoxia-induced metastasis. Finally, clinical analysis confirmed the positive correlation between histone deacetylase 5 and hypoxia-inducible factor-1α in hepatocellular carcinoma specimens and a relatively poor prognosis for the patients with high levels of histone deacetylase 5 and hypoxia-inducible factor-1α. Taken together, our findings demonstrated a novel mechanism underlying the crosstalk between histone deacetylase 5 and hypoxia-inducible factor-1 in hepatocellular carcinoma.
