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Reduction of T-Box 15 gene expression in tumor tissue is a prognostic biomarker for patients with hepatocellular carcinoma.

ABSTRACT: Genome-wide analysis is widely applied to detect molecular alterations during oncogenesis and tumor progression. We analyzed DNA methylation profiles of hepatocellular carcinoma (HCC), and investigated the clinical role of most heypermethylated of tumor, encodes T-box 15 (TBX15), which was originally involved in mesodermal differentiation. We conducted a genome-wide analysis of DNA methylation of tumor and non-tumor tissue of 15 patients with HCC, and revealed TBX15 was the most hypermethylated gene of tumor (Beta-value in tumor tissue = 0.52 compared with non-tumor tissue). Another validation set, which comprised 58 HCC with radical resection, was analyzed to investigate the relationships between tumor phenotype and TBX15 mRNA expression. TBX15 mRNA levels in tumor tissues were significantly lower compared with those of nontumor tissues (p < 0.0001). When we assigned a cutoff value = 0.5-fold, the overall survival 5-year survival rates of the low-expression group (n = 17) were significantly shorter compared with those of the high-expression group (n = 41) (43.3% vs. 86.2%, p = 0.001). Multivariate analysis identified low TBX15 expression as an independent prognostic factor for overall and disease-free survival. Therefore, genome-wide DNA methylation profiling indicates that hypermethylation and reduced expression of TBX15 in tumor tissue represents a potential biomarker for predicting poor survival of patients with HCC.

SUBMITTER: Morine Y

PROVIDER: S-EPMC7779253 | biostudies-literature | 2020 Dec

REPOSITORIES: biostudies-literature

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Reduction of T-Box 15 gene expression in tumor tissue is a prognostic biomarker for patients with hepatocellular carcinoma.

Morine Yuji Y Utsunomiya Tohru T Saito Yu Y Yamada Shinichiro S Imura Satoru S Ikemoto Tetsuya T Kitagawa Akihiro A Kobayashi Yuta Y Takao Seiichiro S Kosai Keisuke K Mimori Koshi K Tanaka Yasuhito Y Shimada Mitsuo M

Oncotarget 20201229 52

Genome-wide analysis is widely applied to detect molecular alterations during oncogenesis and tumor progression. We analyzed DNA methylation profiles of hepatocellular carcinoma (HCC), and investigated the clinical role of most heypermethylated of tumor, encodes T-box 15 (TBX15), which was originally involved in mesodermal differentiation. We conducted a genome-wide analysis of DNA methylation of tumor and non-tumor tissue of 15 patients with HCC, and revealed <i>TBX15</i> was the most hypermeth ...[more]

PMID: 33447348

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Project description:BackgroundHepatocellular carcinoma (HCC) is one of the most common malignancies, and the therapeutic outcome remains undesirable due to its recurrence and metastasis. Gene dysregulation plays a pivotal role in the occurrence and progression of cancer, and the molecular mechanisms are largely unknown.MethodsThe differentially expressed genes of HCC screened from the GSE39791 dataset were used to conduct weighted gene co-expression network analysis. The selected hub genes were validated in The Cancer Genome Atlas (TCGA) database and 11 HCC datasets from the Gene Expression Omnibus (GEO) database. Then, a tissue microarray comprising 90 HCC specimens and 90 adjacent normal specimens was used to validate the hub genes. Moreover, the Hallmark, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases were used to identify enriched pathways. Then, we conducted the immune infiltration analysis.ResultsA total of 17 co-expression modules were obtained by weighted gene co-expression network analysis. The green, blue, and purple modules were the most relevant to HCC samples. Four hub genes, RPL19, RPL35A, RPL27A, and RPS12, were identified. Interestingly, we found that all four genes were highly expressed in HCC and that their high expression was related to a poor prognosis by analyzing the TCGA and GEO databases. Furthermore, we investigated RPL19 in HCC tissue microarrays and demonstrated that RPL19 was overexpressed in tumor tissues compared with non-tumor tissues (p = 0.016). Moreover, overexpression of RPL19 predicted a poor prognosis in hepatocellular carcinoma (p < 0.0007). Then, enrichment analysis revealed that cell cycle pathways were significantly enriched, and bile acid metabolism-related pathways were significantly down-regulated when RPL19 was highly expressed. Furthermore, immune infiltration analysis showed that immune response was suppressed.ConclusionOur study demonstrates that RPL19 may play an important role in promoting tumor progression and is correlated with a poor prognosis in HCC. RPL19 may serve as a promising biomarker and therapeutic target for the precise diagnosis and treatment of HCC in the future.

