Pan-Cancer Analysis Identifies CHD5 as a Potential Biomarker for Glioma

Abstract

The chromodomain helicase DNA binding domain 5 (CHD5) is required for neural development and plays an important role in the regulation of gene expression. Although CHD5 exerts a broad tumor suppressor effect in many tumor types, its specific functions regarding its expression levels, and impact on immune cell infiltration, proliferation and migration in glioma remain unclear. Here, we evaluated the role of CHD5 in tumor immunity in a pan-cancer multi-database using the R language. The Cancer Genome Atlas (TCGA), Genotype Tissue Expression (GTEx), and Cancer Cell Lines Encyclopedia (CCLE) datasets were utilized to determine the role of CHD5 in 33 types of cancers, including the expression level, prognosis, tumor progression, and immune microenvironment. Furthermore, we explored the effect of CHD5 on glioma proliferation and migration using the cell counting kit 8 (CCK-8) assay, transwell assays and western blot analysis. The findings from our pan-cancer analysis showed that CHD5 was differentially expressed in the tumor tissues as compared to the normal tissues. Survival analysis showed that CHD5 was generally associated with the prognosis of glioblastoma (GBM), low Grade Glioma (LGG) and neuroblastoma, where the low expression of CHD5 was associated with a worse prognosis in glioma patients. Then, we confirmed that the expression level of CHD5 was associated with tumor immune infiltration and tumor microenvironment, especially in glioma. Moreover, si-RNA mediated knockdown of CHD5 promoted the proliferation and migration of glioma cells in vitro. In conclusion, CHD5 was found to be differentially expressed in the pan-cancer analysis and might play an important role in antitumor immunity. CHD5 is expected to be a potential tumor prognostic marker, especially in glioma.

TGIF2 is a potential biomarker for diagnosis and prognosis of glioma

“…Furthermore, in the GSE14805 dataset, we identified 2954 DEGs, including 1369 upregulated and 1585 downregulated genes, with TGIF2 significantly upregulated in the tumor group ( Figure 1D ). The ROC analysis indicated similar diagnostic ability for TGIF2 (AUC = 0.971) with established glioma prognostic genes (IDH1, IDH2, EGFR, TP53, CDC6, CDC14B, CHD5) ( 24 – 30 ) ( Figure 1E ). Kaplan-Meyer analysis demonstrated that glioma patients with high TGIF2 expression exhibited poor OS, DSS and PFI ( Figures 1F–H ).…”

“…There is an imperative need for novel early diagnostic and prognostic targets to address the pressing need for glioma treatment. Numerous studies have been devoted to exploring biomarkers in order to open new avenues for glioma treatment ( 28 – 30 , 36 , 37 ). The 1p/19q codeletion and IDH mutation emerged as the initial biomarkers, widely employed in clinical glioma diagnosis and have been associated with a variety of prognostic factors to establish effective clinical prediction model ( 38 – 40 ).…”

Identification of Key Regulators in Pancreatic Ductal Adenocarcinoma using Network theoretical Approach

“…CLDN5 expression levels differ significantly between cancer and normal tissues, and it has been confirmed in multiple studies (71). CLDN5 is implicated in the oncogenesis of diverse cancer types, highlighting its potential significance in cancer biology (72). PCDH1 enhances p65 nuclear localization by interacting with KPNB1, activating the NF-κB signaling pathway and promoting PDAC progression (73).…”

A pan-cancer analysis has uncovered CCDC58, a mitochondrial gene associated with epilepsy, as a potential prognostic and immunotherapeutic biomarker for various cancer types, including gliomas

“…This, in turn, enhances the likelihood of one or more of these neoantigens being immunogenic and eliciting T-cell responses(36). High TMB tumors respond well to immunotherapy and are linked to longer survival times (37). A phenotype of microsatellite sequence changes brought on by errors in DNA mismatch repair is called MSI, and it's linked to a higher risk of developing cancer(38).…”