Potential Diagnostic and Prognostic Values of CBX8 Expression in Liver Hepatocellular Carcinoma, Kidney Renal Clear Cell Carcinoma, and Ovarian Cancer: A Study Based on TCGA Data Mining

Abstract

Background. Chromobox protein homolog 8 (CBX8), a transcriptional repressor, participates in many biological processes in various carcinomas. Cell differentiation, aging, and cell cycle progression are examples of such processes. It is critical to investigate CBX8 expression and its relationship with clinicopathological characteristics in liver hepatocellular carcinoma (LIHC), kidney renal clear cell carcinoma (KIRC), and ovarian cancer (OV) to investigate CBX8’s potential diagnostic and prognostic values. Methods. TCGA and CPTAC databases were used to compare the data between cancer and matched normal tissues on RNA and protein expression profiles and their relevant clinical information to determine the relationship between CBX8 and clinicopathological features. Kaplan–Meier analyses were used to assess CBX8 relationship’s with disease-free survival (DFS), relapse-free survival (RFS), and overall survival (OS). The multivariate Cox regression analysis was used to identify independent risk factors which affect prognosis. DNA methylation and genetic changes and their impact on prognoses were evaluated by cBioPortal and MethSurv websites. Spearman’s correlation was used to determine the relationship of CBX8 expression with somatic mutation. Tumor immune estimation resource (TIMER) was adopted to investigate the relationship between CBX8 and immune cell infiltration (ICI). CBX8-relevant genes and proteins are analyzed by EnhancedVolcano and STRING databases. The gene set enrichment analysis (GSEA) was performed to investigate the potential functions of CBX8. Results. CBX8 RNA and protein overexpression were confirmed in LIHC, KIRC, and OV ( p < 0.05 ). High CBX8 was significantly related to the clinical features and poor prognoses. The CBX8 genetic alteration rate was 3%. DNA methylation was also associated with prognoses. CBX8 closely interacted with ICI, TMB, MSI, purity, and ploidy. GO analyses revealed that CBX8-associated genes were enriched in biological processes, cell cycle regulation, and molecular functions. KEGG analyses exhibited that CBX8 was gathered in signaling pathway regulation. GSEA revealed that cell cycle, DNA replication, and Wnt signaling pathways were differentially enriched in the high CBX8 expression group. Conclusions. CBX8 could be a potential diagnostic and prognostic biomarker for LIHC, KIRC, and OV cancers.

Anti-complement 5 antibody ameliorates antibody-mediated rejection after liver transplantation in rats

“…Differentially expressed genes (DEGs) were calculated with the DESeq2 package, as defined as genes with an adjusted P-value <0.05 and a log 2 -fold change >1. Volcano plots were generated using the Enhanced Volcano package (version 1.14.0) (31). The raw counts were normalized using the DESeq2 package, which were then used to construct the clustering heat maps using the heatmap.2 function from the gplots package (version 3.1.3) (32).…”

Current data and future perspectives on DNA methylation in ovarian cancer (Review)

“…Cell cycle progression, senescence and differentiation are all influenced by CBX8, and the hypomethylation of its promotor leads to an increase in its expression ( 108 ). CBX8 has been shown to play a role in the development of hepatocellular carcinoma, renal cancer and colorectal cancer, among others ( 109 , 110 ). The DNA hypomethylation of CBX8 leads to an enhanced expression, which acts as a potential diagnostic and prognostic biomarker for patients with OC and is associated with a poor prognosis ( 109 ).…”

“…CBX8 has been shown to play a role in the development of hepatocellular carcinoma, renal cancer and colorectal cancer, among others ( 109 , 110 ). The DNA hypomethylation of CBX8 leads to an enhanced expression, which acts as a potential diagnostic and prognostic biomarker for patients with OC and is associated with a poor prognosis ( 109 ). Furthermore, SLC6A12, a betaine/GABA transporter ( 111 ), is overexpressed in OC metastases, negatively affecting patient survival due to its promoter hypomethylation.…”