Project description:BackgroundXanthine dehydrogenase (XDH) is a critical enzyme involved in the oxidative metabolism of purines, pterin and aldehydes and a central component of the innate immune system. However, the prognostic value of XDH in predicting tumor-infiltrating lymphocyte abundance, the immune response, and survival in different cancers, including hepatocellular carcinoma (HCC), is still unclear.MethodsXDH expression was analyzed in multiple databases, including Oncomine, the Tumor Immune Estimation Resource (TIMER), the Kaplan-Meier plotter database, the Gene Expression Profiling Interactive Analysis (GEPIA) database, and The Cancer Genome Atlas (TCGA). XDH-associated transcriptional profiles were detected with an mRNA array, and the levels of infiltrating immune cells were validated by immunohistochemistry (IHC) of HCC tissues. A predictive signature containing multiple XDH-associated immune genes was established using the Cox regression model.ResultsDecreased XDH mRNA expression was detected in human cancers originating from the liver, bladder, breast, colon, bile duct, kidney, and hematolymphoid system. The prognostic potential of XDH mRNA expression was also significant in certain other cancers, including HCC, breast cancer, kidney or bladder carcinoma, gastric cancer, mesothelioma, lung cancer, and ovarian cancer. In HCC, a low XDH mRNA level predicted poorer overall survival, disease-specific survival, disease-free survival, and progression-free survival. The prognostic value of XDH was independent of the clinical features of HCC patients. Indeed, XDH expression in HCC activated several immune-related pathways, including the T cell receptor, PI3K-AKT, and MAPK signaling pathways, which induced a cytotoxic immune response. Importantly, the microenvironment of XDHhigh HCC tumors contained abundant infiltrating CD8 + T cells but not exhausted T cells. A risk prediction signature based on multiple XDH-associated immune genes was revealed as an independent predictor in the TCGA liver cancer cohort.ConclusionThese findings suggest that XDH is a valuable prognostic biomarker in HCC and other cancers and indicate that it may function in tumor immunology. Loss of XDH expression may be an immune evasion mechanism for HCC.

Project description:IntroductionTumor mutation burden (TMB) is an emerging biomarker for immunotherapy of hepatocellular carcinoma (HCC), but its value for clinical application has not been fully revealed.Materials and methodsWe used the Wilcox test to identify the differentially expressed immune-related genes (DEIRGs) in groups with high and low TMB as well as screened the immune gene pairs related to prognosis using univariate Cox regression analysis. A LASSO Cox regression prognostic model was developed by combining The Cancer Genome Atlas Liver Hepatocellular Carcinoma (TCGA-LIHC) with the International Cancer Genome Consortium (ICGC) LIRI-JP cohort, and internal (TCGA, ICGC) and external (GSE14520) validation analyses were conducted on the predictive value of the model. We also explored the relationship between the prognostic model and tumor microenvironment via the ESTIMATE algorithm and performed clinical correlation analysis by the chi-square test, revealing its underlying molecular mechanism with the help of Gene Set Enrichment Analysis (GSEA).ResultsThe prognostic model consisting of 15 immune gene pairs showed high predictive value for short- and long-term survival of HCC in three independent cohorts. Based on univariate multivariate Cox regression analysis, the prognostic model could be used to independently predict the prognosis in each independent cohort. The immune score, stromal score, and estimated score values were lower in the high-risk group than in the low-risk group. As shown by the chi-square test, the prognostic model exhibited an obvious correlation with the tumor stage [American Joint Committee on Cancer tumor-node-metastasis (AJCC-TNM) (p < 0.001), Barcelona Clinic Liver Cancer (BCLC) (p = 0.003)], histopathological grade (p = 0.033), vascular invasion (p = 0.009), maximum tumor diameter (p = 0.013), and background of liver cirrhosis (p < 0.001). GSEA revealed that the high-risk group had an enrichment of many oncology features, including the cell cycle, mismatch repair, DNA replication, RNA degradation, etc.ConclusionOur research developed and validated a reliable prognostic model associated with TMB for HCC, which may help to further enrich the therapeutic targets of HCC.

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Reduction of T-Box 15 gene expression in tumor tissue is a prognostic biomarker for patients with hepatocellular carcinoma.

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Reduction of T-Box 15 gene expression in tumor tissue is a prognostic biomarker for patients with hepatocellular carcinoma.

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